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Robert J. Robbins is a biologist, an educator, a science administrator, a publisher, an information technologist, and an IT leader and manager who specializes in advancing biomedical knowledge and supporting education through the application of information technology. More About: RJR | OUR TEAM | OUR SERVICES | THIS WEBSITE
RJR: Recommended Bibliography 08 Nov 2024 at 01:47 Created:
Publications by FHCRC Researchers
The Fred Hutchinson Cancer Research Center began in 1975, with critical help from Washington State's U.S. Senator Warren Magnuson.
Fred Hutch quickly became the permanent home to Dr. E. Donnall Thomas, who had spent decades developing an innovative treatment for leukemia and other blood cancers. Thomas and his colleagues were working to cure cancer by transplanting human bone marrow after otherwise lethal doses of chemotherapy and radiation. At the Hutch, Thomas improved this treatment and readied it for widespread use. Since then, the pioneering procedure has saved hundreds of thousands of lives worldwide.
While improving bone marrow transplantation remains central to Fred Hutch's research, it is now only part of its efforts. The Hutch is home to five scientific divisions, three Nobel laureates and more than 2,700 faculty, who collectively have published more than 10,000 scientific papers, presented here as a full bibliography.
NOTE: From 1995 to 2009 I served as the Hutch's vice president for information technology — hence my interest in the organization. Although my role was in the admin division, if you dig through this bibliography, you will find a couple of papers with me as an author.
Created with PubMed® Query: ( fhcrc[Affiliation] OR "fred hutchinson"[Affiliation] OR "Fred Hutchinson Cancer Research"[Affiliation] OR "Fred Hutch"[affiliation] ) NOT pmcbook NOT ispreviousversion
Citations The Papers (from PubMed®)
RevDate: 2024-11-07
A Bundle of the "Top 10" Outpatient Parenteral Antimicrobial Therapy Publications in 2023.
Open forum infectious diseases, 11(11):ofae635 pii:ofae635.
Outpatient parenteral antimicrobial therapy (OPAT) has become more common in infectious diseases practice settings. Similarly, OPAT-related publications have also increased. The objective of this article was to summarize clinically important OPAT-related publications from 2023. Eighty-one articles were found on initial search, with 52 meeting inclusion criteria. A survey containing the 19 articles that had at least 1 citation was sent to an email listserv of multidisciplinary clinicians with OPAT experience. This article summarizes the "top 10" 2023 OPAT articles from the survey results.
Additional Links: PMID-39507884
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Citation:
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@article {pmid39507884,
year = {2024},
author = {Childs-Kean, LM and Beieler, AM and Cortés-Penfield, N and Keller, SC and Rivera, CG and Ryan, KL and Yoke, LH and Mahoney, MV},
title = {A Bundle of the "Top 10" Outpatient Parenteral Antimicrobial Therapy Publications in 2023.},
journal = {Open forum infectious diseases},
volume = {11},
number = {11},
pages = {ofae635},
doi = {10.1093/ofid/ofae635},
pmid = {39507884},
issn = {2328-8957},
abstract = {Outpatient parenteral antimicrobial therapy (OPAT) has become more common in infectious diseases practice settings. Similarly, OPAT-related publications have also increased. The objective of this article was to summarize clinically important OPAT-related publications from 2023. Eighty-one articles were found on initial search, with 52 meeting inclusion criteria. A survey containing the 19 articles that had at least 1 citation was sent to an email listserv of multidisciplinary clinicians with OPAT experience. This article summarizes the "top 10" 2023 OPAT articles from the survey results.},
}
RevDate: 2024-11-06
CmpDate: 2024-11-06
A PSA SNP associates with cellular function and clinical outcome in men with prostate cancer.
Nature communications, 15(1):9587.
Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility in men. The non-synonymous KLK3 single nucleotide polymorphism (SNP), rs17632542 (c.536 T > C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity mediates prostate cancer pathogenesis. The 'Thr' PSA variant leads to small subcutaneous tumours, supporting reduced prostate cancer risk. However, 'Thr' PSA also displays higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterisation of this PSA variant demonstrates markedly reduced proteolytic activity that correlates with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele have reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.
Additional Links: PMID-39505858
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@article {pmid39505858,
year = {2024},
author = {Srinivasan, S and Kryza, T and Bock, N and Tse, BWC and Sokolowski, KA and Janaththani, P and Fernando, A and Moya, L and Stephens, C and Dong, Y and Röhl, J and Alinezhad, S and Vela, I and Perry-Keene, JL and Buzacott, K and Nica, R and , and Gago-Dominguez, M and , and Schleutker, J and Maier, C and Muir, K and Tangen, CM and Gronberg, H and Pashayan, N and Albanes, D and Wolk, A and Stanford, JL and Berndt, SI and Mucci, LA and Koutros, S and Cussenot, O and Sorensen, KD and Grindedal, EM and Travis, RC and Haiman, CA and MacInnis, RJ and Vega, A and Wiklund, F and Neal, DE and Kogevinas, M and Penney, KL and Nordestgaard, BG and Brenner, H and John, EM and Gamulin, M and Claessens, F and Melander, O and Dahlin, A and Stattin, P and Hallmans, G and Häggström, C and Johansson, R and Thysell, E and Rönn, AC and Li, W and Brown, N and Dimeski, G and Shepherd, B and Dadaev, T and Brook, MN and Spurdle, AB and Stenman, UH and Koistinen, H and Kote-Jarai, Z and Klein, RJ and Lilja, H and Ecker, RC and Eeles, R and , and , and Clements, J and Batra, J},
title = {A PSA SNP associates with cellular function and clinical outcome in men with prostate cancer.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9587},
pmid = {39505858},
issn = {2041-1723},
support = {AQIRF175-2019RD2//State of Queensland | Advance Queensland/ ; W81XWH-19-1-0343//U.S. Department of Defense (United States Department of Defense)/ ; },
mesh = {Male ; Humans ; *Prostatic Neoplasms/genetics/pathology/metabolism/mortality ; *Polymorphism, Single Nucleotide ; *Prostate-Specific Antigen/blood/metabolism ; *Kallikreins/genetics/metabolism ; Genetic Predisposition to Disease ; Aged ; Animals ; Chromosomes, Human, Pair 19/genetics ; Middle Aged ; Mice ; Alleles ; Cell Line, Tumor ; },
abstract = {Genetic variation at the 19q13.3 KLK locus is linked with prostate cancer susceptibility in men. The non-synonymous KLK3 single nucleotide polymorphism (SNP), rs17632542 (c.536 T > C; Ile163Thr-substitution in PSA) is associated with reduced prostate cancer risk, however, the functional relevance is unknown. Here, we identify that the SNP variant-induced change in PSA biochemical activity mediates prostate cancer pathogenesis. The 'Thr' PSA variant leads to small subcutaneous tumours, supporting reduced prostate cancer risk. However, 'Thr' PSA also displays higher metastatic potential with pronounced osteolytic activity in an experimental metastasis in-vivo model. Biochemical characterisation of this PSA variant demonstrates markedly reduced proteolytic activity that correlates with differences in in-vivo tumour burden. The SNP is associated with increased risk for aggressive disease and prostate cancer-specific mortality in three independent cohorts, highlighting its critical function in mediating metastasis. Carriers of this SNP allele have reduced serum total PSA and a higher free/total PSA ratio that could contribute to late biopsy decisions and delay in diagnosis. Our results provide a molecular explanation for the prominent 19q13.3 KLK locus, rs17632542 SNP, association with a spectrum of prostate cancer clinical outcomes.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Male
Humans
*Prostatic Neoplasms/genetics/pathology/metabolism/mortality
*Polymorphism, Single Nucleotide
*Prostate-Specific Antigen/blood/metabolism
*Kallikreins/genetics/metabolism
Genetic Predisposition to Disease
Aged
Animals
Chromosomes, Human, Pair 19/genetics
Middle Aged
Mice
Alleles
Cell Line, Tumor
RevDate: 2024-11-06
Association of CD19+-Targeted Chimeric Antigen Receptor (CAR) T-cell Therapy with Hypogammaglobulinemia, Infection and Mortality.
The Journal of allergy and clinical immunology pii:S0091-6749(24)01165-5 [Epub ahead of print].
BACKGROUND: CD19-targeted chimeric antigen receptor T-cell therapy (CAR-T therapy) has revolutionized the treatment of hematologic malignancies. As these cells target CD19+ receptors on B-cells, there is the potential for B-cell aplasia and hypogammaglobulinemia. Data on the degree and clinical significance of hypogammaglobulinemia are sparse.
OBJECTIVE: To evaluate hypogammaglobulinemia after CD19-targeted CAR-T therapy and risk factors for hypogammaglobulinemia, infections, and mortality.
METHODS: We performed a retrospective evaluation of 579 patients receiving CD19-directed CAR-T therapy and evaluated demographics, hypogammaglobulinemia (immunoglobulin G [IgG]≤600mg/dL), infections pre- and post-CAR-T therapy, and risk factors for hypogammaglobulinemia, infection, hospitalizations, and mortality.
RESULTS: Patients had a mean age of 64 years and 64% were male. Prior to CAR-T therapy, 60% of patients had hypogammaglobulinemia, which increased to 91% post-CAR-T therapy. Mean IgG levels decreased from pre- to post-CAR-T therapy (587 to 362 mg/dL; p<0.0001). 37% of patients developed a serious infection post-CAR-T therapy. Hypogammaglobulinemia pre-CAR-T therapy was associated with worsening hypogammaglobulinemia post-CAR-T therapy. Hypogammaglobulinemia post-CAR-T therapy was associated with an increased risk of serious infection post-CAR-T therapy (IRR=2.7; 95% CI=1.5-5.2; p=0.002). Risk factors for mortality included mild hypogammaglobulinemia (400mg/dL
CONCLUSIONS: We identified ∼90% of patients with hypogammaglobulinemia after CAR-T therapy. Hypogammaglobulinemia pre-CAR-T therapy was strongly predictive of worsening hypogammaglobulinemia post-CAR-T therapy, which was associated with an increased risk of serious infection and mortality post-CAR-T therapy. Increased immunological monitoring is needed to identify high-risk patients who may benefit from interventions to decrease morbidity and mortality.
Additional Links: PMID-39505278
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PubMed:
Citation:
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@article {pmid39505278,
year = {2024},
author = {Sutherland, NM and Zhou, B and Zhang, L and Ong, MS and Hong, JS and Pak, A and Liu, KJ and Frigault, MJ and Maus, MV and Hill, JA and Reynolds, K and Walter, JE and Camargo, CA and Barmettler, S},
title = {Association of CD19+-Targeted Chimeric Antigen Receptor (CAR) T-cell Therapy with Hypogammaglobulinemia, Infection and Mortality.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2024.10.021},
pmid = {39505278},
issn = {1097-6825},
abstract = {BACKGROUND: CD19-targeted chimeric antigen receptor T-cell therapy (CAR-T therapy) has revolutionized the treatment of hematologic malignancies. As these cells target CD19+ receptors on B-cells, there is the potential for B-cell aplasia and hypogammaglobulinemia. Data on the degree and clinical significance of hypogammaglobulinemia are sparse.
OBJECTIVE: To evaluate hypogammaglobulinemia after CD19-targeted CAR-T therapy and risk factors for hypogammaglobulinemia, infections, and mortality.
METHODS: We performed a retrospective evaluation of 579 patients receiving CD19-directed CAR-T therapy and evaluated demographics, hypogammaglobulinemia (immunoglobulin G [IgG]≤600mg/dL), infections pre- and post-CAR-T therapy, and risk factors for hypogammaglobulinemia, infection, hospitalizations, and mortality.
RESULTS: Patients had a mean age of 64 years and 64% were male. Prior to CAR-T therapy, 60% of patients had hypogammaglobulinemia, which increased to 91% post-CAR-T therapy. Mean IgG levels decreased from pre- to post-CAR-T therapy (587 to 362 mg/dL; p<0.0001). 37% of patients developed a serious infection post-CAR-T therapy. Hypogammaglobulinemia pre-CAR-T therapy was associated with worsening hypogammaglobulinemia post-CAR-T therapy. Hypogammaglobulinemia post-CAR-T therapy was associated with an increased risk of serious infection post-CAR-T therapy (IRR=2.7; 95% CI=1.5-5.2; p=0.002). Risk factors for mortality included mild hypogammaglobulinemia (400mg/dL
CONCLUSIONS: We identified ∼90% of patients with hypogammaglobulinemia after CAR-T therapy. Hypogammaglobulinemia pre-CAR-T therapy was strongly predictive of worsening hypogammaglobulinemia post-CAR-T therapy, which was associated with an increased risk of serious infection and mortality post-CAR-T therapy. Increased immunological monitoring is needed to identify high-risk patients who may benefit from interventions to decrease morbidity and mortality.},
}
RevDate: 2024-11-06
Phase II randomized study of maintenance atezolizumab (A) versus atezolizumab + talazoparib (AT) in patients with SLFN11 positive extensive stage small cell lung cancer. S1929.
Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer pii:S1556-0864(24)02431-6 [Epub ahead of print].
PURPOSE: To evaluate whether the addition of a poly (ADP-ribose) polymerase inhibitor (PARPi) talazoparib to maintenance immune checkpoint inhibitor (ICI) atezolizumab following frontline chemoimmunotherapy improved outcomes in patients with Schlafen 11 (SLFN11)-positive extensive stage small cell lung cancer (ES-SCLC).
METHODS: Patients with newly diagnosed SLFN11 expressing (H-score ≥ 1, evaluated centrally) ES-SCLC were randomized to maintenance atezolizumab (A) versus atezolizumab plus talazoparib (AT) following frontline chemotherapy plus atezolizumab. The primary objective was to compare progression-free survival (PFS) using a 1-sided 10% level stratified log-rank test. Secondary endpoints included objective response rate (ORR), overall survival (OS), and toxicity. Target sample size was 84 eligible patients.
RESULTS: From June 15, 2020 to December 15, 2022, 106 eligible patients were randomized (54 to AT and 52 to A). PFS was improved with AT versus A (hazard ratio [HR], 0.66; 80% confidence interval [CI]: 0.50-0.86; 1-sided P = 0.019) with a median PFS of 2.9 and 2.4 months; OS was not different between groups (HR, 0.98; 80% CI: 0.71-1.36; 1-sided P = 0.47). Grade ≥ 3 non-hematologic treatment-related adverse events (TRAEs) occurred in 17% of patients with AT and 14% of patients with A. Grade ≥ 3 hematological TRAEs were more common in AT (50%) than in A (4%) (P < 0.001).
CONCLUSION: Maintenance AT improved PFS in patients with SLFN11-positive ES-SCLC that did not progress following initial chemo-immunotherapy. Hematologic toxicity, primarily grade 3 anemia, was increased with AT, as expected. Prospective biomarker-selection was demonstrated, paving the way for future evaluation of novel therapies in molecularly defined SCLC populations.
Additional Links: PMID-39505259
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@article {pmid39505259,
year = {2024},
author = {Karim, NA and Miao, J and Reckamp, KL and Gay, CM and Byers, LA and Zhao, YQ and Redman, MW and Carrizosa, DR and Wang, WL and Petty, WJ and Mehta, K and Faller, BA and Agamah, ES and Kasbari, SS and Malisetti, RK and Kumar, A and Schallenkamp, J and Alluri, KC and Gray, JE and Kelly, K},
title = {Phase II randomized study of maintenance atezolizumab (A) versus atezolizumab + talazoparib (AT) in patients with SLFN11 positive extensive stage small cell lung cancer. S1929.},
journal = {Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtho.2024.10.021},
pmid = {39505259},
issn = {1556-1380},
abstract = {PURPOSE: To evaluate whether the addition of a poly (ADP-ribose) polymerase inhibitor (PARPi) talazoparib to maintenance immune checkpoint inhibitor (ICI) atezolizumab following frontline chemoimmunotherapy improved outcomes in patients with Schlafen 11 (SLFN11)-positive extensive stage small cell lung cancer (ES-SCLC).
METHODS: Patients with newly diagnosed SLFN11 expressing (H-score ≥ 1, evaluated centrally) ES-SCLC were randomized to maintenance atezolizumab (A) versus atezolizumab plus talazoparib (AT) following frontline chemotherapy plus atezolizumab. The primary objective was to compare progression-free survival (PFS) using a 1-sided 10% level stratified log-rank test. Secondary endpoints included objective response rate (ORR), overall survival (OS), and toxicity. Target sample size was 84 eligible patients.
RESULTS: From June 15, 2020 to December 15, 2022, 106 eligible patients were randomized (54 to AT and 52 to A). PFS was improved with AT versus A (hazard ratio [HR], 0.66; 80% confidence interval [CI]: 0.50-0.86; 1-sided P = 0.019) with a median PFS of 2.9 and 2.4 months; OS was not different between groups (HR, 0.98; 80% CI: 0.71-1.36; 1-sided P = 0.47). Grade ≥ 3 non-hematologic treatment-related adverse events (TRAEs) occurred in 17% of patients with AT and 14% of patients with A. Grade ≥ 3 hematological TRAEs were more common in AT (50%) than in A (4%) (P < 0.001).
CONCLUSION: Maintenance AT improved PFS in patients with SLFN11-positive ES-SCLC that did not progress following initial chemo-immunotherapy. Hematologic toxicity, primarily grade 3 anemia, was increased with AT, as expected. Prospective biomarker-selection was demonstrated, paving the way for future evaluation of novel therapies in molecularly defined SCLC populations.},
}
RevDate: 2024-11-06
Prospective, multi-site evaluation of the Cepheid Xpert Xpress CoV-2 plus test on nasal and nasopharyngeal swabs.
Journal of clinical microbiology [Epub ahead of print].
UNLABELLED: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues its largely aseasonal spread with millions of cases per year. Highly sensitive, point-of-care testing is critical for rapid detection of coronavirus disease 2019 (COVID-19) cases and initiation of antiviral therapy to avert adverse health outcomes and reduce onward transmission of the virus. While hundreds of COVID-19 diagnostics received emergency use authorization from the FDA during the pandemic, significantly fewer have navigated the course to FDA clearance or approval. Here, we determined the clinical performance of the Cepheid Xpert Xpress CoV-2 plus for detection of SARS-CoV-2 in 3,750 anterior nasal swab (NS) specimens and nasopharyngeal swab (NPS) from 32 sites in comparison to the FDA-authorized BioFire Respiratory Panel 2.1. Three-quarters of specimens collected were tested on the Xpert Xpress CoV-2 plus in the point-of-care setting. Overall positive percent agreement (PPA) was 98.1% (95% CI: 96.7%-98.9%) and negative percent agreement (NPA) was 98.3% (97.7%-98.7%). Performance of the Xpert Xpress CoV-2 plus was slightly improved in NS compared to NPS specimens, with PPA of 99.3% versus 97.0% (Fisher's exact test, P = 0.06) and NPA of 98.3% versus 98.2% (P = 0.89), respectively. Assay PPA was similar between untrained and trained users (98.7% vs 97.3%, P = 0.75), while NPA was slightly improved for untrained users (99.0% vs 97.6%, P = 0.0003). This study showed that Cepheid Xpert Xpress COV-2 plus is highly sensitive and specific/has high PPA and NPA for detection of SARS-CoV-2 from both NS and NPS specimens.
IMPORTANCE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause millions of infections and tens of thousands of deaths per year in the United States. While the FDA authorized hundreds of SARS-CoV-2 tests during the public health emergency, significantly fewer have made the transition to being cleared or approved. There continues to be a need for FDA-authorized point-of-care SARS-CoV-2 testing that can be performed by untrained users. We conducted a large prospective study of the Cepheid Xpert Xpress CoV-2 plus test for detection of SARS-CoV-2 in both nasal and nasopharyngeal swabs by trained and untrained users. The assay demonstrated excellent clinical performance characteristics and, as a result of this study, was cleared by the FDA.
Additional Links: PMID-39503494
Publisher:
PubMed:
Citation:
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@article {pmid39503494,
year = {2024},
author = {Greninger, AL and Larcena, A and Patel, A and Webster, B and Ulen, C and Green, DF and King, D and Patel, DR and McElvania, E and Harnett, G and Jandali, I and Gibson, J and Killion, J and Atwi, J and Bergmann, K and Slade, L and Allen Staat, M and Faron, M and Washington, M and Patel, R and Annamalai, R and Ackerman, R and Stewart, WP and Amador, YM and Rao, D and Liu, X and Raman, A},
title = {Prospective, multi-site evaluation of the Cepheid Xpert Xpress CoV-2 plus test on nasal and nasopharyngeal swabs.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0121924},
doi = {10.1128/jcm.01219-24},
pmid = {39503494},
issn = {1098-660X},
abstract = {UNLABELLED: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues its largely aseasonal spread with millions of cases per year. Highly sensitive, point-of-care testing is critical for rapid detection of coronavirus disease 2019 (COVID-19) cases and initiation of antiviral therapy to avert adverse health outcomes and reduce onward transmission of the virus. While hundreds of COVID-19 diagnostics received emergency use authorization from the FDA during the pandemic, significantly fewer have navigated the course to FDA clearance or approval. Here, we determined the clinical performance of the Cepheid Xpert Xpress CoV-2 plus for detection of SARS-CoV-2 in 3,750 anterior nasal swab (NS) specimens and nasopharyngeal swab (NPS) from 32 sites in comparison to the FDA-authorized BioFire Respiratory Panel 2.1. Three-quarters of specimens collected were tested on the Xpert Xpress CoV-2 plus in the point-of-care setting. Overall positive percent agreement (PPA) was 98.1% (95% CI: 96.7%-98.9%) and negative percent agreement (NPA) was 98.3% (97.7%-98.7%). Performance of the Xpert Xpress CoV-2 plus was slightly improved in NS compared to NPS specimens, with PPA of 99.3% versus 97.0% (Fisher's exact test, P = 0.06) and NPA of 98.3% versus 98.2% (P = 0.89), respectively. Assay PPA was similar between untrained and trained users (98.7% vs 97.3%, P = 0.75), while NPA was slightly improved for untrained users (99.0% vs 97.6%, P = 0.0003). This study showed that Cepheid Xpert Xpress COV-2 plus is highly sensitive and specific/has high PPA and NPA for detection of SARS-CoV-2 from both NS and NPS specimens.
IMPORTANCE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause millions of infections and tens of thousands of deaths per year in the United States. While the FDA authorized hundreds of SARS-CoV-2 tests during the public health emergency, significantly fewer have made the transition to being cleared or approved. There continues to be a need for FDA-authorized point-of-care SARS-CoV-2 testing that can be performed by untrained users. We conducted a large prospective study of the Cepheid Xpert Xpress CoV-2 plus test for detection of SARS-CoV-2 in both nasal and nasopharyngeal swabs by trained and untrained users. The assay demonstrated excellent clinical performance characteristics and, as a result of this study, was cleared by the FDA.},
}
RevDate: 2024-11-06
An integrated view of the structure and function of the human 4D nucleome.
bioRxiv : the preprint server for biology.
The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connections between chromosome folding, nuclear organization, chromatin looping, gene transcription, and DNA replication. We demonstrate the use of computational methods to predict genome folding from DNA sequence, uncovering potential effects of genetic variants on genome structure and function. Together, this comprehensive analysis contributes insights into human genome organization and enhances our understanding of connections between the regulation of genome function and 3D genome organization in general.
Additional Links: PMID-39484446
PubMed:
Citation:
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@article {pmid39484446,
year = {2024},
author = {, and Dekker, J and Oksuz, BA and Zhang, Y and Wang, Y and Minsk, MK and Kuang, S and Yang, L and Gibcus, JH and Krietenstein, N and Rando, OJ and Xu, J and Janssens, DH and Henikoff, S and Kukalev, A and Willemin, A and Winick-Ng, W and Kempfer, R and Pombo, A and Yu, M and Kumar, P and Zhang, L and Belmont, AS and Sasaki, T and van Schaik, T and Brueckner, L and Peric-Hupkes, D and van Steensel, B and Wang, P and Chai, H and Kim, M and Ruan, Y and Zhang, R and Quinodoz, SA and Bhat, P and Guttman, M and Zhao, W and Chien, S and Liu, Y and Venev, SV and Plewczynski, D and Azcarate, II and Szabó, D and Thieme, CJ and Szczepińska, T and Chiliński, M and Sengupta, K and Conte, M and Esposito, A and Abraham, A and Zhang, R and Wang, Y and Wen, X and Wu, Q and Yang, Y and Liu, J and Boninsegna, L and Yildirim, A and Zhan, Y and Chiariello, AM and Bianco, S and Lee, L and Hu, M and Li, Y and Barnett, RJ and Cook, AL and Emerson, DJ and Marchal, C and Zhao, P and Park, P and Alver, BH and Schroeder, A and Navelkar, R and Bakker, C and Ronchetti, W and Ehmsen, S and Veit, A and Gehlenborg, N and Wang, T and Li, D and Wang, X and Nicodemi, M and Ren, B and Zhong, S and Phillips-Cremins, JE and Gilbert, DM and Pollard, KS and Alber, F and Ma, J and Noble, WS and Yue, F},
title = {An integrated view of the structure and function of the human 4D nucleome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39484446},
issn = {2692-8205},
support = {U54 DK107981/DK/NIDDK NIH HHS/United States ; U54 DK107977/DK/NIDDK NIH HHS/United States ; U54 DK107967/DK/NIDDK NIH HHS/United States ; U01 DA052715/DA/NIDA NIH HHS/United States ; U01 CA200060/CA/NCI NIH HHS/United States ; U54 DK107979/DK/NIDDK NIH HHS/United States ; U01 DK127405/DK/NIDDK NIH HHS/United States ; U01 HL129998/HL/NHLBI NIH HHS/United States ; U01 CA200147/CA/NCI NIH HHS/United States ; UM1 HG011593/HG/NHGRI NIH HHS/United States ; U01 HL130007/HL/NHLBI NIH HHS/United States ; UM1 HG011536/HG/NHGRI NIH HHS/United States ; T32 GM152342/GM/NIGMS NIH HHS/United States ; U54 DK107980/DK/NIDDK NIH HHS/United States ; U01 DA052769/DA/NIDA NIH HHS/United States ; U01 DA040612/DA/NIDA NIH HHS/United States ; U01 DK127420/DK/NIDDK NIH HHS/United States ; U54 DK107965/DK/NIDDK NIH HHS/United States ; UM1 HG011585/HG/NHGRI NIH HHS/United States ; U01 CA200059/CA/NCI NIH HHS/United States ; U01 HL157989/HL/NHLBI NIH HHS/United States ; },
abstract = {The dynamic three-dimensional (3D) organization of the human genome (the "4D Nucleome") is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connections between chromosome folding, nuclear organization, chromatin looping, gene transcription, and DNA replication. We demonstrate the use of computational methods to predict genome folding from DNA sequence, uncovering potential effects of genetic variants on genome structure and function. Together, this comprehensive analysis contributes insights into human genome organization and enhances our understanding of connections between the regulation of genome function and 3D genome organization in general.},
}
RevDate: 2024-11-05
CmpDate: 2024-11-05
DNA Damage Response Alterations Predict for Neoadjuvant Chemotherapy Sensitivity in Muscle-Invasive Bladder Cancer: A Correlative Analysis of the SWOG S1314 Trial.
JCO precision oncology, 8:e2400287.
PURPOSE: Alterations in DNA damage response (DDR) genes, including ERCC2, have been correlated with response to neoadjuvant cisplatin-based chemotherapy (NAC) in patients with muscle-invasive bladder cancer (MIBC). The SWOG 1314 (S1314) trial enrolled patients with MIBC who received one of two NAC regimens followed by radical cystectomy. We examined the prevalence of DDR alterations in NAC responders versus nonresponders and correlated DDR alteration status with response.
METHODS: Pretreatment tumor specimens from 179 evaluable patients underwent next-generation sequencing (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets assay). Associations were determined between any or only deleterious alterations within nine predefined DDR genes, or any alterations in ERCC2, and progression-free survival (PFS) and overall survival using Cox regression, and, in a subset of evaluable patients, pathologic response (complete response, pT0, or downstaging to
RESULTS: Deleterious DDR alterations were detected in 41 (23%) of 179 patients. Of the 151 patients evaluable for pathologic response, patients with deleterious DDR alterations (n = 39) demonstrated a higher pathologic response rate than those without (odds ratio [OR], 3.24 [95% CI, 1.51 to 6.94]; P = .003). In 24 ERCC2-mutant patients, the OR for pT0 was 3.33 (95% CI, 1.35 to 8.22; P = .009) and for
CONCLUSION: Deleterious DDR alterations were associated with pathologic response following NAC in S1314. Functional validation of ERCC2 and other DDR alterations is underway to help refine such alterations as biomarkers of NAC in patients with bladder cancer.
Additional Links: PMID-39499893
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PubMed:
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@article {pmid39499893,
year = {2024},
author = {Iyer, G and Tangen, CM and Sarfaty, M and Regazzi, AM and Lee, IL and Fong, M and Choi, W and Dinney, CPN and Flaig, TW and Thompson, IM and Lerner, SP and McConkey, DJ and Rosenberg, JE},
title = {DNA Damage Response Alterations Predict for Neoadjuvant Chemotherapy Sensitivity in Muscle-Invasive Bladder Cancer: A Correlative Analysis of the SWOG S1314 Trial.},
journal = {JCO precision oncology},
volume = {8},
number = {},
pages = {e2400287},
doi = {10.1200/PO.24.00287},
pmid = {39499893},
issn = {2473-4284},
mesh = {Humans ; *Urinary Bladder Neoplasms/drug therapy/genetics/pathology ; Male ; Female ; *Neoadjuvant Therapy ; Middle Aged ; Aged ; *DNA Damage ; Xeroderma Pigmentosum Group D Protein/genetics ; Cisplatin/therapeutic use ; Neoplasm Invasiveness ; Adult ; },
abstract = {PURPOSE: Alterations in DNA damage response (DDR) genes, including ERCC2, have been correlated with response to neoadjuvant cisplatin-based chemotherapy (NAC) in patients with muscle-invasive bladder cancer (MIBC). The SWOG 1314 (S1314) trial enrolled patients with MIBC who received one of two NAC regimens followed by radical cystectomy. We examined the prevalence of DDR alterations in NAC responders versus nonresponders and correlated DDR alteration status with response.
METHODS: Pretreatment tumor specimens from 179 evaluable patients underwent next-generation sequencing (Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets assay). Associations were determined between any or only deleterious alterations within nine predefined DDR genes, or any alterations in ERCC2, and progression-free survival (PFS) and overall survival using Cox regression, and, in a subset of evaluable patients, pathologic response (complete response, pT0, or downstaging to
RESULTS: Deleterious DDR alterations were detected in 41 (23%) of 179 patients. Of the 151 patients evaluable for pathologic response, patients with deleterious DDR alterations (n = 39) demonstrated a higher pathologic response rate than those without (odds ratio [OR], 3.24 [95% CI, 1.51 to 6.94]; P = .003). In 24 ERCC2-mutant patients, the OR for pT0 was 3.33 (95% CI, 1.35 to 8.22; P = .009) and for
CONCLUSION: Deleterious DDR alterations were associated with pathologic response following NAC in S1314. Functional validation of ERCC2 and other DDR alterations is underway to help refine such alterations as biomarkers of NAC in patients with bladder cancer.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Urinary Bladder Neoplasms/drug therapy/genetics/pathology
Male
Female
*Neoadjuvant Therapy
Middle Aged
Aged
*DNA Damage
Xeroderma Pigmentosum Group D Protein/genetics
Cisplatin/therapeutic use
Neoplasm Invasiveness
Adult
RevDate: 2024-11-05
Influence of physical activity measurement on the association between Life's Essential 8 and incident cardiovascular disease in older women.
Preventive medicine reports, 47:102904.
OBJECTIVE: The American Heart Association's Life's Essential 8 (LE8) metric includes self-reported physical activity as one of the metrics for assessing cardiovascular health. Self-reported physical activity is prone to misclassification, whereas accelerometer measures are less biased. We examined associations of LE8 and incident cardiovascular disease (CVD) using self-reported and accelerometer-measured physical activity.
METHODS: Participants in the Women's Health Initiative (WHI) Objective Physical Activity and Cardiovascular Health Study (n = 4,243; mean age = 79 ± 7 years) with no CVD history completed the WHI physical activity questionnaire and the Community Healthy Activities Model Program for Seniors (CHAMPS) questionnaire prior to wearing a hip-worn accelerometer for up to seven days in 2012-2014. LE8 components (physical activity, diet, sleep, body mass index, smoking, blood pressure, non-HDL cholesterol, and glucose) were scored according to guidelines. Scores were created using five physical activity measures: WHI questionnaire (LE8WHI), CHAMPS (LE8CHAMPS), accelerometer-measured physical activity (LE8A), and sample quantiles of accelerometer-measured physical activity (LE8AQ) and daily steps (LE8STEPS). Hazard ratios (HR) for physician-adjudicated CVD were estimated using Cox regression.
RESULTS: 707 incident CVD events occurred over an average 7.5 years. Multivariable HRs (95 % CI) comparing women in the highest vs. lowest quartiles of LE8 scores were: LE8WHI = 0.53 (0.43-0.67), LE8CHAMPS = 0.47 (0.38-0.60), LE8A = 0.44 (0.36-0.56), LE8AQ = 0.44 (0.35-0.55), and LE8STEPS = 0.45 (0.35-0.57).
CONCLUSIONS: The LE8-incident CVD association varies by physical activity measurement, however all methods showed reduced risk. Device-measures of physical activity may be more accurate in the LE8, but when impractical to implement, also support use of self-reported measures.
Additional Links: PMID-39498208
PubMed:
Citation:
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@article {pmid39498208,
year = {2024},
author = {Hyde, ET and Nguyen, S and LaMonte, MJ and Di, C and Bellettiere, J and Tinker, LF and Foraker, RE and Tindle, HA and Stefanick, ML and LaCroix, AZ},
title = {Influence of physical activity measurement on the association between Life's Essential 8 and incident cardiovascular disease in older women.},
journal = {Preventive medicine reports},
volume = {47},
number = {},
pages = {102904},
pmid = {39498208},
issn = {2211-3355},
abstract = {OBJECTIVE: The American Heart Association's Life's Essential 8 (LE8) metric includes self-reported physical activity as one of the metrics for assessing cardiovascular health. Self-reported physical activity is prone to misclassification, whereas accelerometer measures are less biased. We examined associations of LE8 and incident cardiovascular disease (CVD) using self-reported and accelerometer-measured physical activity.
METHODS: Participants in the Women's Health Initiative (WHI) Objective Physical Activity and Cardiovascular Health Study (n = 4,243; mean age = 79 ± 7 years) with no CVD history completed the WHI physical activity questionnaire and the Community Healthy Activities Model Program for Seniors (CHAMPS) questionnaire prior to wearing a hip-worn accelerometer for up to seven days in 2012-2014. LE8 components (physical activity, diet, sleep, body mass index, smoking, blood pressure, non-HDL cholesterol, and glucose) were scored according to guidelines. Scores were created using five physical activity measures: WHI questionnaire (LE8WHI), CHAMPS (LE8CHAMPS), accelerometer-measured physical activity (LE8A), and sample quantiles of accelerometer-measured physical activity (LE8AQ) and daily steps (LE8STEPS). Hazard ratios (HR) for physician-adjudicated CVD were estimated using Cox regression.
RESULTS: 707 incident CVD events occurred over an average 7.5 years. Multivariable HRs (95 % CI) comparing women in the highest vs. lowest quartiles of LE8 scores were: LE8WHI = 0.53 (0.43-0.67), LE8CHAMPS = 0.47 (0.38-0.60), LE8A = 0.44 (0.36-0.56), LE8AQ = 0.44 (0.35-0.55), and LE8STEPS = 0.45 (0.35-0.57).
CONCLUSIONS: The LE8-incident CVD association varies by physical activity measurement, however all methods showed reduced risk. Device-measures of physical activity may be more accurate in the LE8, but when impractical to implement, also support use of self-reported measures.},
}
RevDate: 2024-11-04
CmpDate: 2024-11-04
National Liver Cancer Screening Trial (TRACER) study protocol.
Hepatology communications, 8(11):.
BACKGROUND: Professional guidelines recommend HCC screening in at-risk patients using semi-annual ultrasound with or without alpha-fetoprotein (AFP); however, this strategy has limited effectiveness due to low adherence and sensitivity. Increasing data support the potential role of blood-based biomarker panels, which could improve both aspects. The biomarker panel GALAD, comprised of sex, age, and 3 blood biomarkers (AFP, AFP-L3, and des-carboxy prothrombin des-carboxy prothrombin), has shown high sensitivity and specificity in biomarker phase II (case-control) and phase III (retrospective cohort) validation studies. However, prospective validation in a large phase IV biomarker clinical utility trial is necessary before its adoption in practice.
METHODS: The National Liver Cancer Screening Trial is an adaptive pragmatic randomized phase IV trial, which began enrollment in January 2024, comparing ultrasound-based versus biomarker-based screening in 5500 patients with chronic hepatitis B infection or cirrhosis from any etiology. Eligible patients are randomly assigned in a 1:1 ratio to semi-annual screening with ultrasound ± alpha-fetoprotein (arm A) or semi-annual screening with GALAD (arm B). Randomization is stratified by enrollment site, liver disease severity (per Child-Pugh class), liver disease etiology (viral, nonviral, and noncirrhotic HBV), and sex. Patients are being recruited from 15 sites (a mix of tertiary care academic referral centers, safety-net health systems, and large community health systems) over a 3-year period, and the primary endpoint, reduction in late-stage HCC, will be assessed at the end of year 5.5.
DISCUSSION: The results of this trial will inform the best strategy for HCC screening and early-stage detection in patients with chronic liver diseases. If GALAD shows superiority, HCC screening would primarily shift from an ultrasound-based strategy to the adoption of the biomarker panel.
TRIAL REGISTRATION: NCT06084234.
TRIAL STATUS: The TRACER Study is actively enrolling.
Additional Links: PMID-39495136
PubMed:
Citation:
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@article {pmid39495136,
year = {2024},
author = {Singal, AG and Parikh, ND and Kanwal, F and Marrero, JA and Deodhar, S and Page-Lester, S and Lopez, C and Feng, Z and Tayob, N},
title = {National Liver Cancer Screening Trial (TRACER) study protocol.},
journal = {Hepatology communications},
volume = {8},
number = {11},
pages = {},
pmid = {39495136},
issn = {2471-254X},
mesh = {Humans ; *Liver Neoplasms/diagnosis/blood/diagnostic imaging ; *Early Detection of Cancer/methods ; *alpha-Fetoproteins/analysis ; *Carcinoma, Hepatocellular/diagnosis/blood/diagnostic imaging ; Male ; Female ; *Biomarkers, Tumor/blood ; Prothrombin/analysis ; Ultrasonography ; Hepatitis B, Chronic/diagnosis/blood ; Middle Aged ; Protein Precursors/blood ; Adult ; Liver Cirrhosis/blood/diagnosis/diagnostic imaging ; Aged ; Pragmatic Clinical Trials as Topic ; Biomarkers ; },
abstract = {BACKGROUND: Professional guidelines recommend HCC screening in at-risk patients using semi-annual ultrasound with or without alpha-fetoprotein (AFP); however, this strategy has limited effectiveness due to low adherence and sensitivity. Increasing data support the potential role of blood-based biomarker panels, which could improve both aspects. The biomarker panel GALAD, comprised of sex, age, and 3 blood biomarkers (AFP, AFP-L3, and des-carboxy prothrombin des-carboxy prothrombin), has shown high sensitivity and specificity in biomarker phase II (case-control) and phase III (retrospective cohort) validation studies. However, prospective validation in a large phase IV biomarker clinical utility trial is necessary before its adoption in practice.
METHODS: The National Liver Cancer Screening Trial is an adaptive pragmatic randomized phase IV trial, which began enrollment in January 2024, comparing ultrasound-based versus biomarker-based screening in 5500 patients with chronic hepatitis B infection or cirrhosis from any etiology. Eligible patients are randomly assigned in a 1:1 ratio to semi-annual screening with ultrasound ± alpha-fetoprotein (arm A) or semi-annual screening with GALAD (arm B). Randomization is stratified by enrollment site, liver disease severity (per Child-Pugh class), liver disease etiology (viral, nonviral, and noncirrhotic HBV), and sex. Patients are being recruited from 15 sites (a mix of tertiary care academic referral centers, safety-net health systems, and large community health systems) over a 3-year period, and the primary endpoint, reduction in late-stage HCC, will be assessed at the end of year 5.5.
DISCUSSION: The results of this trial will inform the best strategy for HCC screening and early-stage detection in patients with chronic liver diseases. If GALAD shows superiority, HCC screening would primarily shift from an ultrasound-based strategy to the adoption of the biomarker panel.
TRIAL REGISTRATION: NCT06084234.
TRIAL STATUS: The TRACER Study is actively enrolling.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Liver Neoplasms/diagnosis/blood/diagnostic imaging
*Early Detection of Cancer/methods
*alpha-Fetoproteins/analysis
*Carcinoma, Hepatocellular/diagnosis/blood/diagnostic imaging
Male
Female
*Biomarkers, Tumor/blood
Prothrombin/analysis
Ultrasonography
Hepatitis B, Chronic/diagnosis/blood
Middle Aged
Protein Precursors/blood
Adult
Liver Cirrhosis/blood/diagnosis/diagnostic imaging
Aged
Pragmatic Clinical Trials as Topic
Biomarkers
RevDate: 2024-11-04
A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.
Virus evolution, 10(1):veae083.
In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis.
Additional Links: PMID-39493537
PubMed:
Citation:
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@article {pmid39493537,
year = {2024},
author = {Colquhoun, R and O'Toole, Á and Hill, V and McCrone, JT and Yu, X and Nicholls, SM and Poplawski, R and Whalley, T and Groves, N and Ellaby, N and Loman, N and Connor, T and Rambaut, A},
title = {A phylogenetics and variant calling pipeline to support SARS-CoV-2 genomic epidemiology in the UK.},
journal = {Virus evolution},
volume = {10},
number = {1},
pages = {veae083},
pmid = {39493537},
issn = {2057-1577},
abstract = {In response to the escalating SARS-CoV-2 pandemic, in March 2020 the COVID-19 Genomics UK (COG-UK) consortium was established to enable national-scale genomic surveillance in the UK. By the end of 2020, 49% of all SARS-CoV-2 genome sequences globally had been generated as part of the COG-UK programme, and to date, this system has generated >3 million SARS-CoV-2 genomes. Rapidly and reliably analysing this unprecedented number of genomes was an enormous challenge. To fulfil this need and to inform public health decision-making, we developed a centralized pipeline that performs quality control, alignment, and variant calling and provides the global phylogenetic context of sequences. We present this pipeline and describe how we tailored it as the pandemic progressed to scale with the increasing amounts of data and to provide the most relevant analyses on a daily basis.},
}
RevDate: 2024-11-04
Current and future strategies for the prevention and treatment of cytomegalovirus infections in transplantation.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:7874563 [Epub ahead of print].
Successful prevention and treatment of cytomegalovirus (CMV) infection remains a central focus of clinical care in solid organ and allogeneic hematopoietic cell transplantation. Over the past 5 years, pivotal clinical trials have created new paradigms in CMV prevention, including diverging approaches in HCT and SOT. We review recent advances in CMV risk assessment and progress in antiviral and immune-based strategies for CMV prevention and treatment. We highlight approaches to optimize CMV-specific immunity through vaccination, monoclonal antibodies, and virus-specific T-cells. Observational studies and interventional trials of commercially-available CMV cell-mediated immunity assays for refining preventive and treatment strategies are summarized. Finally, we discuss the importance of enhancing CMV-specific immunity to mitigate the negative impacts of CMV in different transplant settings. CMV infections in recipients of chimeric antigen receptor-T (CAR-T) cell therapies and other immunocompromised populations are growing areas of importance that are beyond the scope of this review.
Additional Links: PMID-39492698
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PubMed:
Citation:
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@article {pmid39492698,
year = {2024},
author = {Heldman, MR and Boeckh, MJ and Limaye, AP},
title = {Current and future strategies for the prevention and treatment of cytomegalovirus infections in transplantation.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciae535},
pmid = {39492698},
issn = {1537-6591},
abstract = {Successful prevention and treatment of cytomegalovirus (CMV) infection remains a central focus of clinical care in solid organ and allogeneic hematopoietic cell transplantation. Over the past 5 years, pivotal clinical trials have created new paradigms in CMV prevention, including diverging approaches in HCT and SOT. We review recent advances in CMV risk assessment and progress in antiviral and immune-based strategies for CMV prevention and treatment. We highlight approaches to optimize CMV-specific immunity through vaccination, monoclonal antibodies, and virus-specific T-cells. Observational studies and interventional trials of commercially-available CMV cell-mediated immunity assays for refining preventive and treatment strategies are summarized. Finally, we discuss the importance of enhancing CMV-specific immunity to mitigate the negative impacts of CMV in different transplant settings. CMV infections in recipients of chimeric antigen receptor-T (CAR-T) cell therapies and other immunocompromised populations are growing areas of importance that are beyond the scope of this review.},
}
RevDate: 2024-11-01
A novel PhoPQ-potentiated mechanism of colistin resistance impairs membrane integrity in Pseudomonas aeruginosa.
bioRxiv : the preprint server for biology.
Polymicrobial communities are often recalcitrant to antibiotic treatment because interactions between different microbes can dramatically alter their responses and susceptibility to antimicrobials. However, the mechanisms of evolving antimicrobial resistance in such polymicrobial environments are poorly understood. We previously reported that Mg[2+] depletion caused by the fungus Candida albicans can enable Pseudomonas aeruginosa to acquire significant resistance to colistin, a last-resort antibiotic targeting bacterial membrane. Here, we dissect the genetic and biochemical basis of this increased colistin resistance. We show that P. aeruginosa cells can acquire colistin resistance using three distinct evolutionary trajectories involving mutations in genes involved in lipid A biosynthesis, lipid A modifications that are dependent on low Mg[2+], and a putative Mg[2+] transporter, PA4824. These mutations confer colistin resistance by altering acyl chains, hydroxylation, and aminoarabinose modification of lipid A moieties on the bacterial outer membrane. In all cases, enhanced colistin resistance initially depends on the low Mg[2+]-responsive PhoPQ pathway, which potentiates the evolution of resistance mutations and lipid A modifications that do not occur without Mg[2+] depletion. However, the PhoPQ pathway is not required to maintain high colistin resistance in all cases. In most cases, the genetic and biochemical changes associated with these novel forms of colistin resistance also impair bacterial membrane integrity, leading to fitness costs. Our findings provide molecular insights into how nutritional competition drives a novel antibiotic resistance mechanism and its ensuing fitness tradeoffs.
Additional Links: PMID-39464160
PubMed:
Citation:
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@article {pmid39464160,
year = {2024},
author = {Hsieh, YP and O'Keefe, IP and Sun, W and Wang, Z and Yang, H and Vu, LM and Ernst, RK and Dandekar, AA and Malik, HS},
title = {A novel PhoPQ-potentiated mechanism of colistin resistance impairs membrane integrity in Pseudomonas aeruginosa.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39464160},
issn = {2692-8205},
support = {R01 AI104895/AI/NIAID NIH HHS/United States ; R35 GM152107/GM/NIGMS NIH HHS/United States ; },
abstract = {Polymicrobial communities are often recalcitrant to antibiotic treatment because interactions between different microbes can dramatically alter their responses and susceptibility to antimicrobials. However, the mechanisms of evolving antimicrobial resistance in such polymicrobial environments are poorly understood. We previously reported that Mg[2+] depletion caused by the fungus Candida albicans can enable Pseudomonas aeruginosa to acquire significant resistance to colistin, a last-resort antibiotic targeting bacterial membrane. Here, we dissect the genetic and biochemical basis of this increased colistin resistance. We show that P. aeruginosa cells can acquire colistin resistance using three distinct evolutionary trajectories involving mutations in genes involved in lipid A biosynthesis, lipid A modifications that are dependent on low Mg[2+], and a putative Mg[2+] transporter, PA4824. These mutations confer colistin resistance by altering acyl chains, hydroxylation, and aminoarabinose modification of lipid A moieties on the bacterial outer membrane. In all cases, enhanced colistin resistance initially depends on the low Mg[2+]-responsive PhoPQ pathway, which potentiates the evolution of resistance mutations and lipid A modifications that do not occur without Mg[2+] depletion. However, the PhoPQ pathway is not required to maintain high colistin resistance in all cases. In most cases, the genetic and biochemical changes associated with these novel forms of colistin resistance also impair bacterial membrane integrity, leading to fitness costs. Our findings provide molecular insights into how nutritional competition drives a novel antibiotic resistance mechanism and its ensuing fitness tradeoffs.},
}
RevDate: 2024-11-03
Efficacy of a conversational chatbot for cigarette smoking cessation: Protocol of the QuitBot full-scale randomized controlled trial.
Contemporary clinical trials pii:S1551-7144(24)00310-0 [Epub ahead of print].
Globally, cigarette smoking results in over 8 million premature annual deaths. Addressing this issue requires high-impact, cost-effective population-level interventions for smoking cessation. Conversational chatbots offer a potential solution given the recent advancements in machine learning and large language models. Chatbots can deliver supportive, empathetic behaviors, personalized responses, and timely advice tailored to users' needs that is engaging through therapeutic conversations aimed at creating lasting social-emotional connections. Despite their promise, little is known about the efficacy and underlying mechanisms of chatbots for cigarette smoking cessation. We developed QuitBot, a quit smoking program of two to three-minute conversations covering topics ranging from motivations to quit, setting a quit date, choosing cessation medications, coping with triggers, maintaining abstinence, and recovering from relapse. QuitBot employs conversational interactions, powered by an expert-curated large language model, allowing users to ask questions and receive personalized guidance on quitting smoking. Here, we report the design and execution of a randomized clinical trial comparing QuitBot (n = 760) against Smokefree TXT (SFT) text messaging program (n = 760), with a 12-month follow-up period. Both interventions include 42-days of content on motivations to quit, skills to cope with triggers, and relapse prevention. The key distinction between QuitBot and SFT is the communication and engagement feature of QuitBot. This study aims to determine: whether QuitBot yields higher quit rates than SFT; and whether therapeutic alliance processes and engagement are mechanisms underlying cessation outcomes. Additionally, we will explore whether baseline factors including trust, social support, and demographics, moderate the efficacy of QuitBot. Trial Registration numberClinicalTrials.govNCT04308759.
Additional Links: PMID-39490766
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PubMed:
Citation:
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@article {pmid39490766,
year = {2024},
author = {Bricker, JB and Sullivan, BM and Mull, KE and Lavista-Ferres, J and Santiago-Torres, M},
title = {Efficacy of a conversational chatbot for cigarette smoking cessation: Protocol of the QuitBot full-scale randomized controlled trial.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107727},
doi = {10.1016/j.cct.2024.107727},
pmid = {39490766},
issn = {1559-2030},
abstract = {Globally, cigarette smoking results in over 8 million premature annual deaths. Addressing this issue requires high-impact, cost-effective population-level interventions for smoking cessation. Conversational chatbots offer a potential solution given the recent advancements in machine learning and large language models. Chatbots can deliver supportive, empathetic behaviors, personalized responses, and timely advice tailored to users' needs that is engaging through therapeutic conversations aimed at creating lasting social-emotional connections. Despite their promise, little is known about the efficacy and underlying mechanisms of chatbots for cigarette smoking cessation. We developed QuitBot, a quit smoking program of two to three-minute conversations covering topics ranging from motivations to quit, setting a quit date, choosing cessation medications, coping with triggers, maintaining abstinence, and recovering from relapse. QuitBot employs conversational interactions, powered by an expert-curated large language model, allowing users to ask questions and receive personalized guidance on quitting smoking. Here, we report the design and execution of a randomized clinical trial comparing QuitBot (n = 760) against Smokefree TXT (SFT) text messaging program (n = 760), with a 12-month follow-up period. Both interventions include 42-days of content on motivations to quit, skills to cope with triggers, and relapse prevention. The key distinction between QuitBot and SFT is the communication and engagement feature of QuitBot. This study aims to determine: whether QuitBot yields higher quit rates than SFT; and whether therapeutic alliance processes and engagement are mechanisms underlying cessation outcomes. Additionally, we will explore whether baseline factors including trust, social support, and demographics, moderate the efficacy of QuitBot. Trial Registration numberClinicalTrials.govNCT04308759.},
}
RevDate: 2024-11-03
A Winding Road to Health Care Equity in Sickle Cell Disease.
Clinics in laboratory medicine, 44(4):693-704.
Sickle cell disease (SCD) is a genetic disorder where red blood cells sickle, causing anemia and pain. Historically linked to marginalized groups, SCD saw little progress in treatment strategies for decades. Addressing these requires holistic strategies including dedicated centers, education, patient inclusion, and tackling implicit bias. Efforts must ensure treatments are accessible and stigma-free. Progress depends on collaboration and advocacy, aiming for an equitable, patient-focused health care system responsive to the unique needs of those with SCD. This review illustrates the actionable steps that the medical community can take to improve care for patients with SCD.
Additional Links: PMID-39490125
Publisher:
PubMed:
Citation:
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@article {pmid39490125,
year = {2024},
author = {Walia, R and Fertrin, KY and Sabath, DE},
title = {A Winding Road to Health Care Equity in Sickle Cell Disease.},
journal = {Clinics in laboratory medicine},
volume = {44},
number = {4},
pages = {693-704},
doi = {10.1016/j.cll.2024.07.005},
pmid = {39490125},
issn = {1557-9832},
abstract = {Sickle cell disease (SCD) is a genetic disorder where red blood cells sickle, causing anemia and pain. Historically linked to marginalized groups, SCD saw little progress in treatment strategies for decades. Addressing these requires holistic strategies including dedicated centers, education, patient inclusion, and tackling implicit bias. Efforts must ensure treatments are accessible and stigma-free. Progress depends on collaboration and advocacy, aiming for an equitable, patient-focused health care system responsive to the unique needs of those with SCD. This review illustrates the actionable steps that the medical community can take to improve care for patients with SCD.},
}
RevDate: 2024-11-03
History, Advances, and Challenges of Sickle Cell Disease Treatment.
Clinics in laboratory medicine, 44(4):679-691.
Sickle cell disease (SCD) is marked by red blood cells that deform into a sickle shape, causing severe health complications. Historic neglect and slow therapeutic progress have left many, especially African descendants, vulnerable. Recent treatment strides include novel drugs and gene therapy, promising improved management. Nonetheless, challenges persist with treatment adoption because of cost, adverse effects, and accessibility. Advancements hold hope for enhanced life quality and longevity for SCD patients.
Additional Links: PMID-39490124
Publisher:
PubMed:
Citation:
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@article {pmid39490124,
year = {2024},
author = {Walia, R and Fertrin, KY and Sabath, DE},
title = {History, Advances, and Challenges of Sickle Cell Disease Treatment.},
journal = {Clinics in laboratory medicine},
volume = {44},
number = {4},
pages = {679-691},
doi = {10.1016/j.cll.2024.07.004},
pmid = {39490124},
issn = {1557-9832},
abstract = {Sickle cell disease (SCD) is marked by red blood cells that deform into a sickle shape, causing severe health complications. Historic neglect and slow therapeutic progress have left many, especially African descendants, vulnerable. Recent treatment strides include novel drugs and gene therapy, promising improved management. Nonetheless, challenges persist with treatment adoption because of cost, adverse effects, and accessibility. Advancements hold hope for enhanced life quality and longevity for SCD patients.},
}
RevDate: 2024-11-03
Introducing a G-Makassar variant in HSCs by in vivo base editing treats sickle cell disease in mice.
Molecular therapy : the journal of the American Society of Gene Therapy pii:S1525-0016(24)00678-6 [Epub ahead of print].
Precise repair of the pathogenic mutation in hematopoietic stem cells (HSCs) represents an ideal cure for patients with sickle cell disease (SCD). Here, we demonstrated correction of the SCD phenotype by converting the sickle mutation codon (GTG) into a benign G-Makassar variant (GCG) using in vivo base editing in HSCs. We demonstrated successful production of helper-dependent adenoviral vectors expressing an all-in-one base editor mapping to the sickle mutation site. In HSC-enriched cells from SCD patients, transduction with the base editing vector in vitro resulted in 35% GTG > GCG conversion and phenotypic improvements of derived red blood cells. After ex vivo transduction of HSCs from a SCD mouse model and subsequent transplantation, we achieved an average of 88% editing at the target site in transplanted mice. Importantly, in vivo HSC base editing followed by selection generated 24.5% Makassar variant in long-term repopulating HSCs of SCD mice. The treated animals demonstrated correction of disease hallmarks without showing noticeable side effects. Off-target analyses at top-scored genomic sites revealed no off-target editing. This in vivo approach requires only one non-integrating vector, only intravenous/subcutaneous injections, and minimal in vivo selection. This technically simple approach has the potential for scalable applications in resource-limiting regions where SCD is prevalent.
Additional Links: PMID-39489920
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@article {pmid39489920,
year = {2024},
author = {Li, C and Georgakopoulou, A and Paschoudi, K and Anderson, AK and Huang, L and Gil, S and Giannaki, M and Vlachaki, E and Newby, GA and Liu, DR and Yannaki, E and Kiem, HP and Lieber, A},
title = {Introducing a G-Makassar variant in HSCs by in vivo base editing treats sickle cell disease in mice.},
journal = {Molecular therapy : the journal of the American Society of Gene Therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymthe.2024.10.018},
pmid = {39489920},
issn = {1525-0024},
abstract = {Precise repair of the pathogenic mutation in hematopoietic stem cells (HSCs) represents an ideal cure for patients with sickle cell disease (SCD). Here, we demonstrated correction of the SCD phenotype by converting the sickle mutation codon (GTG) into a benign G-Makassar variant (GCG) using in vivo base editing in HSCs. We demonstrated successful production of helper-dependent adenoviral vectors expressing an all-in-one base editor mapping to the sickle mutation site. In HSC-enriched cells from SCD patients, transduction with the base editing vector in vitro resulted in 35% GTG > GCG conversion and phenotypic improvements of derived red blood cells. After ex vivo transduction of HSCs from a SCD mouse model and subsequent transplantation, we achieved an average of 88% editing at the target site in transplanted mice. Importantly, in vivo HSC base editing followed by selection generated 24.5% Makassar variant in long-term repopulating HSCs of SCD mice. The treated animals demonstrated correction of disease hallmarks without showing noticeable side effects. Off-target analyses at top-scored genomic sites revealed no off-target editing. This in vivo approach requires only one non-integrating vector, only intravenous/subcutaneous injections, and minimal in vivo selection. This technically simple approach has the potential for scalable applications in resource-limiting regions where SCD is prevalent.},
}
RevDate: 2024-11-02
CmpDate: 2024-11-02
H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells.
Epigenetics & chromatin, 17(1):32.
Canonical histone H3 and histone variant H3.3 are posttranslationally modified with the genomic distribution of these marks denoting different features and these modifications may influence transcription. While the majority of posttranslational modifications occur on histone tails, there are defined modifications within the globular domain, such as acetylation of H3K122/H3.3K122. To understand the function of the amino acid H3.3K122 in transcriptional regulation, we attempted to generate H3.3K122A mouse embryonic stem (mES) cells but were unsuccessful. Through multi-omic profiling of mutant cell lines harboring two or three of four H3.3 targeted alleles, we have uncovered that H3.3K122A is neomorphic and results in lethality. This is surprising as prior studies demonstrate H3.3-null mES cells are viable and pluripotent but exhibit a reduced differentiation capacity. Together, these studies have uncovered a novel dependence of a globular domain residue within H3.3 for viability and broadened our understanding of how histone variants contribute to transcription regulation and pluripotency in mES cells.
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@article {pmid39487536,
year = {2024},
author = {Patty, BJ and Jordan, C and Lardo, SM and Troy, K and Hainer, SJ},
title = {H3.3K122A results in a neomorphic phenotype in mouse embryonic stem cells.},
journal = {Epigenetics & chromatin},
volume = {17},
number = {1},
pages = {32},
pmid = {39487536},
issn = {1756-8935},
support = {R35GM133732/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; *Histones/metabolism ; Mice ; *Mouse Embryonic Stem Cells/metabolism/cytology ; *Phenotype ; Cell Differentiation ; Protein Processing, Post-Translational ; Acetylation ; },
abstract = {Canonical histone H3 and histone variant H3.3 are posttranslationally modified with the genomic distribution of these marks denoting different features and these modifications may influence transcription. While the majority of posttranslational modifications occur on histone tails, there are defined modifications within the globular domain, such as acetylation of H3K122/H3.3K122. To understand the function of the amino acid H3.3K122 in transcriptional regulation, we attempted to generate H3.3K122A mouse embryonic stem (mES) cells but were unsuccessful. Through multi-omic profiling of mutant cell lines harboring two or three of four H3.3 targeted alleles, we have uncovered that H3.3K122A is neomorphic and results in lethality. This is surprising as prior studies demonstrate H3.3-null mES cells are viable and pluripotent but exhibit a reduced differentiation capacity. Together, these studies have uncovered a novel dependence of a globular domain residue within H3.3 for viability and broadened our understanding of how histone variants contribute to transcription regulation and pluripotency in mES cells.},
}
MeSH Terms:
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Animals
*Histones/metabolism
Mice
*Mouse Embryonic Stem Cells/metabolism/cytology
*Phenotype
Cell Differentiation
Protein Processing, Post-Translational
Acetylation
RevDate: 2024-11-01
Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial.
Cancer cell pii:S1535-6108(24)00395-7 [Epub ahead of print].
Intratumoral TLR9 agonists and anti-PD-1 produce clinical responses and broad immune activation. We conducted a single-arm study of neoadjuvant TLR9 agonist vidutolimod combined with anti-PD-1 nivolumab in high-risk resectable melanoma. In 31 evaluable patients, 55% major pathologic response (MPR) was observed, meeting primary endpoint. MPR was associated with necrosis, and melanophagocytosis with increased CD8[+] tumor-infiltrating lymphocytes and plasmacytoid dendritic cells (pDCs) in the tumor microenvironment, and increased frequencies of Ki67[+]CD8[+] T cells peripherally. MPRs had an enriched pre-treatment gene signature of myeloid cells, and response to therapy was associated with gene signatures of immune cells, pDCs, phagocytosis, and macrophage activation. MPRs gut microbiota were enriched for Gram-negative bacteria belonging to the Bacteroidaceae and Enterobacteriaceae families and the small subgroup of Gram-negative Firmicutes. Our findings support that combined vidutolimod and nivolumab stimulates a broad anti-tumor immune response and is associated with distinct baseline myeloid gene signature and gut microbiota. ClinicalTrials.gov identifier: NCT03618641.
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@article {pmid39486411,
year = {2024},
author = {Davar, D and Morrison, RM and Dzutsev, AK and Karunamurthy, A and Chauvin, JM and Amatore, F and Deutsch, JS and Das Neves, RX and Rodrigues, RR and McCulloch, JA and Wang, H and Hartman, DJ and Badger, JH and Fernandes, MR and Bai, Y and Sun, J and Cole, AM and Aggarwal, P and Fang, JR and Deitrick, C and Bao, R and Duvvuri, U and Sridharan, SS and Kim, SW and A Choudry, H and Holtzman, MP and Pingpank, JF and O'Toole, JP and DeBlasio, R and Jin, Y and Ding, Q and Gao, W and Groetsch, C and Pagliano, O and Rose, A and Urban, C and Singh, J and Divarkar, P and Mauro, D and Bobilev, D and Wooldridge, J and Krieg, AM and Fury, MG and Whiteaker, JR and Zhao, L and Paulovich, AG and Najjar, YG and Luke, JJ and Kirkwood, JM and Taube, JM and Park, HJ and Trinchieri, G and Zarour, HM},
title = {Neoadjuvant vidutolimod and nivolumab in high-risk resectable melanoma: A prospective phase II trial.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2024.10.007},
pmid = {39486411},
issn = {1878-3686},
abstract = {Intratumoral TLR9 agonists and anti-PD-1 produce clinical responses and broad immune activation. We conducted a single-arm study of neoadjuvant TLR9 agonist vidutolimod combined with anti-PD-1 nivolumab in high-risk resectable melanoma. In 31 evaluable patients, 55% major pathologic response (MPR) was observed, meeting primary endpoint. MPR was associated with necrosis, and melanophagocytosis with increased CD8[+] tumor-infiltrating lymphocytes and plasmacytoid dendritic cells (pDCs) in the tumor microenvironment, and increased frequencies of Ki67[+]CD8[+] T cells peripherally. MPRs had an enriched pre-treatment gene signature of myeloid cells, and response to therapy was associated with gene signatures of immune cells, pDCs, phagocytosis, and macrophage activation. MPRs gut microbiota were enriched for Gram-negative bacteria belonging to the Bacteroidaceae and Enterobacteriaceae families and the small subgroup of Gram-negative Firmicutes. Our findings support that combined vidutolimod and nivolumab stimulates a broad anti-tumor immune response and is associated with distinct baseline myeloid gene signature and gut microbiota. ClinicalTrials.gov identifier: NCT03618641.},
}
RevDate: 2024-11-01
Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas.
Cell genomics pii:S2666-979X(24)00321-5 [Epub ahead of print].
Latin Americans are underrepresented in genetic studies, increasing disparities in personalized genomic medicine. Despite available genetic data from thousands of Latin Americans, accessing and navigating the bureaucratic hurdles for consent or access remains challenging. To address this, we introduce the Genetics of Latin American Diversity (GLAD) Project, compiling genome-wide information from 53,738 Latin Americans across 39 studies representing 46 geographical regions. Through GLAD, we identified heterogeneous ancestry composition and recent gene flow across the Americas. Additionally, we developed GLAD-match, a simulated annealing-based algorithm, to match the genetic background of external samples to our database, sharing summary statistics (i.e., allele and haplotype frequencies) without transferring individual-level genotypes. Finally, we demonstrate the potential of GLAD as a critical resource for evaluating statistical genetic software in the presence of admixture. By providing this resource, we promote genomic research in Latin Americans and contribute to the promises of personalized medicine to more people.
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@article {pmid39486408,
year = {2024},
author = {Borda, V and Loesch, DP and Guo, B and Laboulaye, R and Veliz-Otani, D and French, JN and Leal, TP and Gogarten, SM and Ikpe, S and Gouveia, MH and Mendes, M and Abecasis, GR and Alvim, I and Arboleda-Bustos, CE and Arboleda, G and Arboleda, H and Barreto, ML and Barwick, L and Bezzera, MA and Blangero, J and Borges, V and Caceres, O and Cai, J and Chana-Cuevas, P and Chen, Z and Custer, B and Dean, M and Dinardo, C and Domingos, I and Duggirala, R and Dieguez, E and Fernandez, W and Ferraz, HB and Gilliland, F and Guio, H and Horta, B and Curran, JE and Johnsen, JM and Kaplan, RC and Kelly, S and Kenny, EE and Konkle, BA and Kooperberg, C and Lescano, A and Lima-Costa, MF and Loos, RJF and Manichaikul, A and Meyers, DA and Naslavsky, MS and Nickerson, DA and North, KE and Padilla, C and Preuss, M and Raggio, V and Reiner, AP and Rich, SS and Rieder, CR and Rienstra, M and Rotter, JI and Rundek, T and Sacco, RL and Sanchez, C and Sankaran, VG and Santos-Lobato, BL and Schumacher-Schuh, AF and Scliar, MO and Silverman, EK and Sofer, T and Lasky-Su, J and Tumas, V and Weiss, ST and , and , and , and Mata, IF and Hernandez, RD and Tarazona-Santos, E and O'Connor, TD},
title = {Genetics of Latin American Diversity Project: Insights into population genetics and association studies in admixed groups in the Americas.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100692},
doi = {10.1016/j.xgen.2024.100692},
pmid = {39486408},
issn = {2666-979X},
abstract = {Latin Americans are underrepresented in genetic studies, increasing disparities in personalized genomic medicine. Despite available genetic data from thousands of Latin Americans, accessing and navigating the bureaucratic hurdles for consent or access remains challenging. To address this, we introduce the Genetics of Latin American Diversity (GLAD) Project, compiling genome-wide information from 53,738 Latin Americans across 39 studies representing 46 geographical regions. Through GLAD, we identified heterogeneous ancestry composition and recent gene flow across the Americas. Additionally, we developed GLAD-match, a simulated annealing-based algorithm, to match the genetic background of external samples to our database, sharing summary statistics (i.e., allele and haplotype frequencies) without transferring individual-level genotypes. Finally, we demonstrate the potential of GLAD as a critical resource for evaluating statistical genetic software in the presence of admixture. By providing this resource, we promote genomic research in Latin Americans and contribute to the promises of personalized medicine to more people.},
}
RevDate: 2024-11-01
Infectious Morbidity and All-cause Mortality of Infants HIV-exposed Uninfected Compared to Infants HIV-unexposed Uninfected in Botswana.
The Pediatric infectious disease journal pii:00006454-990000000-01066 [Epub ahead of print].
Some studies have reported increased infectious morbidity and all-cause mortality risk among infants HIV-exposed uninfected compared with infants HIV-unexposed uninfected. In a retrospective analysis of infants enrolled in the Botswana-based Tshilo Dikotla study, we found no difference in the prevalence of infectious hospitalizations or deaths from any cause in the first year of life by perinatal HIV exposure.
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@article {pmid39486012,
year = {2024},
author = {Dubois, MM and Jao, J and Sun, S and Legbedze, J and Schenkel, S and Mmasa, N and Kgole, SW and Masasa, G and Happel, AU and Iwase, SC and Haghighat, R and Moyo, S and Sharma, TS and Edlefsen, PT and Shao, D and Jaspan, H and Powis, KM},
title = {Infectious Morbidity and All-cause Mortality of Infants HIV-exposed Uninfected Compared to Infants HIV-unexposed Uninfected in Botswana.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004603},
pmid = {39486012},
issn = {1532-0987},
abstract = {Some studies have reported increased infectious morbidity and all-cause mortality risk among infants HIV-exposed uninfected compared with infants HIV-unexposed uninfected. In a retrospective analysis of infants enrolled in the Botswana-based Tshilo Dikotla study, we found no difference in the prevalence of infectious hospitalizations or deaths from any cause in the first year of life by perinatal HIV exposure.},
}
RevDate: 2024-11-01
Prediction of breast cancer risk for adolescents and young adults with Hodgkin lymphoma.
Journal of the National Cancer Institute pii:7863296 [Epub ahead of print].
BACKGROUND: While female survivors of Hodgkin lymphoma (HL) have an increased risk of breast cancer (BC), no BC risk prediction model is available. We developed such models incorporating mean radiation dose to the breast or breast quadrant-specific radiation doses.
METHODS: Relative risks and age-specific incidence for BC and competing events (mortality or other subsequent cancer) were estimated from 1194 Dutch five-year HL survivors, treated at ages 11-40 during 1965-2000. Predictors were doses to ten breast segments or mean breast radiation dose, BC family history, year of and age at HL diagnosis, ages at menopause and first live birth. Models were independently validated using U.S. Childhood Cancer Survivor Study cohort participants.
RESULTS: Predicted absolute BC risks 25 years after HL diagnosis ranged from 1.0% for survivors diagnosed at ages 20-24, with <10 Gy mean breast radiation dose and menopausal 5 years after HL diagnosis, to 22.0% for survivors 25-29 years at diagnosis, ≥25 Gy mean breast dose, and no menopause within 5 years. In external validation, the observed/expected BC case ratio was 1.19 (95% confidence interval 0.97 to 1.47) for the breast segment-specific doses model, and 1.29 (1.05 to 1.60) for the mean breast dose model. The areas under the receiver operating characteristic curve were 0.68 (0.63 to 0.74) and 0.68 (0.62 to 0.73), respectively.
CONCLUSION: Breast segment-specific or mean breast radiation dose with personal and clinical characteristics predicted absolute BC risk in HL survivors with moderate discrimination but good calibration, rendering the models useful for clinical decision-making.
Additional Links: PMID-39485483
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@article {pmid39485483,
year = {2024},
author = {Roberti, S and van Leeuwen, FE and Diallo, I and de Vathaire, F and Schaapveld, M and Leisenring, WM and Howell, RM and Armstrong, GT and Moskowitz, CS and Smith, SA and Aleman, BMP and Krul, IM and Russell, NS and Pfeiffer, RM and Hauptmann, M},
title = {Prediction of breast cancer risk for adolescents and young adults with Hodgkin lymphoma.},
journal = {Journal of the National Cancer Institute},
volume = {},
number = {},
pages = {},
doi = {10.1093/jnci/djae274},
pmid = {39485483},
issn = {1460-2105},
abstract = {BACKGROUND: While female survivors of Hodgkin lymphoma (HL) have an increased risk of breast cancer (BC), no BC risk prediction model is available. We developed such models incorporating mean radiation dose to the breast or breast quadrant-specific radiation doses.
METHODS: Relative risks and age-specific incidence for BC and competing events (mortality or other subsequent cancer) were estimated from 1194 Dutch five-year HL survivors, treated at ages 11-40 during 1965-2000. Predictors were doses to ten breast segments or mean breast radiation dose, BC family history, year of and age at HL diagnosis, ages at menopause and first live birth. Models were independently validated using U.S. Childhood Cancer Survivor Study cohort participants.
RESULTS: Predicted absolute BC risks 25 years after HL diagnosis ranged from 1.0% for survivors diagnosed at ages 20-24, with <10 Gy mean breast radiation dose and menopausal 5 years after HL diagnosis, to 22.0% for survivors 25-29 years at diagnosis, ≥25 Gy mean breast dose, and no menopause within 5 years. In external validation, the observed/expected BC case ratio was 1.19 (95% confidence interval 0.97 to 1.47) for the breast segment-specific doses model, and 1.29 (1.05 to 1.60) for the mean breast dose model. The areas under the receiver operating characteristic curve were 0.68 (0.63 to 0.74) and 0.68 (0.62 to 0.73), respectively.
CONCLUSION: Breast segment-specific or mean breast radiation dose with personal and clinical characteristics predicted absolute BC risk in HL survivors with moderate discrimination but good calibration, rendering the models useful for clinical decision-making.},
}
RevDate: 2024-11-01
CmpDate: 2024-11-01
Kinetochores grip microtubules with directionally asymmetric strength.
The Journal of cell biology, 224(1):.
For accurate mitosis, all chromosomes must achieve "biorientation," with replicated sister chromatids coupled via kinetochores to the plus ends of opposing microtubules. However, kinetochores first bind the sides of microtubules and subsequently find plus ends through a trial-and-error process; accurate biorientation depends on the selective release of erroneous attachments. Proposed mechanisms for error-correction have focused mainly on plus-end attachments. Whether erroneous side attachments are distinguished from correct side attachments is unknown. Here, we show that side-attached kinetochores are very sensitive to microtubule polarity, gripping sixfold more strongly when pulled toward plus versus minus ends. This directionally asymmetric grip is conserved in human and yeast subcomplexes, and it correlates with changes in the axial arrangement of subcomplexes within the kinetochore, suggesting that internal architecture dictates attachment strength. We propose that the kinetochore's directional grip promotes accuracy during early mitosis by stabilizing correct attachments even before both sisters have found plus ends.
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@article {pmid39485274,
year = {2025},
author = {Larson, JD and Heitkamp, NA and Murray, LE and Popchock, AR and Biggins, S and Asbury, CL},
title = {Kinetochores grip microtubules with directionally asymmetric strength.},
journal = {The Journal of cell biology},
volume = {224},
number = {1},
pages = {},
doi = {10.1083/jcb.202405176},
pmid = {39485274},
issn = {1540-8140},
support = {T32HL007312/NH/NIH HHS/United States ; //Washington Research Foundation/ ; //University of Washington/ ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {*Kinetochores/metabolism ; *Microtubules/metabolism ; Humans ; *Mitosis ; Saccharomyces cerevisiae/metabolism/genetics ; Saccharomyces cerevisiae Proteins/metabolism/genetics ; Microtubule-Associated Proteins/metabolism/genetics ; Chromosome Segregation ; HeLa Cells ; },
abstract = {For accurate mitosis, all chromosomes must achieve "biorientation," with replicated sister chromatids coupled via kinetochores to the plus ends of opposing microtubules. However, kinetochores first bind the sides of microtubules and subsequently find plus ends through a trial-and-error process; accurate biorientation depends on the selective release of erroneous attachments. Proposed mechanisms for error-correction have focused mainly on plus-end attachments. Whether erroneous side attachments are distinguished from correct side attachments is unknown. Here, we show that side-attached kinetochores are very sensitive to microtubule polarity, gripping sixfold more strongly when pulled toward plus versus minus ends. This directionally asymmetric grip is conserved in human and yeast subcomplexes, and it correlates with changes in the axial arrangement of subcomplexes within the kinetochore, suggesting that internal architecture dictates attachment strength. We propose that the kinetochore's directional grip promotes accuracy during early mitosis by stabilizing correct attachments even before both sisters have found plus ends.},
}
MeSH Terms:
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*Kinetochores/metabolism
*Microtubules/metabolism
Humans
*Mitosis
Saccharomyces cerevisiae/metabolism/genetics
Saccharomyces cerevisiae Proteins/metabolism/genetics
Microtubule-Associated Proteins/metabolism/genetics
Chromosome Segregation
HeLa Cells
RevDate: 2024-11-01
Metabolic syndrome and risks of breast cancer outcomes for luminal, triple-negative, and HER2-overexpressing subtypes.
Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology pii:749612 [Epub ahead of print].
BACKGROUND: We evaluated the association between metabolic syndrome (obesity plus two metabolic risk factors) and breast cancer outcomes according to molecular subtype.
METHODS: This population-based prospective cohort consisted of 3,267 women aged 20-69 diagnosed with a first primary invasive breast cancer from 2004-2015 in the Seattle-Puget Sound region. Breast cancer was categorized into three subtypes based on estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression: luminal (ER+), triple-negative (ER-/PR-/HER2-), and HER2-overexpressing (H2E) (ER-/HER2+). We used time-varying Cox models to assess the association between prevalent and incident metabolic syndrome and risks of recurrence, breast cancer-specific mortality, and all-cause mortality.
RESULTS: Metabolic syndrome was associated with a greater risk of recurrence (HR:3.24; 95% CI:1.13-9.33) and breast cancer-specific mortality (HR:5.34; 95% CI:2.32-12.31) only for the H2E subtype, and greater risks of all-cause mortality for luminal (HR:1.92; 95% CI:1.37-2.68), H2E (HR:5.09; 95% CI:2.51-10.32), and all cases combined (HR:1.90; 95% CI:1.42,2.53). We also observed heterogeneity in recurrence and mortality outcomes across specific components of metabolic syndrome and molecular subtypes.
CONCLUSIONS: Metabolic syndrome is associated with all-cause mortality among women with breast cancer and with breast cancer-specific mortality among women with the H2E subtype.
IMPACT: These results highlight the importance of managing comorbidities to decrease the risk for adverse outcomes among breast cancer survivors.
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@article {pmid39485107,
year = {2024},
author = {Loroña, NC and Othus, M and Malone, KE and Linden, HM and Tang, MC and Li, CI},
title = {Metabolic syndrome and risks of breast cancer outcomes for luminal, triple-negative, and HER2-overexpressing subtypes.},
journal = {Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1158/1055-9965.EPI-24-1167},
pmid = {39485107},
issn = {1538-7755},
abstract = {BACKGROUND: We evaluated the association between metabolic syndrome (obesity plus two metabolic risk factors) and breast cancer outcomes according to molecular subtype.
METHODS: This population-based prospective cohort consisted of 3,267 women aged 20-69 diagnosed with a first primary invasive breast cancer from 2004-2015 in the Seattle-Puget Sound region. Breast cancer was categorized into three subtypes based on estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression: luminal (ER+), triple-negative (ER-/PR-/HER2-), and HER2-overexpressing (H2E) (ER-/HER2+). We used time-varying Cox models to assess the association between prevalent and incident metabolic syndrome and risks of recurrence, breast cancer-specific mortality, and all-cause mortality.
RESULTS: Metabolic syndrome was associated with a greater risk of recurrence (HR:3.24; 95% CI:1.13-9.33) and breast cancer-specific mortality (HR:5.34; 95% CI:2.32-12.31) only for the H2E subtype, and greater risks of all-cause mortality for luminal (HR:1.92; 95% CI:1.37-2.68), H2E (HR:5.09; 95% CI:2.51-10.32), and all cases combined (HR:1.90; 95% CI:1.42,2.53). We also observed heterogeneity in recurrence and mortality outcomes across specific components of metabolic syndrome and molecular subtypes.
CONCLUSIONS: Metabolic syndrome is associated with all-cause mortality among women with breast cancer and with breast cancer-specific mortality among women with the H2E subtype.
IMPACT: These results highlight the importance of managing comorbidities to decrease the risk for adverse outcomes among breast cancer survivors.},
}
RevDate: 2024-10-31
Carvedilol to Improve Cardiac Remodeling in Anthracycline-Exposed Childhood Cancer Survivors: Subgroup Analysis of COG ALTE1621.
JACC. CardioOncology, 6(5):791-793.
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@article {pmid39479331,
year = {2024},
author = {Armenian, SH and Hudson, MM and Lindenfeld, L and Chen, S and Chow, EJ and Colan, S and Echevarria, M and Wong, FL and Chen, MH and Bhatia, S},
title = {Carvedilol to Improve Cardiac Remodeling in Anthracycline-Exposed Childhood Cancer Survivors: Subgroup Analysis of COG ALTE1621.},
journal = {JACC. CardioOncology},
volume = {6},
number = {5},
pages = {791-793},
pmid = {39479331},
issn = {2666-0873},
}
RevDate: 2024-10-31
CmpDate: 2024-10-31
B7-H3 is widely expressed in soft tissue sarcomas.
BMC cancer, 24(1):1336.
PURPOSE: Targeted therapy development in soft tissue sarcoma (STS) has been burdened by the heterogeneity of this group of rare tumors. B7 homolog 3 protein (B7-H3) is a molecule in the same family as programmed death-ligand 1 (PD-L1). It has limited expression in noncancerous tissues and is overexpressed in many cancers, making it an attractive target for cancer therapy, and clinical trials targeting B7-H3 are actively underway. While available data demonstrate high expression levels of B7-H3 in individual sarcoma subtypes, its expression patterns across STS subtypes are not well described. The purpose of this study was to characterize the expression patterns of B7-H3 in STS.
PATIENTS AND METHODS: This retrospective analysis evaluated STS tumor specimens from patients with a variety of different subtypes. Specimens were evaluated by immunohistochemistry (IHC) for expression and staining pattern of B7-H3 both in tumors and in associated vasculature.
RESULTS: Specimens from 153 sarcoma patients included 15 different STS subtypes. B7-H3 was broadly expressed in 97% of samples (95% CI 0.93-0.99) and 69.2% demonstrated high levels of B7-H3 expression (95% CI 0.61-0.76). No significant association between B7-H3 positivity or expression level and prior treatment(s), tumor size, tumor grade, or patient age. B7-H3 positivity in vessels was found in 94.7% (145/153) of samples. In tumors that had been previously assessed for PD-L1 and PD-1, there was no correlation between B7-H3 positivity or expression and the positivity or expression level of PD-L1 or PD-1.
CONCLUSION: These data show high levels of B7-H3 positivity across soft tissue sarcoma subtypes, suggesting its feasibility as a therapeutic target for future sarcoma treatments. Future clinical trials are needed to evaluate whether targeting B7-H3 can provide clinical benefit to help patients with sarcoma.
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@article {pmid39478506,
year = {2024},
author = {Lynch, MM and Al-Marayaty, R and Obeidin, F and Alexiev, BA and Chen, EY and Viveiros, P and Schroeder, BA and Hudkins, K and Fan, TM and Redman, MW and Baker, KK and Jour, G and Cranmer, LD and Pollack, SM},
title = {B7-H3 is widely expressed in soft tissue sarcomas.},
journal = {BMC cancer},
volume = {24},
number = {1},
pages = {1336},
pmid = {39478506},
issn = {1471-2407},
support = {R01CA244872/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *B7 Antigens/metabolism ; *Sarcoma/metabolism/pathology ; Female ; Male ; Middle Aged ; Retrospective Studies ; Adult ; Aged ; Biomarkers, Tumor/metabolism ; Immunohistochemistry ; Aged, 80 and over ; Young Adult ; Adolescent ; },
abstract = {PURPOSE: Targeted therapy development in soft tissue sarcoma (STS) has been burdened by the heterogeneity of this group of rare tumors. B7 homolog 3 protein (B7-H3) is a molecule in the same family as programmed death-ligand 1 (PD-L1). It has limited expression in noncancerous tissues and is overexpressed in many cancers, making it an attractive target for cancer therapy, and clinical trials targeting B7-H3 are actively underway. While available data demonstrate high expression levels of B7-H3 in individual sarcoma subtypes, its expression patterns across STS subtypes are not well described. The purpose of this study was to characterize the expression patterns of B7-H3 in STS.
PATIENTS AND METHODS: This retrospective analysis evaluated STS tumor specimens from patients with a variety of different subtypes. Specimens were evaluated by immunohistochemistry (IHC) for expression and staining pattern of B7-H3 both in tumors and in associated vasculature.
RESULTS: Specimens from 153 sarcoma patients included 15 different STS subtypes. B7-H3 was broadly expressed in 97% of samples (95% CI 0.93-0.99) and 69.2% demonstrated high levels of B7-H3 expression (95% CI 0.61-0.76). No significant association between B7-H3 positivity or expression level and prior treatment(s), tumor size, tumor grade, or patient age. B7-H3 positivity in vessels was found in 94.7% (145/153) of samples. In tumors that had been previously assessed for PD-L1 and PD-1, there was no correlation between B7-H3 positivity or expression and the positivity or expression level of PD-L1 or PD-1.
CONCLUSION: These data show high levels of B7-H3 positivity across soft tissue sarcoma subtypes, suggesting its feasibility as a therapeutic target for future sarcoma treatments. Future clinical trials are needed to evaluate whether targeting B7-H3 can provide clinical benefit to help patients with sarcoma.},
}
MeSH Terms:
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Humans
*B7 Antigens/metabolism
*Sarcoma/metabolism/pathology
Female
Male
Middle Aged
Retrospective Studies
Adult
Aged
Biomarkers, Tumor/metabolism
Immunohistochemistry
Aged, 80 and over
Young Adult
Adolescent
RevDate: 2024-10-31
Evidence-Informed Provision of Doxycycline Post-Exposure Prophylaxis for Prevention of Bacterial Sexually Transmitted Infections.
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America pii:7852954 [Epub ahead of print].
Doxycycline post-exposure prophylaxis (doxy-PEP) reduces the risk of bacterial sexually transmitted infections (STIs) among men who have sex with men and transgender women. In the United States, doxy-PEP is in an early stage of integration into clinical practice, and national guidelines for its use were recently released. The goal of this manuscript is to provide practical guidance for clinicians who are considering or currently prescribing doxy-PEP. We address five clinical questions using post hoc analyses of data from the DoxyPEP randomized controlled trial and discuss the potential implications and limitations of each question with the goal of informing clinical practice and implementation of doxy-PEP programs. The questions address patient eligibility criteria for doxy-PEP, the expected benefit and associated doxy-PEP doses for the average patient, the initial number of doses prescribed, and laboratory monitoring of persons taking doxy-PEP.
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@article {pmid39478321,
year = {2024},
author = {Dombrowski, JC and Donnell, D and Grabow, C and Cohen, SE and Cannon, CA and Brown, CE and Buchbinder, SP and Celum, C and Luetkemeyer, AF},
title = {Evidence-Informed Provision of Doxycycline Post-Exposure Prophylaxis for Prevention of Bacterial Sexually Transmitted Infections.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciae527},
pmid = {39478321},
issn = {1537-6591},
abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) reduces the risk of bacterial sexually transmitted infections (STIs) among men who have sex with men and transgender women. In the United States, doxy-PEP is in an early stage of integration into clinical practice, and national guidelines for its use were recently released. The goal of this manuscript is to provide practical guidance for clinicians who are considering or currently prescribing doxy-PEP. We address five clinical questions using post hoc analyses of data from the DoxyPEP randomized controlled trial and discuss the potential implications and limitations of each question with the goal of informing clinical practice and implementation of doxy-PEP programs. The questions address patient eligibility criteria for doxy-PEP, the expected benefit and associated doxy-PEP doses for the average patient, the initial number of doses prescribed, and laboratory monitoring of persons taking doxy-PEP.},
}
RevDate: 2024-10-31
Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination.
bioRxiv : the preprint server for biology.
V(D)J recombination generates the diverse B and T cell receptors essential for recognizing a wide array of antigens. This diversity arises from the combinatorial assembly of V(D)J genes and the junctional deletion and insertion of nucleotides. While previous in vitro studies have shown that microhomology--short stretches of sequence homology between gene ends--can bias the recombination process, the extent of microhomology's impact in vivo, particularly in humans, remains unknown. In this paper, we assess how germline-encoded microhomology influences trimming and ligation during V(D)J recombination using statistical inference on previously-published high-throughput TCRα repertoire sequencing data. We find that microhomology increases both trimming and ligation probabilities, making it an important predictor of recombination outcomes. These effects are consistent across different receptor loci and sequence types. Further, we demonstrate that accounting for microhomology effects significantly alters sequence annotation probabilities and rankings, highlighting its practical importance for accurately inferring the V(D)J recombination events that generated an observed sequence. Together, these results enhance our understanding of how microhomologous nucleotides shape the human V(D)J recombination process.
Additional Links: PMID-39464162
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@article {pmid39464162,
year = {2024},
author = {Russell, ML and Trofimov, A and Bradley, P and Matsen, FA},
title = {Statistical analysis of repertoire data demonstrates the influence of microhomology in V(D)J recombination.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39464162},
issn = {2692-8205},
support = {S10 OD028685/OD/NIH HHS/United States ; R01 AI146028/AI/NIAID NIH HHS/United States ; R35 GM142795/GM/NIGMS NIH HHS/United States ; R01 AI136514/AI/NIAID NIH HHS/United States ; R35 GM141457/GM/NIGMS NIH HHS/United States ; },
abstract = {V(D)J recombination generates the diverse B and T cell receptors essential for recognizing a wide array of antigens. This diversity arises from the combinatorial assembly of V(D)J genes and the junctional deletion and insertion of nucleotides. While previous in vitro studies have shown that microhomology--short stretches of sequence homology between gene ends--can bias the recombination process, the extent of microhomology's impact in vivo, particularly in humans, remains unknown. In this paper, we assess how germline-encoded microhomology influences trimming and ligation during V(D)J recombination using statistical inference on previously-published high-throughput TCRα repertoire sequencing data. We find that microhomology increases both trimming and ligation probabilities, making it an important predictor of recombination outcomes. These effects are consistent across different receptor loci and sequence types. Further, we demonstrate that accounting for microhomology effects significantly alters sequence annotation probabilities and rankings, highlighting its practical importance for accurately inferring the V(D)J recombination events that generated an observed sequence. Together, these results enhance our understanding of how microhomologous nucleotides shape the human V(D)J recombination process.},
}
RevDate: 2024-10-31
Efficient multiplex non-viral engineering and expansion of polyclonal γδ CAR-T cells for immunotherapy.
bioRxiv : the preprint server for biology.
Gamma delta (γδ) T cells are defined by their unique ability to recognize a limited repertoire of non-peptide, non-MHC-associated antigens on transformed and pathogen-infected cells. In addition to their lack of alloreactivity, γδ T cells exhibit properties distinct from other lymphocyte subsets, prompting significant interest in their development as an off-the-shelf cellular immunotherapeutic. However, their low abundance in circulation, heterogeneity, limited methods for ex vivo expansion, and under-developed methodologies for genetic modification have hindered basic study and clinical application of γδ T cells. Here, we implement a feeder-free, scalable approach for ex vivo manufacture of polyclonal, non-virally modified, gene edited chimeric antigen receptor (CAR)-γδ T cells in support of therapeutic application. Engineered CAR-γδ T cells demonstrate high function in vitro and and in vivo. Longitudinal in vivo pharmacokinetic profiling of adoptively transferred polyclonal CAR-γδ T cells uncover subset-specific responses to IL-15 cytokine armoring and multiplex base editing. Our results present a robust platform for genetic modification of polyclonal CAR-γδ T cells and present unique opportunities to further define synergy and the contribution of discrete, engineered CAR-γδ T cell subsets to therapeutic efficacy in vivo.
Additional Links: PMID-39464114
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@article {pmid39464114,
year = {2024},
author = {Bridge, J and Johnson, MJ and Kim, J and Wenthe, S and Krueger, J and Wick, B and Kluesner, M and Crane, AT and Bell, J and Skeate, JG and Moriarity, BS and Webber, BR},
title = {Efficient multiplex non-viral engineering and expansion of polyclonal γδ CAR-T cells for immunotherapy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39464114},
issn = {2692-8205},
support = {R01 AI161017/AI/NIAID NIH HHS/United States ; P30 CA077598/CA/NCI NIH HHS/United States ; U24 OD026641/OD/NIH HHS/United States ; R21 CA237789/CA/NCI NIH HHS/United States ; U54 CA232561/CA/NCI NIH HHS/United States ; R21 AI163731/AI/NIAID NIH HHS/United States ; P01 CA254849/CA/NCI NIH HHS/United States ; R01 AI146009/AI/NIAID NIH HHS/United States ; U54 CA268069/CA/NCI NIH HHS/United States ; P50 CA136393/CA/NCI NIH HHS/United States ; },
abstract = {Gamma delta (γδ) T cells are defined by their unique ability to recognize a limited repertoire of non-peptide, non-MHC-associated antigens on transformed and pathogen-infected cells. In addition to their lack of alloreactivity, γδ T cells exhibit properties distinct from other lymphocyte subsets, prompting significant interest in their development as an off-the-shelf cellular immunotherapeutic. However, their low abundance in circulation, heterogeneity, limited methods for ex vivo expansion, and under-developed methodologies for genetic modification have hindered basic study and clinical application of γδ T cells. Here, we implement a feeder-free, scalable approach for ex vivo manufacture of polyclonal, non-virally modified, gene edited chimeric antigen receptor (CAR)-γδ T cells in support of therapeutic application. Engineered CAR-γδ T cells demonstrate high function in vitro and and in vivo. Longitudinal in vivo pharmacokinetic profiling of adoptively transferred polyclonal CAR-γδ T cells uncover subset-specific responses to IL-15 cytokine armoring and multiplex base editing. Our results present a robust platform for genetic modification of polyclonal CAR-γδ T cells and present unique opportunities to further define synergy and the contribution of discrete, engineered CAR-γδ T cell subsets to therapeutic efficacy in vivo.},
}
RevDate: 2024-10-30
FAP and PSMA Expression by Immunohistochemistry and PET Imaging in Castration-Resistant Prostate Cancer: A Translational Pilot Study.
Journal of nuclear medicine : official publication, Society of Nuclear Medicine pii:jnumed.124.268037 [Epub ahead of print].
Prostate-specific membrane antigen (PSMA) is a theranostic target for metastatic prostate cancer (PCa). However, castration-resistant PCa (CRPC) may lose PSMA expression after systemic therapy. Fibroblast activation protein (FAP), expressed by carcinoma-associated fibroblasts in various cancer types, including PCa, has the potential to be an alternative target. In this study, we evaluated FAP expression in CRPC to assess its potential, using PSMA as a comparison. Methods: FAP expression was assessed using immunohistochemistry in 116 CRPC tumors: 78 adenocarcinomas, 11 small cell carcinomas, and 27 anaplastic carcinomas. Correlation analysis between manual scoring and automated scoring was performed on 54 whole-slide sections of metastatic CRPC. Paired FAP and PSMA stains were assessed in tissue microarray cores of CRPC (n = 62), consisting of locally advanced CRPC (n = 9) and metastatic CRPC (n = 53). FAP and PSMA positivity was defined by an immunohistochemistry score of at least 10. To explore the correlation of PSMA and FAP inhibitor (FAPi) PET imaging and immunohistochemistry, a preliminary analysis of 4 patients included in a [[68]Ga]-FAPi-46 imaging trial (NCT04457232) was conducted. Results: Manual and automated scoring of FAP yielded results with strong correlations. Overall, FAP expression in CRPC was notably lower than PSMA expression (median immunoscores, 14 vs. 72; P < 0.001). Different histologic subtypes of CRPC demonstrated distinct levels of PSMA expression, whereas their FAP expression levels were comparable. Among the 19 PSMA-negative tumors, 11 (58%) exhibited FAP positivity. FAP expression levels in lymph node metastases were significantly lower than those in nonnodal metastases (P = 0.021). Liver metastases showed significant enrichment of tumors with strong FAP expression compared with nonliver lesions (P = 0.016). In the 4 clinical trial patients, the biopsied metastatic lesions showed lower uptake on FAPi PET than on PSMA PET (median SUVmax, 9.6 vs. 14.5), consistent with FAP expression that was lower than PSMA expression in the corresponding tumor biopsy samples (median immunoscores, 30 vs. 160). Conclusion: Because of the low FAP expression levels in CRPC, the utility of FAPi PET imaging may be limited. Although FAPi PET imaging may be further tested in PSMA-negative CRPC, such as small cell carcinoma, other molecular imaging modalities should be evaluated as alternative choices.
Additional Links: PMID-39477498
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PubMed:
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@article {pmid39477498,
year = {2024},
author = {Huang, RR and Zuo, C and Mona, CE and Holzgreve, A and Morrissey, C and Nelson, PS and Brady, L and True, L and Sisk, A and Czernin, J and Calais, J and Ye, H},
title = {FAP and PSMA Expression by Immunohistochemistry and PET Imaging in Castration-Resistant Prostate Cancer: A Translational Pilot Study.},
journal = {Journal of nuclear medicine : official publication, Society of Nuclear Medicine},
volume = {},
number = {},
pages = {},
doi = {10.2967/jnumed.124.268037},
pmid = {39477498},
issn = {1535-5667},
abstract = {Prostate-specific membrane antigen (PSMA) is a theranostic target for metastatic prostate cancer (PCa). However, castration-resistant PCa (CRPC) may lose PSMA expression after systemic therapy. Fibroblast activation protein (FAP), expressed by carcinoma-associated fibroblasts in various cancer types, including PCa, has the potential to be an alternative target. In this study, we evaluated FAP expression in CRPC to assess its potential, using PSMA as a comparison. Methods: FAP expression was assessed using immunohistochemistry in 116 CRPC tumors: 78 adenocarcinomas, 11 small cell carcinomas, and 27 anaplastic carcinomas. Correlation analysis between manual scoring and automated scoring was performed on 54 whole-slide sections of metastatic CRPC. Paired FAP and PSMA stains were assessed in tissue microarray cores of CRPC (n = 62), consisting of locally advanced CRPC (n = 9) and metastatic CRPC (n = 53). FAP and PSMA positivity was defined by an immunohistochemistry score of at least 10. To explore the correlation of PSMA and FAP inhibitor (FAPi) PET imaging and immunohistochemistry, a preliminary analysis of 4 patients included in a [[68]Ga]-FAPi-46 imaging trial (NCT04457232) was conducted. Results: Manual and automated scoring of FAP yielded results with strong correlations. Overall, FAP expression in CRPC was notably lower than PSMA expression (median immunoscores, 14 vs. 72; P < 0.001). Different histologic subtypes of CRPC demonstrated distinct levels of PSMA expression, whereas their FAP expression levels were comparable. Among the 19 PSMA-negative tumors, 11 (58%) exhibited FAP positivity. FAP expression levels in lymph node metastases were significantly lower than those in nonnodal metastases (P = 0.021). Liver metastases showed significant enrichment of tumors with strong FAP expression compared with nonliver lesions (P = 0.016). In the 4 clinical trial patients, the biopsied metastatic lesions showed lower uptake on FAPi PET than on PSMA PET (median SUVmax, 9.6 vs. 14.5), consistent with FAP expression that was lower than PSMA expression in the corresponding tumor biopsy samples (median immunoscores, 30 vs. 160). Conclusion: Because of the low FAP expression levels in CRPC, the utility of FAPi PET imaging may be limited. Although FAPi PET imaging may be further tested in PSMA-negative CRPC, such as small cell carcinoma, other molecular imaging modalities should be evaluated as alternative choices.},
}
RevDate: 2024-10-30
Association of Tumor Mutational Burden and PD-L1 with the Efficacy of Pembrolizumab with or without Chemotherapy versus Chemotherapy in Advanced Urothelial Carcinoma.
Clinical cancer research : an official journal of the American Association for Cancer Research pii:749557 [Epub ahead of print].
PURPOSE: The three-arm, phase III KEYNOTE-361 study did not meet its dual primary endpoints of progression-free survival (PFS) or overall survival (OS) with first-line pembrolizumab plus chemotherapy versus chemotherapy in advanced urothelial carcinoma. This prespecified exploratory analysis assessed the association of tumor mutational burden (TMB) and PD-L1 combined positive score (CPS) with clinical outcomes.
PATIENTS AND METHODS: TMB and PD-L1 CPS were determined via whole-exome sequencing and PD-L1 IHC 22C3 pharmDx, respectively. The association was evaluated in each treatment arm using logistic regression [objective response rate (ORR)] and Cox proportional hazards regression models (PFS and OS); one-sided (pembrolizumab monotherapy; pembrolizumab plus chemotherapy) and two-sided (chemotherapy) nominal P values were calculated. Significance was prespecified at α = 0.05 without multiplicity adjustment. Efficacy was evaluated by prespecified cutoffs of 175 mutations/exome (TMB) and CPS 10 (PD-L1).
RESULTS: Of the 993 treated patients, 820 (82.6%) and 993 (100%) had evaluable TMB and CPS data, respectively. Continuous TMB was positively associated with ORR, PFS, and OS for pembrolizumab monotherapy (one-sided P < 0.001, P < 0.001, and P = 0.007, respectively); PFS and OS for pembrolizumab plus chemotherapy (one-sided P = 0.007 and P = 0.010, respectively); and OS for chemotherapy alone (two-sided P = 0.040). Continuous PD-L1 CPS showed evidence of anticipated association with ORR and PFS for pembrolizumab monotherapy. The subgroup with TMB ≥175 mutations/exome and PD-L1 CPS ≥10 had the highest PFS and OS improvements with pembrolizumab alone or with chemotherapy versus chemotherapy alone.
CONCLUSIONS: These data suggest that TMB may be predictive of the response to pembrolizumab alone or with chemotherapy in advanced urothelial carcinoma.
Additional Links: PMID-39475359
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@article {pmid39475359,
year = {2024},
author = {Fléchon, A and Morales-Barrera, R and Powles, T and Alva, A and Özgüroğlu, M and Csöszi, T and Loriot, Y and Rodriguez-Vida, A and Géczi, L and Cheng, SY and Fradet, Y and Oudard, S and Vulsteke, C and Gunduz, S and Mamtani, R and Yu, EY and Montesa Pino, A and Anido, U and Sendur, MAN and Gravis, G and Révész, J and Kostorov, V and Huillard, O and Ma, J and Rajasagi, M and Vajdi, A and Lunceford, J and Cristescu, R and Imai, K and Homet Moreno, B and Matsubara, N},
title = {Association of Tumor Mutational Burden and PD-L1 with the Efficacy of Pembrolizumab with or without Chemotherapy versus Chemotherapy in Advanced Urothelial Carcinoma.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {OF1-OF12},
doi = {10.1158/1078-0432.CCR-23-3518},
pmid = {39475359},
issn = {1557-3265},
abstract = {PURPOSE: The three-arm, phase III KEYNOTE-361 study did not meet its dual primary endpoints of progression-free survival (PFS) or overall survival (OS) with first-line pembrolizumab plus chemotherapy versus chemotherapy in advanced urothelial carcinoma. This prespecified exploratory analysis assessed the association of tumor mutational burden (TMB) and PD-L1 combined positive score (CPS) with clinical outcomes.
PATIENTS AND METHODS: TMB and PD-L1 CPS were determined via whole-exome sequencing and PD-L1 IHC 22C3 pharmDx, respectively. The association was evaluated in each treatment arm using logistic regression [objective response rate (ORR)] and Cox proportional hazards regression models (PFS and OS); one-sided (pembrolizumab monotherapy; pembrolizumab plus chemotherapy) and two-sided (chemotherapy) nominal P values were calculated. Significance was prespecified at α = 0.05 without multiplicity adjustment. Efficacy was evaluated by prespecified cutoffs of 175 mutations/exome (TMB) and CPS 10 (PD-L1).
RESULTS: Of the 993 treated patients, 820 (82.6%) and 993 (100%) had evaluable TMB and CPS data, respectively. Continuous TMB was positively associated with ORR, PFS, and OS for pembrolizumab monotherapy (one-sided P < 0.001, P < 0.001, and P = 0.007, respectively); PFS and OS for pembrolizumab plus chemotherapy (one-sided P = 0.007 and P = 0.010, respectively); and OS for chemotherapy alone (two-sided P = 0.040). Continuous PD-L1 CPS showed evidence of anticipated association with ORR and PFS for pembrolizumab monotherapy. The subgroup with TMB ≥175 mutations/exome and PD-L1 CPS ≥10 had the highest PFS and OS improvements with pembrolizumab alone or with chemotherapy versus chemotherapy alone.
CONCLUSIONS: These data suggest that TMB may be predictive of the response to pembrolizumab alone or with chemotherapy in advanced urothelial carcinoma.},
}
RevDate: 2024-10-30
CmpDate: 2024-10-30
A prediction model for differential resilience to the effects of combat-related stressors in US army soldiers.
International journal of methods in psychiatric research, 33(4):e70006.
OBJECTIVES: To develop a composite score for differential resilience to effects of combat-related stressors (CRS) on persistent DSM-IV post-traumatic stress disorder (PTSD) among US Army combat arms soldiers using survey data collected before deployment.
METHODS: A sample of n = 2542 US Army combat arms soldiers completed a survey shortly before deployment to Afghanistan and then again two to three and 8-9 months after redeployment. Retrospective self-reports were obtained about CRS. Precision treatment methods were used to determine whether differential resilience to persistent PTSD in the follow-up surveys could be developed from pre-deployment survey data in a 60% training sample and validated in a 40% test sample.
RESULTS: 40.8% of respondents experienced high CRS and 5.4% developed persistent PTSD. Significant test sample heterogeneity was found in resilience (t = 2.1, p = 0.032), with average treatment effect (ATE) of high CRS in the 20% least resilient soldiers of 17.1% (SE = 5.5%) compared to ATE = 3.8% (SE = 1.2%) in the remaining 80%. The most important predictors involved recent and lifetime pre-deployment distress disorders.
CONCLUSIONS: A reliable pre-deployment resilience score can be constructed to predict variation in the effects of high CRS on persistent PTSD among combat arms soldiers. Such a score could be used to target preventive interventions to reduce PTSD or other resilience-related outcomes.
Additional Links: PMID-39475323
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@article {pmid39475323,
year = {2024},
author = {Kessler, RC and Bossarte, RM and Hwang, I and Luedtke, A and Naifeh, JA and Nock, MK and Petukhova, M and Sadikova, E and Sampson, NA and Sverdrup, E and Zubizarreta, JR and Wager, S and Wagner, J and Stein, MB and Ursano, RJ},
title = {A prediction model for differential resilience to the effects of combat-related stressors in US army soldiers.},
journal = {International journal of methods in psychiatric research},
volume = {33},
number = {4},
pages = {e70006},
doi = {10.1002/mpr.70006},
pmid = {39475323},
issn = {1557-0657},
support = {U01MH087981/MH/NIMH NIH HHS/United States ; HU0001-15-2-0004//U.S. Department of Defense/ ; U01MH087981//U.S. Army/ ; },
mesh = {Humans ; *Military Personnel/psychology ; *Resilience, Psychological ; Adult ; Male ; Female ; *Stress Disorders, Post-Traumatic/diagnosis ; United States ; Young Adult ; *Combat Disorders/diagnosis ; Follow-Up Studies ; Afghan Campaign 2001- ; Retrospective Studies ; Adolescent ; Stress, Psychological ; },
abstract = {OBJECTIVES: To develop a composite score for differential resilience to effects of combat-related stressors (CRS) on persistent DSM-IV post-traumatic stress disorder (PTSD) among US Army combat arms soldiers using survey data collected before deployment.
METHODS: A sample of n = 2542 US Army combat arms soldiers completed a survey shortly before deployment to Afghanistan and then again two to three and 8-9 months after redeployment. Retrospective self-reports were obtained about CRS. Precision treatment methods were used to determine whether differential resilience to persistent PTSD in the follow-up surveys could be developed from pre-deployment survey data in a 60% training sample and validated in a 40% test sample.
RESULTS: 40.8% of respondents experienced high CRS and 5.4% developed persistent PTSD. Significant test sample heterogeneity was found in resilience (t = 2.1, p = 0.032), with average treatment effect (ATE) of high CRS in the 20% least resilient soldiers of 17.1% (SE = 5.5%) compared to ATE = 3.8% (SE = 1.2%) in the remaining 80%. The most important predictors involved recent and lifetime pre-deployment distress disorders.
CONCLUSIONS: A reliable pre-deployment resilience score can be constructed to predict variation in the effects of high CRS on persistent PTSD among combat arms soldiers. Such a score could be used to target preventive interventions to reduce PTSD or other resilience-related outcomes.},
}
MeSH Terms:
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Humans
*Military Personnel/psychology
*Resilience, Psychological
Adult
Male
Female
*Stress Disorders, Post-Traumatic/diagnosis
United States
Young Adult
*Combat Disorders/diagnosis
Follow-Up Studies
Afghan Campaign 2001-
Retrospective Studies
Adolescent
Stress, Psychological
RevDate: 2024-10-30
Metastatic SMARCB1-Deficient Renal Medullary Carcinoma without Hemoglobinopathy with Durable and Dramatic Response to Pembrolizumab plus Lenvatinib: Case Report.
Case reports in oncology, 17(1):1025-1033.
INTRODUCTION: Renal medullary carcinoma (RMC) is a rare form of renal cell carcinoma (RCC) that is typically associated with a loss of function in SMARCB1 and diagnosis of sickle cell or other hemoglobinopathy. In rare cases, this disease can be seen in patients without hemoglobinopathy and is classified as "SMARCB1-deficient RMC without hemoglobinopathy" or referred to as "RCC unclassified with medullary phenotype" in some of the literature. Platinum-based cytotoxic chemotherapy is currently the recommended first-line treatment for this rare disease.
CASE PRESENTATION: Here we report a 53-year-old male who was diagnosed with metastatic SMARCB1-deficient RMC without hemoglobinopathy after presenting with left flank and abdominal pain. After initiating first-line pembrolizumab and lenvatinib systemic therapy, imaging showed regression at 6 weeks. To date, this patient continues to show a near complete response to this treatment regimen.
CONCLUSION: To our knowledge, this is the first documented case of SMARCB1-deficient RMC without hemoglobinopathy to receive this treatment regimen and show such a response.
Additional Links: PMID-39474526
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@article {pmid39474526,
year = {2024},
author = {McCamy, W and Yousefiasl, M and Tretiakova, M and Jagtiani, M and Hall, E},
title = {Metastatic SMARCB1-Deficient Renal Medullary Carcinoma without Hemoglobinopathy with Durable and Dramatic Response to Pembrolizumab plus Lenvatinib: Case Report.},
journal = {Case reports in oncology},
volume = {17},
number = {1},
pages = {1025-1033},
pmid = {39474526},
issn = {1662-6575},
abstract = {INTRODUCTION: Renal medullary carcinoma (RMC) is a rare form of renal cell carcinoma (RCC) that is typically associated with a loss of function in SMARCB1 and diagnosis of sickle cell or other hemoglobinopathy. In rare cases, this disease can be seen in patients without hemoglobinopathy and is classified as "SMARCB1-deficient RMC without hemoglobinopathy" or referred to as "RCC unclassified with medullary phenotype" in some of the literature. Platinum-based cytotoxic chemotherapy is currently the recommended first-line treatment for this rare disease.
CASE PRESENTATION: Here we report a 53-year-old male who was diagnosed with metastatic SMARCB1-deficient RMC without hemoglobinopathy after presenting with left flank and abdominal pain. After initiating first-line pembrolizumab and lenvatinib systemic therapy, imaging showed regression at 6 weeks. To date, this patient continues to show a near complete response to this treatment regimen.
CONCLUSION: To our knowledge, this is the first documented case of SMARCB1-deficient RMC without hemoglobinopathy to receive this treatment regimen and show such a response.},
}
RevDate: 2024-10-30
Advancements in genetic research by the Hispanic Community Health Study/Study of Latinos (HCHS/SOL): A 10-year Retrospective Review.
HGG advances pii:S2666-2477(24)00116-7 [Epub ahead of print].
The Hispanic Community Health Study/Study of Latinos (HCHS/SOL) is a multicenter, longitudinal cohort study designed to evaluate environmental, lifestyle, and genetic risk factors as they relate to cardiometabolic and other chronic diseases among Hispanic/Latino populations in the United States. Since the study's inception in 2008, as a result of the study's robust genetic measures, HCHS/SOL has facilitated major contributions to the field of genetic research. This 15-year retrospective review highlights the major findings for genotype phenotype relationships and advancements in statistical methods owing to the HCHS/SOL. Furthermore, we discuss the ethical and societal challenges of genetic research, especially among Hispanic/Latino adults in the U.S. Continued genetic research, ancillary study expansion, and consortia collaboration through HCHS/SOL will further drive knowledge and advancements in human genetics research.
Additional Links: PMID-39473183
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@article {pmid39473183,
year = {2024},
author = {Rao, H and Weiss, MC and Moon, JY and Perreira, KM and Daviglus, ML and Kaplan, R and North, KE and Argos, M and Fernández-Rhodes, L and Sofer, T},
title = {Advancements in genetic research by the Hispanic Community Health Study/Study of Latinos (HCHS/SOL): A 10-year Retrospective Review.},
journal = {HGG advances},
volume = {},
number = {},
pages = {100376},
doi = {10.1016/j.xhgg.2024.100376},
pmid = {39473183},
issn = {2666-2477},
abstract = {The Hispanic Community Health Study/Study of Latinos (HCHS/SOL) is a multicenter, longitudinal cohort study designed to evaluate environmental, lifestyle, and genetic risk factors as they relate to cardiometabolic and other chronic diseases among Hispanic/Latino populations in the United States. Since the study's inception in 2008, as a result of the study's robust genetic measures, HCHS/SOL has facilitated major contributions to the field of genetic research. This 15-year retrospective review highlights the major findings for genotype phenotype relationships and advancements in statistical methods owing to the HCHS/SOL. Furthermore, we discuss the ethical and societal challenges of genetic research, especially among Hispanic/Latino adults in the U.S. Continued genetic research, ancillary study expansion, and consortia collaboration through HCHS/SOL will further drive knowledge and advancements in human genetics research.},
}
RevDate: 2024-10-30
CmpDate: 2024-10-30
MLL oncoprotein levels influence leukemia lineage identities.
Nature communications, 15(1):9341.
Chromosomal translocations involving the mixed-lineage leukemia (MLL) locus generate potent oncogenic fusion proteins (oncoproteins) that disrupt regulation of developmental gene expression. By profiling the oncoprotein-target sites of 36 broadly representative MLL-rearranged leukemia samples, including three samples that underwent a lymphoid-to-myeloid lineage-switching event in response to therapy, we find the genomic enrichment of the oncoprotein is highly variable between samples and subject to dynamic regulation. At high levels of expression, the oncoproteins preferentially activate either an acute lymphoblastic leukemia (ALL) program, enriched for pro-B-cell genes, or an acute myeloid leukemia (AML) program, enriched for hematopoietic-stem-cell genes. The fusion-partner-specific-binding patterns over these gene sets are highly correlated with the prevalence of each mutation in ALL versus AML. In lineage-switching samples the oncoprotein levels are reduced and the oncoproteins preferentially activate granulocyte-monocyte progenitor (GMP) genes. In a sample that lineage switched during treatment with the menin inhibitor revumenib, the oncoprotein and menin are reduced to undetectable levels, but ENL, a transcriptional cofactor of the oncoprotein, persists on numerous oncoprotein-target loci, including genes in the GMP-like lineage-switching program. We propose MLL oncoproteins promote lineage-switching events through dynamic chromatin binding at lineage-specific target genes, and may support resistance to menin inhibitors through similar changes in chromatin occupancy.
Additional Links: PMID-39472576
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@article {pmid39472576,
year = {2024},
author = {Janssens, DH and Duran, M and Otto, DJ and Wu, W and Xu, Y and Kirkey, D and Mullighan, CG and Yi, JS and Meshinchi, S and Sarthy, JF and Ahmad, K and Henikoff, S},
title = {MLL oncoprotein levels influence leukemia lineage identities.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9341},
pmid = {39472576},
issn = {2041-1723},
support = {Henikoff//Howard Hughes Medical Institute (HHMI)/ ; R01 HG010492/HG/NHGRI NIH HHS/United States ; Derek Janssens//Hartwell Foundation (The Hartwell Foundation)/ ; NCI R35 CA297695//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; Mullighan//American Lebanese Syrian Associated Charities (ALSAC)/ ; },
mesh = {*Myeloid-Lymphoid Leukemia Protein/metabolism/genetics ; Humans ; *Leukemia, Myeloid, Acute/genetics/metabolism ; *Oncogene Proteins, Fusion/metabolism/genetics ; *Cell Lineage/genetics ; *Histone-Lysine N-Methyltransferase/metabolism/genetics ; Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics/metabolism/pathology ; Gene Expression Regulation, Leukemic ; Proto-Oncogene Proteins/metabolism/genetics ; Mutation ; Translocation, Genetic ; Hematopoietic Stem Cells/metabolism ; Chromatin/metabolism ; },
abstract = {Chromosomal translocations involving the mixed-lineage leukemia (MLL) locus generate potent oncogenic fusion proteins (oncoproteins) that disrupt regulation of developmental gene expression. By profiling the oncoprotein-target sites of 36 broadly representative MLL-rearranged leukemia samples, including three samples that underwent a lymphoid-to-myeloid lineage-switching event in response to therapy, we find the genomic enrichment of the oncoprotein is highly variable between samples and subject to dynamic regulation. At high levels of expression, the oncoproteins preferentially activate either an acute lymphoblastic leukemia (ALL) program, enriched for pro-B-cell genes, or an acute myeloid leukemia (AML) program, enriched for hematopoietic-stem-cell genes. The fusion-partner-specific-binding patterns over these gene sets are highly correlated with the prevalence of each mutation in ALL versus AML. In lineage-switching samples the oncoprotein levels are reduced and the oncoproteins preferentially activate granulocyte-monocyte progenitor (GMP) genes. In a sample that lineage switched during treatment with the menin inhibitor revumenib, the oncoprotein and menin are reduced to undetectable levels, but ENL, a transcriptional cofactor of the oncoprotein, persists on numerous oncoprotein-target loci, including genes in the GMP-like lineage-switching program. We propose MLL oncoproteins promote lineage-switching events through dynamic chromatin binding at lineage-specific target genes, and may support resistance to menin inhibitors through similar changes in chromatin occupancy.},
}
MeSH Terms:
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*Myeloid-Lymphoid Leukemia Protein/metabolism/genetics
Humans
*Leukemia, Myeloid, Acute/genetics/metabolism
*Oncogene Proteins, Fusion/metabolism/genetics
*Cell Lineage/genetics
*Histone-Lysine N-Methyltransferase/metabolism/genetics
Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics/metabolism/pathology
Gene Expression Regulation, Leukemic
Proto-Oncogene Proteins/metabolism/genetics
Mutation
Translocation, Genetic
Hematopoietic Stem Cells/metabolism
Chromatin/metabolism
RevDate: 2024-10-30
CmpDate: 2024-10-30
Accumulation of Oncogenic Mutations During Progression from Healthy Tissue to Cancer.
Bulletin of mathematical biology, 86(12):142.
Cancers are typically fueled by sequential accumulation of driver mutations in a previously healthy cell. Some of these mutations, such as inactivation of the first copy of a tumor suppressor gene, can be neutral, and some, like those resulting in activation of oncogenes, may provide cells with a selective growth advantage. We study a multi-type branching process that starts with healthy tissue in homeostasis and models accumulation of neutral and advantageous mutations on the way to cancer. We provide results regarding the sizes of premalignant populations and the waiting times to the first cell with a particular combination of mutations, including the waiting time to malignancy. Finally, we apply our results to two specific biological settings: initiation of colorectal cancer and age incidence of chronic myeloid leukemia. Our model allows for any order of neutral and advantageous mutations and can be applied to other evolutionary settings.
Additional Links: PMID-39472320
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@article {pmid39472320,
year = {2024},
author = {Zhang, R and Bozic, I},
title = {Accumulation of Oncogenic Mutations During Progression from Healthy Tissue to Cancer.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {12},
pages = {142},
pmid = {39472320},
issn = {1522-9602},
support = {DMS-2045166//National Science Foundation/ ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology ; *Disease Progression ; *Mutation ; *Mathematical Concepts ; *Oncogenes/genetics ; *Models, Genetic ; *Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics/pathology ; Neoplasms/genetics/pathology ; Carcinogenesis/genetics ; Mutation Accumulation ; Precancerous Conditions/genetics/pathology ; Computer Simulation ; },
abstract = {Cancers are typically fueled by sequential accumulation of driver mutations in a previously healthy cell. Some of these mutations, such as inactivation of the first copy of a tumor suppressor gene, can be neutral, and some, like those resulting in activation of oncogenes, may provide cells with a selective growth advantage. We study a multi-type branching process that starts with healthy tissue in homeostasis and models accumulation of neutral and advantageous mutations on the way to cancer. We provide results regarding the sizes of premalignant populations and the waiting times to the first cell with a particular combination of mutations, including the waiting time to malignancy. Finally, we apply our results to two specific biological settings: initiation of colorectal cancer and age incidence of chronic myeloid leukemia. Our model allows for any order of neutral and advantageous mutations and can be applied to other evolutionary settings.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Colorectal Neoplasms/genetics/pathology
*Disease Progression
*Mutation
*Mathematical Concepts
*Oncogenes/genetics
*Models, Genetic
*Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics/pathology
Neoplasms/genetics/pathology
Carcinogenesis/genetics
Mutation Accumulation
Precancerous Conditions/genetics/pathology
Computer Simulation
RevDate: 2024-10-29
What's in a Name? Why Words Matter in Advanced Prostate Cancer.
Much of the disease nomenclature used for patients with advanced prostate cancer has negative connotations and can be confusing or intimidating. Experts in the field convened to recommend a clearer and more accurate approach to defining the nomenclature.
Additional Links: PMID-39472202
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@article {pmid39472202,
year = {2024},
author = {Oh, WK and Agarwal, N and Bryce, A and Barata, P and Bugler, C and Carlsson, SV and Cornell, B and Dahut, W and George, D and Loeb, S and Montgomery, B and Morris, D and Mucci, LA and Omlin, A and Palapattu, G and Riaz, IB and Ryan, C and Schoen, MW and Washington, SL and Gillessen, S},
title = {What's in a Name? Why Words Matter in Advanced Prostate Cancer.},
journal = {European urology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eururo.2024.10.017},
pmid = {39472202},
issn = {1873-7560},
abstract = {Much of the disease nomenclature used for patients with advanced prostate cancer has negative connotations and can be confusing or intimidating. Experts in the field convened to recommend a clearer and more accurate approach to defining the nomenclature.},
}
RevDate: 2024-10-29
Immunological and molecular features of the tumor microenvironment of long-term survivors of ovarian cancer.
The Journal of clinical investigation pii:179501 [Epub ahead of print].
BACKGROUND: Despite an overall poor prognosis, about 15% of patients with advanced-stage tubo-ovarian high-grade serous carcinoma (HGSC) survive ten or more years after standard treatment.
METHODS: We evaluated the tumor microenvironment of this exceptional, understudied group using a large international cohort enriched for long-term survivors (LTS; 10+ years; n = 374) compared to medium-term (MTS; 5-7.99 years; n = 433) and short-term survivors (STS; 2-4.99 years; n = 416). Primary tumor samples were immunostained and scored for intra-epithelial and intra-stromal densities of 10 immune-cell subsets (including T cells, B cells, plasma cells, myeloid cells, PD-1+ cells, and PD-L1+ cells) and epithelial content.
RESULTS: Positive associations with LTS compared to STS were seen for 9/10 immune-cell subsets. In particular, the combination of intra-epithelial CD8+ T cells and intra-stromal B cells showed near five-fold increased odds of LTS compared to STS. All of these associations were stronger in tumors with high epithelial content and/or the C4/Differentiated molecular subtype, despite immune-cell densities generally being higher in tumors with low epithelial content and/or the C2/Immunoreactive molecular subtype.
CONCLUSIONS: The tumor microenvironment of HGSC long-term survivors is distinguished by the intersection of T and B cell co-infiltration, high epithelial content and C4/Differentiated molecular subtype, features which may inspire new approaches to immunotherapy.
FUNDING: Ovarian Cancer Research Program (OCRP) of the Congressionally Directed Medical Research Program (CDMRP), U.S. Department of Defense (DOD); American Cancer Society; BC Cancer Foundation; Canada's Networks of Centres of Excellence; Canadian Cancer Society; Canadian Institutes of Health Research; Cancer Councils of New South Wales, Victoria, Queensland, South Australia and Tasmania, Cancer Foundation of Western Australia; Cancer Institute NSW; Cancer Research UK; Deutsche Forschungsgesellschaft; ELAN Funds of the University of Erlangen-Nuremberg; Fred C. and Katherine B. Andersen Foundation; Genome BC; German Cancer Research Center; German Federal Ministry of Education and Research, Programme of Clinical Biomedical Research; Instituto de Salud Carlos III; Mayo Foundation; Minnesota Ovarian Cancer Alliance; Ministerio de Economía y Competitividad; MRC; National Center for Advancing Translational Sciences; National Health and Medical Research Council of Australia (NHMRC); Ovarian Cancer Australia; Peter MacCallum Foundation; Sydney West Translational Cancer Research Centre; Terry Fox Research Institute; The Eve Appeal (The Oak Foundation); UK National Institute for Health Research Biomedical Research Centres at the University of Cambridge; University of Pittsburgh School of Medicine; U.S. National Cancer Institute of the National Institutes of Health; VGH & UBC Hospital Foundation; Victorian Cancer Agency.
Additional Links: PMID-39470729
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PubMed:
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@article {pmid39470729,
year = {2024},
author = {Nelson, BH and Hamilton, PT and Phung, MT and Milne, K and Harris, B and Thornton, S and Stevens, DL and Kalaria, S and Singh, K and Laumont, CM and Moss, E and Alimujiang, A and Meagher, NS and Bolithon, A and Fereday, S and Kennedy, CJ and Hendley, J and Ariyaratne, D and Alsop, K and Traficante, N and Goode, EL and Karnezis, AN and Shen, H and Richardson, J and McKinnon Deurloo, C and Chase, A and Grout, B and Doherty, JA and Harris, HR and Cushing-Haugen, KL and Anglesio, MS and Heinze, K and Huntsman, D and Talhouk, A and Hanley, GE and Alsop, J and Jimenez-Linan, M and Pharoah, PD and Boros, J and Brand, AH and Harnett, PR and Sharma, R and Hecht, JL and Sasamoto, N and Terry, KL and Karlan, BY and Lester, J and Carney, ME and Goodman, MT and Hernandez, BY and Wilkens, LR and Behrens, S and Turzanski Fortner, R and Fasching, PA and Bisinotto, C and Candido Dos Reis, FJ and Ghatage, P and Köbel, M and Elishaev, E and Modugno, F and Cook, LS and Le, ND and Gentry-Maharaj, A and Menon, U and García, MJ and Rodriguez-Antona, C and Farrington, KM and Kelemen, LE and Kommoss, S and Staebler, A and Garsed, DW and Brenton, JD and Piskorz, AM and Bowtell, DD and DeFazio, A and Ramus, SJ and Pike, MC and Pearce, CL},
title = {Immunological and molecular features of the tumor microenvironment of long-term survivors of ovarian cancer.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI179501},
pmid = {39470729},
issn = {1558-8238},
abstract = {BACKGROUND: Despite an overall poor prognosis, about 15% of patients with advanced-stage tubo-ovarian high-grade serous carcinoma (HGSC) survive ten or more years after standard treatment.
METHODS: We evaluated the tumor microenvironment of this exceptional, understudied group using a large international cohort enriched for long-term survivors (LTS; 10+ years; n = 374) compared to medium-term (MTS; 5-7.99 years; n = 433) and short-term survivors (STS; 2-4.99 years; n = 416). Primary tumor samples were immunostained and scored for intra-epithelial and intra-stromal densities of 10 immune-cell subsets (including T cells, B cells, plasma cells, myeloid cells, PD-1+ cells, and PD-L1+ cells) and epithelial content.
RESULTS: Positive associations with LTS compared to STS were seen for 9/10 immune-cell subsets. In particular, the combination of intra-epithelial CD8+ T cells and intra-stromal B cells showed near five-fold increased odds of LTS compared to STS. All of these associations were stronger in tumors with high epithelial content and/or the C4/Differentiated molecular subtype, despite immune-cell densities generally being higher in tumors with low epithelial content and/or the C2/Immunoreactive molecular subtype.
CONCLUSIONS: The tumor microenvironment of HGSC long-term survivors is distinguished by the intersection of T and B cell co-infiltration, high epithelial content and C4/Differentiated molecular subtype, features which may inspire new approaches to immunotherapy.
FUNDING: Ovarian Cancer Research Program (OCRP) of the Congressionally Directed Medical Research Program (CDMRP), U.S. Department of Defense (DOD); American Cancer Society; BC Cancer Foundation; Canada's Networks of Centres of Excellence; Canadian Cancer Society; Canadian Institutes of Health Research; Cancer Councils of New South Wales, Victoria, Queensland, South Australia and Tasmania, Cancer Foundation of Western Australia; Cancer Institute NSW; Cancer Research UK; Deutsche Forschungsgesellschaft; ELAN Funds of the University of Erlangen-Nuremberg; Fred C. and Katherine B. Andersen Foundation; Genome BC; German Cancer Research Center; German Federal Ministry of Education and Research, Programme of Clinical Biomedical Research; Instituto de Salud Carlos III; Mayo Foundation; Minnesota Ovarian Cancer Alliance; Ministerio de Economía y Competitividad; MRC; National Center for Advancing Translational Sciences; National Health and Medical Research Council of Australia (NHMRC); Ovarian Cancer Australia; Peter MacCallum Foundation; Sydney West Translational Cancer Research Centre; Terry Fox Research Institute; The Eve Appeal (The Oak Foundation); UK National Institute for Health Research Biomedical Research Centres at the University of Cambridge; University of Pittsburgh School of Medicine; U.S. National Cancer Institute of the National Institutes of Health; VGH & UBC Hospital Foundation; Victorian Cancer Agency.},
}
RevDate: 2024-10-29
Clinical validation of an RSV neutralization assay and analysis of cross-sectional sera associated with 2021-2023 RSV outbreaks to investigate the immunity debt hypothesis.
Microbiology spectrum [Epub ahead of print].
UNLABELLED: Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections and hospitalization in infants and the elderly. Newly approved vaccines and the prophylactic antibody nirsevimab have heightened interest in RSV immunologic surveillance, necessitating the development of high-throughput assays assessing anti-RSV neutralizing activity. Quantitative viral neutralization remains the best correlate of protection for RSV infection and the gold standard for RSV immunological testing. Here, we developed a high-throughput RSV strain A2 focus-reduction neutralization test validated to Clinical Laboratory Improvement Amendments (CLIA)/ Good Clinical Laboratory Practices (GCLP) standards using both clinical specimens and commercially available reference sera. The assay is highly accurate, generating reference serum neutralizing titers within twofold of established assays, with an analytical measurement range between 8 and 1,798 international units per mL (IU/mL). Neutralizing activity measured by the assay strongly correlated with antibody titer determined via indirect enzyme-linked immunosorbent assay (ELISA) (ρ = 1.0, P = 0.0014). Individuals recently having tested positive via quantitative reverse transcription polymerase chain reaction (RT-qPCR) for RSV had a 9.1-fold higher geometric mean neutralizing titer relative to RSV PCR negatives (P-value = 0.09). The validated assay was then used to investigate the immunity debt hypothesis for resurgent RSV outbreaks in the 2022-2023 season, using adult clinical remnant sera sent for herpes simplex virus (HSV)-1/2 antibody testing. There was no difference in geometric mean anti-RSV neutralizing titers between sera sampled before and after the 2022-2023 RSV outbreak (P = 0.68). These data are consistent with limited changes in RSV-neutralizing antibody levels in adults across the 2022-23 RSV outbreak.
IMPORTANCE: Population surveillance studies of serum-neutralizing activity against RSV are crucial for evaluating RSV vaccine efficacy and vulnerabilities to new strains. Here, we designed and validated a high-throughput assay for assessing anti-RSV neutralizing activity, standardized its measurements for comparison with other methodologies, and demonstrated its applicability to real-world samples. Our assay is precise, linear, and yields measurements consistent with other standardized assays, offering a methodology useful for large-scale studies of RSV immunity. We also find no significant difference in neutralizing titers among adults between those taken before and after large RSV outbreaks associated with the latter stages of the coronavirus disease of 2019 (COVID-19) public health emergency, underlining the need for a greater understanding of the dynamics of serological responses to RSV infection.
Additional Links: PMID-39470275
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@article {pmid39470275,
year = {2024},
author = {Piliper, EA and Reed, JC and Greninger, AL},
title = {Clinical validation of an RSV neutralization assay and analysis of cross-sectional sera associated with 2021-2023 RSV outbreaks to investigate the immunity debt hypothesis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0211524},
doi = {10.1128/spectrum.02115-24},
pmid = {39470275},
issn = {2165-0497},
abstract = {UNLABELLED: Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections and hospitalization in infants and the elderly. Newly approved vaccines and the prophylactic antibody nirsevimab have heightened interest in RSV immunologic surveillance, necessitating the development of high-throughput assays assessing anti-RSV neutralizing activity. Quantitative viral neutralization remains the best correlate of protection for RSV infection and the gold standard for RSV immunological testing. Here, we developed a high-throughput RSV strain A2 focus-reduction neutralization test validated to Clinical Laboratory Improvement Amendments (CLIA)/ Good Clinical Laboratory Practices (GCLP) standards using both clinical specimens and commercially available reference sera. The assay is highly accurate, generating reference serum neutralizing titers within twofold of established assays, with an analytical measurement range between 8 and 1,798 international units per mL (IU/mL). Neutralizing activity measured by the assay strongly correlated with antibody titer determined via indirect enzyme-linked immunosorbent assay (ELISA) (ρ = 1.0, P = 0.0014). Individuals recently having tested positive via quantitative reverse transcription polymerase chain reaction (RT-qPCR) for RSV had a 9.1-fold higher geometric mean neutralizing titer relative to RSV PCR negatives (P-value = 0.09). The validated assay was then used to investigate the immunity debt hypothesis for resurgent RSV outbreaks in the 2022-2023 season, using adult clinical remnant sera sent for herpes simplex virus (HSV)-1/2 antibody testing. There was no difference in geometric mean anti-RSV neutralizing titers between sera sampled before and after the 2022-2023 RSV outbreak (P = 0.68). These data are consistent with limited changes in RSV-neutralizing antibody levels in adults across the 2022-23 RSV outbreak.
IMPORTANCE: Population surveillance studies of serum-neutralizing activity against RSV are crucial for evaluating RSV vaccine efficacy and vulnerabilities to new strains. Here, we designed and validated a high-throughput assay for assessing anti-RSV neutralizing activity, standardized its measurements for comparison with other methodologies, and demonstrated its applicability to real-world samples. Our assay is precise, linear, and yields measurements consistent with other standardized assays, offering a methodology useful for large-scale studies of RSV immunity. We also find no significant difference in neutralizing titers among adults between those taken before and after large RSV outbreaks associated with the latter stages of the coronavirus disease of 2019 (COVID-19) public health emergency, underlining the need for a greater understanding of the dynamics of serological responses to RSV infection.},
}
RevDate: 2024-10-29
CmpDate: 2024-10-29
Loss of myosin light chain kinase induces the cellular senescence associated secretory phenotype to promote breast epithelial cell migration.
Scientific reports, 14(1):25786.
Overexpression or activation of oncogenes or loss of tumor-suppressor genes can induce cellular senescence as a defense mechanism against tumor development, thereby maintaining cellular homeostasis. However, cancer cells can circumvent this senescent state and continue to spread. Myosin light chain kinase (MLCK) is downregulated in many breast cancers. Here we report that downregulation of MLCK in normal breast epithelial cells induces a senescence-associated secretory phenotype and stimulates migration. The reduction of MLCK results in increased p21[Cip1] expression, dependent on p53 and the AKT-mammalian target of rapamycin pathway. Subsequently, p21[Cip1] promotes the secretion of soluble ICAM-1, IL-1α, IL-6 and IL-8, thereby enhancing collective cell migration in a non-cell-autonomous manner. These findings provide new mechanistic insights into the role of MLCK in cellular senescence and cancer progression.
Additional Links: PMID-39468273
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@article {pmid39468273,
year = {2024},
author = {Kim, D and Cooper, JA and Helfman, DM},
title = {Loss of myosin light chain kinase induces the cellular senescence associated secretory phenotype to promote breast epithelial cell migration.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {25786},
pmid = {39468273},
issn = {2045-2322},
support = {NFR 2018R1A2A2A05021262//National Research Foundation of Korea/ ; NFR 2018R1A2A2A05021262//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Myosin-Light-Chain Kinase/metabolism/genetics ; *Cell Movement ; *Epithelial Cells/metabolism ; Female ; *Cyclin-Dependent Kinase Inhibitor p21/metabolism/genetics ; TOR Serine-Threonine Kinases/metabolism ; Tumor Suppressor Protein p53/metabolism/genetics ; Senescence-Associated Secretory Phenotype ; Proto-Oncogene Proteins c-akt/metabolism ; Cellular Senescence ; Signal Transduction ; Intercellular Adhesion Molecule-1/metabolism/genetics ; Breast/metabolism/pathology ; Breast Neoplasms/pathology/metabolism/genetics ; },
abstract = {Overexpression or activation of oncogenes or loss of tumor-suppressor genes can induce cellular senescence as a defense mechanism against tumor development, thereby maintaining cellular homeostasis. However, cancer cells can circumvent this senescent state and continue to spread. Myosin light chain kinase (MLCK) is downregulated in many breast cancers. Here we report that downregulation of MLCK in normal breast epithelial cells induces a senescence-associated secretory phenotype and stimulates migration. The reduction of MLCK results in increased p21[Cip1] expression, dependent on p53 and the AKT-mammalian target of rapamycin pathway. Subsequently, p21[Cip1] promotes the secretion of soluble ICAM-1, IL-1α, IL-6 and IL-8, thereby enhancing collective cell migration in a non-cell-autonomous manner. These findings provide new mechanistic insights into the role of MLCK in cellular senescence and cancer progression.},
}
MeSH Terms:
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hide MeSH Terms
Humans
*Myosin-Light-Chain Kinase/metabolism/genetics
*Cell Movement
*Epithelial Cells/metabolism
Female
*Cyclin-Dependent Kinase Inhibitor p21/metabolism/genetics
TOR Serine-Threonine Kinases/metabolism
Tumor Suppressor Protein p53/metabolism/genetics
Senescence-Associated Secretory Phenotype
Proto-Oncogene Proteins c-akt/metabolism
Cellular Senescence
Signal Transduction
Intercellular Adhesion Molecule-1/metabolism/genetics
Breast/metabolism/pathology
Breast Neoplasms/pathology/metabolism/genetics
RevDate: 2024-10-29
Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping.
Nature methods [Epub ahead of print].
RNA molecules form complex networks of molecular interactions that are central to their function and to cellular architecture. But these interaction networks are difficult to probe in situ. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a method for elucidating the biomolecules near an RNA of interest, within its native context. O-MAP uses RNA-fluorescence in situ hybridization-like oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA in situ, enabling nearby molecules to be enriched by streptavidin pulldown. This induces exceptionally precise biotinylation that can be easily optimized and ported to new targets or sample types. Using the noncoding RNAs 47S, 7SK and Xist as models, we develop O-MAP workflows for discovering RNA-proximal proteins, transcripts and genomic loci, yielding a multiomic characterization of these RNAs' subcellular compartments and new regulatory interactions. O-MAP requires no genetic manipulation, uses exclusively off-the-shelf parts and requires orders of magnitude fewer cells than established methods, making it accessible to most laboratories.
Additional Links: PMID-39468212
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@article {pmid39468212,
year = {2024},
author = {Tsue, AF and Kania, EE and Lei, DQ and Fields, R and McGann, CD and Marciniak, DM and Hershberg, EA and Deng, X and Kihiu, M and Ong, SE and Disteche, CM and Kugel, S and Beliveau, BJ and Schweppe, DK and Shechner, DM},
title = {Multiomic characterization of RNA microenvironments by oligonucleotide-mediated proximity-interactome mapping.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {39468212},
issn = {1548-7105},
support = {1R01GM138799-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R01GM138799-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM007750//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R01GM138799-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM007750//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R01GM138799-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM150919-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM150919-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM137916//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; GM131745//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM129090//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; GM131745//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM137916//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R35GM150919-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01GM129090//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 1R01HL160825-01//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1R01HL160825-01//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1R01HL160825-01//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 902616//American Heart Association (American Heart Association, Inc.)/ ; DEB2016186//National Science Foundation (NSF)/ ; T32HG000035//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; UM1HG011586//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; UM1HG011586//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; S10OD021502//U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)/ ; S10OD021502//U.S. Department of Health & Human Services | NIH | NIH Office of the Director (OD)/ ; R37CA241472//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {RNA molecules form complex networks of molecular interactions that are central to their function and to cellular architecture. But these interaction networks are difficult to probe in situ. Here, we introduce Oligonucleotide-mediated proximity-interactome MAPping (O-MAP), a method for elucidating the biomolecules near an RNA of interest, within its native context. O-MAP uses RNA-fluorescence in situ hybridization-like oligonucleotide probes to deliver proximity-biotinylating enzymes to a target RNA in situ, enabling nearby molecules to be enriched by streptavidin pulldown. This induces exceptionally precise biotinylation that can be easily optimized and ported to new targets or sample types. Using the noncoding RNAs 47S, 7SK and Xist as models, we develop O-MAP workflows for discovering RNA-proximal proteins, transcripts and genomic loci, yielding a multiomic characterization of these RNAs' subcellular compartments and new regulatory interactions. O-MAP requires no genetic manipulation, uses exclusively off-the-shelf parts and requires orders of magnitude fewer cells than established methods, making it accessible to most laboratories.},
}
RevDate: 2024-10-28
Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses.
PLoS pathogens, 20(10):e1012650 pii:PPATHOGENS-D-24-00874 [Epub ahead of print].
The recurring spillover of pathogenic coronaviruses and demonstrated capacity of sarbecoviruses, such SARS-CoV-2, to rapidly evolve in humans underscores the need to better understand immune responses to this virus family. For this purpose, we characterized the functional breadth and potency of antibodies targeting the receptor binding domain (RBD) of the spike glycoprotein that exhibited cross-reactivity against SARS-CoV-2 variants, SARS-CoV-1 and sarbecoviruses from diverse clades and animal origins with spillover potential. One neutralizing antibody, C68.61, showed remarkable neutralization breadth against both SARS-CoV-2 variants and viruses from different sarbecovirus clades. C68.61, which targets a conserved RBD class 5 epitope, did not select for escape variants of SARS-CoV-2 or SARS-CoV-1 in culture nor have predicted escape variants among circulating SARS-CoV-2 strains, suggesting this epitope is functionally constrained. We identified 11 additional SARS-CoV-2/SARS-CoV-1 cross-reactive antibodies that target the more sequence conserved class 4 and class 5 epitopes within RBD that show activity against a subset of diverse sarbecoviruses with one antibody binding every single sarbecovirus RBD tested. A subset of these antibodies exhibited Fc-mediated effector functions as potent as antibodies that impact infection outcome in animal models. Thus, our study identified antibodies targeting conserved regions across SARS-CoV-2 variants and sarbecoviruses that may serve as therapeutics for pandemic preparedness as well as blueprints for the design of immunogens capable of eliciting cross-neutralizing responses.
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@article {pmid39466880,
year = {2024},
author = {Ruiz, F and Foreman, WB and Lilly, M and Baharani, VA and Depierreux, DM and Chohan, V and Taylor, AL and Guenthoer, J and Ralph, D and Matsen Iv, FA and Chu, HY and Bieniasz, PD and Côté, M and Starr, TN and Overbaugh, J},
title = {Delineating the functional activity of antibodies with cross-reactivity to SARS-CoV-2, SARS-CoV-1 and related sarbecoviruses.},
journal = {PLoS pathogens},
volume = {20},
number = {10},
pages = {e1012650},
doi = {10.1371/journal.ppat.1012650},
pmid = {39466880},
issn = {1553-7374},
abstract = {The recurring spillover of pathogenic coronaviruses and demonstrated capacity of sarbecoviruses, such SARS-CoV-2, to rapidly evolve in humans underscores the need to better understand immune responses to this virus family. For this purpose, we characterized the functional breadth and potency of antibodies targeting the receptor binding domain (RBD) of the spike glycoprotein that exhibited cross-reactivity against SARS-CoV-2 variants, SARS-CoV-1 and sarbecoviruses from diverse clades and animal origins with spillover potential. One neutralizing antibody, C68.61, showed remarkable neutralization breadth against both SARS-CoV-2 variants and viruses from different sarbecovirus clades. C68.61, which targets a conserved RBD class 5 epitope, did not select for escape variants of SARS-CoV-2 or SARS-CoV-1 in culture nor have predicted escape variants among circulating SARS-CoV-2 strains, suggesting this epitope is functionally constrained. We identified 11 additional SARS-CoV-2/SARS-CoV-1 cross-reactive antibodies that target the more sequence conserved class 4 and class 5 epitopes within RBD that show activity against a subset of diverse sarbecoviruses with one antibody binding every single sarbecovirus RBD tested. A subset of these antibodies exhibited Fc-mediated effector functions as potent as antibodies that impact infection outcome in animal models. Thus, our study identified antibodies targeting conserved regions across SARS-CoV-2 variants and sarbecoviruses that may serve as therapeutics for pandemic preparedness as well as blueprints for the design of immunogens capable of eliciting cross-neutralizing responses.},
}
RevDate: 2024-10-28
HIV DNA Levels in Persons Who Acquired HIV in the Setting of Long-Acting Cabotegravir for HIV Prevention: Analysis of Cases from HPTN 083 and 084.
AIDS research and human retroviruses [Epub ahead of print].
We evaluated HIV DNA levels in individuals who received long-acting cabotegravir (CAB-LA) or tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) pre-exposure prophylaxis in the HPTN 083 and 084 trials and had HIV DNA testing performed to help determine HIV status. HIV DNA testing was performed using peripheral blood mononuclear cell (PBMC) samples collected after a reactive HIV test was obtained at a study site. DNA was quantified using droplet digital PCR (lower limit of detection [LLOD]: 4.09 copies/million PBMCs). Final HIV status and the timing of the first HIV-positive visit were determined by an independent adjudication committee based on HIV test results from real-time site testing and retrospective testing at a centralized laboratory. HIV DNA testing was performed for 133 participants [21 HIV-positive (7 CAB-LA arm, 14 TDF/FTC arm) and 112 HIV-negative; 1-6 tests/person]. For persons with HIV, the time between the first HIV-positive visit and collection of the first sample for DNA testing was a median of 81 days for those receiving CAB-LA (range 41-246) and 11 days for those receiving TDF/FTC (range 3-127). Four (57.1%) of the seven CAB-LA cases with infection had a low initial DNA result [three detected
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@article {pmid39466048,
year = {2024},
author = {Fogel, JM and Persaud, D and Piwowar-Manning, E and Richardson, P and Szewczyk, J and Marzinke, MA and Wang, Z and Guo, X and McCauley, M and Farrior, J and Tran, HV and Ungsedhapand, C and Mathew, CA and Mpendo, J and Rinehart, AR and Rooney, JF and Cohen, MS and Hanscom, B and Grinsztejn, B and Hosseinipour, MC and Delany-Moretlwe, S and Landovitz, RJ and Eshleman, SH and , },
title = {HIV DNA Levels in Persons Who Acquired HIV in the Setting of Long-Acting Cabotegravir for HIV Prevention: Analysis of Cases from HPTN 083 and 084.},
journal = {AIDS research and human retroviruses},
volume = {},
number = {},
pages = {},
doi = {10.1089/aid.2024.0049},
pmid = {39466048},
issn = {1931-8405},
abstract = {We evaluated HIV DNA levels in individuals who received long-acting cabotegravir (CAB-LA) or tenofovir disoproxil fumarate/emtricitabine (TDF/FTC) pre-exposure prophylaxis in the HPTN 083 and 084 trials and had HIV DNA testing performed to help determine HIV status. HIV DNA testing was performed using peripheral blood mononuclear cell (PBMC) samples collected after a reactive HIV test was obtained at a study site. DNA was quantified using droplet digital PCR (lower limit of detection [LLOD]: 4.09 copies/million PBMCs). Final HIV status and the timing of the first HIV-positive visit were determined by an independent adjudication committee based on HIV test results from real-time site testing and retrospective testing at a centralized laboratory. HIV DNA testing was performed for 133 participants [21 HIV-positive (7 CAB-LA arm, 14 TDF/FTC arm) and 112 HIV-negative; 1-6 tests/person]. For persons with HIV, the time between the first HIV-positive visit and collection of the first sample for DNA testing was a median of 81 days for those receiving CAB-LA (range 41-246) and 11 days for those receiving TDF/FTC (range 3-127). Four (57.1%) of the seven CAB-LA cases with infection had a low initial DNA result [three detected
RevDate: 2024-10-28
Phase 1 Study of ROR1 Specific CAR T Cells in Advanced Hematopoietic and Epithelial Malignancies.
Clinical cancer research : an official journal of the American Association for Cancer Research pii:749523 [Epub ahead of print].
PURPOSE: The receptor tyrosine kinase-like orphan receptor 1 (ROR1) is expressed in hematopoietic and epithelial cancers but has limited expression on normal adult tissues. This phase 1 study evaluated the safety of targeting ROR1 with autologous T-lymphocytes engineered to express a ROR1 chimeric antigen receptor (CAR). Secondary objectives evaluated persistence, trafficking, and antitumor activity of CAR T cells.
PATIENTS & METHODS: Twenty-one patients with ROR1+ tumors received CAR T cells at one of four dose levels (DL): 3.3x105/1x106/3.3x106/1x107 cells/kg, administered after lymphodepletion with Cyclophosphamide/Fludarabine (Cy/Flu) or Oxaliplatin/Cyclophosphamide (Ox/Cy). Cohort A included patients with chronic lymphocytic leukemia (CLL, n=3); cohort B included patients with triple-negative breast cancer (TNBC, n=10) or non-small-cell lung cancer (NSCLC, n=8). A second infusion was administered to one patient in cohort A with residual CLL in the marrow and three patients in cohort B with stable disease after first infusion.
RESULTS: Treatment was well tolerated apart from one dose limiting toxicity at DL4 in a patient with advanced NSCLC. Two of the three (67%) CLL patients showed robust CAR T expansion and a rapid antitumor response. In patients with NSCLC and TNBC, CAR T cells expanded to variable levels, infiltrated tumor poorly, and one of eighteen patients (5.5%) achieved partial response by RECIST 1.1.
CONCLUSION: ROR1 CAR T cells were well tolerated in most patients. Antitumor activity was observed in CLL but was limited in TNBC and NSCLC. Immunogenicity of the CAR and lack of sustained tumor infiltration were identified as limitations.
Additional Links: PMID-39466024
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@article {pmid39466024,
year = {2024},
author = {Jaeger-Ruckstuhl, CA and Specht, JM and Voutsinas, JM and MacMillan, HR and Wu, QV and Muhunthan, V and Berger, C and Pullarkat, S and Wright, JH and Yeung, CCS and Hyun, TS and Seaton, B and Aicher, LD and Song, X and Pierce, RH and Lo, Y and Cole, GO and Lee, SM and Newell, EW and Maloney, DG and Riddell, SR},
title = {Phase 1 Study of ROR1 Specific CAR T Cells in Advanced Hematopoietic and Epithelial Malignancies.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-24-2172},
pmid = {39466024},
issn = {1557-3265},
abstract = {PURPOSE: The receptor tyrosine kinase-like orphan receptor 1 (ROR1) is expressed in hematopoietic and epithelial cancers but has limited expression on normal adult tissues. This phase 1 study evaluated the safety of targeting ROR1 with autologous T-lymphocytes engineered to express a ROR1 chimeric antigen receptor (CAR). Secondary objectives evaluated persistence, trafficking, and antitumor activity of CAR T cells.
PATIENTS & METHODS: Twenty-one patients with ROR1+ tumors received CAR T cells at one of four dose levels (DL): 3.3x105/1x106/3.3x106/1x107 cells/kg, administered after lymphodepletion with Cyclophosphamide/Fludarabine (Cy/Flu) or Oxaliplatin/Cyclophosphamide (Ox/Cy). Cohort A included patients with chronic lymphocytic leukemia (CLL, n=3); cohort B included patients with triple-negative breast cancer (TNBC, n=10) or non-small-cell lung cancer (NSCLC, n=8). A second infusion was administered to one patient in cohort A with residual CLL in the marrow and three patients in cohort B with stable disease after first infusion.
RESULTS: Treatment was well tolerated apart from one dose limiting toxicity at DL4 in a patient with advanced NSCLC. Two of the three (67%) CLL patients showed robust CAR T expansion and a rapid antitumor response. In patients with NSCLC and TNBC, CAR T cells expanded to variable levels, infiltrated tumor poorly, and one of eighteen patients (5.5%) achieved partial response by RECIST 1.1.
CONCLUSION: ROR1 CAR T cells were well tolerated in most patients. Antitumor activity was observed in CLL but was limited in TNBC and NSCLC. Immunogenicity of the CAR and lack of sustained tumor infiltration were identified as limitations.},
}
RevDate: 2024-10-28
Efficacy and safety of pembrolizumab in patients with advanced urothelial carcinoma deemed potentially ineligible for platinum-containing chemotherapy: Post hoc analysis of KEYNOTE-052 and LEAP-011.
Cancer [Epub ahead of print].
BACKGROUND: First-line pembrolizumab monotherapy is a standard of care for platinum-ineligible patients with advanced urothelial carcinoma (UC). No global standardized definition of platinum ineligibility exists. This study aimed to evaluate the efficacy and safety of pembrolizumab monotherapy in patients with UC who met various criteria for platinum ineligibility.
METHODS: Patients from KEYNOTE-052 and LEAP-011 deemed potentially platinum ineligible were pooled for this post hoc exploratory analysis as follows: group 1: Eastern Cooperative Oncology Group performance status (ECOG PS) 2; group 2: ECOG PS 2 and age ≥80 years, renal dysfunction, or visceral disease; and group 3: any two other factors regardless of ECOG PS. Patients received pembrolizumab 200 mg intravenously every 3 weeks. End points included objective response rate (ORR), progression-free survival (PFS) per Response Evaluation Criteria in Solid Tumors, version 1.1, by blinded independent central review, overall survival (OS), and safety.
RESULTS: A total of 612 patients treated with pembrolizumab from KEYNOTE-052 (n = 370) and LEAP-011 (n = 242) were included; the median (range) follow-up was 56.3 months (51.2-65.3 months) and 12.8 months (0.2-25.1 months), respectively. For group 1, ORR was 26.2%, median PFS was 2.7 months, and median OS was 10.1 months. For group 2, ORR ranged from 23.5% to 33.3%, median PFS ranged from 2.1 to 4.4 months, and median OS ranged from 9.1 to 10.1 months. For group 3, ORR ranged from 25.7% to 27.9%, median PFS ranged from 2.1 to 2.8 months, and median OS ranged from 9.0 to 10.6 months. Treatment-related adverse event rates were consistent across groups.
CONCLUSIONS: Frontline pembrolizumab has consistent antitumor activity and safety in patients with advanced UC categorized as potentially ineligible for platinum-based chemotherapy, regardless of the variable definitions of platinum ineligibility used.
Additional Links: PMID-39465550
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@article {pmid39465550,
year = {2024},
author = {O'Donnell, PH and Loriot, Y and Csoszi, T and Matsubara, N and Shin, SJ and Park, SH and Atduev, V and Gumus, M and Karaca, SB and Grivas, P and de Wit, R and Castellano, DE and Powles, T and Vuky, J and Zhao, Y and O'Hara, K and Okpara, CE and Franco, S and Homet Moreno, B and Żołnierek, J and Siefker-Radtke, AO},
title = {Efficacy and safety of pembrolizumab in patients with advanced urothelial carcinoma deemed potentially ineligible for platinum-containing chemotherapy: Post hoc analysis of KEYNOTE-052 and LEAP-011.},
journal = {Cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/cncr.35601},
pmid = {39465550},
issn = {1097-0142},
support = {//Merck Sharp & Dohme LLC, a subsidiary of Merck & Co, Inc. (Rahway, New Jersey, USA)/ ; },
abstract = {BACKGROUND: First-line pembrolizumab monotherapy is a standard of care for platinum-ineligible patients with advanced urothelial carcinoma (UC). No global standardized definition of platinum ineligibility exists. This study aimed to evaluate the efficacy and safety of pembrolizumab monotherapy in patients with UC who met various criteria for platinum ineligibility.
METHODS: Patients from KEYNOTE-052 and LEAP-011 deemed potentially platinum ineligible were pooled for this post hoc exploratory analysis as follows: group 1: Eastern Cooperative Oncology Group performance status (ECOG PS) 2; group 2: ECOG PS 2 and age ≥80 years, renal dysfunction, or visceral disease; and group 3: any two other factors regardless of ECOG PS. Patients received pembrolizumab 200 mg intravenously every 3 weeks. End points included objective response rate (ORR), progression-free survival (PFS) per Response Evaluation Criteria in Solid Tumors, version 1.1, by blinded independent central review, overall survival (OS), and safety.
RESULTS: A total of 612 patients treated with pembrolizumab from KEYNOTE-052 (n = 370) and LEAP-011 (n = 242) were included; the median (range) follow-up was 56.3 months (51.2-65.3 months) and 12.8 months (0.2-25.1 months), respectively. For group 1, ORR was 26.2%, median PFS was 2.7 months, and median OS was 10.1 months. For group 2, ORR ranged from 23.5% to 33.3%, median PFS ranged from 2.1 to 4.4 months, and median OS ranged from 9.1 to 10.1 months. For group 3, ORR ranged from 25.7% to 27.9%, median PFS ranged from 2.1 to 2.8 months, and median OS ranged from 9.0 to 10.6 months. Treatment-related adverse event rates were consistent across groups.
CONCLUSIONS: Frontline pembrolizumab has consistent antitumor activity and safety in patients with advanced UC categorized as potentially ineligible for platinum-based chemotherapy, regardless of the variable definitions of platinum ineligibility used.},
}
RevDate: 2024-10-28
Management of human leukocyte antigen-mediated platelet transfusion refractoriness: Brief synopsis and recent literature review.
Transfusion [Epub ahead of print].
Additional Links: PMID-39462857
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@article {pmid39462857,
year = {2024},
author = {Panch, SR and Vassallo, RR and Adams, S and Borge, DP and Gammon, R and Gandhi, MJ and Philogene, M and Sullivan, HC and Wu, Y and Kopko, P},
title = {Management of human leukocyte antigen-mediated platelet transfusion refractoriness: Brief synopsis and recent literature review.},
journal = {Transfusion},
volume = {},
number = {},
pages = {},
doi = {10.1111/trf.18036},
pmid = {39462857},
issn = {1537-2995},
}
RevDate: 2024-10-26
Optimizing Siglec-8-Directed Immunotherapy for Eosinophilic and Mast Cell Disorders.
Cancers, 16(20): pii:cancers16203476.
Background/Objective: Current treatments for eosinophilic and mast cell disorders are often ineffective. One promising target to improve outcomes is sialic acid-binding immunoglobulin-like lectin-8 (Siglec-8). As limitations, there are few Siglec-8 monoclonal antibodies (mAbs) available to date, and Siglec-8-directed treatments have so far primarily focused on unconjugated mAbs, which may be inadequate, especially against mast cells. Methods: Here, we used transgenic mice to raise a diverse panel of fully human mAbs that either recognize the V-set domain, membrane-distal C2-set domain, or membrane-proximal C2-set domain of full-length Siglec-8 as a basis for novel therapeutics. Results: All mAbs were efficiently internalized into Siglec-8-expressing cells, suggesting their potential to deliver cytotoxic payloads. Tool T cell-engaging bispecific antibodies (BiAbs) and chimeric antigen receptor (CAR)-modified natural killer (NK) cells using single-chain variable fragments from Siglec-8 mAbs showed highly potent cytolytic activity against Siglec-8-positive cells even in cases of very low target antigen abundance, whereas they elicited no cytolytic activity against Siglec-8-negative target cells. Siglec-8[V-set]-directed T cell-engaging BiAbs and Siglec-8[V-set]-directed CAR-modified NK cells induced substantially greater cytotoxicity against cells expressing an artificial smaller Siglec-8 variant containing only the V-set domain than cells expressing full-length Siglec-8, consistent with the notion that targeting membrane-proximal epitopes enhances effector functions of Siglec-8 antibody-based therapeutics. Indeed, unconjugated Siglec-8[C2-set] mAbs, Siglec-8[C2-set]-directed T cell-engaging BiAbs, and Siglec-8[C2-set]-directed CAR-modified NK cells showed high antigen-specific cytolytic activity against Siglec-8-positive human cell lines and primary patient eosinophils. Conclusions: Together, these data demonstrate Siglec-8-directed immunotherapies can be highly potent, supporting their further development for eosinophilic and mast cell disorders.
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@article {pmid39456570,
year = {2024},
author = {Lim, SYT and Huo, J and Laszlo, GS and Cole, FM and Kehret, AR and Li, J and Lunn-Halbert, MC and Persicke, JL and Rupert, PB and Strong, RK and Walter, RB},
title = {Optimizing Siglec-8-Directed Immunotherapy for Eosinophilic and Mast Cell Disorders.},
journal = {Cancers},
volume = {16},
number = {20},
pages = {},
doi = {10.3390/cancers16203476},
pmid = {39456570},
issn = {2072-6694},
support = {R21-AI150566//National Institute of Health (NIH)/National Institute of Allergy and Infectious Diseases/ ; },
abstract = {Background/Objective: Current treatments for eosinophilic and mast cell disorders are often ineffective. One promising target to improve outcomes is sialic acid-binding immunoglobulin-like lectin-8 (Siglec-8). As limitations, there are few Siglec-8 monoclonal antibodies (mAbs) available to date, and Siglec-8-directed treatments have so far primarily focused on unconjugated mAbs, which may be inadequate, especially against mast cells. Methods: Here, we used transgenic mice to raise a diverse panel of fully human mAbs that either recognize the V-set domain, membrane-distal C2-set domain, or membrane-proximal C2-set domain of full-length Siglec-8 as a basis for novel therapeutics. Results: All mAbs were efficiently internalized into Siglec-8-expressing cells, suggesting their potential to deliver cytotoxic payloads. Tool T cell-engaging bispecific antibodies (BiAbs) and chimeric antigen receptor (CAR)-modified natural killer (NK) cells using single-chain variable fragments from Siglec-8 mAbs showed highly potent cytolytic activity against Siglec-8-positive cells even in cases of very low target antigen abundance, whereas they elicited no cytolytic activity against Siglec-8-negative target cells. Siglec-8[V-set]-directed T cell-engaging BiAbs and Siglec-8[V-set]-directed CAR-modified NK cells induced substantially greater cytotoxicity against cells expressing an artificial smaller Siglec-8 variant containing only the V-set domain than cells expressing full-length Siglec-8, consistent with the notion that targeting membrane-proximal epitopes enhances effector functions of Siglec-8 antibody-based therapeutics. Indeed, unconjugated Siglec-8[C2-set] mAbs, Siglec-8[C2-set]-directed T cell-engaging BiAbs, and Siglec-8[C2-set]-directed CAR-modified NK cells showed high antigen-specific cytolytic activity against Siglec-8-positive human cell lines and primary patient eosinophils. Conclusions: Together, these data demonstrate Siglec-8-directed immunotherapies can be highly potent, supporting their further development for eosinophilic and mast cell disorders.},
}
RevDate: 2024-10-25
Ibrutinib for therapy of steroid-refractory chronic graft vs. host disease: A multicenter real-world analysis.
Blood advances pii:525803 [Epub ahead of print].
To examine activity of ibrutinib in steroid-refractory chronic GVHD (SR-cGVHD) after FDA approval, we conducted a multicenter retrospective study. Data were standardly collected (N=270 from 19 centers). Involved organs included skin (75%), eye (61%), mouth (54%), joint/fascia (47%), GI (26%), lung (27%), liver (19%), genital (7%), other (4.4%). NIH severity was mild in 5.7%, moderate 42%, severe 53%. 39% had overlap subtype. KPS was ≥ 80% in 72%. Median prednisone (mg/kg) was 0.21 (0-2.27). Ibrutinib was started at median of 18.2 months after cGVHD onset and in earlier lines of therapy (2nd line: 26%, 3rd: 30%, 4th: 21%, 5th: 9.6%, 6th: 10%, 7th or higher: 1.2%)). Among evaluable subjects, the 6 month NIH overall response rate (CR/PR) was 45% (PR 42%, CR 3%). Median duration of response was 15 months (range 1-46). Liver involvement had association with 6 month ORR (multivariate (MVA) OR 5.49 (95% CI 2.3-14.2, p <0.001). Best overall response was 56%, with most (86%) achieving by 1-3 months. With median follow up for survivors of 30.5 months, FFS was 59% (53-65%) at 6 months and 41% (36-48%) at 12 months. On MVA, increased age (HR 1.01, 95% CI 1.0-1.02, p=0.033), higher baseline prednisone (HR 1.92, 1.09-3.38, p=0.032), and lung involvement (HR 1.58, 1.1-2.28, p=0.016) had worse FFS. Ibrutinib discontinuation was most commonly due to progressive cGVHD (44%) or toxicity (42%). These data support that ibrutinib has activity in SR-cGVHD, provide new insight into factors associated with response and FFS, and demonstrate the toxicity profile associated with discontinuation.
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@article {pmid39454280,
year = {2024},
author = {Pidala, JA and Kim, J and Kalos, D and Cutler, CS and DeFilipp, Z and Flowers, ME and Hamilton, BK and Chin, KK and Rotta, M and El Jurdi, N and Hamadani, M and Ahmed, G and Kitko, CL and Ponce, DM and Sung, AD and Tang, H and Farhadfar, N and Nemecek, ER and Pusic, I and Qayed, M and Rangarajan, HG and Hogan, WJ and Etra, AM and Jaglowski, SM},
title = {Ibrutinib for therapy of steroid-refractory chronic graft vs. host disease: A multicenter real-world analysis.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024014374},
pmid = {39454280},
issn = {2473-9537},
abstract = {To examine activity of ibrutinib in steroid-refractory chronic GVHD (SR-cGVHD) after FDA approval, we conducted a multicenter retrospective study. Data were standardly collected (N=270 from 19 centers). Involved organs included skin (75%), eye (61%), mouth (54%), joint/fascia (47%), GI (26%), lung (27%), liver (19%), genital (7%), other (4.4%). NIH severity was mild in 5.7%, moderate 42%, severe 53%. 39% had overlap subtype. KPS was ≥ 80% in 72%. Median prednisone (mg/kg) was 0.21 (0-2.27). Ibrutinib was started at median of 18.2 months after cGVHD onset and in earlier lines of therapy (2nd line: 26%, 3rd: 30%, 4th: 21%, 5th: 9.6%, 6th: 10%, 7th or higher: 1.2%)). Among evaluable subjects, the 6 month NIH overall response rate (CR/PR) was 45% (PR 42%, CR 3%). Median duration of response was 15 months (range 1-46). Liver involvement had association with 6 month ORR (multivariate (MVA) OR 5.49 (95% CI 2.3-14.2, p <0.001). Best overall response was 56%, with most (86%) achieving by 1-3 months. With median follow up for survivors of 30.5 months, FFS was 59% (53-65%) at 6 months and 41% (36-48%) at 12 months. On MVA, increased age (HR 1.01, 95% CI 1.0-1.02, p=0.033), higher baseline prednisone (HR 1.92, 1.09-3.38, p=0.032), and lung involvement (HR 1.58, 1.1-2.28, p=0.016) had worse FFS. Ibrutinib discontinuation was most commonly due to progressive cGVHD (44%) or toxicity (42%). These data support that ibrutinib has activity in SR-cGVHD, provide new insight into factors associated with response and FFS, and demonstrate the toxicity profile associated with discontinuation.},
}
RevDate: 2024-10-25
Global, regional, and national burden of injuries, and burden attributable to injuries risk factors, 1990 to 2019: results from the Global Burden of Disease study 2019.
Public health, 237:212-231 pii:S0033-3506(24)00252-X [Epub ahead of print].
OBJECTIVES: In this study, the trends and current situation of the injury burden as well as attributable burden to injury risk factors at global, regional, and national levels based on the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 are presented.
STUDY DESIGN: To assess the attributable burden of injury risk factors, the data of interest on data sources were retrieved from the Global Health Data Exchange (GHDx) and analyzed.
METHODS: Cause-specific death from injuries was estimated using the Cause of Death Ensemble model in the GBD 2019. The burden attributable to each injury risk factor was incorporated in the population attributable fraction to estimate the total attributable deaths and disability-adjusted life years. The Socio-demographic Index (SDI) was used to evaluate countries' developmental status.
RESULTS: Globally, there were 713.9 million (95% uncertainty interval [UI]: 663.8 to 766.9) injuries incidence and 4.3 million (UI: 3.9 to 4.6) deaths caused by injuries in 2019. There was an inverse relationship between age-standardized disability-adjusted life year rate and SDI quintiles in 2019. Overall, low bone mineral density was the leading risk factor of injury deaths in 2019, with a contribution of 10.5% (UI: 9.0 to 11.6) of total injuries and age-standardized deaths, followed by occupational risks (7.0% [UI: 6.3-7.9]) and alcohol use (6.8% [UI: 5.2 to 8.5]).
CONCLUSION: Various risks were responsible for the imposed burden of injuries. This study highlighted the small but persistent share of injuries in the global burden of diseases and injuries to provide beneficial data to produce proper policies to reach an effective global injury prevention plan.
Additional Links: PMID-39454232
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PubMed:
Citation:
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@article {pmid39454232,
year = {2024},
author = {, },
title = {Global, regional, and national burden of injuries, and burden attributable to injuries risk factors, 1990 to 2019: results from the Global Burden of Disease study 2019.},
journal = {Public health},
volume = {237},
number = {},
pages = {212-231},
doi = {10.1016/j.puhe.2024.06.011},
pmid = {39454232},
issn = {1476-5616},
abstract = {OBJECTIVES: In this study, the trends and current situation of the injury burden as well as attributable burden to injury risk factors at global, regional, and national levels based on the Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) 2019 are presented.
STUDY DESIGN: To assess the attributable burden of injury risk factors, the data of interest on data sources were retrieved from the Global Health Data Exchange (GHDx) and analyzed.
METHODS: Cause-specific death from injuries was estimated using the Cause of Death Ensemble model in the GBD 2019. The burden attributable to each injury risk factor was incorporated in the population attributable fraction to estimate the total attributable deaths and disability-adjusted life years. The Socio-demographic Index (SDI) was used to evaluate countries' developmental status.
RESULTS: Globally, there were 713.9 million (95% uncertainty interval [UI]: 663.8 to 766.9) injuries incidence and 4.3 million (UI: 3.9 to 4.6) deaths caused by injuries in 2019. There was an inverse relationship between age-standardized disability-adjusted life year rate and SDI quintiles in 2019. Overall, low bone mineral density was the leading risk factor of injury deaths in 2019, with a contribution of 10.5% (UI: 9.0 to 11.6) of total injuries and age-standardized deaths, followed by occupational risks (7.0% [UI: 6.3-7.9]) and alcohol use (6.8% [UI: 5.2 to 8.5]).
CONCLUSION: Various risks were responsible for the imposed burden of injuries. This study highlighted the small but persistent share of injuries in the global burden of diseases and injuries to provide beneficial data to produce proper policies to reach an effective global injury prevention plan.},
}
RevDate: 2024-10-25
Reply to Letter to Editor by Fingrut, et al.
Blood advances pii:525801 [Epub ahead of print].
Additional Links: PMID-39454203
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PubMed:
Citation:
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@article {pmid39454203,
year = {2024},
author = {Farhadfar, N and Lee, SJ},
title = {Reply to Letter to Editor by Fingrut, et al.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024014712},
pmid = {39454203},
issn = {2473-9537},
}
RevDate: 2024-10-25
Randomized Controlled Trial of Acceptance and Commitment Therapy for Fatigue Interference With Functioning in Metastatic Breast Cancer.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology [Epub ahead of print].
PURPOSE: Fatigue is a highly prevalent and disabling symptom for patients with metastatic breast cancer (MBC). Evidence-based interventions for managing fatigue in advanced cancer populations are lacking. This phase II randomized controlled trial tested the effect of acceptance and commitment therapy (ACT) on fatigue interference with functioning in patients with MBC.
METHODS: Eligible patients were women with stage IV breast cancer who had moderate to severe fatigue interference. Patients completed a baseline assessment that included self-report measures of fatigue interference with activities, mood, and cognition (primary outcome) and sleep interference with functioning, engagement in daily activities, and quality of life (QOL; secondary outcomes). Then patients were randomly assigned to six weekly telephone-delivered sessions of either ACT (n = 116) or education/support (n = 120). Follow-up assessments occurred at 2 weeks, 3 months, and 6 months postintervention (means, 9.69, 20.51, and 33.59 weeks postbaseline, respectively).
RESULTS: Linear mixed model analyses showed that compared with patients in the education/support condition, patients in the ACT condition reported significantly less fatigue interference (P = .018). These results were significant at 2 weeks and 6 months postintervention. ACT's effect on sleep interference was not statistically significant after the Sidak adjustment for multiple comparisons (P = .037). ACT patients showed a steady decline in sleep interference, a trend that was not found for education/support patients. Engagement in daily activities and QOL did not significantly differ between study groups, except for functional QOL (P = .006). Compared with education/support patients, ACT patients showed significantly better functional QOL at 2 weeks and 6 months postintervention.
CONCLUSION: Results suggest that a brief, telephone-delivered ACT intervention can reduce fatigue interference with functioning in patients with MBC.
Additional Links: PMID-39454125
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PubMed:
Citation:
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@article {pmid39454125,
year = {2024},
author = {Mosher, CE and Lee, S and Addington, EL and Park, S and Lewson, AB and Snyder, S and Hirsh, AT and Bricker, JB and Miller, KD and Ballinger, TJ and Schneider, BP and Storniolo, AM and Newton, EV and Champion, VL and Johns, SA},
title = {Randomized Controlled Trial of Acceptance and Commitment Therapy for Fatigue Interference With Functioning in Metastatic Breast Cancer.},
journal = {Journal of clinical oncology : official journal of the American Society of Clinical Oncology},
volume = {},
number = {},
pages = {JCO2400965},
doi = {10.1200/JCO.24.00965},
pmid = {39454125},
issn = {1527-7755},
abstract = {PURPOSE: Fatigue is a highly prevalent and disabling symptom for patients with metastatic breast cancer (MBC). Evidence-based interventions for managing fatigue in advanced cancer populations are lacking. This phase II randomized controlled trial tested the effect of acceptance and commitment therapy (ACT) on fatigue interference with functioning in patients with MBC.
METHODS: Eligible patients were women with stage IV breast cancer who had moderate to severe fatigue interference. Patients completed a baseline assessment that included self-report measures of fatigue interference with activities, mood, and cognition (primary outcome) and sleep interference with functioning, engagement in daily activities, and quality of life (QOL; secondary outcomes). Then patients were randomly assigned to six weekly telephone-delivered sessions of either ACT (n = 116) or education/support (n = 120). Follow-up assessments occurred at 2 weeks, 3 months, and 6 months postintervention (means, 9.69, 20.51, and 33.59 weeks postbaseline, respectively).
RESULTS: Linear mixed model analyses showed that compared with patients in the education/support condition, patients in the ACT condition reported significantly less fatigue interference (P = .018). These results were significant at 2 weeks and 6 months postintervention. ACT's effect on sleep interference was not statistically significant after the Sidak adjustment for multiple comparisons (P = .037). ACT patients showed a steady decline in sleep interference, a trend that was not found for education/support patients. Engagement in daily activities and QOL did not significantly differ between study groups, except for functional QOL (P = .006). Compared with education/support patients, ACT patients showed significantly better functional QOL at 2 weeks and 6 months postintervention.
CONCLUSION: Results suggest that a brief, telephone-delivered ACT intervention can reduce fatigue interference with functioning in patients with MBC.},
}
RevDate: 2024-10-25
Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference.
Systematic biology pii:7841849 [Epub ahead of print].
Online phylogenetic inference methods add sequentially arriving sequences to an inferred phylogeny without the need to recompute the entire tree from scratch. Some online method implementations exist already, but there remains concern that additional sequences may change the topological relationship among the original set of taxa. We call such a change in tree topology a lack of stability for the inferred tree. In this paper, we analyze the stability of single taxon addition in a Maximum Likelihood framework across 1, 000 empirical datasets. We find that instability occurs in almost 90% of our examples, although observed topological differences do not always reach significance under the AU-test. Changes in tree topology after addition of a taxon rarely occur close to its attachment location, and are more frequently observed in more distant tree locations carrying low bootstrap support. To investigate whether instability is predictable, we hypothesize sources of instability and design summary statistics addressing these hypotheses. Using these summary statistics as input features for machine learning under random forests, we are able to predict instability and can identify the most influential features. In summary, it does not appear that a strict insertion-only online inference method will deliver globally optimal trees, although relaxing insertion strictness by allowing for a small number of final tree rearrangements or accepting slightly suboptimal solutions appears feasible.
Additional Links: PMID-39453463
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PubMed:
Citation:
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@article {pmid39453463,
year = {2024},
author = {Collienne, L and Barker, M and Suchard, MA and Matsen Iv, FA},
title = {Phylogenetic tree instability after taxon addition: empirical frequency, predictability, and consequences for online inference.},
journal = {Systematic biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/sysbio/syae059},
pmid = {39453463},
issn = {1076-836X},
abstract = {Online phylogenetic inference methods add sequentially arriving sequences to an inferred phylogeny without the need to recompute the entire tree from scratch. Some online method implementations exist already, but there remains concern that additional sequences may change the topological relationship among the original set of taxa. We call such a change in tree topology a lack of stability for the inferred tree. In this paper, we analyze the stability of single taxon addition in a Maximum Likelihood framework across 1, 000 empirical datasets. We find that instability occurs in almost 90% of our examples, although observed topological differences do not always reach significance under the AU-test. Changes in tree topology after addition of a taxon rarely occur close to its attachment location, and are more frequently observed in more distant tree locations carrying low bootstrap support. To investigate whether instability is predictable, we hypothesize sources of instability and design summary statistics addressing these hypotheses. Using these summary statistics as input features for machine learning under random forests, we are able to predict instability and can identify the most influential features. In summary, it does not appear that a strict insertion-only online inference method will deliver globally optimal trees, although relaxing insertion strictness by allowing for a small number of final tree rearrangements or accepting slightly suboptimal solutions appears feasible.},
}
RevDate: 2024-10-25
Early Changes in Health-Related Quality of Life as a Biomarker of Survival in African Patients with HIV-Associated Kaposi Sarcoma.
Tropical medicine and infectious disease, 9(10): pii:tropicalmed9100244.
Sub-Saharan Africa bears the largest public health burden of Kaposi sarcoma (KS), a leading cause of cancer mortality. Quality of life (QOL) assessments in cancer patients can provide information on prognosis beyond traditional biomarkers or biological measures. The prognostic value of QOL measures in patients with HIV-KS was evaluated. Prognostic associations of baseline QOL scores (by quartiles or thresholds for clinical importance) and changes in QOL scores (using minimum important difference) over the first 3 months of therapy were evaluated in 112 participants with HIV-KS randomised to receive ART, with or without chemotherapy. Cox's regression analysis assessed the prognostic contribution of QOL scores from the EORTC QLQ-C30 questionnaire. Survival curves were generated using the Kaplan-Meier method. Baseline QOL scores did not predict overall survival. The change in the 3-month QOL scores for the global health scale, fatigue, and pain domains was prognostic; the hazard ratios were 3.88 (95% CI 1.32-11.38, p = 0.01), 3.72 (95% CI 1.61-8.62, p = 0.00) and 5.96 (95% CI 2.46-14.43, p = 0.00), respectively. QOL assessments can provide useful prognostic information in patients with HIV-KS. Patients lacking meaningful improvement early into treatment represent a population at high risk of death.
Additional Links: PMID-39453271
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PubMed:
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@article {pmid39453271,
year = {2024},
author = {Shaik, F and Uldrick, TS and Mazinu, M and Gwebushe, N and Mosam, A},
title = {Early Changes in Health-Related Quality of Life as a Biomarker of Survival in African Patients with HIV-Associated Kaposi Sarcoma.},
journal = {Tropical medicine and infectious disease},
volume = {9},
number = {10},
pages = {},
doi = {10.3390/tropicalmed9100244},
pmid = {39453271},
issn = {2414-6366},
support = {SELF-INITIATED RESEARCH (SIR) GRANT//South African Medical Research Council/ ; },
abstract = {Sub-Saharan Africa bears the largest public health burden of Kaposi sarcoma (KS), a leading cause of cancer mortality. Quality of life (QOL) assessments in cancer patients can provide information on prognosis beyond traditional biomarkers or biological measures. The prognostic value of QOL measures in patients with HIV-KS was evaluated. Prognostic associations of baseline QOL scores (by quartiles or thresholds for clinical importance) and changes in QOL scores (using minimum important difference) over the first 3 months of therapy were evaluated in 112 participants with HIV-KS randomised to receive ART, with or without chemotherapy. Cox's regression analysis assessed the prognostic contribution of QOL scores from the EORTC QLQ-C30 questionnaire. Survival curves were generated using the Kaplan-Meier method. Baseline QOL scores did not predict overall survival. The change in the 3-month QOL scores for the global health scale, fatigue, and pain domains was prognostic; the hazard ratios were 3.88 (95% CI 1.32-11.38, p = 0.01), 3.72 (95% CI 1.61-8.62, p = 0.00) and 5.96 (95% CI 2.46-14.43, p = 0.00), respectively. QOL assessments can provide useful prognostic information in patients with HIV-KS. Patients lacking meaningful improvement early into treatment represent a population at high risk of death.},
}
RevDate: 2024-10-25
Epidemiology and Outcomes of Recurrent C Difficile Infection Among Hematopoietic Cell Transplant Recipients: A Single-center, Retrospective 10-year Study.
Open forum infectious diseases, 11(10):ofae570.
BACKGROUND: There are limited data on the contemporary epidemiology of recurrent Clostridioides difficile infection (CDI) among hematopoietic cell transplant (HCT) recipients. We aimed to determine the incidence, risk factors, and outcomes for recurrent CDI among HCT recipients.
METHODS: We conducted a retrospective study of adult HCT recipients between 2012 and 2021 diagnosed with index CDI between HCT day -7 and +100. Recurrent CDI was defined as new symptoms and a positive test within 12 weeks after treatment for index CDI. Cox proportional hazards models were used to investigate associations between prespecified variables (age, neutropenia, exposure to antibiotics with antianaerobic coverage, cytomegalovirus viremia/disease, and metronidazole monotherapy) and recurrent infection, presented as hazard ratios with 95% confidence intervals (CI).
RESULTS: Of 3479 HCT recipients, 416 (12%) had index CDI and were treated with oral vancomycin (31%), metronidazole (41%), oral vancomycin and metronidazole (29%). Of 381 patients eligible for recurrent CDI analysis, 35 had recurrent infection; cumulative incidence was 10% (95% CI, 7-13) at 12 weeks. In the 14 days after recurrence, 2/25 (8%) patients required hospital admission; none died within 30 days. Metronidazole monotherapy for treatment of index CDI was associated with an increased rate of recurrence (adjusted hazard ratio, 2.0; 95% CI, 1.0-4.0; P = .048).
CONCLUSIONS: Recurrent CDI occurred in 10% of HCT recipients in the early posttransplant period and was associated with use of metronidazole. Further study is needed to characterize risk factors for recurrent CDI among HCT recipients to guide use of agents aimed at preventing recurrence.
Additional Links: PMID-39450393
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Citation:
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@article {pmid39450393,
year = {2024},
author = {Sanchez, E and Krantz, EM and Escobar, ZK and Tverdek, F and Rosen, EA and Oshima, MU and Carpenter, PA and Pergam, SA and Liu, C},
title = {Epidemiology and Outcomes of Recurrent C Difficile Infection Among Hematopoietic Cell Transplant Recipients: A Single-center, Retrospective 10-year Study.},
journal = {Open forum infectious diseases},
volume = {11},
number = {10},
pages = {ofae570},
pmid = {39450393},
issn = {2328-8957},
abstract = {BACKGROUND: There are limited data on the contemporary epidemiology of recurrent Clostridioides difficile infection (CDI) among hematopoietic cell transplant (HCT) recipients. We aimed to determine the incidence, risk factors, and outcomes for recurrent CDI among HCT recipients.
METHODS: We conducted a retrospective study of adult HCT recipients between 2012 and 2021 diagnosed with index CDI between HCT day -7 and +100. Recurrent CDI was defined as new symptoms and a positive test within 12 weeks after treatment for index CDI. Cox proportional hazards models were used to investigate associations between prespecified variables (age, neutropenia, exposure to antibiotics with antianaerobic coverage, cytomegalovirus viremia/disease, and metronidazole monotherapy) and recurrent infection, presented as hazard ratios with 95% confidence intervals (CI).
RESULTS: Of 3479 HCT recipients, 416 (12%) had index CDI and were treated with oral vancomycin (31%), metronidazole (41%), oral vancomycin and metronidazole (29%). Of 381 patients eligible for recurrent CDI analysis, 35 had recurrent infection; cumulative incidence was 10% (95% CI, 7-13) at 12 weeks. In the 14 days after recurrence, 2/25 (8%) patients required hospital admission; none died within 30 days. Metronidazole monotherapy for treatment of index CDI was associated with an increased rate of recurrence (adjusted hazard ratio, 2.0; 95% CI, 1.0-4.0; P = .048).
CONCLUSIONS: Recurrent CDI occurred in 10% of HCT recipients in the early posttransplant period and was associated with use of metronidazole. Further study is needed to characterize risk factors for recurrent CDI among HCT recipients to guide use of agents aimed at preventing recurrence.},
}
RevDate: 2024-10-25
CmpDate: 2024-10-25
Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk.
BMC medical genomics, 17(1):255.
The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase approximately 50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.
Additional Links: PMID-39449055
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Citation:
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@article {pmid39449055,
year = {2024},
author = {Behera, S and Belyeu, JR and Chen, X and Paulin, LF and Nguyen, NQH and Newman, E and Mahmoud, M and Menon, VK and Qi, Q and Joshi, P and Marcovina, S and Rossi, M and Roller, E and Han, J and Onuchic, V and Avery, CL and Ballantyne, CM and Rodriguez, CJ and Kaplan, RC and Muzny, DM and Metcalf, GA and Gibbs, RA and Yu, B and Boerwinkle, E and Eberle, MA and Sedlazeck, FJ},
title = {Identification of allele-specific KIV-2 repeats and impact on Lp(a) measurements for cardiovascular disease risk.},
journal = {BMC medical genomics},
volume = {17},
number = {1},
pages = {255},
pmid = {39449055},
issn = {1755-8794},
mesh = {Humans ; *Cardiovascular Diseases/genetics ; *Alleles ; *Lipoprotein(a)/genetics/blood ; DNA Copy Number Variations ; Genetic Predisposition to Disease ; Polymorphism, Single Nucleotide ; },
abstract = {The abundance of Lp(a) protein holds significant implications for the risk of cardiovascular disease (CVD), which is directly impacted by the copy number (CN) of KIV-2, a 5.5 kbp sub-region. KIV-2 is highly polymorphic in the population and accurate analysis is challenging. In this study, we present the DRAGEN KIV-2 CN caller, which utilizes short reads. Data across 166 WGS show that the caller has high accuracy, compared to optical mapping and can further phase approximately 50% of the samples. We compared KIV-2 CN numbers to 24 previously postulated KIV-2 relevant SNVs, revealing that many are ineffective predictors of KIV-2 copy number. Population studies, including USA-based cohorts, showed distinct KIV-2 CN, distributions for European-, African-, and Hispanic-American populations and further underscored the limitations of SNV predictors. We demonstrate that the CN estimates correlate significantly with the available Lp(a) protein levels and that phasing is highly important.},
}
MeSH Terms:
show MeSH Terms
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Humans
*Cardiovascular Diseases/genetics
*Alleles
*Lipoprotein(a)/genetics/blood
DNA Copy Number Variations
Genetic Predisposition to Disease
Polymorphism, Single Nucleotide
RevDate: 2024-10-25
CmpDate: 2024-10-25
Acceptability of six-monthly PrEP dispensing supported with interim HIV self-testing to simplify PrEP delivery in Kenya: findings from qualitative research.
BMC health services research, 24(1):1281.
BACKGROUND: In Africa, dispensing oral HIV pre-exposure prophylaxis (PrEP) within already strained public health facilities has led to prolonged waiting periods and suboptimal experiences for clients. We sought to explore the acceptability of dispensing PrEP semiannually with interim HIV self-testing (HIVST) versus quarterly PrEP dispensing with clinic-based HIV testing to optimize clinic-delivered PrEP services.
METHODS: We conducted a qualitative study within a non-inferiority individual-level randomized controlled trial testing the effect of six-monthly PrEP dispensing with HIVST compared to the standard-of-care three-monthly PrEP dispensing on PrEP clinical outcomes in Kenya (ClinicalTrials.gov: NCT03593629). Eligible participants were ≥ 18 years, refilling PrEP for the first time, and either in an HIV serodifferent relationship (men and women) or singly enrolled (women only). A subset of participants in the intervention group completed serial in-depth interviews (IDIs) at enrollment, six months, and 12 months. We utilized stratified purposive sampling to ensure representation across participant groups. We analyzed our qualitative data thematically using a combination of inductive and deductive approaches, the latter guided by the Theoretical Framework of Acceptability (TFA).
RESULTS: Between May 2018 and June 2021, we conducted 120 serial IDIs with 55 participants; 64% (35/55) were in a serodifferent relationship, 64% (35/55) were women, and the median age was 32 years (IQR 27-40). Overall, participants found this novel PrEP delivery model highly acceptable; it was well-liked, private (TFA construct: affective attitude), and less burdensome (TFA construct: burden) compared to standard PrEP delivery. Additionally, participants were confident in their ability to participate in the intervention (TFA construct: self-efficacy). Some participants, however, highlighted model disadvantages, including fewer opportunities for in-person counseling and potentially less accurate HIV testing (TFA construct: opportunity costs). Ultimately, most participants reported that the intervention allowed them to achieve their HIV prevention goals (TFA construct: perceived effectiveness) and that their confidence in at-home HIVST and PrEP continuation increased following each semiannual clinic visit.
CONCLUSIONS: Semiannual PrEP clinic visits supported with six-monthly drug dispensing and interim HIVST was acceptable among PrEP users who experienced the intervention in Kenya. More comprehensive pre-intervention counseling and training on HIVST may help alleviate the client concerns presented, which were often resolved over time with intervention experience.
Additional Links: PMID-39448999
PubMed:
Citation:
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@article {pmid39448999,
year = {2024},
author = {Thuo, N and Bardon, AR and Mogere, P and Kiptinness, C and Casmir, E and Wairimu, N and Owidi, E and Okello, P and Mugo, NR and Baeten, JM and Ngure, K and Ortblad, KF},
title = {Acceptability of six-monthly PrEP dispensing supported with interim HIV self-testing to simplify PrEP delivery in Kenya: findings from qualitative research.},
journal = {BMC health services research},
volume = {24},
number = {1},
pages = {1281},
pmid = {39448999},
issn = {1472-6963},
support = {R01 MH113572/MH/NIMH NIH HHS/United States ; R01 MH113572/MH/NIMH NIH HHS/United States ; R00 MH121166/MH/NIMH NIH HHS/United States ; },
mesh = {Humans ; Kenya ; *Pre-Exposure Prophylaxis/methods ; Female ; Male ; *HIV Infections/prevention & control ; Adult ; *Qualitative Research ; *Self-Testing ; *Patient Acceptance of Health Care/statistics & numerical data ; Anti-HIV Agents/therapeutic use/administration & dosage ; Young Adult ; HIV Testing/methods ; Interviews as Topic ; },
abstract = {BACKGROUND: In Africa, dispensing oral HIV pre-exposure prophylaxis (PrEP) within already strained public health facilities has led to prolonged waiting periods and suboptimal experiences for clients. We sought to explore the acceptability of dispensing PrEP semiannually with interim HIV self-testing (HIVST) versus quarterly PrEP dispensing with clinic-based HIV testing to optimize clinic-delivered PrEP services.
METHODS: We conducted a qualitative study within a non-inferiority individual-level randomized controlled trial testing the effect of six-monthly PrEP dispensing with HIVST compared to the standard-of-care three-monthly PrEP dispensing on PrEP clinical outcomes in Kenya (ClinicalTrials.gov: NCT03593629). Eligible participants were ≥ 18 years, refilling PrEP for the first time, and either in an HIV serodifferent relationship (men and women) or singly enrolled (women only). A subset of participants in the intervention group completed serial in-depth interviews (IDIs) at enrollment, six months, and 12 months. We utilized stratified purposive sampling to ensure representation across participant groups. We analyzed our qualitative data thematically using a combination of inductive and deductive approaches, the latter guided by the Theoretical Framework of Acceptability (TFA).
RESULTS: Between May 2018 and June 2021, we conducted 120 serial IDIs with 55 participants; 64% (35/55) were in a serodifferent relationship, 64% (35/55) were women, and the median age was 32 years (IQR 27-40). Overall, participants found this novel PrEP delivery model highly acceptable; it was well-liked, private (TFA construct: affective attitude), and less burdensome (TFA construct: burden) compared to standard PrEP delivery. Additionally, participants were confident in their ability to participate in the intervention (TFA construct: self-efficacy). Some participants, however, highlighted model disadvantages, including fewer opportunities for in-person counseling and potentially less accurate HIV testing (TFA construct: opportunity costs). Ultimately, most participants reported that the intervention allowed them to achieve their HIV prevention goals (TFA construct: perceived effectiveness) and that their confidence in at-home HIVST and PrEP continuation increased following each semiannual clinic visit.
CONCLUSIONS: Semiannual PrEP clinic visits supported with six-monthly drug dispensing and interim HIVST was acceptable among PrEP users who experienced the intervention in Kenya. More comprehensive pre-intervention counseling and training on HIVST may help alleviate the client concerns presented, which were often resolved over time with intervention experience.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Kenya
*Pre-Exposure Prophylaxis/methods
Female
Male
*HIV Infections/prevention & control
Adult
*Qualitative Research
*Self-Testing
*Patient Acceptance of Health Care/statistics & numerical data
Anti-HIV Agents/therapeutic use/administration & dosage
Young Adult
HIV Testing/methods
Interviews as Topic
RevDate: 2024-10-24
Pediatric Central Nervous System Embryonal Tumors: Presentation, Diagnosis, Therapeutic Strategies, and Survivorship-A Review.
Pediatric neurology, 161:237-246 pii:S0887-8994(24)00356-4 [Epub ahead of print].
Central nervous system (CNS) embryonal tumors represent a diverse group of neoplasms and have a peak incidence in early childhood. These tumors can be located anywhere within the CNS, and presenting symptoms typically represent tumor location. These tumors display distinctive findings on neuroimaging and are staged using magnetic resonance imaging of the brain and spine as well as evaluation of cerebrospinal fluid. Diagnosis is made based on an integrated analysis of histologic and molecular features via tissue sampling. Risk stratification is based on integration of clinical staging and extent of resection with histologic and molecular risk factors. The therapeutic approach for these tumors is multimodal and includes surgery, chemotherapy, and radiation, tailored to the individual patient factors (including age) and specific tumor type. Comprehensive supportive care including management of nausea, nutrition support, pain, fertility preservation, and mitigation of therapy-related morbidity (including hearing protection) is imperative through treatment of CNS embryonal tumors. Despite advances in therapy and supportive care, the long-term consequences of current treatment strategies are substantial. Integration of less toxic, molecularly targeted therapies and a comprehensive, multidisciplinary approach to survivorship care are essential to improving survival and the overall quality of life for survivors.
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@article {pmid39447443,
year = {2024},
author = {Ronsley, R and Cole, B and Ketterl, T and Wright, J and Ermoian, R and Hoffman, LM and Margol, AS and Leary, SES},
title = {Pediatric Central Nervous System Embryonal Tumors: Presentation, Diagnosis, Therapeutic Strategies, and Survivorship-A Review.},
journal = {Pediatric neurology},
volume = {161},
number = {},
pages = {237-246},
doi = {10.1016/j.pediatrneurol.2024.09.031},
pmid = {39447443},
issn = {1873-5150},
abstract = {Central nervous system (CNS) embryonal tumors represent a diverse group of neoplasms and have a peak incidence in early childhood. These tumors can be located anywhere within the CNS, and presenting symptoms typically represent tumor location. These tumors display distinctive findings on neuroimaging and are staged using magnetic resonance imaging of the brain and spine as well as evaluation of cerebrospinal fluid. Diagnosis is made based on an integrated analysis of histologic and molecular features via tissue sampling. Risk stratification is based on integration of clinical staging and extent of resection with histologic and molecular risk factors. The therapeutic approach for these tumors is multimodal and includes surgery, chemotherapy, and radiation, tailored to the individual patient factors (including age) and specific tumor type. Comprehensive supportive care including management of nausea, nutrition support, pain, fertility preservation, and mitigation of therapy-related morbidity (including hearing protection) is imperative through treatment of CNS embryonal tumors. Despite advances in therapy and supportive care, the long-term consequences of current treatment strategies are substantial. Integration of less toxic, molecularly targeted therapies and a comprehensive, multidisciplinary approach to survivorship care are essential to improving survival and the overall quality of life for survivors.},
}
RevDate: 2024-10-24
Long-term 3-year follow-up of mosunetuzumab in relapsed or refractory follicular lymphoma after ≥2 prior therapies.
Blood pii:525779 [Epub ahead of print].
Mosunetuzumab, a CD20xCD3 T-cell engaging bispecific antibody, redirects T cells to eliminate malignant B cells. We present updated efficacy and safety data of a pivotal phase 1/2 study after a median follow-up of 37.4 months in 90 patients with relapsed/refractory (R/R) follicular lymphoma (FL) and ≥2 prior lines of therapy treated with fixed-duration mosunetuzumab. Investigator-assessed complete response (CR) rate and objective response rate (ORR) were 60.0% (95% confidence interval [CI], 49.1-70.2) and 77.8% (95% CI, 67.8-85.9), respectively. Among 70 responders, median duration of response was 35.9 months (95% CI, 20.7-not estimable [NE]). Among 54 patients who achieved CR, 49 remained in CR at the end of treatment; median duration of complete response was not reached (NR) (95% CI, 33.0-NE); Kaplan-Meier-estimated 30-month remission rate was 72.4% (95% CI, 59.2-85.6). Estimated 36-month overall survival (OS) rate was 82.4% (95% CI, 73.8-91.0); median OS was NR (95% CI, NE-NE). Median progression-free survival was 24.0 months (95% CI, 12.0-NE). Median time to CD19+ B-cell recovery was 18.4 months (95% CI, 12.8-25.0) following 8 cycles of mosunetuzumab treatment. No new cytokine release syndrome events or fatal, serious, or Grade ≥3 adverse events were reported. With extended follow-up, mosunetuzumab demonstrated high response rates, durable remissions and manageable safety with no long-term concerns. This supports outpatient mosunetuzumab administration as an off-the-shelf, fixed-duration, safe and effective treatment for patients with R/R FL, including those with high-risk disease. Trial registration: www.clinicaltrials.gov (NCT02500407).
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@article {pmid39447094,
year = {2024},
author = {Sehn, LH and Bartlett, NL and Matasar, MJ and Schuster, SJ and Assouline, SE and Giri, P and Kuruvilla, J and Shadman, M and Cheah, CY and Dietrich, S and Fay, K and Ku, M and Nastoupil, LJ and Wei, MC and Yin, S and To, I and Kaufman, D and Kwan, A and Penuel, E and Bolen, CR and Budde, LE},
title = {Long-term 3-year follow-up of mosunetuzumab in relapsed or refractory follicular lymphoma after ≥2 prior therapies.},
journal = {Blood},
volume = {},
number = {},
pages = {},
doi = {10.1182/blood.2024025454},
pmid = {39447094},
issn = {1528-0020},
abstract = {Mosunetuzumab, a CD20xCD3 T-cell engaging bispecific antibody, redirects T cells to eliminate malignant B cells. We present updated efficacy and safety data of a pivotal phase 1/2 study after a median follow-up of 37.4 months in 90 patients with relapsed/refractory (R/R) follicular lymphoma (FL) and ≥2 prior lines of therapy treated with fixed-duration mosunetuzumab. Investigator-assessed complete response (CR) rate and objective response rate (ORR) were 60.0% (95% confidence interval [CI], 49.1-70.2) and 77.8% (95% CI, 67.8-85.9), respectively. Among 70 responders, median duration of response was 35.9 months (95% CI, 20.7-not estimable [NE]). Among 54 patients who achieved CR, 49 remained in CR at the end of treatment; median duration of complete response was not reached (NR) (95% CI, 33.0-NE); Kaplan-Meier-estimated 30-month remission rate was 72.4% (95% CI, 59.2-85.6). Estimated 36-month overall survival (OS) rate was 82.4% (95% CI, 73.8-91.0); median OS was NR (95% CI, NE-NE). Median progression-free survival was 24.0 months (95% CI, 12.0-NE). Median time to CD19+ B-cell recovery was 18.4 months (95% CI, 12.8-25.0) following 8 cycles of mosunetuzumab treatment. No new cytokine release syndrome events or fatal, serious, or Grade ≥3 adverse events were reported. With extended follow-up, mosunetuzumab demonstrated high response rates, durable remissions and manageable safety with no long-term concerns. This supports outpatient mosunetuzumab administration as an off-the-shelf, fixed-duration, safe and effective treatment for patients with R/R FL, including those with high-risk disease. Trial registration: www.clinicaltrials.gov (NCT02500407).},
}
RevDate: 2024-10-24
Randomized pilot trial of an unconditional cash transfer intervention to address food insecurity in oncology.
JNCI cancer spectrum pii:7840267 [Epub ahead of print].
Screening for food insecurity and other social determinants of health is being integrated into oncology practice. We performed a pilot randomized trial to investigate whether an unconditional cash transfer (UCT) could be used to address food insecurity among female breast and gynecologic cancer survivors. Food insecure cancer survivors completed a baseline survey and were randomized to receive $100/month for three months (UCT) or usual care (UC). Participants (n = 14) completed a follow-up survey after 3-months and we compared changes in health-related quality of life, indicators of food insecurity, diet quality, and whether a participant had to forgo, delay, or make changes to medical care because of cost. The UCT was associated with higher physical health scores, fewer indicators of food insecurity, better diet quality, and a lower likelihood of forgoing medical care than those who received UC. Our results suggest that UCTs can improve outcomes for food insecure cancer survivors.
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@article {pmid39447043,
year = {2024},
author = {Mcdougall, JA and Adler Jaffe, S and Jacobson, K and Shaver, TL and Wilson, JLF and Baca, K and Boyce, T and Tawfik, B and Page-Reeves, J},
title = {Randomized pilot trial of an unconditional cash transfer intervention to address food insecurity in oncology.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkae107},
pmid = {39447043},
issn = {2515-5091},
abstract = {Screening for food insecurity and other social determinants of health is being integrated into oncology practice. We performed a pilot randomized trial to investigate whether an unconditional cash transfer (UCT) could be used to address food insecurity among female breast and gynecologic cancer survivors. Food insecure cancer survivors completed a baseline survey and were randomized to receive $100/month for three months (UCT) or usual care (UC). Participants (n = 14) completed a follow-up survey after 3-months and we compared changes in health-related quality of life, indicators of food insecurity, diet quality, and whether a participant had to forgo, delay, or make changes to medical care because of cost. The UCT was associated with higher physical health scores, fewer indicators of food insecurity, better diet quality, and a lower likelihood of forgoing medical care than those who received UC. Our results suggest that UCTs can improve outcomes for food insecure cancer survivors.},
}
RevDate: 2024-10-24
Promising results of HIV prevention trials highlight the benefits of collaboration in global health: The perspective of the Forum HIV Recency Assay Working Group.
PLOS global public health, 4(10):e0003878 pii:PGPH-D-24-02139.
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@article {pmid39446892,
year = {2024},
author = {Schaefer, R and Donaldson, L and Leus, M and Osakwe, CE and Chimukangara, B and Dalal, S and Duerr, A and Gao, F and Glidden, DV and Grinsztejn, B and Justman, J and Kumwenda, G and Laeyendecker, O and Lee, HY and Maldarelli, F and Mayer, KH and Murray, J and Parekh, BS and Rice, B and Robertson, MN and Saito, S and Vannappagari, V and Warren, M and Zeballos, D and Zinserling, J and Miller, V},
title = {Promising results of HIV prevention trials highlight the benefits of collaboration in global health: The perspective of the Forum HIV Recency Assay Working Group.},
journal = {PLOS global public health},
volume = {4},
number = {10},
pages = {e0003878},
doi = {10.1371/journal.pgph.0003878},
pmid = {39446892},
issn = {2767-3375},
}
RevDate: 2024-10-24
Hoping to Adhere? Examining the Relationship Between Hope and Pre-exposure Prophylaxis Willingness, Adherence, and Persistence Among Young Women in South Africa and Zimbabwe (HPTN 082).
AIDS and behavior [Epub ahead of print].
Hope is a powerful psychological construct which is linked to positive health. Greater hope is associated with improved antiretroviral therapy adherence; however, less is known about the impact of hope on oral pre-exposure prophylaxis (PrEP) outcomes. HIV Prevention Trials Network 082, was an open-label PrEP study among young women (ages 16-25) in South Africa and Zimbabwe. Hope was measured at baseline and follow-up using a subset of the Hope for the Future Scale (score range 6-24) and PrEP willingness was measured using a subscale of the HIV Prevention Readiness Measure (score range 6-30). Intracellular tenofovir-diphosphate (TFV-DP) concentrations were obtained from dried blood spot samples at weeks 13, 26, and 52; high PrEP adherence was defined as TFV-DP concentrations ≥ 700 fmol/punch. Persistence was defined as TFV-DP > 16 fmol/punch at weeks 26 and 52. Linear regression and generalized estimating equations were used to assess the relationship between hope and PrEP willingness, adherence, and persistence. The median age of participants (n = 432) was 21 years (interquartile range [IQR]: 19-22). The mean hope score at baseline was 21.0 (SD = 3.4). Although hope was positively associated with PrEP willingness (β = 0.22, 95% CI 0.15, 0.37), it was not associated with high PrEP adherence (aRR = 1.00, 95% CI 0.96, 1.05), or persistence at follow-up (aRR = 1.02, 95% CI 0.99, 1.05). While cultivating hope may be an important strategy in building willingness to take oral PrEP, it may not be enough to sustain PrEP adherence or persistence.
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@article {pmid39446266,
year = {2024},
author = {Gichane, MW and Velloza, J and Hosek, S and Beauchamp, G and Anderson, P and Delany-Moretlwe, S and Celum, C and , },
title = {Hoping to Adhere? Examining the Relationship Between Hope and Pre-exposure Prophylaxis Willingness, Adherence, and Persistence Among Young Women in South Africa and Zimbabwe (HPTN 082).},
journal = {AIDS and behavior},
volume = {},
number = {},
pages = {},
pmid = {39446266},
issn = {1573-3254},
support = {UM1AI068619//National Institute of Allergy and Infectious Diseases/ ; UM1AI068617//National Institute of Allergy and Infectious Diseases/ ; UM1AI068613//National Institute of Allergy and Infectious Diseases/ ; K01MH134775/MH/NIMH NIH HHS/United States ; },
abstract = {Hope is a powerful psychological construct which is linked to positive health. Greater hope is associated with improved antiretroviral therapy adherence; however, less is known about the impact of hope on oral pre-exposure prophylaxis (PrEP) outcomes. HIV Prevention Trials Network 082, was an open-label PrEP study among young women (ages 16-25) in South Africa and Zimbabwe. Hope was measured at baseline and follow-up using a subset of the Hope for the Future Scale (score range 6-24) and PrEP willingness was measured using a subscale of the HIV Prevention Readiness Measure (score range 6-30). Intracellular tenofovir-diphosphate (TFV-DP) concentrations were obtained from dried blood spot samples at weeks 13, 26, and 52; high PrEP adherence was defined as TFV-DP concentrations ≥ 700 fmol/punch. Persistence was defined as TFV-DP > 16 fmol/punch at weeks 26 and 52. Linear regression and generalized estimating equations were used to assess the relationship between hope and PrEP willingness, adherence, and persistence. The median age of participants (n = 432) was 21 years (interquartile range [IQR]: 19-22). The mean hope score at baseline was 21.0 (SD = 3.4). Although hope was positively associated with PrEP willingness (β = 0.22, 95% CI 0.15, 0.37), it was not associated with high PrEP adherence (aRR = 1.00, 95% CI 0.96, 1.05), or persistence at follow-up (aRR = 1.02, 95% CI 0.99, 1.05). While cultivating hope may be an important strategy in building willingness to take oral PrEP, it may not be enough to sustain PrEP adherence or persistence.},
}
RevDate: 2024-10-24
Cancer Prevalence across Vertebrates.
Cancer discovery pii:749321 [Epub ahead of print].
Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.
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@article {pmid39445720,
year = {2024},
author = {Compton, ZT and Mellon, W and Harris, VK and Rupp, S and Mallo, D and Kapsetaki, SE and Wilmot, M and Kennington, R and Noble, K and Baciu, C and Ramirez, LN and Peraza, A and Martins, B and Sudhakar, S and Aksoy, S and Furukawa, G and Vincze, O and Giraudeau, M and Duke, EG and Spiro, S and Flach, E and Davidson, H and Li, CI and Zehnder, A and Graham, TA and Troan, BV and Harrison, TM and Tollis, M and Schiffman, JD and Aktipis, CA and Abegglen, LM and Maley, CC and Boddy, AM},
title = {Cancer Prevalence across Vertebrates.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {OF1-OF18},
doi = {10.1158/2159-8290.CD-24-0573},
pmid = {39445720},
issn = {2159-8290},
support = {U54 CA217376/CA/NCI NIH HHS/United States ; T32 CA272303/CA/NCI NIH HHS/United States ; BC132057//Congressionally Directed Medical Research Programs (CDMRP)/ ; ADHS18-198847//Arizona Biomedical Research Commission (ABRC)/ ; //Hyundai Hope On Wheels (Hope On Wheels)/ ; COVER ANR-23-CE02-0019//Agence Nationale de la Recherche (ANR)/ ; OTKA K143421//Agence Nationale de la Recherche (ANR)/ ; },
abstract = {Cancer is pervasive across multicellular species, but what explains the differences in cancer prevalence across species? Using 16,049 necropsy records for 292 species spanning three clades of tetrapods (amphibians, sauropsids, and mammals), we found that neoplasia and malignancy prevalence increases with adult mass (contrary to Peto's paradox) and somatic mutation rate but decreases with gestation time. The relationship between adult mass and malignancy prevalence was only apparent when we controlled for gestation time. Evolution of cancer susceptibility appears to have undergone sudden shifts followed by stabilizing selection. Outliers for neoplasia prevalence include the common porpoise (<1.3%), the Rodrigues fruit bat (<1.6%), the black-footed penguin (<0.4%), ferrets (63%), and opossums (35%). Discovering why some species have particularly high or low levels of cancer may lead to a better understanding of cancer syndromes and novel strategies for the management and prevention of cancer. Significance: Evolution has discovered mechanisms for suppressing cancer in a wide variety of species. By analyzing veterinary necropsy records, we can identify species with exceptionally high or low cancer prevalence. Discovering the mechanisms of cancer susceptibility and resistance may help improve cancer prevention and explain cancer syndromes.},
}
RevDate: 2024-10-23
A phase III trial of adjuvant ribociclib plus endocrine therapy vs endocrine therapy alone in patients with HR+/HER2- early breast cancer: final invasive disease-free survival results from the NATALEE trial.
Annals of oncology : official journal of the European Society for Medical Oncology pii:S0923-7534(24)04064-X [Epub ahead of print].
BACKGROUND: NATALEE assessed efficacy and tolerability of 3 years of adjuvant ribociclib plus NSAI compared with a nonsteroidal aromatase inhibitor (NSAI) alone in a broad population of patients with HR+/HER2- early breast cancer, including a select group without nodal involvement. This is the final preplanned analysis of invasive disease-free survival (iDFS).
PATIENTS AND METHODS: Premenopausal/postmenopausal women and men were randomized 1:1 to ribociclib (n=2549; 400 mg/day, 3 weeks on/1 week off for 36 months) plus NSAI (letrozole 2.5 mg/day or anastrozole 1 mg/day for 60 months) or NSAI alone (n=2552). Men and premenopausal women also received goserelin (3.6 mg once every 28 days). Patients had anatomical stage IIA (N0 with additional risk factors or N1), IIB, or III disease. The primary endpoint was iDFS. Secondary efficacy endpoints were recurrence-free survival (RFS), distant DFS (DDFS), and overall survival (OS). This final iDFS analysis was planned after ≈500 events.
RESULTS: At data cutoff (21 July 2023), ribociclib was stopped for 1996 patients (78.3%); 1091 (42.8%) completed 3 years of ribociclib, and ribociclib treatment was ongoing for 528 (20.7%). Median follow-up for iDFS was 33.3 months. Overall, 226 and 283 iDFS events occurred with ribociclib plus NSAI vs NSAI alone, respectively. Ribociclib plus NSAI demonstrated significant iDFS benefit over NSAI alone (Hazard Ratio 0.749, 95% Confidence Interval [CI] 0.628-0.892; P=0.0012). The 3-year iDFS rates were 90.7% (95% CI 89.3%-91.8%) vs 87.6% (95% CI 86.1%-88.9%). A consistent benefit was observed across prespecified subgroups, including stage (II/III) and nodal status (+/-). DDFS and RFS favored ribociclib plus NSAI. OS data were immature. No new safety signals were observed.
CONCLUSIONS: With longer follow-up and most patients off ribociclib, NATALEE continues to demonstrate iDFS benefit with ribociclib plus NSAI over NSAI alone in the overall population and across key subgroups. Observed adverse events remained stable.
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@article {pmid39442617,
year = {2024},
author = {Hortobagyi, GN and Lacko, A and Sohn, J and Cruz, F and Borrego, MR and Manikhas, A and Park, YH and Stroyakovskiy, D and Yardley, DA and Huang, CS and Fasching, PA and Crown, J and Bardia, A and Chia, S and Im, SA and Martin, M and Loi, S and Xu, B and Hurvitz, S and Barrios, C and Untch, M and Moroose, R and Visco, F and Parnizari, F and Zarate, JP and Li, Z and Waters, S and Chakravartty, A and Slamon, D},
title = {A phase III trial of adjuvant ribociclib plus endocrine therapy vs endocrine therapy alone in patients with HR+/HER2- early breast cancer: final invasive disease-free survival results from the NATALEE trial.},
journal = {Annals of oncology : official journal of the European Society for Medical Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.annonc.2024.10.015},
pmid = {39442617},
issn = {1569-8041},
abstract = {BACKGROUND: NATALEE assessed efficacy and tolerability of 3 years of adjuvant ribociclib plus NSAI compared with a nonsteroidal aromatase inhibitor (NSAI) alone in a broad population of patients with HR+/HER2- early breast cancer, including a select group without nodal involvement. This is the final preplanned analysis of invasive disease-free survival (iDFS).
PATIENTS AND METHODS: Premenopausal/postmenopausal women and men were randomized 1:1 to ribociclib (n=2549; 400 mg/day, 3 weeks on/1 week off for 36 months) plus NSAI (letrozole 2.5 mg/day or anastrozole 1 mg/day for 60 months) or NSAI alone (n=2552). Men and premenopausal women also received goserelin (3.6 mg once every 28 days). Patients had anatomical stage IIA (N0 with additional risk factors or N1), IIB, or III disease. The primary endpoint was iDFS. Secondary efficacy endpoints were recurrence-free survival (RFS), distant DFS (DDFS), and overall survival (OS). This final iDFS analysis was planned after ≈500 events.
RESULTS: At data cutoff (21 July 2023), ribociclib was stopped for 1996 patients (78.3%); 1091 (42.8%) completed 3 years of ribociclib, and ribociclib treatment was ongoing for 528 (20.7%). Median follow-up for iDFS was 33.3 months. Overall, 226 and 283 iDFS events occurred with ribociclib plus NSAI vs NSAI alone, respectively. Ribociclib plus NSAI demonstrated significant iDFS benefit over NSAI alone (Hazard Ratio 0.749, 95% Confidence Interval [CI] 0.628-0.892; P=0.0012). The 3-year iDFS rates were 90.7% (95% CI 89.3%-91.8%) vs 87.6% (95% CI 86.1%-88.9%). A consistent benefit was observed across prespecified subgroups, including stage (II/III) and nodal status (+/-). DDFS and RFS favored ribociclib plus NSAI. OS data were immature. No new safety signals were observed.
CONCLUSIONS: With longer follow-up and most patients off ribociclib, NATALEE continues to demonstrate iDFS benefit with ribociclib plus NSAI over NSAI alone in the overall population and across key subgroups. Observed adverse events remained stable.},
}
RevDate: 2024-10-23
Imlunestrant, an oral selective estrogen receptor degrader, as monotherapy and combined with abemaciclib, in recurrent/advanced ER-positive endometrioid endometrial cancer: Results from the phase 1a/1b EMBER study.
Gynecologic oncology, 191:172-181 pii:S0090-8258(24)01156-9 [Epub ahead of print].
OBJECTIVE: Imlunestrant is a next-generation oral selective estrogen receptor degrader designed to deliver continuous estrogen receptor (ER) target inhibition. EMBER is a phase 1a/b trial of imlunestrant, as monotherapy and combined with targeted therapy, in patients with ER+ advanced breast cancer or endometrioid endometrial cancer (EEC). This report focuses on patients with ER+ EEC.
METHODS: EMBER used an i3 + 3 dose-escalation design to determine the recommended phase 2 dose (RP2D) followed by dose-expansion cohorts (1:1 randomization): imlunestrant monotherapy and imlunestrant plus abemaciclib (150 mg twice daily). Eligible patients had measurable disease and progression or recurrence after platinum-containing chemotherapy. Prior fulvestrant or aromatase inhibitor was not allowed. Secondary endpoints included safety, pharmacokinetics and antitumor activity.
RESULTS: In total, 72 patients with a median of 2 prior anticancer therapies were treated. Among the 39 patients who received imlunestrant (400 mg [RP2D], n = 33; 800 mg, n = 6), the most common treatment-emergent adverse events (TEAEs) were grade 1-2 nausea (35.9 %), diarrhea (25.6 %), urinary tract infection (25.6 %), and abdominal pain (20.5 %). Overall response rate (ORR) was 10.3 %, clinical benefit rate (CBR) was 33.3 %, and median progression-free survival (mPFS) was 3.8 months (95 % CI, 1.8-6.7). Among the 33 patients who received imlunestrant (400 mg [RP2D], n = 29; 800 mg, n = 4) plus abemaciclib, the most common TEAEs were diarrhea (87.9 %), nausea (66.7 %), fatigue (48.5 %), and anemia (45.5 %). ORR was 18.2 %, CBR was 42.4 %, and mPFS was 6.8 months (95 % CI, 2.1-12).
CONCLUSION: Imlunestrant, as monotherapy and combined with abemaciclib, has a manageable safety profile with preliminary evidence of antitumor activity in patients with ER+ EEC.
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@article {pmid39442371,
year = {2024},
author = {Yonemori, K and Boni, V and Min, KG and Meniawy, TM and Lombard, J and Kaufman, PA and Richardson, DL and Bender, L and Okera, M and Matsumoto, K and Giridhar, KV and García-Sáenz, JA and Prenen, H and de Speville Uribe, BD and Dizon, DS and Garcia-Corbacho, J and Van Nieuwenhuysen, E and Li, Y and Estrem, ST and Nguyen, B and Bacchion, F and Ismail-Khan, R and Jhaveri, K and Banda, K},
title = {Imlunestrant, an oral selective estrogen receptor degrader, as monotherapy and combined with abemaciclib, in recurrent/advanced ER-positive endometrioid endometrial cancer: Results from the phase 1a/1b EMBER study.},
journal = {Gynecologic oncology},
volume = {191},
number = {},
pages = {172-181},
doi = {10.1016/j.ygyno.2024.10.006},
pmid = {39442371},
issn = {1095-6859},
abstract = {OBJECTIVE: Imlunestrant is a next-generation oral selective estrogen receptor degrader designed to deliver continuous estrogen receptor (ER) target inhibition. EMBER is a phase 1a/b trial of imlunestrant, as monotherapy and combined with targeted therapy, in patients with ER+ advanced breast cancer or endometrioid endometrial cancer (EEC). This report focuses on patients with ER+ EEC.
METHODS: EMBER used an i3 + 3 dose-escalation design to determine the recommended phase 2 dose (RP2D) followed by dose-expansion cohorts (1:1 randomization): imlunestrant monotherapy and imlunestrant plus abemaciclib (150 mg twice daily). Eligible patients had measurable disease and progression or recurrence after platinum-containing chemotherapy. Prior fulvestrant or aromatase inhibitor was not allowed. Secondary endpoints included safety, pharmacokinetics and antitumor activity.
RESULTS: In total, 72 patients with a median of 2 prior anticancer therapies were treated. Among the 39 patients who received imlunestrant (400 mg [RP2D], n = 33; 800 mg, n = 6), the most common treatment-emergent adverse events (TEAEs) were grade 1-2 nausea (35.9 %), diarrhea (25.6 %), urinary tract infection (25.6 %), and abdominal pain (20.5 %). Overall response rate (ORR) was 10.3 %, clinical benefit rate (CBR) was 33.3 %, and median progression-free survival (mPFS) was 3.8 months (95 % CI, 1.8-6.7). Among the 33 patients who received imlunestrant (400 mg [RP2D], n = 29; 800 mg, n = 4) plus abemaciclib, the most common TEAEs were diarrhea (87.9 %), nausea (66.7 %), fatigue (48.5 %), and anemia (45.5 %). ORR was 18.2 %, CBR was 42.4 %, and mPFS was 6.8 months (95 % CI, 2.1-12).
CONCLUSION: Imlunestrant, as monotherapy and combined with abemaciclib, has a manageable safety profile with preliminary evidence of antitumor activity in patients with ER+ EEC.},
}
RevDate: 2024-10-23
CmpDate: 2024-10-23
Characterization of clonal dynamics using duplex sequencing in donor-recipient pairs decades after hematopoietic cell transplantation.
Science translational medicine, 16(770):eado5108.
After allogeneic hematopoietic cell transplantation (HCT), a very small number of donor stem cells reconstitute the recipient hematopoietic system, whereas the donor is left with a near-normal pool of stem cells. We hypothesized that the increased replicative stress on transplanted donor cells in the recipient could lead to the disproportionate proliferation of clonal hematopoiesis (CH) variants. We obtained blood samples from 16 related donor-recipient pairs at a median of 33.8 years (range: 6.6 to 45.7) after HCT, including the longest surviving HCT recipients in the world. For 11 of 16 pairs, a donor sample from the time of HCT was available for comparison. We performed ultrasensitive duplex sequencing of genes recurrently mutated in myeloid malignancies and CH, as well as a set of functionally neutral genomic regions representative of human genomic content at large. CH variants were observed in all donors, even those as young as 12 years old. Where donor pre-HCT sample was available, the average mutation rate in donors compared to recipients post-HCT was similar (2.0% versus 2.6% per year, respectively) within genes recurrently mutated in myeloid malignancies. Twenty-two (5.6%) of the 393 variants shared between paired donors and recipients post-HCT showed ≥10-fold higher variant allele frequency (VAF) in the recipient. A longer time since HCT was positively associated with the expansion of shared variant VAFs in the recipient. In conclusion, even decades after HCT, there does not appear to be widespread accelerated clonal expansion in the transplanted cells, highlighting the immense regenerative capacity of the human hematopoietic system.
Additional Links: PMID-39441907
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PubMed:
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@article {pmid39441907,
year = {2024},
author = {Oshima, MU and Higgins, J and Jenkins, I and Randolph, T and Smith, T and Valentine, C and Salk, J and Yeung, C and Beppu, L and Campbell, J and Carpenter, PA and Lee, SJ and Flowers, ME and Radich, JP and Storb, R},
title = {Characterization of clonal dynamics using duplex sequencing in donor-recipient pairs decades after hematopoietic cell transplantation.},
journal = {Science translational medicine},
volume = {16},
number = {770},
pages = {eado5108},
doi = {10.1126/scitranslmed.ado5108},
pmid = {39441907},
issn = {1946-6242},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation ; *Tissue Donors ; Adult ; Middle Aged ; Male ; Mutation/genetics ; Female ; Young Adult ; Child ; Clonal Hematopoiesis/genetics ; Transplant Recipients ; Adolescent ; },
abstract = {After allogeneic hematopoietic cell transplantation (HCT), a very small number of donor stem cells reconstitute the recipient hematopoietic system, whereas the donor is left with a near-normal pool of stem cells. We hypothesized that the increased replicative stress on transplanted donor cells in the recipient could lead to the disproportionate proliferation of clonal hematopoiesis (CH) variants. We obtained blood samples from 16 related donor-recipient pairs at a median of 33.8 years (range: 6.6 to 45.7) after HCT, including the longest surviving HCT recipients in the world. For 11 of 16 pairs, a donor sample from the time of HCT was available for comparison. We performed ultrasensitive duplex sequencing of genes recurrently mutated in myeloid malignancies and CH, as well as a set of functionally neutral genomic regions representative of human genomic content at large. CH variants were observed in all donors, even those as young as 12 years old. Where donor pre-HCT sample was available, the average mutation rate in donors compared to recipients post-HCT was similar (2.0% versus 2.6% per year, respectively) within genes recurrently mutated in myeloid malignancies. Twenty-two (5.6%) of the 393 variants shared between paired donors and recipients post-HCT showed ≥10-fold higher variant allele frequency (VAF) in the recipient. A longer time since HCT was positively associated with the expansion of shared variant VAFs in the recipient. In conclusion, even decades after HCT, there does not appear to be widespread accelerated clonal expansion in the transplanted cells, highlighting the immense regenerative capacity of the human hematopoietic system.},
}
MeSH Terms:
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hide MeSH Terms
Humans
*Hematopoietic Stem Cell Transplantation
*Tissue Donors
Adult
Middle Aged
Male
Mutation/genetics
Female
Young Adult
Child
Clonal Hematopoiesis/genetics
Transplant Recipients
Adolescent
RevDate: 2024-10-23
Trends in Age and Prostate-Specific Antigen at Prostate Cancer Diagnosis between 2010 and 2019.
JNCI cancer spectrum pii:7833368 [Epub ahead of print].
Recent studies have shown that de novo metastatic prostate cancer incidence in the U.S. increased from 2010 to 2019. Plausible explanations include delayed detection following recommendations against prostate cancer screening or upstaging associated with use of more sensitive imaging technologies. Using Surveillance, Epidemiology and End Results cases and controlling for aging of the population, we found the median age and prostate-specific antigen (PSA) level at prostate cancer diagnosis increased by 1.4 years of age (95% CI 1.3-1.5) and 1.4 ng/mL (95% CI 1.4-1.5) over this period, consistent with the delayed detection hypothesis. Racial differences were noted, with 75th percentiles of PSA at diagnosis increasing by 4.3 ng/mL (95% CI 3.7-4.8) over this time period for non-Hispanic Black men compared to 3.0 ng/mL (95% CI 2.8-3.2) for non-Hispanic White men. Overall, patient characteristics at diagnosis suggest that delayed detection contributed at least in part to increases in de novo metastatic disease.
Additional Links: PMID-39441819
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PubMed:
Citation:
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@article {pmid39441819,
year = {2024},
author = {Owens, L and Brahme, O and Gulati, R and Etzioni, R},
title = {Trends in Age and Prostate-Specific Antigen at Prostate Cancer Diagnosis between 2010 and 2019.},
journal = {JNCI cancer spectrum},
volume = {},
number = {},
pages = {},
doi = {10.1093/jncics/pkae106},
pmid = {39441819},
issn = {2515-5091},
abstract = {Recent studies have shown that de novo metastatic prostate cancer incidence in the U.S. increased from 2010 to 2019. Plausible explanations include delayed detection following recommendations against prostate cancer screening or upstaging associated with use of more sensitive imaging technologies. Using Surveillance, Epidemiology and End Results cases and controlling for aging of the population, we found the median age and prostate-specific antigen (PSA) level at prostate cancer diagnosis increased by 1.4 years of age (95% CI 1.3-1.5) and 1.4 ng/mL (95% CI 1.4-1.5) over this period, consistent with the delayed detection hypothesis. Racial differences were noted, with 75th percentiles of PSA at diagnosis increasing by 4.3 ng/mL (95% CI 3.7-4.8) over this time period for non-Hispanic Black men compared to 3.0 ng/mL (95% CI 2.8-3.2) for non-Hispanic White men. Overall, patient characteristics at diagnosis suggest that delayed detection contributed at least in part to increases in de novo metastatic disease.},
}
RevDate: 2024-10-23
Evolving strategies to overcome barriers in CAR-T cell therapy for acute myeloid leukemia.
Expert review of hematology [Epub ahead of print].
INTRODUCTION: Acute myeloid leukemia (AML) is a complex and heterogeneous disease characterized by an aggressive clinical course and limited efficacious treatment options in the relapsed/refractory (R/R) setting. Chimeric antigen receptor (CAR)-modified T (CAR-T) cell immunotherapy is an investigational treatment strategy for R/R AML that has shown some promise. However, obstacles to successful CAR-T cell immunotherapy for AML remain.
AREAS COVERED: In analyses of clinical trials of CAR-T cell therapy for R/R AML, complete responses without measurable residual disease have been reported, but the durability of those responses remains unclear. Significant barriers to successful CAR-T cell therapy in AML include the scarcity of suitable tumor-target antigens (TTA), inherent T cell functional deficits, and the immunoinhibitory and hostile tumor microenvironment (TME). This review will focus on these barriers to successful CAR-T cell therapy in AML, and discuss scientific advancements and evolving strategies to overcome them.
EXPERT OPINION: Achieving durable remissions in R/R AML will likely require a multifaceted approach that integrates advancements in TTA selection, enhancement of the intrinsic quality of CAR-T cells, and development of strategies to overcome inhibitory mechanisms in the AML TME.
Additional Links: PMID-39439295
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PubMed:
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@article {pmid39439295,
year = {2024},
author = {Colonne, CK and Kimble, EL and Turtle, CJ},
title = {Evolving strategies to overcome barriers in CAR-T cell therapy for acute myeloid leukemia.},
journal = {Expert review of hematology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474086.2024.2420614},
pmid = {39439295},
issn = {1747-4094},
abstract = {INTRODUCTION: Acute myeloid leukemia (AML) is a complex and heterogeneous disease characterized by an aggressive clinical course and limited efficacious treatment options in the relapsed/refractory (R/R) setting. Chimeric antigen receptor (CAR)-modified T (CAR-T) cell immunotherapy is an investigational treatment strategy for R/R AML that has shown some promise. However, obstacles to successful CAR-T cell immunotherapy for AML remain.
AREAS COVERED: In analyses of clinical trials of CAR-T cell therapy for R/R AML, complete responses without measurable residual disease have been reported, but the durability of those responses remains unclear. Significant barriers to successful CAR-T cell therapy in AML include the scarcity of suitable tumor-target antigens (TTA), inherent T cell functional deficits, and the immunoinhibitory and hostile tumor microenvironment (TME). This review will focus on these barriers to successful CAR-T cell therapy in AML, and discuss scientific advancements and evolving strategies to overcome them.
EXPERT OPINION: Achieving durable remissions in R/R AML will likely require a multifaceted approach that integrates advancements in TTA selection, enhancement of the intrinsic quality of CAR-T cells, and development of strategies to overcome inhibitory mechanisms in the AML TME.},
}
RevDate: 2024-10-23
Suspended Tissue Open Microfluidic Patterning (STOMP).
bioRxiv : the preprint server for biology.
Cell-laden hydrogel constructs suspended between pillars are powerful tools for modeling tissue structure and physiology, though current fabrication techniques often limit them to uniform compositions. In contrast, tissues are complex in nature with spatial arrangements of cell types and extracellular matrices. Thus, we present Suspended Tissue Open Microfluidic Patterning (STOMP), which utilizes a removable, open microfluidic patterning channel to pattern multiple spatial regions across a single suspended tissue. The STOMP platform contains capillary pinning features along the open channel that controls the fluid front, allowing multiple cell and extracellular matrix precursors to be pipetted into one tissue. We have used this technique to pattern suspended tissues with multiple regional components using a variety of native and synthetic extracellular matrices, including fibrin, collagen, and poly(ethylene glycol). Here, we demonstrate that STOMP models a region of fibrosis in a functional heart tissue and a bone-ligament junction in periodontal tissues. Additionally, the STOMP platform can be customized to allow patterning of suspended cores and more spatial configurations, enhancing its utility in complex tissue modeling. STOMP is a versatile technique for generating suspended tissue models with increased control over cell and hydrogel composition to model interfacial tissue regions in a suspended tissue.
Additional Links: PMID-39416011
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Citation:
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@article {pmid39416011,
year = {2024},
author = {Haack, AJ and Brown, LG and Goldstein, AJ and Mulimani, P and Berthier, J and Viswanathan, AR and Kopyeva, I and Whitten, JM and Lin, A and Nguyen, SH and Leahy, TP and Bouker, EE and Padgett, RM and Mazzawi, NA and Tokihiro, JC and Bretherton, RC and Wu, A and Tapscott, SJ and DeForest, CA and Popowics, TE and Berthier, E and Sniadecki, NJ and Theberge, AB},
title = {Suspended Tissue Open Microfluidic Patterning (STOMP).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416011},
issn = {2692-8205},
support = {F30 HL158030/HL/NHLBI NIH HHS/United States ; R01 HL149734/HL/NHLBI NIH HHS/United States ; R90 DE023059/DE/NIDCR NIH HHS/United States ; R35 GM128648/GM/NIGMS NIH HHS/United States ; TL1 TR002318/TR/NCATS NIH HHS/United States ; R03 DE029827/DE/NIDCR NIH HHS/United States ; R35 GM138036/GM/NIGMS NIH HHS/United States ; T32 CA080416/CA/NCI NIH HHS/United States ; P50 AR065139/AR/NIAMS NIH HHS/United States ; },
abstract = {Cell-laden hydrogel constructs suspended between pillars are powerful tools for modeling tissue structure and physiology, though current fabrication techniques often limit them to uniform compositions. In contrast, tissues are complex in nature with spatial arrangements of cell types and extracellular matrices. Thus, we present Suspended Tissue Open Microfluidic Patterning (STOMP), which utilizes a removable, open microfluidic patterning channel to pattern multiple spatial regions across a single suspended tissue. The STOMP platform contains capillary pinning features along the open channel that controls the fluid front, allowing multiple cell and extracellular matrix precursors to be pipetted into one tissue. We have used this technique to pattern suspended tissues with multiple regional components using a variety of native and synthetic extracellular matrices, including fibrin, collagen, and poly(ethylene glycol). Here, we demonstrate that STOMP models a region of fibrosis in a functional heart tissue and a bone-ligament junction in periodontal tissues. Additionally, the STOMP platform can be customized to allow patterning of suspended cores and more spatial configurations, enhancing its utility in complex tissue modeling. STOMP is a versatile technique for generating suspended tissue models with increased control over cell and hydrogel composition to model interfacial tissue regions in a suspended tissue.},
}
RevDate: 2024-10-22
Combined PD-1 and CTLA-4 Blockade in an International Cohort of Patients with Acral Lentiginous Melanoma.
The British journal of dermatology pii:7831584 [Epub ahead of print].
BACKGROUND: Combination immune checkpoint blockade targeting PD-1 and CTLA-4 leads to high response rates and improved survival in advanced cutaneous melanoma (CM). Less is known about the efficacy of this combination in acral lentiginous melanoma (ALM).
OBJECTIVES: To determine the efficacy of combination immune checkpoint blockade targeting PD-1 and CTLA-4 in a real-world, diverse population of ALM.
METHODS: This multi-institutional retrospective study analyzed patients with histologically confirmed ALM treated with the combination of PD-1 and CTLA-4 inhibitors between 2010-2022. The primary objective of the study was objective response rate (ORR) per RECIST criteria. The secondary objectives were progression-free survival (PFS) and overall survival (OS).
RESULTS: In total, 109 patients with advanced ALM treated with combined PD-1 and CTLA-4 blockade in any line of treatment were included. The majority of patients had stage IV disease (n=81, 74.2%). The ORR for the entire cohort was 18.3% (95% CI 11.6-26.9%), with 9 (8.3%) complete responses (CR) and 11 (10.1%) partial responses (PR). An additional 22 patients (20.2%) had stable disease (SD), and the disease control rate (DCR) was 38.5%. The median PFS was 4.2 months [95% CI 3.25-5.62], while the median OS was 17 months [95% CI 12.4%-23.1%]. A total of 95 patients (87.2%) had a treatment-related adverse event, with 40.4% (n=44/109) experiencing at least one grade 3 or 4 toxicity. Elevated LDH (p=.04), 2+ lines of prior therapy (p=.03), and Asian race/ethnicity (p=.04) were associated with worse OS, while Hispanic/Latino race/ethnicity was associated with better OS (p=.02).
CONCLUSIONS: Combination of PD-1 and CTLA-4 blockade is less effective for ALM, as compared to CM, despite similar toxicity. Asian patients, in particular, appear to derive lower benefit from this regimen. Novel treatment approaches are needed for this rare melanoma subtype.
Additional Links: PMID-39438074
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PubMed:
Citation:
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@article {pmid39438074,
year = {2024},
author = {McGillivray, E and Ashouri, K and Chatziioannou, E and Gallegos, JAO and Zarka, J and Kechter, J and Hwang, AS and Zhang, K and Barros, M and Yeh, J and Okazaki, I and Crocker, AB and Maeda, T and Park, SJ and Choi, J and Andreoli, M and Darwish, T and Savage, DJ and Kim, KB and Gupta, J and Shen, J and Shirai, K and Choi, A and Pai, L and de Lima Vazquez, V and Moser, J and Amaral, T and Hernandez Aya, LF and Lutzky, J and Najjar, YG and Costello, CM and Mangold, AR and Bhatia, S and Gibney, GT and Farma, JM and Daniels, GA and Sosman, J and Chandra, S and Mangla, A and Bollin, K and Abrão Possik, P and Robles Espinoza, CD and Ito, F and In, GK},
title = {Combined PD-1 and CTLA-4 Blockade in an International Cohort of Patients with Acral Lentiginous Melanoma.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljae401},
pmid = {39438074},
issn = {1365-2133},
abstract = {BACKGROUND: Combination immune checkpoint blockade targeting PD-1 and CTLA-4 leads to high response rates and improved survival in advanced cutaneous melanoma (CM). Less is known about the efficacy of this combination in acral lentiginous melanoma (ALM).
OBJECTIVES: To determine the efficacy of combination immune checkpoint blockade targeting PD-1 and CTLA-4 in a real-world, diverse population of ALM.
METHODS: This multi-institutional retrospective study analyzed patients with histologically confirmed ALM treated with the combination of PD-1 and CTLA-4 inhibitors between 2010-2022. The primary objective of the study was objective response rate (ORR) per RECIST criteria. The secondary objectives were progression-free survival (PFS) and overall survival (OS).
RESULTS: In total, 109 patients with advanced ALM treated with combined PD-1 and CTLA-4 blockade in any line of treatment were included. The majority of patients had stage IV disease (n=81, 74.2%). The ORR for the entire cohort was 18.3% (95% CI 11.6-26.9%), with 9 (8.3%) complete responses (CR) and 11 (10.1%) partial responses (PR). An additional 22 patients (20.2%) had stable disease (SD), and the disease control rate (DCR) was 38.5%. The median PFS was 4.2 months [95% CI 3.25-5.62], while the median OS was 17 months [95% CI 12.4%-23.1%]. A total of 95 patients (87.2%) had a treatment-related adverse event, with 40.4% (n=44/109) experiencing at least one grade 3 or 4 toxicity. Elevated LDH (p=.04), 2+ lines of prior therapy (p=.03), and Asian race/ethnicity (p=.04) were associated with worse OS, while Hispanic/Latino race/ethnicity was associated with better OS (p=.02).
CONCLUSIONS: Combination of PD-1 and CTLA-4 blockade is less effective for ALM, as compared to CM, despite similar toxicity. Asian patients, in particular, appear to derive lower benefit from this regimen. Novel treatment approaches are needed for this rare melanoma subtype.},
}
RevDate: 2024-10-22
Vaccine hesitancy and routine revaccination among adult HCT survivors in the United States: A convergent mixed methods analysis.
Vaccine, 42(26):126374 pii:S0264-410X(24)01056-9 [Epub ahead of print].
Revaccination to restore immunity to vaccine-preventable diseases (VPDs) is essential risk mitigation in the prevention of infectious morbidity and mortality after hematopoietic cell transplantation (HCT). However, revaccination rates have been shown to be insufficient and to what extent vaccine hesitancy contributes to survivors not becoming fully revaccinated is unknown. We performed a cross-sectional, mixed methods survey-based study to explore how vaccine hesitancy influences revaccination among US adult HCT survivors who were 2 to 8 years after transplant. Participants were asked to complete the Vaccination Confidence Scale (VCS) and open-ended survey items regarding vaccine confidence. The survey response rate was 30 %; among 332 respondents, vaccine confidence was high in 69 %, medium in 20 %, and low in 11 %. On multivariable analysis, four factors associated with high vaccine confidence were: predominantly Democrat zip codes (per 2020 election results), ability to pay for revaccination out of pocket, receipt of pre-HCT adult vaccines, and receipt of COVID-19 vaccines. From 189 participants who also answered open-ended items, 14 themes associated with vaccine confidence were identified and collapsed into 4 categories based on the VCS: Benefits, Harms, Trust, and Other. Merged analysis showed congruence between VCS scores and open-ended survey responses and created a narrative about the relative importance of the constructs when approaching revaccination by vaccine confidence level. These findings significantly expand our knowledge of how vaccine hesitancy influences revaccination uptake among US adult HCT survivors. Population-specific interventions to approach vaccine-hesitant survivors should be developed and tested.
Additional Links: PMID-39437647
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PubMed:
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@article {pmid39437647,
year = {2024},
author = {Wickline, MM and Carpenter, PA and Harris, JR and Iribarren, SJ and Reding, KW and Pike, KC and Lee, SJ and Salit, RB and Oshima, MU and Vo, PT and Berry, DL},
title = {Vaccine hesitancy and routine revaccination among adult HCT survivors in the United States: A convergent mixed methods analysis.},
journal = {Vaccine},
volume = {42},
number = {26},
pages = {126374},
doi = {10.1016/j.vaccine.2024.126374},
pmid = {39437647},
issn = {1873-2518},
abstract = {Revaccination to restore immunity to vaccine-preventable diseases (VPDs) is essential risk mitigation in the prevention of infectious morbidity and mortality after hematopoietic cell transplantation (HCT). However, revaccination rates have been shown to be insufficient and to what extent vaccine hesitancy contributes to survivors not becoming fully revaccinated is unknown. We performed a cross-sectional, mixed methods survey-based study to explore how vaccine hesitancy influences revaccination among US adult HCT survivors who were 2 to 8 years after transplant. Participants were asked to complete the Vaccination Confidence Scale (VCS) and open-ended survey items regarding vaccine confidence. The survey response rate was 30 %; among 332 respondents, vaccine confidence was high in 69 %, medium in 20 %, and low in 11 %. On multivariable analysis, four factors associated with high vaccine confidence were: predominantly Democrat zip codes (per 2020 election results), ability to pay for revaccination out of pocket, receipt of pre-HCT adult vaccines, and receipt of COVID-19 vaccines. From 189 participants who also answered open-ended items, 14 themes associated with vaccine confidence were identified and collapsed into 4 categories based on the VCS: Benefits, Harms, Trust, and Other. Merged analysis showed congruence between VCS scores and open-ended survey responses and created a narrative about the relative importance of the constructs when approaching revaccination by vaccine confidence level. These findings significantly expand our knowledge of how vaccine hesitancy influences revaccination uptake among US adult HCT survivors. Population-specific interventions to approach vaccine-hesitant survivors should be developed and tested.},
}
RevDate: 2024-10-22
Cellular Characterization of Breast Cancer Using Microstructural Diffusion MRI.
Radiology, 313(1):e242268.
Additional Links: PMID-39436293
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PubMed:
Citation:
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@article {pmid39436293,
year = {2024},
author = {Partridge, SC and Xu, J},
title = {Cellular Characterization of Breast Cancer Using Microstructural Diffusion MRI.},
journal = {Radiology},
volume = {313},
number = {1},
pages = {e242268},
doi = {10.1148/radiol.242268},
pmid = {39436293},
issn = {1527-1315},
}
RevDate: 2024-10-22
CmpDate: 2024-10-16
NCCN Guidelines® Insights: Ovarian Cancer/Fallopian Tube Cancer/Primary Peritoneal Cancer, Version 3.2024.
Journal of the National Comprehensive Cancer Network : JNCCN, 22(8):512-519.
The NCCN Guidelines for Ovarian Cancer/Fallopian Tube Cancer/Primary Peritoneal Cancer provide multidisciplinary diagnostic workup, staging, and treatment recommendations for this disease. These NCCN Guidelines Insights detail how the evolution of the use of PARP inhibitors as maintenance and single-agent regimens for the treatment of ovarian cancer informed panel recommendations in the guidelines.
Additional Links: PMID-39413835
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@article {pmid39413835,
year = {2024},
author = {Liu, J and Berchuck, A and Backes, FJ and Cohen, J and Grisham, R and Leath, CA and Martin, L and Matei, D and Miller, DS and Robertson, S and Barroilhet, L and Uppal, S and Hendrickson, AW and Gershenson, DM and Gray, HJ and Hakam, A and Jain, A and Konecny, GE and Moroney, J and Ratner, E and Schorge, J and Thaker, PH and Werner, TL and Zsiros, E and Behbakht, K and Chen, LM and DeRosa, M and Eisenhauer, EL and Leiserowitz, G and Litkouhi, B and McHale, M and Percac-Lima, S and Rodabaugh, K and Vargas, R and Jones, F and Kovach, E and Hang, L and Ramakrishnan, S and Alvarez, RD and Armstrong, DK},
title = {NCCN Guidelines® Insights: Ovarian Cancer/Fallopian Tube Cancer/Primary Peritoneal Cancer, Version 3.2024.},
journal = {Journal of the National Comprehensive Cancer Network : JNCCN},
volume = {22},
number = {8},
pages = {512-519},
doi = {10.6004/jnccn.2024.0052},
pmid = {39413835},
issn = {1540-1413},
mesh = {Humans ; Female ; *Ovarian Neoplasms/diagnosis/therapy/pathology ; *Peritoneal Neoplasms/therapy/diagnosis ; *Fallopian Tube Neoplasms/diagnosis/therapy/pathology ; Medical Oncology/standards/methods ; Neoplasm Staging ; Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use ; },
abstract = {The NCCN Guidelines for Ovarian Cancer/Fallopian Tube Cancer/Primary Peritoneal Cancer provide multidisciplinary diagnostic workup, staging, and treatment recommendations for this disease. These NCCN Guidelines Insights detail how the evolution of the use of PARP inhibitors as maintenance and single-agent regimens for the treatment of ovarian cancer informed panel recommendations in the guidelines.},
}
MeSH Terms:
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Humans
Female
*Ovarian Neoplasms/diagnosis/therapy/pathology
*Peritoneal Neoplasms/therapy/diagnosis
*Fallopian Tube Neoplasms/diagnosis/therapy/pathology
Medical Oncology/standards/methods
Neoplasm Staging
Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use
RevDate: 2024-10-22
CmpDate: 2024-10-16
Acute Lymphoblastic Leukemia, Version 2.2024, NCCN Clinical Practice Guidelines in Oncology.
Journal of the National Comprehensive Cancer Network : JNCCN, 22(8):563-576.
The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for acute lymphoblastic leukemia (ALL) provide recommendations for management of ALL, with a focus on the classification of ALL subtypes based on immunophenotype and cytogenetic/molecular markers; risk assessment and stratification for risk-adapted therapy; treatment strategies for Philadelphia chromosome (Ph)-positive and Ph-negative ALL for both adolescent and young adult and adult patients; and supportive care considerations. This selection from the NCCN Guidelines for ALL focuses on treatment recommendations for adults with newly diagnosed Ph-negative ALL based on current evidence.
Additional Links: PMID-39413812
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@article {pmid39413812,
year = {2024},
author = {Shah, B and Mattison, RJ and Abboud, R and Abdelmessieh, P and Aldoss, I and Burke, PW and DeAngelo, DJ and Dinner, S and Fathi, AT and Gauthier, J and Haddadin, M and Jain, N and Jonas, B and Kirby, S and Liedtke, M and Litzow, M and Logan, A and Long, M and Luger, S and Mangan, JK and Massaro, S and May, W and Oluwole, O and Park, J and Przespolewski, A and Rangaraju, S and Saygin, C and Schwartz, M and Shami, P and Tomlinson, B and Webster, J and Awotiwon, A and Stehman, K},
title = {Acute Lymphoblastic Leukemia, Version 2.2024, NCCN Clinical Practice Guidelines in Oncology.},
journal = {Journal of the National Comprehensive Cancer Network : JNCCN},
volume = {22},
number = {8},
pages = {563-576},
doi = {10.6004/jnccn.2024.0051},
pmid = {39413812},
issn = {1540-1413},
mesh = {Humans ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy/diagnosis ; Medical Oncology/standards/methods ; Adult ; Philadelphia Chromosome ; Adolescent ; },
abstract = {The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for acute lymphoblastic leukemia (ALL) provide recommendations for management of ALL, with a focus on the classification of ALL subtypes based on immunophenotype and cytogenetic/molecular markers; risk assessment and stratification for risk-adapted therapy; treatment strategies for Philadelphia chromosome (Ph)-positive and Ph-negative ALL for both adolescent and young adult and adult patients; and supportive care considerations. This selection from the NCCN Guidelines for ALL focuses on treatment recommendations for adults with newly diagnosed Ph-negative ALL based on current evidence.},
}
MeSH Terms:
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Humans
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy/diagnosis
Medical Oncology/standards/methods
Adult
Philadelphia Chromosome
Adolescent
RevDate: 2024-10-21
Alendronate preserves bone mineral density in adults with sickle cell disease and osteoporosis.
Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA [Epub ahead of print].
UNLABELLED: Low bone mineral density is highly prevalent in sickle cell disease (SCD); whether bisphosphonates can safely preserve or increase bone mass in SCD adults remains unknown. In this study, lumbar spine bone density remained stable with alendronate use, and treatment-related side effects were mostly mild and self-limited.
PURPOSE: To describe the effects of alendronate in adults with sickle cell disease (SCD) and osteoporosis.
METHODS: We reviewed retrospective clinical data from adults with SCD and osteoporosis treated with alendronate at a single center in Brazil (2009-2019). Bone mineral density (BMD) was measured by dual-energy X-ray absorptiometry (DXA) of the lumbar spine, femoral neck, and total hip. We analyzed BMD changes by alendronate treatment duration (months), stratified by sex, skeletal site, and SCD genotype.
RESULTS: Sixty-four SCD adults with osteoporosis (69% females, 73% HbSS, mean age ± standard deviation 42.4 ± 10.9 years) received alendronate for a median (interquartile range) of 48 (29, 73) months. Compared with males, females had significantly lower baseline BMD (g/cm[2]) at the femoral neck (0.72 vs 0.85, p = < 0.001) and total hip (0.79 vs 0.88, p = 0.009). The between-sex differences in BMD changes were insignificant. Mean lumbar spine BMD significantly changed by 0.0357 g/cm[2] (p = 0.028) in those on alendronate for > 5 years. Four adults (6.3%) reported mild therapy-related side effects. An atypical femoral diaphysis fracture, attributed to alendronate, was incidentally noted in a 37-year-old man on treatment for 4 years.
CONCLUSION: In this retrospective cohort of adults with SCD and osteoporosis on alendronate for a median of 48 months, we found no significant interactions between sex and changes in lumbar spine, femoral neck, or total hip BMD with alendronate. Lumbar spine BMD was stable in those on alendronate for < 5 years. Side effects of alendronate were mild, though one patient developed an atypical femoral fracture.
Additional Links: PMID-39433652
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Citation:
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@article {pmid39433652,
year = {2024},
author = {Adesina, OO and Jenkins, IC and Galvão, F and de Moura, AC and Fertrin, KY and Zemel, BS and Saad, STO},
title = {Alendronate preserves bone mineral density in adults with sickle cell disease and osteoporosis.},
journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA},
volume = {},
number = {},
pages = {},
pmid = {39433652},
issn = {1433-2965},
support = {5K23HL148310-02/HL/NHLBI NIH HHS/United States ; CSDA 2020095/DDCF/Doris Duke Charitable Foundation/United States ; },
abstract = {UNLABELLED: Low bone mineral density is highly prevalent in sickle cell disease (SCD); whether bisphosphonates can safely preserve or increase bone mass in SCD adults remains unknown. In this study, lumbar spine bone density remained stable with alendronate use, and treatment-related side effects were mostly mild and self-limited.
PURPOSE: To describe the effects of alendronate in adults with sickle cell disease (SCD) and osteoporosis.
METHODS: We reviewed retrospective clinical data from adults with SCD and osteoporosis treated with alendronate at a single center in Brazil (2009-2019). Bone mineral density (BMD) was measured by dual-energy X-ray absorptiometry (DXA) of the lumbar spine, femoral neck, and total hip. We analyzed BMD changes by alendronate treatment duration (months), stratified by sex, skeletal site, and SCD genotype.
RESULTS: Sixty-four SCD adults with osteoporosis (69% females, 73% HbSS, mean age ± standard deviation 42.4 ± 10.9 years) received alendronate for a median (interquartile range) of 48 (29, 73) months. Compared with males, females had significantly lower baseline BMD (g/cm[2]) at the femoral neck (0.72 vs 0.85, p = < 0.001) and total hip (0.79 vs 0.88, p = 0.009). The between-sex differences in BMD changes were insignificant. Mean lumbar spine BMD significantly changed by 0.0357 g/cm[2] (p = 0.028) in those on alendronate for > 5 years. Four adults (6.3%) reported mild therapy-related side effects. An atypical femoral diaphysis fracture, attributed to alendronate, was incidentally noted in a 37-year-old man on treatment for 4 years.
CONCLUSION: In this retrospective cohort of adults with SCD and osteoporosis on alendronate for a median of 48 months, we found no significant interactions between sex and changes in lumbar spine, femoral neck, or total hip BMD with alendronate. Lumbar spine BMD was stable in those on alendronate for < 5 years. Side effects of alendronate were mild, though one patient developed an atypical femoral fracture.},
}
RevDate: 2024-10-21
CmpDate: 2024-10-21
Heterogeneity-aware integrative regression for ancestry-specific association studies.
Biometrics, 80(4):.
Ancestry-specific proteome-wide association studies (PWAS) based on genetically predicted protein expression can reveal complex disease etiology specific to certain ancestral groups. These studies require ancestry-specific models for protein expression as a function of SNP genotypes. In order to improve protein expression prediction in ancestral populations historically underrepresented in genomic studies, we propose a new penalized maximum likelihood estimator for fitting ancestry-specific joint protein quantitative trait loci models. Our estimator borrows information across ancestral groups, while simultaneously allowing for heterogeneous error variances and regression coefficients. We propose an alternative parameterization of our model that makes the objective function convex and the penalty scale invariant. To improve computational efficiency, we propose an approximate version of our method and study its theoretical properties. Our method provides a substantial improvement in protein expression prediction accuracy in individuals of African ancestry, and in a downstream PWAS analysis, leads to the discovery of multiple associations between protein expression and blood lipid traits in the African ancestry population.
Additional Links: PMID-39432443
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PubMed:
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@article {pmid39432443,
year = {2024},
author = {Molstad, AJ and Cai, Y and Reiner, AP and Kooperberg, C and Sun, W and Hsu, L},
title = {Heterogeneity-aware integrative regression for ancestry-specific association studies.},
journal = {Biometrics},
volume = {80},
number = {4},
pages = {},
doi = {10.1093/biomtc/ujae109},
pmid = {39432443},
issn = {1541-0420},
support = {//WHI/ ; /HL/NHLBI NIH HHS/United States ; R01 HL145806/NH/NIH HHS/United States ; 75N92021D00001/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Genome-Wide Association Study/statistics & numerical data ; Regression Analysis ; Likelihood Functions ; Black People/genetics/statistics & numerical data ; Proteome ; Computer Simulation ; Models, Statistical ; Biometry/methods ; },
abstract = {Ancestry-specific proteome-wide association studies (PWAS) based on genetically predicted protein expression can reveal complex disease etiology specific to certain ancestral groups. These studies require ancestry-specific models for protein expression as a function of SNP genotypes. In order to improve protein expression prediction in ancestral populations historically underrepresented in genomic studies, we propose a new penalized maximum likelihood estimator for fitting ancestry-specific joint protein quantitative trait loci models. Our estimator borrows information across ancestral groups, while simultaneously allowing for heterogeneous error variances and regression coefficients. We propose an alternative parameterization of our model that makes the objective function convex and the penalty scale invariant. To improve computational efficiency, we propose an approximate version of our method and study its theoretical properties. Our method provides a substantial improvement in protein expression prediction accuracy in individuals of African ancestry, and in a downstream PWAS analysis, leads to the discovery of multiple associations between protein expression and blood lipid traits in the African ancestry population.},
}
MeSH Terms:
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hide MeSH Terms
Humans
*Polymorphism, Single Nucleotide
*Quantitative Trait Loci
Genome-Wide Association Study/statistics & numerical data
Regression Analysis
Likelihood Functions
Black People/genetics/statistics & numerical data
Proteome
Computer Simulation
Models, Statistical
Biometry/methods
RevDate: 2024-10-21
Structure-Based Engineering of Monoclonal Antibodies for Improved Binding to Counteract the Effects of Fentanyl and Carfentanil.
ACS omega, 9(41):42506-42519.
The opioid overdose epidemic is a growing and evolving public health crisis fueled by the widespread presence of fentanyl and fentanyl analogues (F/FAs) in both street mixtures and counterfeit pills. To expand current treatment options, drug-targeting monoclonal antibodies (mAbs) offer a viable therapeutic for both pre- and postexposure clinical scenarios. This study reports the isolation, in vitro characterization, and in vivo efficacy of two murine mAb families targeting fentanyl, carfentanil, or both. Because humanization of the mAbs by CDR grafting negatively impacted affinity for both fentanyl and carfentanil, crystal structures of mAbs in complex with fentanyl or carfentanil were analyzed to identify key residues involved in ligand binding in murine versus humanized structures, and site-directed mutagenesis was used to verify their functional importance. The structural analysis identified a framework residue, Tyr36, present in the murine germline sequence of two mAbs, which was critical for binding to fentanyl and carfentanil. These studies emphasize the importance of structural considerations in mAb engineering to optimize mAbs targeting small molecules including opioids and other drugs of public health interest.
Additional Links: PMID-39431098
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@article {pmid39431098,
year = {2024},
author = {Rodarte, J and Baehr, C and Hicks, D and McGovern, M and Zhang, Y and Silva-Ortiz, P and Hannon, B and Duddu, S and Pancera, M and Pravetoni, M},
title = {Structure-Based Engineering of Monoclonal Antibodies for Improved Binding to Counteract the Effects of Fentanyl and Carfentanil.},
journal = {ACS omega},
volume = {9},
number = {41},
pages = {42506-42519},
pmid = {39431098},
issn = {2470-1343},
abstract = {The opioid overdose epidemic is a growing and evolving public health crisis fueled by the widespread presence of fentanyl and fentanyl analogues (F/FAs) in both street mixtures and counterfeit pills. To expand current treatment options, drug-targeting monoclonal antibodies (mAbs) offer a viable therapeutic for both pre- and postexposure clinical scenarios. This study reports the isolation, in vitro characterization, and in vivo efficacy of two murine mAb families targeting fentanyl, carfentanil, or both. Because humanization of the mAbs by CDR grafting negatively impacted affinity for both fentanyl and carfentanil, crystal structures of mAbs in complex with fentanyl or carfentanil were analyzed to identify key residues involved in ligand binding in murine versus humanized structures, and site-directed mutagenesis was used to verify their functional importance. The structural analysis identified a framework residue, Tyr36, present in the murine germline sequence of two mAbs, which was critical for binding to fentanyl and carfentanil. These studies emphasize the importance of structural considerations in mAb engineering to optimize mAbs targeting small molecules including opioids and other drugs of public health interest.},
}
RevDate: 2024-10-21
Stem-like exhausted CD8 T cells in pleural effusions predict improved survival in non-small cell lung cancer (NSCLC) and mesothelioma.
Translational lung cancer research, 13(9):2352-2372.
BACKGROUND: Anti-tumor CD8 T cells are important for immunity but can become 'exhausted' and hence ineffective. Tumor-infiltrating exhausted CD8[+] T cells include less differentiated stem-like exhausted T (Tex[stem]) cells and terminally exhausted T (Tex[term]) cells. Both subsets have been proposed as prognostic biomarkers in cancer patients. In this study, we retrospectively investigated their prognostic significance in patients with metastatic non-small cell lung cancer (NSCLC) and validated our findings in a mesothelioma cohort.
METHODS: Pre-treatment malignant pleural effusions (PEs) from 43 NSCLC (41 non-squamous, 2 squamous) patients were analyzed by flow cytometry. The percentages of Tex[stem] and Tex[term] CD8 T cells were correlated with overall survival (OS) after adjusting for clinicopathological variables. Findings were validated using a mesothelioma cohort (n=49). Mass cytometry was performed on 16 pre-treatment PE samples from 5 mesothelioma and 3 NSCLC patients for T-cell phenotyping. Single-cell multi-omics analysis was performed on 4 pre-treatment PE samples from 2 NSCLC patients and 2 mesothelioma patients for analysis of the transcriptomic profiles, surface markers and T cell receptor (TCR) repertoire.
RESULTS: Higher frequency of Tex[stem] was associated with significantly increased OS [median 9.9 vs. 3.4 months, hazard ratio (HR) 0.36, 95% CI: 0.16-0.79, P=0.01]. The frequency of Tex[term] was not associated with OS. These findings were validated in the mesothelioma cohort (high vs. low Tex[stem], median OS 32.1 vs. 19.8 months, HR 0.31, 95% CI: 0.10-0.96, P=0.04). Detailed single-cell sequencing and mass cytometry profiling revealed that exhausted T cells from NSCLC expressed greater stem-likeness and less inhibitory markers than those from mesothelioma and that Tex[stem] cells also contained 'bystander' virus-specific T cells.
CONCLUSIONS: This study demonstrates that PE CD8 Tex[stem] cell abundance is associated with better survival outcomes, and thus may be a useful prognostic biomarker.
Additional Links: PMID-39430319
PubMed:
Citation:
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@article {pmid39430319,
year = {2024},
author = {Ye, L and Ryu, H and Granadier, D and Nguyen, LT and Simoni, Y and Dick, I and Firth, T and Rouse, E and Chiang, P and Lee, YCG and Robinson, BW and Creaney, J and Newell, EW and Redwood, AJ},
title = {Stem-like exhausted CD8 T cells in pleural effusions predict improved survival in non-small cell lung cancer (NSCLC) and mesothelioma.},
journal = {Translational lung cancer research},
volume = {13},
number = {9},
pages = {2352-2372},
pmid = {39430319},
issn = {2218-6751},
abstract = {BACKGROUND: Anti-tumor CD8 T cells are important for immunity but can become 'exhausted' and hence ineffective. Tumor-infiltrating exhausted CD8[+] T cells include less differentiated stem-like exhausted T (Tex[stem]) cells and terminally exhausted T (Tex[term]) cells. Both subsets have been proposed as prognostic biomarkers in cancer patients. In this study, we retrospectively investigated their prognostic significance in patients with metastatic non-small cell lung cancer (NSCLC) and validated our findings in a mesothelioma cohort.
METHODS: Pre-treatment malignant pleural effusions (PEs) from 43 NSCLC (41 non-squamous, 2 squamous) patients were analyzed by flow cytometry. The percentages of Tex[stem] and Tex[term] CD8 T cells were correlated with overall survival (OS) after adjusting for clinicopathological variables. Findings were validated using a mesothelioma cohort (n=49). Mass cytometry was performed on 16 pre-treatment PE samples from 5 mesothelioma and 3 NSCLC patients for T-cell phenotyping. Single-cell multi-omics analysis was performed on 4 pre-treatment PE samples from 2 NSCLC patients and 2 mesothelioma patients for analysis of the transcriptomic profiles, surface markers and T cell receptor (TCR) repertoire.
RESULTS: Higher frequency of Tex[stem] was associated with significantly increased OS [median 9.9 vs. 3.4 months, hazard ratio (HR) 0.36, 95% CI: 0.16-0.79, P=0.01]. The frequency of Tex[term] was not associated with OS. These findings were validated in the mesothelioma cohort (high vs. low Tex[stem], median OS 32.1 vs. 19.8 months, HR 0.31, 95% CI: 0.10-0.96, P=0.04). Detailed single-cell sequencing and mass cytometry profiling revealed that exhausted T cells from NSCLC expressed greater stem-likeness and less inhibitory markers than those from mesothelioma and that Tex[stem] cells also contained 'bystander' virus-specific T cells.
CONCLUSIONS: This study demonstrates that PE CD8 Tex[stem] cell abundance is associated with better survival outcomes, and thus may be a useful prognostic biomarker.},
}
RevDate: 2024-10-21
In vitro and in vivo expansion of CD33/HBG promoter-edited HSPCs with Mylotarg.
Molecular therapy. Methods & clinical development, 32(4):101343.
We developed an in vivo HSC gene therapy approach that consists of HSC mobilization and intravenous injection of HSC-tropic HDAd vectors. To achieve therapeutically relevant numbers of corrected cells, we incorporated in vivo expansion of transduced cells. We used an HDAd vector for a multiplex adenine base editing approach to (1) remove the region within CD33 that is recognized by gemtuzumab ozogamicin (GO) (Mylotarg), and (2) create therapeutic edits within the HBG1/2 promoters to reactivate γ-globin/HbF. In vitro studies with HDAd-transduced human CD34[+] cells showed editing of both targeted sites and a 2- to 3-fold GO-mediated expansion of edited erythroid/myeloid progenitors. After erythroid in vitro differentiation, up to 40% of erythrocytes were HbF positive. For in vivo studies, mice were transplanted with human CD34[+] cells. After engraftment, HSCs were mobilized with G-CSF/AMD3100 followed by an intravenous HDAd injection and GO-mediated in vivo selection. Two months later, editing in human cells within the bone marrow was significantly higher in GO-treated mice. The percentage of HbF[+] human erythroid cells was 2.5-fold greater compared with untreated mice. These data indicate that in vivo GO selection can increase edited erythroid cells.
Additional Links: PMID-39429723
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Citation:
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@article {pmid39429723,
year = {2024},
author = {Georgakopoulou, A and Li, C and Kiem, HP and Lieber, A},
title = {In vitro and in vivo expansion of CD33/HBG promoter-edited HSPCs with Mylotarg.},
journal = {Molecular therapy. Methods & clinical development},
volume = {32},
number = {4},
pages = {101343},
pmid = {39429723},
issn = {2329-0501},
abstract = {We developed an in vivo HSC gene therapy approach that consists of HSC mobilization and intravenous injection of HSC-tropic HDAd vectors. To achieve therapeutically relevant numbers of corrected cells, we incorporated in vivo expansion of transduced cells. We used an HDAd vector for a multiplex adenine base editing approach to (1) remove the region within CD33 that is recognized by gemtuzumab ozogamicin (GO) (Mylotarg), and (2) create therapeutic edits within the HBG1/2 promoters to reactivate γ-globin/HbF. In vitro studies with HDAd-transduced human CD34[+] cells showed editing of both targeted sites and a 2- to 3-fold GO-mediated expansion of edited erythroid/myeloid progenitors. After erythroid in vitro differentiation, up to 40% of erythrocytes were HbF positive. For in vivo studies, mice were transplanted with human CD34[+] cells. After engraftment, HSCs were mobilized with G-CSF/AMD3100 followed by an intravenous HDAd injection and GO-mediated in vivo selection. Two months later, editing in human cells within the bone marrow was significantly higher in GO-treated mice. The percentage of HbF[+] human erythroid cells was 2.5-fold greater compared with untreated mice. These data indicate that in vivo GO selection can increase edited erythroid cells.},
}
RevDate: 2024-10-21
CmpDate: 2024-10-21
Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.
Gut microbes, 16(1):2414975.
BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with the maturation of the adaptive immune system. However, little is known about the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n = 94) from a cohort of infants (n = 15) at monthly intervals in the first 6 months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.
RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.
CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort, we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.
Additional Links: PMID-39428758
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PubMed:
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@article {pmid39428758,
year = {2024},
author = {Minot, SS and Mayer-Blackwell, K and Fiore-Gartland, A and Johnson, A and Self, S and Bhatti, P and Yao, L and Liu, L and Sun, X and Jinfa, Y and Kublin, J},
title = {Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2414975},
doi = {10.1080/19490976.2024.2414975},
pmid = {39428758},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Metagenomics ; Microbial Consortia ; Metagenome ; Infant, Newborn ; Cohort Studies ; Cystic Fibrosis/microbiology ; },
abstract = {BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with the maturation of the adaptive immune system. However, little is known about the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n = 94) from a cohort of infants (n = 15) at monthly intervals in the first 6 months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.
RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.
CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort, we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome
Infant
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Female
Metagenomics
Microbial Consortia
Metagenome
Infant, Newborn
Cohort Studies
Cystic Fibrosis/microbiology
RevDate: 2024-10-20
CmpDate: 2024-10-20
Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data.
Briefings in bioinformatics, 25(6):.
Multiplexed spatial proteomics reveals the spatial organization of cells in tumors, which is associated with important clinical outcomes such as survival and treatment response. This spatial organization is often summarized using spatial summary statistics, including Ripley's K and Besag's L. However, if multiple regions of the same tumor are imaged, it is unclear how to synthesize the relationship with a single patient-level endpoint. We evaluate extant approaches for accommodating multiple images within the context of associating summary statistics with outcomes. First, we consider averaging-based approaches wherein multiple summaries for a single sample are combined in a weighted mean. We then propose a novel class of ensemble testing approaches in which we simulate random weights used to aggregate summaries, test for an association with outcomes, and combine the $P$-values. We systematically evaluate the performance of these approaches via simulation and application to data from non-small cell lung cancer, colorectal cancer, and triple negative breast cancer. We find that the optimal strategy varies, but a simple weighted average of the summary statistics based on the number of cells in each image often offers the highest power and controls type I error effectively. When the size of the imaged regions varies, incorporating this variation into the weighted aggregation may yield additional power in cases where the varying size is informative. Ensemble testing (but not resampling) offered high power and type I error control across conditions in our simulated data sets.
Additional Links: PMID-39428129
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@article {pmid39428129,
year = {2024},
author = {Samorodnitsky, S and Wu, MC},
title = {Statistical analysis of multiple regions-of-interest in multiplexed spatial proteomics data.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {6},
pages = {},
doi = {10.1093/bib/bbae522},
pmid = {39428129},
issn = {1477-4054},
support = {U10 CA180819/GF/NIH HHS/United States ; //Hope Foundation for Cancer Research/ ; },
mesh = {Humans ; *Proteomics/methods ; Neoplasms/metabolism/genetics ; Carcinoma, Non-Small-Cell Lung/metabolism/pathology/genetics ; Triple Negative Breast Neoplasms/pathology/metabolism/genetics ; Colorectal Neoplasms/metabolism/pathology/genetics ; Lung Neoplasms/metabolism/pathology/genetics ; Data Interpretation, Statistical ; Algorithms ; },
abstract = {Multiplexed spatial proteomics reveals the spatial organization of cells in tumors, which is associated with important clinical outcomes such as survival and treatment response. This spatial organization is often summarized using spatial summary statistics, including Ripley's K and Besag's L. However, if multiple regions of the same tumor are imaged, it is unclear how to synthesize the relationship with a single patient-level endpoint. We evaluate extant approaches for accommodating multiple images within the context of associating summary statistics with outcomes. First, we consider averaging-based approaches wherein multiple summaries for a single sample are combined in a weighted mean. We then propose a novel class of ensemble testing approaches in which we simulate random weights used to aggregate summaries, test for an association with outcomes, and combine the $P$-values. We systematically evaluate the performance of these approaches via simulation and application to data from non-small cell lung cancer, colorectal cancer, and triple negative breast cancer. We find that the optimal strategy varies, but a simple weighted average of the summary statistics based on the number of cells in each image often offers the highest power and controls type I error effectively. When the size of the imaged regions varies, incorporating this variation into the weighted aggregation may yield additional power in cases where the varying size is informative. Ensemble testing (but not resampling) offered high power and type I error control across conditions in our simulated data sets.},
}
MeSH Terms:
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Humans
*Proteomics/methods
Neoplasms/metabolism/genetics
Carcinoma, Non-Small-Cell Lung/metabolism/pathology/genetics
Triple Negative Breast Neoplasms/pathology/metabolism/genetics
Colorectal Neoplasms/metabolism/pathology/genetics
Lung Neoplasms/metabolism/pathology/genetics
Data Interpretation, Statistical
Algorithms
RevDate: 2024-10-21
Heterozygous and generalist MxA super-restrictors overcome breadth-specificity tradeoffs in antiviral restriction.
bioRxiv : the preprint server for biology.
Antiviral restriction factors such as MxA (myxovirus resistance protein A) inhibit a broad range of viruses. However, they face the challenge of maintaining this breadth as viruses evolve to escape their defense. Viral escape drives restriction factors to evolve rapidly, selecting for amino acid changes at their virus-binding interfaces to regain defense. How do restriction factors balance the breadth of antiviral functions against the need to evolve specificity against individual escaping viruses? We explored this question in human MxA, which uses its rapidly evolving loop L4 as the specificity determinant for orthomyxoviruses such as THOV and IAV. Previous combinatorial mutagenesis of rapidly evolving residues in human MxA loop L4 revealed variants with a ten-fold increase in potency against THOV. However, this strategy did not yield improved IAV restriction, suggesting a strong tradeoff between antiviral specificity and breadth. Here, using a modified combinatorial mutagenesis strategy, we find 'super-restrictor' MxA variants with over ten-fold enhanced restriction of the avian IAV strain H5N1 but reduced THOV restriction. Analysis of super-restrictor MxA variants reveals that the identity of residue 561 explains most of MxA's breadth-specificity tradeoff in H5N1 versus THOV restriction. However, rare 'generalist' super-restrictors with enhanced restriction of both viruses allow MxA to overcome the breadth-specificity tradeoff. Finally, we show that a heterozygous combination of two 'specialist' super-restrictors, one against THOV and the other against IAV, enhances restriction against both viruses. Thus, two strategies enable restriction factors such as MxA to increase their restriction of diverse viruses to overcome breadth-specificity tradeoffs that may be pervasive in host-virus conflicts.
Additional Links: PMID-39416221
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@article {pmid39416221,
year = {2024},
author = {Geiger, RA and Khera, D and Tenthorey, JL and Kochs, G and Graf, L and Emerman, M and Malik, HS},
title = {Heterozygous and generalist MxA super-restrictors overcome breadth-specificity tradeoffs in antiviral restriction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416221},
issn = {2692-8205},
support = {T32 HG000035/HG/NHGRI NIH HHS/United States ; U54 AI170792/AI/NIAID NIH HHS/United States ; },
abstract = {Antiviral restriction factors such as MxA (myxovirus resistance protein A) inhibit a broad range of viruses. However, they face the challenge of maintaining this breadth as viruses evolve to escape their defense. Viral escape drives restriction factors to evolve rapidly, selecting for amino acid changes at their virus-binding interfaces to regain defense. How do restriction factors balance the breadth of antiviral functions against the need to evolve specificity against individual escaping viruses? We explored this question in human MxA, which uses its rapidly evolving loop L4 as the specificity determinant for orthomyxoviruses such as THOV and IAV. Previous combinatorial mutagenesis of rapidly evolving residues in human MxA loop L4 revealed variants with a ten-fold increase in potency against THOV. However, this strategy did not yield improved IAV restriction, suggesting a strong tradeoff between antiviral specificity and breadth. Here, using a modified combinatorial mutagenesis strategy, we find 'super-restrictor' MxA variants with over ten-fold enhanced restriction of the avian IAV strain H5N1 but reduced THOV restriction. Analysis of super-restrictor MxA variants reveals that the identity of residue 561 explains most of MxA's breadth-specificity tradeoff in H5N1 versus THOV restriction. However, rare 'generalist' super-restrictors with enhanced restriction of both viruses allow MxA to overcome the breadth-specificity tradeoff. Finally, we show that a heterozygous combination of two 'specialist' super-restrictors, one against THOV and the other against IAV, enhances restriction against both viruses. Thus, two strategies enable restriction factors such as MxA to increase their restriction of diverse viruses to overcome breadth-specificity tradeoffs that may be pervasive in host-virus conflicts.},
}
RevDate: 2024-10-21
MAX inactivation deregulates the MYC network and induces neuroendocrine neoplasia in multiple tissues.
bioRxiv : the preprint server for biology.
The MYC transcription factor requires MAX for DNA binding and widespread activation of gene expression in both normal and neoplastic cells. Surprisingly, inactivating mutations in MAX are associated with a subset of neuroendocrine cancers including pheochromocytoma, pituitary adenoma and small cell lung cancer. Neither the extent nor the mechanisms of MAX tumor suppression are well understood. Delet-ing Max across multiple mouse neuroendocrine tissues, we find Max inactivation alone produces pituitary adenomas while Max loss cooperates with Rb1/Trp53 loss to accelerate medullary thyroid C-cell and pituitary adenoma development. In the thyroid tumor cell lines, MAX loss triggers a striking shift in genomic occupancy by other members of the MYC network (MNT, MLX, MondoA) supporting metabolism, survival and proliferation of neoplastic neuroendocrine cells. Our work reveals MAX as a broad suppressor of neuroendocrine tumorigenesis through its ability to maintain a balance of genomic occupancies among the diverse transcription factors in the MYC network.
Additional Links: PMID-39386474
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@article {pmid39386474,
year = {2024},
author = {Freie, B and Ibrahim, AH and Carroll, PA and Bronson, RT and Augert, A and MacPherson, D and Eisenman, RN},
title = {MAX inactivation deregulates the MYC network and induces neuroendocrine neoplasia in multiple tissues.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39386474},
issn = {2692-8205},
support = {P30 CA015704/CA/NCI NIH HHS/United States ; R01 CA248762/CA/NCI NIH HHS/United States ; R35 CA231989/CA/NCI NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; },
abstract = {The MYC transcription factor requires MAX for DNA binding and widespread activation of gene expression in both normal and neoplastic cells. Surprisingly, inactivating mutations in MAX are associated with a subset of neuroendocrine cancers including pheochromocytoma, pituitary adenoma and small cell lung cancer. Neither the extent nor the mechanisms of MAX tumor suppression are well understood. Delet-ing Max across multiple mouse neuroendocrine tissues, we find Max inactivation alone produces pituitary adenomas while Max loss cooperates with Rb1/Trp53 loss to accelerate medullary thyroid C-cell and pituitary adenoma development. In the thyroid tumor cell lines, MAX loss triggers a striking shift in genomic occupancy by other members of the MYC network (MNT, MLX, MondoA) supporting metabolism, survival and proliferation of neoplastic neuroendocrine cells. Our work reveals MAX as a broad suppressor of neuroendocrine tumorigenesis through its ability to maintain a balance of genomic occupancies among the diverse transcription factors in the MYC network.},
}
RevDate: 2024-10-18
Performance of Digital Breast Tomosynthesis Versus Digital Mammography in Women With a Family History of Breast Cancer: A Systematic Review.
Clinical breast cancer pii:S1526-8209(24)00274-X [Epub ahead of print].
BACKGROUND: There is limited evidence on the performance of digital breast tomosynthesis (DBT) in populations at increased risk of breast cancer. Our objective was to systematically review evidence on the performance of DBT versus digital mammography (DM) in women with a family history of breast cancer (FHBC).
METHODS: We searched 5 databases (2011-January 2024) for studies comparing DBT and DM in women with a FHBC that reported any measure of cancer detection, recall, sensitivity and specificity. Findings were presented using a descriptive and narrative approach. Risk of bias was assessed using QUADAS-2/C.
RESULTS: Five (4 screening, 1 diagnostic) studies were included (total 3089 DBT, 3024 DM) with most (4/5) being prospective including 1 RCT. All studies were assessed as being at high risk of bias or applicability concern. Four screening studies reported recall rate (range: DBT: 2.7%-4.5%, DM: 2.8%-11.5%) with 3 reporting DBT had lower rates than DM. Cancer detection rates (CDR) were reported in the same studies (DBT: 5.1-11.6 per 1000, DM: 3.8-8.3); 3 reported higher CDR for DBT (vs. DM), and 1 reported same CDR for both. Compared with DM, higher values for sensitivity, specificity and PPV for DBT were reported in 2 studies.
CONCLUSION: This review provides early evidence that DBT may outperform DM for screening women with a FHBC. Our findings support further evaluation of DBT in this population. However, summarized findings were based on few studies and participants, and high-quality studies with improved methodology are needed to address biases identified in our review.
Additional Links: PMID-39424451
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PubMed:
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@article {pmid39424451,
year = {2024},
author = {Li, T and Isautier, J and Lee, JM and Marinovich, ML and Houssami, N},
title = {Performance of Digital Breast Tomosynthesis Versus Digital Mammography in Women With a Family History of Breast Cancer: A Systematic Review.},
journal = {Clinical breast cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clbc.2024.09.013},
pmid = {39424451},
issn = {1938-0666},
abstract = {BACKGROUND: There is limited evidence on the performance of digital breast tomosynthesis (DBT) in populations at increased risk of breast cancer. Our objective was to systematically review evidence on the performance of DBT versus digital mammography (DM) in women with a family history of breast cancer (FHBC).
METHODS: We searched 5 databases (2011-January 2024) for studies comparing DBT and DM in women with a FHBC that reported any measure of cancer detection, recall, sensitivity and specificity. Findings were presented using a descriptive and narrative approach. Risk of bias was assessed using QUADAS-2/C.
RESULTS: Five (4 screening, 1 diagnostic) studies were included (total 3089 DBT, 3024 DM) with most (4/5) being prospective including 1 RCT. All studies were assessed as being at high risk of bias or applicability concern. Four screening studies reported recall rate (range: DBT: 2.7%-4.5%, DM: 2.8%-11.5%) with 3 reporting DBT had lower rates than DM. Cancer detection rates (CDR) were reported in the same studies (DBT: 5.1-11.6 per 1000, DM: 3.8-8.3); 3 reported higher CDR for DBT (vs. DM), and 1 reported same CDR for both. Compared with DM, higher values for sensitivity, specificity and PPV for DBT were reported in 2 studies.
CONCLUSION: This review provides early evidence that DBT may outperform DM for screening women with a FHBC. Our findings support further evaluation of DBT in this population. However, summarized findings were based on few studies and participants, and high-quality studies with improved methodology are needed to address biases identified in our review.},
}
RevDate: 2024-10-18
Reassessing the burden of food insecurity in youth and young adults with youth-onset diabetes: The importance of marginal food security.
Canadian journal of diabetes pii:S1499-2671(24)00338-1 [Epub ahead of print].
INTRODUCTION: Whereas marginal food insecurity has been recognized as important in Canadian food security policy, the category of marginal food security (MFS) is often ignored in US food security research.
METHODS: Prevalence of FI was estimated according to the conventional and an alternate classification of MFS with food insecurity among 938 youth and young adults (YYA) with youth-onset type 1 diabetes (T1D) and 156 with youth-onset of type 2 diabetes (T2D) from the SEARCH Food Security Cohort Study (2018-2021). Multivariable regression was used to estimate the association of MFS and conventionally defined food insecurity (FI) ascertained with diabetes-related outcomes, including acute diabetes complications, health care utilization, and diabetes self-management among YYA with T1D.
RESULTS: MFS affected 10% of participants with T1D diabetes and 20% of participants with T2D. Classifying MFS with FI increased FI prevalence from 18.0% to 27.8% in participants with T1D and 34.6% to 55.1% in participants with T2D. Compared to T1D with high food security, YYA with T1D who were FI had higher odds hypoglycemia (2.1, 95%CI 1.2-3.6) and ketoacidosis (1.6, 95%CI 1.0-2.6), but no association was seen in MFS. The FI group also had higher odds of emergency department use and hospitalization (2.3, 95%CI 1.5-3.4; 2.4, 95%CI 1.5-3.9) and lower odds of technology use and checking glucose (0.6, 95%CI 0.4-0.9; 0.3, 95%CI 0.1-0.6). The MFS group exhibited associations of similar directions.
DISCUSSION AND CONCLUSIONS: Health care providers should consider care of patients with T1D and MFS the same way they care for patients with FI.
Additional Links: PMID-39424273
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PubMed:
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@article {pmid39424273,
year = {2024},
author = {Liese, AD and Julceus, EF and Brown, AD and Pihoker, C and Frongillo, EA and Sauder, KA and Malik, FS and Bellatorre, A and Reboussin, BA and Mendoza, JA},
title = {Reassessing the burden of food insecurity in youth and young adults with youth-onset diabetes: The importance of marginal food security.},
journal = {Canadian journal of diabetes},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcjd.2024.10.006},
pmid = {39424273},
issn = {2352-3840},
abstract = {INTRODUCTION: Whereas marginal food insecurity has been recognized as important in Canadian food security policy, the category of marginal food security (MFS) is often ignored in US food security research.
METHODS: Prevalence of FI was estimated according to the conventional and an alternate classification of MFS with food insecurity among 938 youth and young adults (YYA) with youth-onset type 1 diabetes (T1D) and 156 with youth-onset of type 2 diabetes (T2D) from the SEARCH Food Security Cohort Study (2018-2021). Multivariable regression was used to estimate the association of MFS and conventionally defined food insecurity (FI) ascertained with diabetes-related outcomes, including acute diabetes complications, health care utilization, and diabetes self-management among YYA with T1D.
RESULTS: MFS affected 10% of participants with T1D diabetes and 20% of participants with T2D. Classifying MFS with FI increased FI prevalence from 18.0% to 27.8% in participants with T1D and 34.6% to 55.1% in participants with T2D. Compared to T1D with high food security, YYA with T1D who were FI had higher odds hypoglycemia (2.1, 95%CI 1.2-3.6) and ketoacidosis (1.6, 95%CI 1.0-2.6), but no association was seen in MFS. The FI group also had higher odds of emergency department use and hospitalization (2.3, 95%CI 1.5-3.4; 2.4, 95%CI 1.5-3.9) and lower odds of technology use and checking glucose (0.6, 95%CI 0.4-0.9; 0.3, 95%CI 0.1-0.6). The MFS group exhibited associations of similar directions.
DISCUSSION AND CONCLUSIONS: Health care providers should consider care of patients with T1D and MFS the same way they care for patients with FI.},
}
RevDate: 2024-10-18
Werner syndrome RECQ helicase participates in and directs maintenance of the protein complexes of constitutive heterochromatin in proliferating human cells.
Aging, null: pii:206132 [Epub ahead of print].
Werner syndrome of premature aging is caused by mutations in the WRN RECQ helicase/exonuclease, which functions in DNA replication, repair, transcription, and telomere maintenance. How the loss of WRN accelerates aging is not understood in full. Here we show that WRN is necessary for optimal constitutive heterochromatin levels in proliferating human fibroblasts. Locally, WRN deficiency derepresses SATII pericentromeric satellite repeats but does not reduce replication fork progression on SATII repeats. Globally, WRN loss reduces a subset of protein-protein interactions responsible for the organization of constitutive heterochromatin in the nucleus, namely, the interactions involving Lamin B1 and Lamin B receptor, LBR. Both the mRNA level and subcellular distribution of LBR are affected by WRN deficiency, and unlike the former, the latter phenotype does not require WRN catalytic activities. The phenotypes of heterochromatin disruption seen in WRN-deficient proliferating fibroblasts are also observed in WRN-proficient fibroblasts undergoing replicative or oncogene-induced senescence. WRN interacts with histone deacetylase 2, HDAC2; WRN/HDAC2 association is mediated by heterochromatin protein alpha, HP1α, and WRN complexes with HP1α and HDAC2 are downregulated in senescing cells. The data suggest that the effect of WRN loss on heterochromatin is separable from senescence program, but mimics at least some of the heterochromatin changes associated with it.
Additional Links: PMID-39422615
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@article {pmid39422615,
year = {2024},
author = {Lazarchuk, P and Nguyen, MM and Curca, CM and Pavlova, MN and Oshima, J and Sidorova, JM},
title = {Werner syndrome RECQ helicase participates in and directs maintenance of the protein complexes of constitutive heterochromatin in proliferating human cells.},
journal = {Aging},
volume = {null},
number = {},
pages = {},
doi = {10.18632/aging.206132},
pmid = {39422615},
issn = {1945-4589},
abstract = {Werner syndrome of premature aging is caused by mutations in the WRN RECQ helicase/exonuclease, which functions in DNA replication, repair, transcription, and telomere maintenance. How the loss of WRN accelerates aging is not understood in full. Here we show that WRN is necessary for optimal constitutive heterochromatin levels in proliferating human fibroblasts. Locally, WRN deficiency derepresses SATII pericentromeric satellite repeats but does not reduce replication fork progression on SATII repeats. Globally, WRN loss reduces a subset of protein-protein interactions responsible for the organization of constitutive heterochromatin in the nucleus, namely, the interactions involving Lamin B1 and Lamin B receptor, LBR. Both the mRNA level and subcellular distribution of LBR are affected by WRN deficiency, and unlike the former, the latter phenotype does not require WRN catalytic activities. The phenotypes of heterochromatin disruption seen in WRN-deficient proliferating fibroblasts are also observed in WRN-proficient fibroblasts undergoing replicative or oncogene-induced senescence. WRN interacts with histone deacetylase 2, HDAC2; WRN/HDAC2 association is mediated by heterochromatin protein alpha, HP1α, and WRN complexes with HP1α and HDAC2 are downregulated in senescing cells. The data suggest that the effect of WRN loss on heterochromatin is separable from senescence program, but mimics at least some of the heterochromatin changes associated with it.},
}
RevDate: 2024-10-18
Reverse Selection Designs for Accommodating Multiple Control Arms.
Clinical cancer research : an official journal of the American Association for Cancer Research pii:749184 [Epub ahead of print].
Evaluating a novel treatment in a randomized controlled trial requires comparison against existing therapies. If several existing therapies of similar benefit exist, the identification of a single control regimen may be difficult. For this situation, we propose a reverse selection design which, in its simplest form, includes a single experimental treatment arm and two control arms. Rather than carrying both control arms through the entire trial, the control arms are compared at an early interim analysis, ideally while accrual is ongoing. At this time, the worst-performing control arm is dropped and randomization continues to the remaining arms. At the end of the study, we compare the treatment to the remaining control arm. When no head-to-head comparison of the extant therapies is available or feasible, this design requires a smaller sample size than a traditional three-arm design or two sequential trials in which the extant therapies are compared and the better treatment is used in a subsequent trial as the control arm. This is because the final comparison is only between two arms and because the early interim analysis occurs prior to the end of accrual - yet with enough information such that any substantially better control arm will be selected. We evaluate the operating characteristics of a reverse selection design via simulation and show that it reduces the required sample size needed to compare the treatment against the best control, controls type I error, and likely selects the right control arm to use in the final analysis.
Additional Links: PMID-39422601
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PubMed:
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@article {pmid39422601,
year = {2024},
author = {Samorodnitsky, S and Othus, M and LeBlanc, M and Wu, MC},
title = {Reverse Selection Designs for Accommodating Multiple Control Arms.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-24-1282},
pmid = {39422601},
issn = {1557-3265},
abstract = {Evaluating a novel treatment in a randomized controlled trial requires comparison against existing therapies. If several existing therapies of similar benefit exist, the identification of a single control regimen may be difficult. For this situation, we propose a reverse selection design which, in its simplest form, includes a single experimental treatment arm and two control arms. Rather than carrying both control arms through the entire trial, the control arms are compared at an early interim analysis, ideally while accrual is ongoing. At this time, the worst-performing control arm is dropped and randomization continues to the remaining arms. At the end of the study, we compare the treatment to the remaining control arm. When no head-to-head comparison of the extant therapies is available or feasible, this design requires a smaller sample size than a traditional three-arm design or two sequential trials in which the extant therapies are compared and the better treatment is used in a subsequent trial as the control arm. This is because the final comparison is only between two arms and because the early interim analysis occurs prior to the end of accrual - yet with enough information such that any substantially better control arm will be selected. We evaluate the operating characteristics of a reverse selection design via simulation and show that it reduces the required sample size needed to compare the treatment against the best control, controls type I error, and likely selects the right control arm to use in the final analysis.},
}
RevDate: 2024-10-18
Healthcare Utilization in Pediatric Cancer Patients Near the End-of-Life.
The American journal of hospice & palliative care [Epub ahead of print].
Objective: Describe the healthcare utilization in the last 60 days of life in pediatric patients with cancer who died at home under hospice care and those that died in the hospital. Methods: Retrospective chart review of the medical records of those children with cancer diagnosis with palliative care consult and died either under hospice care at home or in the hospital. Results: Patients dying under hospice care spent a median of 44 days at home. Patients dying in the hospital spent a median of 30.5 days in the hospital, 10.5 days in the intensive care unit, and underwent 3.5 procedures requiring anesthesia. 45% of those that died in the hospital were compassionately extubated. Conclusion: For those dying with a cancer diagnosis, hospice care can allow for significant time at home with minimal healthcare while those dying in the hospital do spend a significant time in the hospital. This provides more information to both providers and families about end-of-life healthcare utilization.
Additional Links: PMID-39420548
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PubMed:
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@article {pmid39420548,
year = {2024},
author = {Kelly, JP and Runco, DV and Slaven, JE and Niehaus, JZ},
title = {Healthcare Utilization in Pediatric Cancer Patients Near the End-of-Life.},
journal = {The American journal of hospice & palliative care},
volume = {},
number = {},
pages = {10499091241294055},
doi = {10.1177/10499091241294055},
pmid = {39420548},
issn = {1938-2715},
abstract = {Objective: Describe the healthcare utilization in the last 60 days of life in pediatric patients with cancer who died at home under hospice care and those that died in the hospital. Methods: Retrospective chart review of the medical records of those children with cancer diagnosis with palliative care consult and died either under hospice care at home or in the hospital. Results: Patients dying under hospice care spent a median of 44 days at home. Patients dying in the hospital spent a median of 30.5 days in the hospital, 10.5 days in the intensive care unit, and underwent 3.5 procedures requiring anesthesia. 45% of those that died in the hospital were compassionately extubated. Conclusion: For those dying with a cancer diagnosis, hospice care can allow for significant time at home with minimal healthcare while those dying in the hospital do spend a significant time in the hospital. This provides more information to both providers and families about end-of-life healthcare utilization.},
}
RevDate: 2024-10-17
Incidence of bacterial blood stream infections in patients with acute GVHD.
Bone marrow transplantation [Epub ahead of print].
Bacterial bloodstream infections (BSI) can be a substantial contributor to complications of GVHD treatment. The aim of this study was to determine the risk for BSI from neutrophil engraftment through day 100 post transplant in patients with acute GVHD (AGVHD) based on organ involvement and severity. Patients (n = 4064) who underwent an allogeneic hematopoietic stem cell transplant (HCT) reported to the CIBMTR registry were analyzed. Grade II-IV AGVHD occurred in 1607 (39.5%) patients and was associated with a greater day-100 incidence of post engraftment BSI than with grade 0/I (24.9 vs. 15.3%). Patients with grade III/IV AGVHD had the highest BSI risk (HR 2.45; 95% CI 1.99-3.0; p < 0.0001). Lower GI involvement increased BSI risk (HR 1.54; 95% CI 1.17-2.02; p = 0.0019). BSI post-engraftment through day 100 was associated with worse survival (HR 1.64, 95% CI 1.43-1.87; p < 0.001) and higher non-relapse mortality (NRM), (HR 2.22; 95% CI 1.91-2.59; p < 0.001). Those with stage III/IV GI involvement are at highest risk for BSI. Future studies evaluating novel methods for preventing BSI in these high risk populations are needed to reduce mortality associated with AGVHD.
Additional Links: PMID-39420192
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@article {pmid39420192,
year = {2024},
author = {Wallis, W and Gulbis, AM and Wang, T and Lee, CJ and Sharma, A and Williams, KM and Nishihori, T and Prestidge, T and Gowda, L and Byrne, M and Krem, MM and MacMillan, ML and Kitko, CL and Pidala, J and Spellman, SR and Lee, SJ and Alousi, AM},
title = {Incidence of bacterial blood stream infections in patients with acute GVHD.},
journal = {Bone marrow transplantation},
volume = {},
number = {},
pages = {},
pmid = {39420192},
issn = {1476-5365},
abstract = {Bacterial bloodstream infections (BSI) can be a substantial contributor to complications of GVHD treatment. The aim of this study was to determine the risk for BSI from neutrophil engraftment through day 100 post transplant in patients with acute GVHD (AGVHD) based on organ involvement and severity. Patients (n = 4064) who underwent an allogeneic hematopoietic stem cell transplant (HCT) reported to the CIBMTR registry were analyzed. Grade II-IV AGVHD occurred in 1607 (39.5%) patients and was associated with a greater day-100 incidence of post engraftment BSI than with grade 0/I (24.9 vs. 15.3%). Patients with grade III/IV AGVHD had the highest BSI risk (HR 2.45; 95% CI 1.99-3.0; p < 0.0001). Lower GI involvement increased BSI risk (HR 1.54; 95% CI 1.17-2.02; p = 0.0019). BSI post-engraftment through day 100 was associated with worse survival (HR 1.64, 95% CI 1.43-1.87; p < 0.001) and higher non-relapse mortality (NRM), (HR 2.22; 95% CI 1.91-2.59; p < 0.001). Those with stage III/IV GI involvement are at highest risk for BSI. Future studies evaluating novel methods for preventing BSI in these high risk populations are needed to reduce mortality associated with AGVHD.},
}
RevDate: 2024-10-17
Anything you can do, glycans do better: deglycosylation and noncanonical ubiquitination vie to rule the proteasome.
Trends in biochemical sciences pii:S0968-0004(24)00226-3 [Epub ahead of print].
The Nrf1/Nfe2L1 transcription factor is a master regulator of proteasome biogenesis. New work by Yoshida and colleagues reveals a surprising mechanism by which ubiquitination of N-glycosylated Nrf1 controls its function.
Additional Links: PMID-39419747
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@article {pmid39419747,
year = {2024},
author = {Lehrbach, N},
title = {Anything you can do, glycans do better: deglycosylation and noncanonical ubiquitination vie to rule the proteasome.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2024.10.001},
pmid = {39419747},
issn = {0968-0004},
abstract = {The Nrf1/Nfe2L1 transcription factor is a master regulator of proteasome biogenesis. New work by Yoshida and colleagues reveals a surprising mechanism by which ubiquitination of N-glycosylated Nrf1 controls its function.},
}
RevDate: 2024-10-17
Lower-intensity CPX-351 plus venetoclax induction for adults with newly diagnosed AML unfit for intensive chemotherapy.
Blood advances pii:518219 [Epub ahead of print].
Preclinical data suggest a rationale for combining CPX-351, a dual-drug liposomal encapsulation of daunorubicin and cytarabine, with venetoclax, a B-cell lymphoma-2 (BCL-2) inhibitor. This phase 1b study evaluated lower-intensity CPX-351 combined with venetoclax in adults with acute myeloid leukemia (AML) considered unfit/ineligible for intensive chemotherapy. In a dose-exploration phase using a 3+3 design, patients received stepwise dosing of CPX‑351 intravenously on days 1 and 3 plus venetoclax 400 mg orally on days 2-21 per cycle to determine the recommended phase 2 dose (RP2D) for this combination. During the expansion phase, additional patients received CPX-351 plus venetoclax at the identified RP2D. The primary endpoints were the RP2D and safety of CPX‑351 combined with venetoclax. Secondary endpoints included preliminary efficacy and pharmacokinetics. Overall, 35 patients were enrolled in the study. A RP2D of CPX-351 30 units/m2 (daunorubicin 13.2 mg/m2 and cytarabine 30 mg/m2) plus venetoclax 400 mg was established. The safety profile of the combination was consistent with the known safety profiles of CPX-351 and venetoclax. Complete remission (CR)/CR with incomplete hematologic recovery (CRi) was achieved by 17/35 (49%) patients, all after cycle 1; of these, 14 were negative for measurable residual disease. CR was achieved by 1/8 (13%) patients with a mutation in TP53, and CR/CRi was achieved by 15/26 (58%) patients with wild-type TP53. This study highlights that lower-intensity therapy of CPX-351 plus venetoclax as induction therapy provides a well-tolerated treatment option in adults with AML deemed unfit for intensive chemotherapy. This trial was registered at www.clinicaltrials.gov as #NCT04038437.
Additional Links: PMID-39418644
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@article {pmid39418644,
year = {2024},
author = {Uy, GL and Pullarkat, VA and Baratam, P and Stuart, RK and Walter, RB and Winer, ES and Wang, Q and Faderl, S and Chakravarthy, D and Menno, D and Cheung, RS and Lin, TL},
title = {Lower-intensity CPX-351 plus venetoclax induction for adults with newly diagnosed AML unfit for intensive chemotherapy.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2024013687},
pmid = {39418644},
issn = {2473-9537},
abstract = {Preclinical data suggest a rationale for combining CPX-351, a dual-drug liposomal encapsulation of daunorubicin and cytarabine, with venetoclax, a B-cell lymphoma-2 (BCL-2) inhibitor. This phase 1b study evaluated lower-intensity CPX-351 combined with venetoclax in adults with acute myeloid leukemia (AML) considered unfit/ineligible for intensive chemotherapy. In a dose-exploration phase using a 3+3 design, patients received stepwise dosing of CPX‑351 intravenously on days 1 and 3 plus venetoclax 400 mg orally on days 2-21 per cycle to determine the recommended phase 2 dose (RP2D) for this combination. During the expansion phase, additional patients received CPX-351 plus venetoclax at the identified RP2D. The primary endpoints were the RP2D and safety of CPX‑351 combined with venetoclax. Secondary endpoints included preliminary efficacy and pharmacokinetics. Overall, 35 patients were enrolled in the study. A RP2D of CPX-351 30 units/m2 (daunorubicin 13.2 mg/m2 and cytarabine 30 mg/m2) plus venetoclax 400 mg was established. The safety profile of the combination was consistent with the known safety profiles of CPX-351 and venetoclax. Complete remission (CR)/CR with incomplete hematologic recovery (CRi) was achieved by 17/35 (49%) patients, all after cycle 1; of these, 14 were negative for measurable residual disease. CR was achieved by 1/8 (13%) patients with a mutation in TP53, and CR/CRi was achieved by 15/26 (58%) patients with wild-type TP53. This study highlights that lower-intensity therapy of CPX-351 plus venetoclax as induction therapy provides a well-tolerated treatment option in adults with AML deemed unfit for intensive chemotherapy. This trial was registered at www.clinicaltrials.gov as #NCT04038437.},
}
RevDate: 2024-10-17
SWOG/NCI Phase II Dual Anti-CTLA-4/PD-1 Blockade in Rare Tumors (DART): Non-Epithelial Ovarian Cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research pii:749166 [Epub ahead of print].
BACKGROUND: The role of dual checkpoint inhibition in advanced rare/ultra-rare non-epithelial ovarian cancers (NEOCs) is yet to be explored.
METHODS: DART is a prospective, multicenter (1,016 US sites), multi-cohort, single-arm phase II trial conducted through the Early Therapeutics and Rare Cancer SWOG/NCI Committee, assessing ipilimumab (anti-CTLA-4) (1mg/kg every 6 weeks) and nivolumab (anti-PD-1) (240mg every 2 weeks) in adults with advanced NEOCs who lack beneficial standard therapy. Primary outcome was overall response rate [ORR; complete response (CR)/partial response (PR)]; secondary outcomes were progression-free survival (PFS), overall survival (OS), clinical benefit rate [CBR; stable disease (SD) ≥6 months plus ORR], and toxicity.
RESULTS: Seventeen patients (median age: 64; number of prior therapies ranged from 0-8 with no immunotherapy exposure; 8 granulosa, 6 carcinosarcomas, 1 Sertoli-Leydig, 1 yolk sac, 1 Wolffian) were evaluated. In granulosa cell tumors, ORR was 25% (n=2/8; 1 CR, 1 PR) and CBR, 50% (n=4/8); PFS of 58.3 (CR), 50.7+ (PR), 30.4 (SD), and 8.7 (SD) months. Median PFS was 3.5 months (95% confidence intervals (CI) 1.7-11.2 months); median OS, 42.5 months (95% CI 10.1 months-not reached). One Sertoli-Leydig cell tumor showed a 22% regression (PFS 11.2 months). Carcinosarcomas had no response. Three participants (18%) discontinued treatment due to grade 3-4 adverse events.
CONCLUSIONS: Ipilimumab-nivolumab shows activity in treatment-refractory granulosa cell tumors, with 25% (n=2/8) of patients experiencing either CR or PR lasting over 4 years..
Additional Links: PMID-39417692
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PubMed:
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@article {pmid39417692,
year = {2024},
author = {Chae, YK and Othus, M and Patel, SP and Wilkinson, KJ and Whitman-Purves, EM and Lea, J and Schallenkamp, JM and Adra, N and Appleman, LJ and Alden, M and Thomes Pepin, J and Ellerton, JA and Poklepovic, A and Walter, A and Rampurwala, MM and Robinson, WR and Kim, HS and Chung, LI and McLeod, CM and Lopez, G and Chen, HX and Sharon, E and Streicher, H and Ryan, CW and Blanke, CD and Kurzrock, R},
title = {SWOG/NCI Phase II Dual Anti-CTLA-4/PD-1 Blockade in Rare Tumors (DART): Non-Epithelial Ovarian Cancer.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-24-0606},
pmid = {39417692},
issn = {1557-3265},
abstract = {BACKGROUND: The role of dual checkpoint inhibition in advanced rare/ultra-rare non-epithelial ovarian cancers (NEOCs) is yet to be explored.
METHODS: DART is a prospective, multicenter (1,016 US sites), multi-cohort, single-arm phase II trial conducted through the Early Therapeutics and Rare Cancer SWOG/NCI Committee, assessing ipilimumab (anti-CTLA-4) (1mg/kg every 6 weeks) and nivolumab (anti-PD-1) (240mg every 2 weeks) in adults with advanced NEOCs who lack beneficial standard therapy. Primary outcome was overall response rate [ORR; complete response (CR)/partial response (PR)]; secondary outcomes were progression-free survival (PFS), overall survival (OS), clinical benefit rate [CBR; stable disease (SD) ≥6 months plus ORR], and toxicity.
RESULTS: Seventeen patients (median age: 64; number of prior therapies ranged from 0-8 with no immunotherapy exposure; 8 granulosa, 6 carcinosarcomas, 1 Sertoli-Leydig, 1 yolk sac, 1 Wolffian) were evaluated. In granulosa cell tumors, ORR was 25% (n=2/8; 1 CR, 1 PR) and CBR, 50% (n=4/8); PFS of 58.3 (CR), 50.7+ (PR), 30.4 (SD), and 8.7 (SD) months. Median PFS was 3.5 months (95% confidence intervals (CI) 1.7-11.2 months); median OS, 42.5 months (95% CI 10.1 months-not reached). One Sertoli-Leydig cell tumor showed a 22% regression (PFS 11.2 months). Carcinosarcomas had no response. Three participants (18%) discontinued treatment due to grade 3-4 adverse events.
CONCLUSIONS: Ipilimumab-nivolumab shows activity in treatment-refractory granulosa cell tumors, with 25% (n=2/8) of patients experiencing either CR or PR lasting over 4 years..},
}
RevDate: 2024-10-17
Molecular profiling of invertebrate glia.
Glia [Epub ahead of print].
Caenorhabditis elegans and Drosophila melanogaster are powerful experimental models for uncovering fundamental tenets of nervous system organization and function. Findings over the last two decades show that molecular and cellular features are broadly conserved between invertebrates and vertebrates, indicating that insights derived from invertebrate models can broadly inform our understanding of glial operating principles across diverse species. In recent years, these model systems have led to exciting discoveries in glial biology and mechanisms of glia-neuron interactions. Here, we summarize studies that have applied current state-of-the-art "-omics" techniques to C. elegans and D. melanogaster glia. Coupled with the remarkable acceleration in the pace of mechanistic studies of glia biology in recent years, these indicate that invertebrate glia also exhibit striking molecular complexity, specificity, and heterogeneity. We provide an overview of these studies and discuss their implications as well as emerging questions where C. elegans and D. melanogaster are well-poised to fill critical knowledge gaps in our understanding of glial biology.
Additional Links: PMID-39415317
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PubMed:
Citation:
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@article {pmid39415317,
year = {2024},
author = {Purice, MD and Lago-Baldaia, I and Fernandes, VM and Singhvi, A},
title = {Molecular profiling of invertebrate glia.},
journal = {Glia},
volume = {},
number = {},
pages = {},
doi = {10.1002/glia.24623},
pmid = {39415317},
issn = {1098-1136},
support = {5T32CA080416-25/NH/NIH HHS/United States ; NS114222/NH/NIH HHS/United States ; 227823//Esther A. and Joseph Klingenstein Fund/ ; BRFSG-2023-10//Brain Research Foundation/ ; 225986/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; //Washington Research Foundation/ ; },
abstract = {Caenorhabditis elegans and Drosophila melanogaster are powerful experimental models for uncovering fundamental tenets of nervous system organization and function. Findings over the last two decades show that molecular and cellular features are broadly conserved between invertebrates and vertebrates, indicating that insights derived from invertebrate models can broadly inform our understanding of glial operating principles across diverse species. In recent years, these model systems have led to exciting discoveries in glial biology and mechanisms of glia-neuron interactions. Here, we summarize studies that have applied current state-of-the-art "-omics" techniques to C. elegans and D. melanogaster glia. Coupled with the remarkable acceleration in the pace of mechanistic studies of glia biology in recent years, these indicate that invertebrate glia also exhibit striking molecular complexity, specificity, and heterogeneity. We provide an overview of these studies and discuss their implications as well as emerging questions where C. elegans and D. melanogaster are well-poised to fill critical knowledge gaps in our understanding of glial biology.},
}
RevDate: 2024-10-16
CmpDate: 2024-10-16
snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.
Communications biology, 7(1):1340.
Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3' and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.
Additional Links: PMID-39414943
PubMed:
Citation:
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@article {pmid39414943,
year = {2024},
author = {Wang, T and Roach, MJ and Harvey, K and Morlanes, JE and Kiedik, B and Al-Eryani, G and Greenwald, A and Kalavros, N and Dezem, FS and Ma, Y and Pita-Juarez, YH and Wise, K and Degletagne, C and Elz, A and Hadadianpour, A and Johanneson, J and Pakiam, F and Ryu, H and Newell, EW and Tonon, L and Kohlway, A and Drennon, T and Abousoud, J and Stott, R and Lund, P and Durruthy, J and Vallejo, AF and Li, W and Salomon, R and Kaczorowski, D and Warren, J and Butler, LM and O'Toole, S and Plummer, J and Vlachos, IS and Lundeberg, J and Swarbrick, A and Martelotto, LG},
title = {snPATHO-seq, a versatile FFPE single-nucleus RNA sequencing method to unlock pathology archives.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1340},
pmid = {39414943},
issn = {2399-3642},
support = {APP2004774//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {*Paraffin Embedding/methods ; Humans ; *Sequence Analysis, RNA/methods ; *Tissue Fixation/methods ; *Single-Cell Analysis/methods ; Formaldehyde/chemistry ; Transcriptome ; Gene Expression Profiling/methods ; Workflow ; },
abstract = {Formalin-fixed paraffin-embedded (FFPE) samples are valuable but underutilized in single-cell omics research due to their low RNA quality. In this study, leveraging a recent advance in single-cell genomic technology, we introduce snPATHO-seq, a versatile method to derive high-quality single-nucleus transcriptomic data from FFPE samples. We benchmarked the performance of the snPATHO-seq workflow against existing 10x 3' and Flex assays designed for frozen or fresh samples and highlighted the consistency in snRNA-seq data produced by all workflows. The snPATHO-seq workflow also demonstrated high robustness when tested across a wide range of healthy and diseased FFPE tissue samples. When combined with FFPE spatial transcriptomic technologies such as FFPE Visium, the snPATHO-seq provides a multi-modal sampling approach for FFPE samples, allowing more comprehensive transcriptomic characterization.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Paraffin Embedding/methods
Humans
*Sequence Analysis, RNA/methods
*Tissue Fixation/methods
*Single-Cell Analysis/methods
Formaldehyde/chemistry
Transcriptome
Gene Expression Profiling/methods
Workflow
RevDate: 2024-10-16
CmpDate: 2024-10-16
Immune effector cell-associated enterocolitis following chimeric antigen receptor T-cell therapy in multiple myeloma.
Blood cancer journal, 14(1):180.
We report 14 cases of immune effector cell (IEC)-associated enterocolitis following chimeric antigen receptor T-cell (CAR-T) therapy in multiple myeloma, with a 1.2% incidence overall (0.2% for idecabtagene vicleucel and 2.2% for ciltacabtagene autoleucel). Patients developed acute-onset symptoms (typically non-bloody Grade 3+ diarrhea) with negative infectious workup beginning a median of 92.5 days (range: 22-210 days) after CAR-T therapy and a median of 85 days after cytokine release syndrome resolution. Gut biopsies uniformly demonstrated inflammation, including intra-epithelial lymphocytosis and villous blunting. In one case where CAR-specific immunofluorescence stains were available, CAR T-cell presence was confirmed within the lamina propria. Systemic corticosteroids were initiated in 10 patients (71%) a median of 25.5 days following symptom onset, with symptom improvement in 40%. Subsequent infliximab or vedolizumab led to improvement in 50% and 33% of corticosteroid-refractory patients, respectively. Five patients (36%) have died from bowel perforation or treatment-emergent sepsis. In conclusion, IEC-associated enterocolitis is a distinct but rare complication of CAR-T therapy typically beginning 1-3 months after infusion. Thorough diagnostic workup is essential, including evaluation for potential T-cell malignancies. The early use of infliximab or vedolizumab may potentially hasten symptom resolution and lower reliance on high-dose corticosteroids during the post-CAR-T period.
Additional Links: PMID-39414769
PubMed:
Citation:
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@article {pmid39414769,
year = {2024},
author = {Fortuna, GG and Banerjee, R and Savid-Frontera, C and Song, J and Morán-Segura, CM and Nguyen, JV and Lekakis, L and Fernandez-Pol, S and Samraj, AN and Naresh, KN and Vazquez-Martinez, M and Baz, RC and Spiegel, JY and Mikkilineni, L and Gubatan, JM and Sidana, S and de Menezes Silva Corraes, A and Kalariya, NM and Patel, KK and Shim, KG and Fonseca, R and Ferreri, C and Voorhees, PM and Richard, S and Valdes, CR and Sireesha Asoori, and Wolf, JL and Cowan, AJ and Sborov, DW and Locke, FL and Lin, Y and Wang, Y and Hansen, DK},
title = {Immune effector cell-associated enterocolitis following chimeric antigen receptor T-cell therapy in multiple myeloma.},
journal = {Blood cancer journal},
volume = {14},
number = {1},
pages = {180},
pmid = {39414769},
issn = {2044-5385},
mesh = {Humans ; *Multiple Myeloma/therapy/immunology/drug therapy ; *Enterocolitis/etiology/therapy/immunology ; Male ; Middle Aged ; Female ; Aged ; *Immunotherapy, Adoptive/adverse effects ; Adult ; Receptors, Chimeric Antigen/therapeutic use/immunology ; },
abstract = {We report 14 cases of immune effector cell (IEC)-associated enterocolitis following chimeric antigen receptor T-cell (CAR-T) therapy in multiple myeloma, with a 1.2% incidence overall (0.2% for idecabtagene vicleucel and 2.2% for ciltacabtagene autoleucel). Patients developed acute-onset symptoms (typically non-bloody Grade 3+ diarrhea) with negative infectious workup beginning a median of 92.5 days (range: 22-210 days) after CAR-T therapy and a median of 85 days after cytokine release syndrome resolution. Gut biopsies uniformly demonstrated inflammation, including intra-epithelial lymphocytosis and villous blunting. In one case where CAR-specific immunofluorescence stains were available, CAR T-cell presence was confirmed within the lamina propria. Systemic corticosteroids were initiated in 10 patients (71%) a median of 25.5 days following symptom onset, with symptom improvement in 40%. Subsequent infliximab or vedolizumab led to improvement in 50% and 33% of corticosteroid-refractory patients, respectively. Five patients (36%) have died from bowel perforation or treatment-emergent sepsis. In conclusion, IEC-associated enterocolitis is a distinct but rare complication of CAR-T therapy typically beginning 1-3 months after infusion. Thorough diagnostic workup is essential, including evaluation for potential T-cell malignancies. The early use of infliximab or vedolizumab may potentially hasten symptom resolution and lower reliance on high-dose corticosteroids during the post-CAR-T period.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Multiple Myeloma/therapy/immunology/drug therapy
*Enterocolitis/etiology/therapy/immunology
Male
Middle Aged
Female
Aged
*Immunotherapy, Adoptive/adverse effects
Adult
Receptors, Chimeric Antigen/therapeutic use/immunology
RevDate: 2024-10-16
Isotope Dilution Space Ratio Declines Above the Age of 60 Years, Potentially Impacting Estimates of Total Energy Expenditure by the Doubly Labeled Water Method[1-3,] *[, ˆ].
The Journal of nutrition pii:S0022-3166(24)01093-9 [Epub ahead of print].
Doubly labeled water is gold standard for measuring total energy expenditure (TEE). Measurements using the method are sensitive to the isotope dilution space ratio (DSR). Accuracy and precision of the method might be improved if we could identify factors influencing DSR. We evaluated the potential associations of age, sex, ethnicity, anthropometry, body composition, turnover rates of the isotopes, and geographical elevation with DSR. We used univariate regression analysis to explore the relationships between the continuous variables and analysis of variance to test the relationships between the categorical variables with DSR. Subsequently, we used General Linear Modeling (GLM) and One-way ANOVA to evaluate the simultaneous associations of age, sex, ethnicity, fat-free mass (FFM) and fat mass (FM) on DSR. From 5,678 measurements complied from studies around the world with diverse ethnicity and living at various elevations, the average DSR was 1.0364 ± 0.0141 (mean ± SD). No meaningful physiological effect of any of the continuous and categorical variable on DSR was detected. GLM analysis revealed no effect of FFM and FM (P > 0.33) on DSR, but DSR decreased with age (P < 0.001) among those 60 years of age and older regardless of sex. Among the White who were younger than 60 years of age, DSR was not related to FFM and FM (P = 0.73) but was affected by both age and sex (P < 0.001). Previous estimates of age-related decline in TEE may have overestimated TEE at age 90. Validation studies on older participants are required to confirm this finding.
Additional Links: PMID-39414027
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PubMed:
Citation:
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@article {pmid39414027,
year = {2024},
author = {Wong, WW and Speakman, JR and Ainslie, PN and Anderson, LJ and Arab, L and Baddou, I and Bedu-Addo, K and Blaak, EE and Blanc, S and Bonomi, AG and Bouten, CVC and Bovet, P and Buchowski, MS and Butte, NF and Camps, SG and Casper, R and Close, GL and Colbert, LH and Cooper, JA and Das, SK and Davies, PSW and Eaton, S and Ekelund, U and Hambly, C and El Hamdouchi, A and Entringer, S and Fudge, BW and Gillingham, M and Goris, AH and Gurven, M and Hoos, MB and Hu, S and Joosen, A and Katzmarzyk, PT and Kempen, KP and Kimura, M and Kraus, WE and Kushner, RF and Larsson, CL and Morehen, JC and Morton, JP and Neuhouser, ML and Nicklas, TA and Ojiambo, RM and Pietilainen, KH and Pitsiladis, YP and Plasqui, G and Prentice, RL and Rabinovich, R and Racette, SB and Raichen, DA and Redman, L and Ravussin, E and Reilly, JJ and Roberts, S and Scuitt, AJ and Sjödin, AM and Stice, E and Urlacher, SS and Valenti, G and van Etten, LM and Van Mil, EA and Verbunt, JA and Wells, JCK and Wilson, G and Yoshida, T and Zhang, X and Loechl, CU and Luke, A and Murphy-Alford, AJ and Pontzer, H and Sagayama, H and Rood, JC and Schoeller, DA and Westerterp, KR and Yamada, Y and , },
title = {Isotope Dilution Space Ratio Declines Above the Age of 60 Years, Potentially Impacting Estimates of Total Energy Expenditure by the Doubly Labeled Water Method[1-3,] *[, ˆ].},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.10.016},
pmid = {39414027},
issn = {1541-6100},
abstract = {Doubly labeled water is gold standard for measuring total energy expenditure (TEE). Measurements using the method are sensitive to the isotope dilution space ratio (DSR). Accuracy and precision of the method might be improved if we could identify factors influencing DSR. We evaluated the potential associations of age, sex, ethnicity, anthropometry, body composition, turnover rates of the isotopes, and geographical elevation with DSR. We used univariate regression analysis to explore the relationships between the continuous variables and analysis of variance to test the relationships between the categorical variables with DSR. Subsequently, we used General Linear Modeling (GLM) and One-way ANOVA to evaluate the simultaneous associations of age, sex, ethnicity, fat-free mass (FFM) and fat mass (FM) on DSR. From 5,678 measurements complied from studies around the world with diverse ethnicity and living at various elevations, the average DSR was 1.0364 ± 0.0141 (mean ± SD). No meaningful physiological effect of any of the continuous and categorical variable on DSR was detected. GLM analysis revealed no effect of FFM and FM (P > 0.33) on DSR, but DSR decreased with age (P < 0.001) among those 60 years of age and older regardless of sex. Among the White who were younger than 60 years of age, DSR was not related to FFM and FM (P = 0.73) but was affected by both age and sex (P < 0.001). Previous estimates of age-related decline in TEE may have overestimated TEE at age 90. Validation studies on older participants are required to confirm this finding.},
}
RevDate: 2024-10-16
CmpDate: 2024-10-16
Nivolumab+AVD in Advanced-Stage Classic Hodgkin's Lymphoma.
The New England journal of medicine, 391(15):1379-1389.
BACKGROUND: Incorporating brentuximab vedotin into the treatment of advanced-stage classic Hodgkin's lymphoma improves outcomes in adult and pediatric patients. However, brentuximab vedotin increases the toxic effects of treatment in adults, more than half of pediatric patients who receive the drug undergo consolidative radiation, and relapse remains a challenge. Programmed death 1 blockade is effective in Hodgkin's lymphoma, including in preliminary studies involving previously untreated patients.
METHODS: We conducted a phase 3, multicenter, open-label, randomized trial involving patients at least 12 years of age with stage III or IV newly diagnosed Hodgkin's lymphoma. Patients were randomly assigned to receive brentuximab vedotin with doxorubicin, vinblastine, and dacarbazine (BV+AVD) or nivolumab with doxorubicin, vinblastine, and dacarbazine (N+AVD). Prespecified patients could receive radiation therapy directed to residual metabolically active lesions. The primary end point was progression-free survival, defined as the time from randomization to the first observation of progressive disease or death from any cause.
RESULTS: Of 994 patients who underwent randomization, 970 were included in the intention-to-treat population for efficacy analyses. At the second planned interim analysis, with a median follow-up of 12.1 months, the threshold for efficacy was crossed, indicating that N+AVD significantly improved progression-free survival as compared with BV+AVD (hazard ratio for disease progression or death, 0.48; 99% confidence interval [CI], 0.27 to 0.87; two-sided P = 0.001). Owing to the short follow-up time, we repeated the analysis with longer follow-up; with a median follow-up of 2.1 years (range, 0 to 4.2 years), the 2-year progression-free survival was 92% (95% CI, 89 to 94) with N+AVD, as compared with 83% (95% CI, 79 to 86) with BV+AVD (hazard ratio for disease progression or death, 0.45; 95% CI, 0.30 to 0.65). Overall, 7 patients received radiation therapy. Immune-related adverse events were infrequent with nivolumab; brentuximab vedotin was associated with more treatment discontinuation.
CONCLUSIONS: N+AVD resulted in longer progression-free survival than BV+AVD in adolescents and adults with stage III or IV advanced-stage classic Hodgkin's lymphoma and had a better side-effect profile. (Funded by the National Cancer Institute of the National Institutes of Health and others; S1826 ClinicalTrials.gov number, NCT03907488.).
Additional Links: PMID-39413375
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PubMed:
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@article {pmid39413375,
year = {2024},
author = {Herrera, AF and LeBlanc, M and Castellino, SM and Li, H and Rutherford, SC and Evens, AM and Davison, K and Punnett, A and Parsons, SK and Ahmed, S and Casulo, C and Bartlett, NL and Tuscano, JM and Mei, MG and Hess, BT and Jacobs, R and Saeed, H and Torka, P and Hu, B and Moskowitz, C and Kaur, S and Goyal, G and Forlenza, C and Doan, A and Lamble, A and Kumar, P and Chowdhury, S and Brinker, B and Sharma, N and Singh, A and Blum, KA and Perry, AM and Kovach, A and Hodgson, D and Constine, LS and Shields, LK and Prica, A and Dillon, H and Little, RF and Shipp, MA and Crump, M and Kahl, B and Leonard, JP and Smith, SM and Song, JY and Kelly, KM and Friedberg, JW},
title = {Nivolumab+AVD in Advanced-Stage Classic Hodgkin's Lymphoma.},
journal = {The New England journal of medicine},
volume = {391},
number = {15},
pages = {1379-1389},
doi = {10.1056/NEJMoa2405888},
pmid = {39413375},
issn = {1533-4406},
support = {U10CA180819/NH/NIH HHS/United States ; U10CA180820/NH/NIH HHS/United States ; U10CA180821/NH/NIH HHS/United States ; U10CA180863/NH/NIH HHS/United States ; U10CA180888/NH/NIH HHS/United States ; UG1CA189955/NH/NIH HHS/United States ; },
mesh = {Humans ; *Hodgkin Disease/drug therapy/mortality/radiotherapy/pathology ; *Nivolumab/therapeutic use/adverse effects ; Male ; Female ; Adult ; *Vinblastine/therapeutic use/adverse effects ; *Brentuximab Vedotin/therapeutic use/adverse effects ; *Dacarbazine/therapeutic use/adverse effects ; Adolescent ; *Progression-Free Survival ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects ; Middle Aged ; Young Adult ; *Doxorubicin/therapeutic use/adverse effects ; Aged ; Neoplasm Staging ; Intention to Treat Analysis ; Kaplan-Meier Estimate ; Child ; },
abstract = {BACKGROUND: Incorporating brentuximab vedotin into the treatment of advanced-stage classic Hodgkin's lymphoma improves outcomes in adult and pediatric patients. However, brentuximab vedotin increases the toxic effects of treatment in adults, more than half of pediatric patients who receive the drug undergo consolidative radiation, and relapse remains a challenge. Programmed death 1 blockade is effective in Hodgkin's lymphoma, including in preliminary studies involving previously untreated patients.
METHODS: We conducted a phase 3, multicenter, open-label, randomized trial involving patients at least 12 years of age with stage III or IV newly diagnosed Hodgkin's lymphoma. Patients were randomly assigned to receive brentuximab vedotin with doxorubicin, vinblastine, and dacarbazine (BV+AVD) or nivolumab with doxorubicin, vinblastine, and dacarbazine (N+AVD). Prespecified patients could receive radiation therapy directed to residual metabolically active lesions. The primary end point was progression-free survival, defined as the time from randomization to the first observation of progressive disease or death from any cause.
RESULTS: Of 994 patients who underwent randomization, 970 were included in the intention-to-treat population for efficacy analyses. At the second planned interim analysis, with a median follow-up of 12.1 months, the threshold for efficacy was crossed, indicating that N+AVD significantly improved progression-free survival as compared with BV+AVD (hazard ratio for disease progression or death, 0.48; 99% confidence interval [CI], 0.27 to 0.87; two-sided P = 0.001). Owing to the short follow-up time, we repeated the analysis with longer follow-up; with a median follow-up of 2.1 years (range, 0 to 4.2 years), the 2-year progression-free survival was 92% (95% CI, 89 to 94) with N+AVD, as compared with 83% (95% CI, 79 to 86) with BV+AVD (hazard ratio for disease progression or death, 0.45; 95% CI, 0.30 to 0.65). Overall, 7 patients received radiation therapy. Immune-related adverse events were infrequent with nivolumab; brentuximab vedotin was associated with more treatment discontinuation.
CONCLUSIONS: N+AVD resulted in longer progression-free survival than BV+AVD in adolescents and adults with stage III or IV advanced-stage classic Hodgkin's lymphoma and had a better side-effect profile. (Funded by the National Cancer Institute of the National Institutes of Health and others; S1826 ClinicalTrials.gov number, NCT03907488.).},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Hodgkin Disease/drug therapy/mortality/radiotherapy/pathology
*Nivolumab/therapeutic use/adverse effects
Male
Female
Adult
*Vinblastine/therapeutic use/adverse effects
*Brentuximab Vedotin/therapeutic use/adverse effects
*Dacarbazine/therapeutic use/adverse effects
Adolescent
*Progression-Free Survival
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/adverse effects
Middle Aged
Young Adult
*Doxorubicin/therapeutic use/adverse effects
Aged
Neoplasm Staging
Intention to Treat Analysis
Kaplan-Meier Estimate
Child
RevDate: 2024-10-16
CmpDate: 2024-10-16
WhatsApp Versus SMS for 2-Way, Text-Based Follow-Up After Voluntary Medical Male Circumcision in South Africa: Exploration of Messaging Platform Choice.
JMIR formative research, 8:e62762 pii:v8i1e62762.
BACKGROUND: Telehealth is growing, especially in areas where access to health facilities is difficult. We previously used 2-way texting (2wT) via SMS to improve the quality of postoperative care after voluntary medical male circumcision in South Africa. In this study, we offered males aged 15 years and older WhatsApp or SMS as their message delivery and interaction platform to explore user preferences and behaviors.
OBJECTIVE: The objectives of this process evaluation embedded within a larger 2wT expansion trial were to (1) explore 2wT client preferences, including client satisfaction, with WhatsApp or SMS; (2) examine response rates (participation) by SMS and WhatsApp; and (3) gather feedback from the 2wT implementation team on the WhatsApp approach.
METHODS: Males aged 15 years and older undergoing voluntary medical male circumcision in program sites could choose their follow-up approach, selecting 2wT via SMS or WhatsApp or routine care (in-person postoperative visits). The 2wT system provided 1-way educational messages and an open 2-way communication channel between providers and clients. We analyzed quantitative data from the 2wT database on message delivery platforms (WhatsApp vs SMS), response rates, and user behaviors using chi-square tests, z tests, and t tests. The team conducted short phone calls with WhatsApp and SMS clients about their perceptions of this 2wT platform using a short, structured interview guide. We consider informal reflections from the technical team members on the use of WhatsApp. We applied an implementation science lens using the RE-AIM (reach, effectiveness, adoption, implementation, and maintenance) framework to focus results on practice and policy improvement.
RESULTS: Over a 2-month period-from August to October, 2023-337 males enrolled in 2wT and were offered WhatsApp or SMS and were included in the analysis. For 2wT reach, 177 (53%) participants chose WhatsApp as their platform (P=.38). Mean client age was 30 years, and 253 (75%) participants chose English for automated messages. From quality assurance calls, almost all respondents (87/89, 98%) were happy with the way they were followed up. For effectiveness, on average for the days on which responses were requested, 58 (33%) WhatsApp clients and 44 (28%) SMS clients responded (P=.50). All 2wT team members believed WhatsApp limited the automated message content, language choices, and inclusivity as compared with the SMS-based 2wT approach.
CONCLUSIONS: When presented with a choice of 2wT communication platform, clients appear evenly split between SMS and WhatsApp. However, WhatsApp requires a smartphone and data plan, potentially reducing reach at scale. Clients using both platforms responded to 2wT interactive prompts, demonstrating similar effectiveness in engaging clients in follow-up. For telehealth interventions, digital health designers should maintain an SMS-based platform and carefully consider adding WhatsApp as an option for clients, using an implementation science approach to present evidence that guides the best implementation approach for their setting.
Additional Links: PMID-39412842
Publisher:
PubMed:
Citation:
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@article {pmid39412842,
year = {2024},
author = {Fabens, I and Makhele, C and Igaba, NK and Hlongwane, S and Phohole, M and Waweru, E and Oni, F and Khwepeya, M and Sardini, M and Moyo, K and Tweya, H and Wafula, MB and Pienaar, J and Ndebele, F and Setswe, G and Dong, TQ and Feldacker, C},
title = {WhatsApp Versus SMS for 2-Way, Text-Based Follow-Up After Voluntary Medical Male Circumcision in South Africa: Exploration of Messaging Platform Choice.},
journal = {JMIR formative research},
volume = {8},
number = {},
pages = {e62762},
doi = {10.2196/62762},
pmid = {39412842},
issn = {2561-326X},
mesh = {Humans ; Male ; *Circumcision, Male/psychology ; *Text Messaging ; South Africa ; Adult ; Adolescent ; *Mobile Applications ; Telemedicine ; Young Adult ; Patient Satisfaction ; Middle Aged ; Aftercare/methods ; },
abstract = {BACKGROUND: Telehealth is growing, especially in areas where access to health facilities is difficult. We previously used 2-way texting (2wT) via SMS to improve the quality of postoperative care after voluntary medical male circumcision in South Africa. In this study, we offered males aged 15 years and older WhatsApp or SMS as their message delivery and interaction platform to explore user preferences and behaviors.
OBJECTIVE: The objectives of this process evaluation embedded within a larger 2wT expansion trial were to (1) explore 2wT client preferences, including client satisfaction, with WhatsApp or SMS; (2) examine response rates (participation) by SMS and WhatsApp; and (3) gather feedback from the 2wT implementation team on the WhatsApp approach.
METHODS: Males aged 15 years and older undergoing voluntary medical male circumcision in program sites could choose their follow-up approach, selecting 2wT via SMS or WhatsApp or routine care (in-person postoperative visits). The 2wT system provided 1-way educational messages and an open 2-way communication channel between providers and clients. We analyzed quantitative data from the 2wT database on message delivery platforms (WhatsApp vs SMS), response rates, and user behaviors using chi-square tests, z tests, and t tests. The team conducted short phone calls with WhatsApp and SMS clients about their perceptions of this 2wT platform using a short, structured interview guide. We consider informal reflections from the technical team members on the use of WhatsApp. We applied an implementation science lens using the RE-AIM (reach, effectiveness, adoption, implementation, and maintenance) framework to focus results on practice and policy improvement.
RESULTS: Over a 2-month period-from August to October, 2023-337 males enrolled in 2wT and were offered WhatsApp or SMS and were included in the analysis. For 2wT reach, 177 (53%) participants chose WhatsApp as their platform (P=.38). Mean client age was 30 years, and 253 (75%) participants chose English for automated messages. From quality assurance calls, almost all respondents (87/89, 98%) were happy with the way they were followed up. For effectiveness, on average for the days on which responses were requested, 58 (33%) WhatsApp clients and 44 (28%) SMS clients responded (P=.50). All 2wT team members believed WhatsApp limited the automated message content, language choices, and inclusivity as compared with the SMS-based 2wT approach.
CONCLUSIONS: When presented with a choice of 2wT communication platform, clients appear evenly split between SMS and WhatsApp. However, WhatsApp requires a smartphone and data plan, potentially reducing reach at scale. Clients using both platforms responded to 2wT interactive prompts, demonstrating similar effectiveness in engaging clients in follow-up. For telehealth interventions, digital health designers should maintain an SMS-based platform and carefully consider adding WhatsApp as an option for clients, using an implementation science approach to present evidence that guides the best implementation approach for their setting.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Male
*Circumcision, Male/psychology
*Text Messaging
South Africa
Adult
Adolescent
*Mobile Applications
Telemedicine
Young Adult
Patient Satisfaction
Middle Aged
Aftercare/methods
RevDate: 2024-10-16
Assessing Radiology and Radiation Therapy Needs for Cancer Care in Low-and-Middle-Income Countries: Insight From a Global Survey of Departmental and Institutional Leaders.
Advances in radiation oncology, 9(11):101615.
PURPOSE: The global cancer burden and mortality rates are increasing, with significant disparities in access to care in low- and middle-income countries (LMICs). This study aimed to identify radiology and radiation therapy needs in LMICs from the perspective of departmental and institutional leaders.
METHODS AND MATERIALS: A survey was developed and conducted by the American Association of Physicists in Medicine Global Needs Assessment Committee and the American Association of Physicists in Medicine International Council. The survey, organized into 5 sections (Introduction, Infrastructure Needs, Education Needs, Research Needs, and General Information), was open to respondents from March 1, to August 16, 2022.
RESULTS: A total of 175 responses were received from 6 global regions: Africa (31.4%), the Americas (17.7%), the Eastern Mediterranean (14.3%), Europe (9.1%), Southeast Asia (23.4%), and the Western Pacific (4.0%). The greatest reported need was for new or updated equipment, particularly positron emission tomography/computed tomography imaging technology. There was also a high demand for clinical and equipment training. Approximately 25% of institutions reported a lack of radiology-based cancer screening programs because of high health care costs and a shortage of specialized equipment. Many institutions that expressed interest in research face funding and grant challenges.
CONCLUSIONS: The findings highlight critical areas where organizations can support LMICs in enhancing radiology and radiation therapy services to mitigate the growing cancer burden.
Additional Links: PMID-39410956
PubMed:
Citation:
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@article {pmid39410956,
year = {2024},
author = {Parker, SA and Weygand, J and Bernat, BG and Jackson, AM and Mawlawi, O and Barreto, I and Hao, Y and Khan, R and Yorke, AA and Swanson, W and Huq, MS and Lief, E and Biancia, CD and Njeh, CF and Al-Basheer, A and Chau, OW and Avery, S and Ngwa, W and Sandwall, PA},
title = {Assessing Radiology and Radiation Therapy Needs for Cancer Care in Low-and-Middle-Income Countries: Insight From a Global Survey of Departmental and Institutional Leaders.},
journal = {Advances in radiation oncology},
volume = {9},
number = {11},
pages = {101615},
pmid = {39410956},
issn = {2452-1094},
abstract = {PURPOSE: The global cancer burden and mortality rates are increasing, with significant disparities in access to care in low- and middle-income countries (LMICs). This study aimed to identify radiology and radiation therapy needs in LMICs from the perspective of departmental and institutional leaders.
METHODS AND MATERIALS: A survey was developed and conducted by the American Association of Physicists in Medicine Global Needs Assessment Committee and the American Association of Physicists in Medicine International Council. The survey, organized into 5 sections (Introduction, Infrastructure Needs, Education Needs, Research Needs, and General Information), was open to respondents from March 1, to August 16, 2022.
RESULTS: A total of 175 responses were received from 6 global regions: Africa (31.4%), the Americas (17.7%), the Eastern Mediterranean (14.3%), Europe (9.1%), Southeast Asia (23.4%), and the Western Pacific (4.0%). The greatest reported need was for new or updated equipment, particularly positron emission tomography/computed tomography imaging technology. There was also a high demand for clinical and equipment training. Approximately 25% of institutions reported a lack of radiology-based cancer screening programs because of high health care costs and a shortage of specialized equipment. Many institutions that expressed interest in research face funding and grant challenges.
CONCLUSIONS: The findings highlight critical areas where organizations can support LMICs in enhancing radiology and radiation therapy services to mitigate the growing cancer burden.},
}
RevDate: 2024-10-15
CmpDate: 2024-10-15
Accurate identification of locally aneuploid cells by incorporating cytogenetic information in single cell data analysis.
Scientific reports, 14(1):24152.
Single-cell RNA sequencing is a powerful tool to investigate the cellular makeup of tumor samples. However, due to the sparse data and the complex tumor microenvironment, it can be challenging to identify neoplastic cells that play important roles in tumor growth and disease progression. This is especially relevant for blood cancers, where neoplastic cells may be highly similar to normal cells. To address this challenge, we have developed partCNV and partCNVH, two methods for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. PartCNV uses an expectation-maximization (EM) algorithm with mixtures of Poisson distributions and incorporates cytogenetic information to guide the classification. PartCNVH further improves partCNV by integrating a hidden Markov model for feature selection. We have thoroughly evaluated the performance of partCNV and partCNVH through simulation studies and real data analysis using three scRNA-seq datasets from blood cancer patients. Our results show that partCNV and partCNVH have favorable accuracy and provide more interpretable results compared to existing methods. In the real data analysis, we have identified multiple biological processes involved in the oncogenesis of myelodysplastic syndromes and acute myeloid leukemia.
Additional Links: PMID-39406835
PubMed:
Citation:
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@article {pmid39406835,
year = {2024},
author = {Li, Z and Li, R and Ganan-Gomez, I and Abbas, HA and Garcia-Manero, G and Sun, W},
title = {Accurate identification of locally aneuploid cells by incorporating cytogenetic information in single cell data analysis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24152},
pmid = {39406835},
issn = {2045-2322},
support = {R03CA270725/NH/NIH HHS/United States ; R03CA270725/NH/NIH HHS/United States ; R01GM105785/NH/NIH HHS/United States ; },
mesh = {Humans ; *Single-Cell Analysis/methods ; *Aneuploidy ; *Algorithms ; Cytogenetic Analysis/methods ; Markov Chains ; Sequence Analysis, RNA/methods ; Leukemia, Myeloid, Acute/genetics/pathology ; Data Analysis ; },
abstract = {Single-cell RNA sequencing is a powerful tool to investigate the cellular makeup of tumor samples. However, due to the sparse data and the complex tumor microenvironment, it can be challenging to identify neoplastic cells that play important roles in tumor growth and disease progression. This is especially relevant for blood cancers, where neoplastic cells may be highly similar to normal cells. To address this challenge, we have developed partCNV and partCNVH, two methods for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. PartCNV uses an expectation-maximization (EM) algorithm with mixtures of Poisson distributions and incorporates cytogenetic information to guide the classification. PartCNVH further improves partCNV by integrating a hidden Markov model for feature selection. We have thoroughly evaluated the performance of partCNV and partCNVH through simulation studies and real data analysis using three scRNA-seq datasets from blood cancer patients. Our results show that partCNV and partCNVH have favorable accuracy and provide more interpretable results compared to existing methods. In the real data analysis, we have identified multiple biological processes involved in the oncogenesis of myelodysplastic syndromes and acute myeloid leukemia.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Single-Cell Analysis/methods
*Aneuploidy
*Algorithms
Cytogenetic Analysis/methods
Markov Chains
Sequence Analysis, RNA/methods
Leukemia, Myeloid, Acute/genetics/pathology
Data Analysis
RevDate: 2024-10-15
Trastuzumab Deruxtecan With Nivolumab in HER2-Expressing Metastatic Breast or Urothelial Cancer: Analysis of the Phase Ib DS8201-A-U105 Study.
Clinical cancer research : an official journal of the American Association for Cancer Research pii:749101 [Epub ahead of print].
PURPOSE: This multicenter phase Ib study investigated trastuzumab deruxtecan (T-DXd) plus nivolumab in patients with HER2-expressing metastatic breast cancer (mBC) and metastatic urothelial cancer (mUC).
PATIENTS AND METHODS: Part 1 determined the recommended dose for expansion (RDE) of T-DXd plus nivolumab. Part 2 evaluated efficacy and safety; the primary endpoint was confirmed objective response rate (cORR) by independent central review.
RESULTS: Seven patients with mBC were enrolled in part 1 and received T-DXd 3.2 mg/kg (4 patients) or 5.4 mg/kg (3 patients) plus nivolumab. The RDE for T-DXd was 5.4 mg/kg plus nivolumab 360 mg intravenously/3 weeks. In part 2, 32 patients with HER2-positive mBC (cohort 1; inclusive of 3 administered 5.4 mg/kg in part 1), 16 with HER2-low mBC (cohort 2), 30 with HER2-high mUC (cohort 3), and 4 with HER2-low mUC (cohort 4) were enrolled. At data cutoff (July 22, 2021), the cORR (95% CI) for cohorts 1-4 was 65.6% (46.8%-81.4%), 50.0% (24.7%-75.3%), 36.7% (19.9%-56.1%), and not assessed due to small sample size, respectively. Median treatment duration (range) with T-DXd in cohorts 1-4 was 8.9 (1-23), 6.9 (1-21), 3.9 (1-21) months, and not assessed; most common treatment-emergent adverse event was nausea (55.2%, 62.5%, 73.3%, 75.0%). Adjudicated drug-related ILD/pneumonitis rates (cohorts 1-3) were 20.7%, 0%, and 20.0% (1 grade 5 each, cohorts 1 and 3).
CONCLUSION: T-DXd plus nivolumab demonstrated promising antitumor activity in HER2-expressing mBC or mUC and safety consistent with the known profile of T‑DXd. ILD/pneumonitis is an important risk and requires careful monitoring and prompt intervention.
Additional Links: PMID-39405343
Publisher:
PubMed:
Citation:
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@article {pmid39405343,
year = {2024},
author = {Hamilton, E and Galsky, MD and Ochsenreither, S and Del Conte, G and Martín, M and de Miguel, MJ and Yu, EY and Williams, A and Gion, M and Tan, AR and Agrawal, L and Rutten, A and Machiels, JP and Cresta, S and Debruyne, PR and Hennequin, A and Moreno, V and Minchom, A and Valdes-Albini, F and Petrylak, D and Li, L and Tsuchihashi, Z and Suto, F and Cheng, FC and Kandil, M and Barrios, D and Hurvitz, S},
title = {Trastuzumab Deruxtecan With Nivolumab in HER2-Expressing Metastatic Breast or Urothelial Cancer: Analysis of the Phase Ib DS8201-A-U105 Study.},
journal = {Clinical cancer research : an official journal of the American Association for Cancer Research},
volume = {},
number = {},
pages = {},
doi = {10.1158/1078-0432.CCR-24-1513},
pmid = {39405343},
issn = {1557-3265},
abstract = {PURPOSE: This multicenter phase Ib study investigated trastuzumab deruxtecan (T-DXd) plus nivolumab in patients with HER2-expressing metastatic breast cancer (mBC) and metastatic urothelial cancer (mUC).
PATIENTS AND METHODS: Part 1 determined the recommended dose for expansion (RDE) of T-DXd plus nivolumab. Part 2 evaluated efficacy and safety; the primary endpoint was confirmed objective response rate (cORR) by independent central review.
RESULTS: Seven patients with mBC were enrolled in part 1 and received T-DXd 3.2 mg/kg (4 patients) or 5.4 mg/kg (3 patients) plus nivolumab. The RDE for T-DXd was 5.4 mg/kg plus nivolumab 360 mg intravenously/3 weeks. In part 2, 32 patients with HER2-positive mBC (cohort 1; inclusive of 3 administered 5.4 mg/kg in part 1), 16 with HER2-low mBC (cohort 2), 30 with HER2-high mUC (cohort 3), and 4 with HER2-low mUC (cohort 4) were enrolled. At data cutoff (July 22, 2021), the cORR (95% CI) for cohorts 1-4 was 65.6% (46.8%-81.4%), 50.0% (24.7%-75.3%), 36.7% (19.9%-56.1%), and not assessed due to small sample size, respectively. Median treatment duration (range) with T-DXd in cohorts 1-4 was 8.9 (1-23), 6.9 (1-21), 3.9 (1-21) months, and not assessed; most common treatment-emergent adverse event was nausea (55.2%, 62.5%, 73.3%, 75.0%). Adjudicated drug-related ILD/pneumonitis rates (cohorts 1-3) were 20.7%, 0%, and 20.0% (1 grade 5 each, cohorts 1 and 3).
CONCLUSION: T-DXd plus nivolumab demonstrated promising antitumor activity in HER2-expressing mBC or mUC and safety consistent with the known profile of T‑DXd. ILD/pneumonitis is an important risk and requires careful monitoring and prompt intervention.},
}
RevDate: 2024-10-15
SurvBal: Compositional microbiome balances for survival outcomes.
Bioinformatics (Oxford, England) pii:7822443 [Epub ahead of print].
SUMMARY: Identification of balances of bacterial taxa in relation to continuous and dichotomous outcomes is an increasingly frequent analytic objective in microbiome profiling experiments. SurvBal enables the selection of balances in relation to censored survival or time-to-event outcomes which are of considerable interest in many biomedical studies. The most commonly used survival models-the Cox proportional hazards and parametric survival models are included in the package, which are used in combination with step-wise selection procedures to identify the optimal associated balance of microbiome, i.e., the ratio of the geometric means of two groups of taxa's relative abundances.
The SurvBal R package and Shiny app can be accessed at https://github.com/yinglia/SurvBal and https://yinglistats.shinyapps.io/shinyapp-survbal/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Additional Links: PMID-39404767
Publisher:
PubMed:
Citation:
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@article {pmid39404767,
year = {2024},
author = {Li, Y and Lee, T and Marin, K and Hua, X and Srinivasan, S and Fredricks, DN and Lee, JR and Ling, W},
title = {SurvBal: Compositional microbiome balances for survival outcomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae612},
pmid = {39404767},
issn = {1367-4811},
abstract = {SUMMARY: Identification of balances of bacterial taxa in relation to continuous and dichotomous outcomes is an increasingly frequent analytic objective in microbiome profiling experiments. SurvBal enables the selection of balances in relation to censored survival or time-to-event outcomes which are of considerable interest in many biomedical studies. The most commonly used survival models-the Cox proportional hazards and parametric survival models are included in the package, which are used in combination with step-wise selection procedures to identify the optimal associated balance of microbiome, i.e., the ratio of the geometric means of two groups of taxa's relative abundances.
The SurvBal R package and Shiny app can be accessed at https://github.com/yinglia/SurvBal and https://yinglistats.shinyapps.io/shinyapp-survbal/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
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RJR Experience and Expertise
Researcher
Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.
Educator
Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.
Administrator
Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.
Technologist
Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.
Publisher
While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.
Speaker
Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.
Facilitator
Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.
Designer
Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.
RJR Picks from Around the Web (updated 11 MAY 2018 )
Old Science
Weird Science
Treating Disease with Fecal Transplantation
Fossils of miniature humans (hobbits) discovered in Indonesia
Paleontology
Dinosaur tail, complete with feathers, found preserved in amber.
Astronomy
Mysterious fast radio burst (FRB) detected in the distant universe.
Big Data & Informatics
Big Data: Buzzword or Big Deal?
Hacking the genome: Identifying anonymized human subjects using publicly available data.