Nature geneticsPub Date : 2024-10-08DOI: 10.1038/s41588-024-01947-9
Alicia Huerta-Chagoya, Philip Schroeder, Ravi Mandla, Jiang Li, Lowri Morris, Maheak Vora, Ahmed Alkanaq, Dorka Nagy, Lukasz Szczerbinski, Jesper G. S. Madsen, Silvia Bonàs-Guarch, Fanny Mollandin, Joanne B. Cole, Bianca Porneala, Kenneth Westerman, Josephine H. Li, Toni I. Pollin, Jose C. Florez, Anna L. Gloyn, David J. Carey, Inês Cebola, Uyenlinh L. Mirshahi, Alisa K. Manning, Aaron Leong, Miriam Udler, Josep M. Mercader
{"title":"Rare variant analyses in 51,256 type 2 diabetes cases and 370,487 controls reveal the pathogenicity spectrum of monogenic diabetes genes","authors":"Alicia Huerta-Chagoya, Philip Schroeder, Ravi Mandla, Jiang Li, Lowri Morris, Maheak Vora, Ahmed Alkanaq, Dorka Nagy, Lukasz Szczerbinski, Jesper G. S. Madsen, Silvia Bonàs-Guarch, Fanny Mollandin, Joanne B. Cole, Bianca Porneala, Kenneth Westerman, Josephine H. Li, Toni I. Pollin, Jose C. Florez, Anna L. Gloyn, David J. Carey, Inês Cebola, Uyenlinh L. Mirshahi, Alisa K. Manning, Aaron Leong, Miriam Udler, Josep M. Mercader","doi":"10.1038/s41588-024-01947-9","DOIUrl":"10.1038/s41588-024-01947-9","url":null,"abstract":"Type 2 diabetes (T2D) genome-wide association studies (GWASs) often overlook rare variants as a result of previous imputation panels’ limitations and scarce whole-genome sequencing (WGS) data. We used TOPMed imputation and WGS to conduct the largest T2D GWAS meta-analysis involving 51,256 cases of T2D and 370,487 controls, targeting variants with a minor allele frequency as low as 5 × 10−5. We identified 12 new variants, including a rare African/African American-enriched enhancer variant near the LEP gene (rs147287548), associated with fourfold increased T2D risk. We also identified a rare missense variant in HNF4A (p.Arg114Trp), associated with eightfold increased T2D risk, previously reported in maturity-onset diabetes of the young with reduced penetrance, but observed here in a T2D GWAS. We further leveraged these data to analyze 1,634 ClinVar variants in 22 genes related to monogenic diabetes, identifying two additional rare variants in HNF1A and GCK associated with fivefold and eightfold increased T2D risk, respectively, the effects of which were modified by the individual’s polygenic risk score. For 21% of the variants with conflicting interpretations or uncertain significance in ClinVar, we provided support of being benign based on their lack of association with T2D. Our work provides a framework for using rare variant GWASs to identify large-effect variants and assess variant pathogenicity in monogenic diabetes genes. Rare variant analyses identify a new type 2 diabetes risk allele near the LEP gene, which encodes leptin, and other risk alleles of intermediate penetrance in genes previously implicated in monogenic forms of diabetes.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2370-2379"},"PeriodicalIF":31.7,"publicationDate":"2024-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01947-9.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142384474","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-07DOI: 10.1038/s41588-024-01940-2
Julia Sidorenko, Baptiste Couvy-Duchesne, Kathryn E. Kemper, Gunn-Helen Moen, Laxmi Bhatta, Bjørn Olav Åsvold, Reedik Mägi, Estonian Biobank Research Team, Alireza Ani, Rujia Wang, Ilja M. Nolte, Lifelines Cohort Study, Scott Gordon, Caroline Hayward, Archie Campbell, Daniel J. Benjamin, David Cesarini, David M. Evans, Michael E. Goddard, Chris S. Haley, David Porteous, Sarah E. Medland, Nicholas G. Martin, Harold Snieder, Andres Metspalu, Kristian Hveem, Ben Brumpton, Peter M. Visscher, Loic Yengo
{"title":"Genetic architecture reconciles linkage and association studies of complex traits","authors":"Julia Sidorenko, Baptiste Couvy-Duchesne, Kathryn E. Kemper, Gunn-Helen Moen, Laxmi Bhatta, Bjørn Olav Åsvold, Reedik Mägi, Estonian Biobank Research Team, Alireza Ani, Rujia Wang, Ilja M. Nolte, Lifelines Cohort Study, Scott Gordon, Caroline Hayward, Archie Campbell, Daniel J. Benjamin, David Cesarini, David M. Evans, Michael E. Goddard, Chris S. Haley, David Porteous, Sarah E. Medland, Nicholas G. Martin, Harold Snieder, Andres Metspalu, Kristian Hveem, Ben Brumpton, Peter M. Visscher, Loic Yengo","doi":"10.1038/s41588-024-01940-2","DOIUrl":"10.1038/s41588-024-01940-2","url":null,"abstract":"Linkage studies have successfully mapped loci underlying monogenic disorders, but mostly failed when applied to common diseases. Conversely, genome-wide association studies (GWASs) have identified replicable associations between thousands of SNPs and complex traits, yet capture less than half of the total heritability. In the present study we reconcile these two approaches by showing that linkage signals of height and body mass index (BMI) from 119,000 sibling pairs colocalize with GWAS-identified loci. Concordant with polygenicity, we observed the following: a genome-wide inflation of linkage test statistics; that GWAS results predict linkage signals; and that adjusting phenotypes for polygenic scores reduces linkage signals. Finally, we developed a method using recombination rate-stratified, identity-by-descent sharing between siblings to unbiasedly estimate heritability of height (0.76 ± 0.05) and BMI (0.55 ± 0.07). Our results imply that substantial heritability remains unaccounted for by GWAS-identified loci and this residual genetic variation is polygenic and enriched near these loci. Analyses of height and body mass index in 119,000 sibling pairs show that linkage and genome-wide association signals colocalize. Further analyses suggest that family-based linkage signals are fully consistent with a highly polygenic architecture.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2352-2360"},"PeriodicalIF":31.7,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142383640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-04DOI: 10.1038/s41588-024-01929-x
Andrew Stiff, Maarten Fornerod, Bailee N. Kain, Deedra Nicolet, Benjamin J. Kelly, Katherine E. Miller, Krzysztof Mrózek, Isaiah Boateng, Audrey Bollas, Elizabeth A. R. Garfinkle, Omolegho Momoh, Foluke A. Fasola, Hannah O. Olawumi, Nuria Mencia-Trinchant, Jean F. Kloppers, Anne-Cecilia van Marle, Eileen Hu, Saranga Wijeratne, Gregory Wheeler, Christopher J. Walker, Jill Buss, Adrienne Heyrosa, Helee Desai, Andrea Laganson, Ethan Hamp, Yazan Abu-Shihab, Hasan Abaza, Parker Kronen, Sidharth Sen, Megan E. Johnstone, Kate Quinn, Ben Wronowski, Erin Hertlein, Linde A. Miles, Alice S. Mims, Christopher C. Oakes, James S. Blachly, Karilyn T. Larkin, Bethany Mundy-Bosse, Andrew J. Carroll, Bayard L. Powell, Jonathan E. Kolitz, Richard M. Stone, Cassandra Duarte, Diana Abbott, Maria L. Amaya, Craig T. Jordan, Geoffrey L. Uy, Wendy Stock, Kellie J. Archer, Electra D. Paskett, Monica L. Guzman, Ross L. Levine, Kamal Menghrajani, Debyani Chakravarty, Michael F. Berger, Daniel Bottomly, Shannon K. McWeeney, Jeffrey W. Tyner, John C. Byrd, Nathan Salomonis, H. Leighton Grimes, Elaine R. Mardis, Ann-Kathrin Eisfeld
{"title":"Multiomic profiling identifies predictors of survival in African American patients with acute myeloid leukemia","authors":"Andrew Stiff, Maarten Fornerod, Bailee N. Kain, Deedra Nicolet, Benjamin J. Kelly, Katherine E. Miller, Krzysztof Mrózek, Isaiah Boateng, Audrey Bollas, Elizabeth A. R. Garfinkle, Omolegho Momoh, Foluke A. Fasola, Hannah O. Olawumi, Nuria Mencia-Trinchant, Jean F. Kloppers, Anne-Cecilia van Marle, Eileen Hu, Saranga Wijeratne, Gregory Wheeler, Christopher J. Walker, Jill Buss, Adrienne Heyrosa, Helee Desai, Andrea Laganson, Ethan Hamp, Yazan Abu-Shihab, Hasan Abaza, Parker Kronen, Sidharth Sen, Megan E. Johnstone, Kate Quinn, Ben Wronowski, Erin Hertlein, Linde A. Miles, Alice S. Mims, Christopher C. Oakes, James S. Blachly, Karilyn T. Larkin, Bethany Mundy-Bosse, Andrew J. Carroll, Bayard L. Powell, Jonathan E. Kolitz, Richard M. Stone, Cassandra Duarte, Diana Abbott, Maria L. Amaya, Craig T. Jordan, Geoffrey L. Uy, Wendy Stock, Kellie J. Archer, Electra D. Paskett, Monica L. Guzman, Ross L. Levine, Kamal Menghrajani, Debyani Chakravarty, Michael F. Berger, Daniel Bottomly, Shannon K. McWeeney, Jeffrey W. Tyner, John C. Byrd, Nathan Salomonis, H. Leighton Grimes, Elaine R. Mardis, Ann-Kathrin Eisfeld","doi":"10.1038/s41588-024-01929-x","DOIUrl":"10.1038/s41588-024-01929-x","url":null,"abstract":"Genomic profiles and prognostic biomarkers in patients with acute myeloid leukemia (AML) from ancestry-diverse populations are underexplored. We analyzed the exomes and transcriptomes of 100 patients with AML with genomically confirmed African ancestry (Black; Alliance) and compared their somatic mutation frequencies with those of 323 self-reported white patients with AML, 55% of whom had genomically confirmed European ancestry (white; BeatAML). Here we find that 73% of 162 gene mutations recurrent in Black patients, including a hitherto unreported PHIP alteration detected in 7% of patients, were found in one white patient or not detected. Black patients with myelodysplasia-related AML were younger than white patients suggesting intrinsic and/or extrinsic dysplasia-causing stressors. On multivariable analyses of Black patients, NPM1 and NRAS mutations were associated with inferior disease-free and IDH1 and IDH2 mutations with reduced overall survival. Inflammatory profiles, cell type distributions and transcriptional profiles differed between Black and white patients with NPM1 mutations. Incorporation of ancestry-specific risk markers into the 2022 European LeukemiaNet genetic risk stratification changed risk group assignment for one-third of Black patients and improved their outcome prediction. Analysis of exomes and transcriptomes from 100 African American patients with acute myeloid leukemia identifies ancestry-related variation in mutation profiles and survival. Refined risk classification suggests clinical relevance of these ancestry-associated differences.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2434-2446"},"PeriodicalIF":31.7,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01929-x.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142369986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-04DOI: 10.1038/s41588-024-01869-6
Evelyn M. Jiagge
{"title":"Genetic African ancestry modifies the biology of acute myeloid leukemia","authors":"Evelyn M. Jiagge","doi":"10.1038/s41588-024-01869-6","DOIUrl":"10.1038/s41588-024-01869-6","url":null,"abstract":"African American patients were under-represented in the studies that led to the current patient classification system for acute myeloid leukemia (AML). A new in-depth analysis of the genetics of AML in African Americans suggests that this omission has implications for patient care.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2299-2301"},"PeriodicalIF":31.7,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142369985","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Population-specific putative causal variants shape quantitative traits","authors":"Satoshi Koyama, Xiaoxi Liu, Yoshinao Koike, Keiko Hikino, Masaru Koido, Wei Li, Kotaro Akaki, Kohei Tomizuka, Shuji Ito, Nao Otomo, Hiroyuki Suetsugu, Soichiro Yoshino, Masato Akiyama, Kohei Saito, Yuki Ishikawa, Christian Benner, Pradeep Natarajan, Patrick T. Ellinor, Taisei Mushiroda, Momoko Horikoshi, Masashi Ikeda, Nakao Iwata, Koichi Matsuda, Biobank Japan Project, Shumpei Niida, Kouichi Ozaki, Yukihide Momozawa, Shiro Ikegawa, Osamu Takeuchi, Kaoru Ito, Chikashi Terao","doi":"10.1038/s41588-024-01913-5","DOIUrl":"10.1038/s41588-024-01913-5","url":null,"abstract":"Human genetic variants are associated with many traits through largely unknown mechanisms. Here, combining approximately 260,000 Japanese study participants, a Japanese-specific genotype reference panel and statistical fine-mapping, we identified 4,423 significant loci across 63 quantitative traits, among which 601 were new, and 9,406 putatively causal variants. New associations included Japanese-specific coding, splicing and noncoding variants, exemplified by a damaging missense variant rs730881101 in TNNT2 associated with lower heart function and increased risk for heart failure (P = 1.4 × 10−15 and odds ratio = 4.5, 95% confidence interval = 3.1–6.5). Putative causal noncoding variants were supported by state-of-art in silico functional assays and had comparable effect sizes to coding variants. A plausible example of new mechanisms of causal variants is an enrichment of causal variants in 3′ untranslated regions (UTRs), including the Japanese-specific rs13306436 in IL6 associated with pro-inflammatory traits and protection against tuberculosis. We experimentally showed that transcripts with rs13306436 are resistant to mRNA degradation by regnase-1, an RNA-binding protein. Our study provides a list of fine-mapped causal variants to be tested for functionality and underscores the importance of sequencing, genotyping and association efforts in diverse populations. Genome-wide association and fine-mapping analyses in approximately 260,000 Japanese individuals combined with a newly constructed Japanese-specific genotype reference panel identify hundreds of new loci and putative causal variants for 63 quantitative traits.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 10","pages":"2027-2035"},"PeriodicalIF":31.7,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01913-5.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142368959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-03DOI: 10.1038/s41588-024-01892-7
Judith F. Kribelbauer-Swietek, Olga Pushkarev, Vincent Gardeux, Katerina Faltejskova, Julie Russeil, Guido van Mierlo, Bart Deplancke
{"title":"Context transcription factors establish cooperative environments and mediate enhancer communication","authors":"Judith F. Kribelbauer-Swietek, Olga Pushkarev, Vincent Gardeux, Katerina Faltejskova, Julie Russeil, Guido van Mierlo, Bart Deplancke","doi":"10.1038/s41588-024-01892-7","DOIUrl":"10.1038/s41588-024-01892-7","url":null,"abstract":"Many enhancers control gene expression by assembling regulatory factor clusters, also referred to as condensates. This process is vital for facilitating enhancer communication and establishing cellular identity. However, how DNA sequence and transcription factor (TF) binding instruct the formation of high regulatory factor environments remains poorly understood. Here we developed a new approach leveraging enhancer-centric chromatin accessibility quantitative trait loci (caQTLs) to nominate regulatory factor clusters genome-wide. By analyzing TF-binding signatures within the context of caQTLs and comparing episomal versus endogenous enhancer activities, we discovered a class of regulators, ‘context-only’ TFs, that amplify the activity of cell type-specific caQTL-binding TFs, that is, ‘context-initiator’ TFs. Similar to super-enhancers, enhancers enriched for context-only TF-binding sites display high coactivator binding and sensitivity to bromodomain-inhibiting molecules. We further show that binding sites for context-only and context-initiator TFs underlie enhancer coordination, providing a mechanistic rationale for how a loose TF syntax confers regulatory specificity. This study identifies context-only transcription factors (TFs), a TF class that enhances DNA accessibility initiated by cell type-specific TFs and establishes cooperative environments. Enhancers enriched with motifs of both TF classes show high coactivator binding, enhanced coordination and sensitivity to bromodomain inhibitors.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 10","pages":"2199-2212"},"PeriodicalIF":31.7,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01892-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142368958","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-03DOI: 10.1038/s41588-024-01932-2
{"title":"Pan-African analysis identifies genetic differences in prostate cancer risk","authors":"","doi":"10.1038/s41588-024-01932-2","DOIUrl":"10.1038/s41588-024-01932-2","url":null,"abstract":"To understand the genetic basis of disease, it is essential to study diverse populations. We conducted the largest study to date of African men to evaluate the evolutionary genetics and causes of prostate cancer. Our findings reveal novel genetic associations, including those that were not observed in studies of non-African populations.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 10","pages":"2006-2007"},"PeriodicalIF":31.7,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142369924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-02DOI: 10.1038/s41588-024-01938-w
Peter J. Freeman, John F. Wagstaff, Ivo F. A. C. Fokkema, Garry R. Cutting, Heidi L. Rehm, Angela C. Davies, Johan T. den Dunnen, Liam J. Gretton, Raymond Dalgleish
{"title":"Standardizing variant naming in literature with VariantValidator to increase diagnostic rates","authors":"Peter J. Freeman, John F. Wagstaff, Ivo F. A. C. Fokkema, Garry R. Cutting, Heidi L. Rehm, Angela C. Davies, Johan T. den Dunnen, Liam J. Gretton, Raymond Dalgleish","doi":"10.1038/s41588-024-01938-w","DOIUrl":"10.1038/s41588-024-01938-w","url":null,"abstract":"Accurate naming of genetic variants is essential to identify clinical data that interpret the consequences of such variants. In partnership with the Human Genome Organization, we advocate for integration of VariantValidator in publishing of journals and databases, to improve the quality of shared genetic data and ultimately patient outcomes.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 11","pages":"2284-2286"},"PeriodicalIF":31.7,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142362745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-02DOI: 10.1038/s41588-024-01883-8
Clare Puttick, Thomas P. Jones, Michelle M. Leung, Felipe Galvez-Cancino, Jiali Liu, Manuel Varas-Godoy, Andrew Rowan, Oriol Pich, Carlos Martinez-Ruiz, Robert Bentham, Krijn K. Dijkstra, James R. M. Black, Rachel Rosenthal, Nnennaya Kanu, Kevin Litchfield, Roberto Salgado, David A. Moore, Peter Van Loo, Mariam Jamal-Hanjani, Sergio A. Quezada, TRACERx Consortium, Charles Swanton, Nicholas McGranahan
{"title":"MHC Hammer reveals genetic and non-genetic HLA disruption in cancer evolution","authors":"Clare Puttick, Thomas P. Jones, Michelle M. Leung, Felipe Galvez-Cancino, Jiali Liu, Manuel Varas-Godoy, Andrew Rowan, Oriol Pich, Carlos Martinez-Ruiz, Robert Bentham, Krijn K. Dijkstra, James R. M. Black, Rachel Rosenthal, Nnennaya Kanu, Kevin Litchfield, Roberto Salgado, David A. Moore, Peter Van Loo, Mariam Jamal-Hanjani, Sergio A. Quezada, TRACERx Consortium, Charles Swanton, Nicholas McGranahan","doi":"10.1038/s41588-024-01883-8","DOIUrl":"10.1038/s41588-024-01883-8","url":null,"abstract":"Disruption of the class I human leukocyte antigen (HLA) molecules has important implications for immune evasion and tumor evolution. We developed major histocompatibility complex loss of heterozygosity (LOH), allele-specific mutation and measurement of expression and repression (MHC Hammer). We identified extensive variability in HLA allelic expression and pervasive HLA alternative splicing in normal lung and breast tissue. In lung TRACERx and lung and breast TCGA cohorts, 61% of lung adenocarcinoma (LUAD), 76% of lung squamous cell carcinoma (LUSC) and 35% of estrogen receptor-positive (ER+) cancers harbored class I HLA transcriptional repression, while HLA tumor-enriched alternative splicing occurred in 31%, 11% and 15% of LUAD, LUSC and ER+ cancers. Consistent with the importance of HLA dysfunction in tumor evolution, in LUADs, HLA LOH was associated with metastasis and LUAD primary tumor regions seeding a metastasis had a lower effective neoantigen burden than non-seeding regions. These data highlight the extent and importance of HLA transcriptomic disruption, including repression and alternative splicing in cancer evolution. Major histocompatibility complex (MHC) loss of heterozygosity, allele-specific mutation and measurement of expression and repression (MHC Hammer) detects disruption to human leukocyte antigens due to mutations, loss of heterogeneity, altered gene expression or alternative splicing. Applied to lung and breast cancer datasets, the tool shows that these aberrations are common across cancer and can have clinical implications.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 10","pages":"2121-2131"},"PeriodicalIF":31.7,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41588-024-01883-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142362747","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nature geneticsPub Date : 2024-10-02DOI: 10.1038/s41588-024-01931-3
Rohini Janivara, Wenlong C. Chen, Ujani Hazra, Shakuntala Baichoo, Ilir Agalliu, Paidamoyo Kachambwa, Corrine N. Simonti, Lyda M. Brown, Saanika P. Tambe, Michelle S. Kim, Maxine Harlemon, Mohamed Jalloh, Dillon Muzondiwa, Daphne Naidoo, Olabode O. Ajayi, Nana Yaa Snyper, Lamine Niang, Halimatou Diop, Medina Ndoye, James E. Mensah, Afua O. D. Abrahams, Richard Biritwum, Andrew A. Adjei, Akindele O. Adebiyi, Olayiwola Shittu, Olufemi Ogunbiyi, Sikiru Adebayo, Maxwell M. Nwegbu, Hafees O. Ajibola, Olabode P. Oluwole, Mustapha A. Jamda, Audrey Pentz, Christopher A. Haiman, Petrus V. Spies, André van der Merwe, Michael B. Cook, Stephen J. Chanock, Sonja I. Berndt, Stephen Watya, Alexander Lubwama, Mazvita Muchengeti, Sean Doherty, Natalie Smyth, David Lounsbury, Brian Fortier, Thomas E. Rohan, Judith S. Jacobson, Alfred I. Neugut, Ann W. Hsing, Alexander Gusev, Oseremen I. Aisuodionoe-Shadrach, Maureen Joffe, Ben Adusei, Serigne M. Gueye, Pedro W. Fernandez, Jo McBride, Caroline Andrews, Lindsay N. Petersen, Joseph Lachance, Timothy R. Rebbeck
{"title":"Heterogeneous genetic architectures of prostate cancer susceptibility in sub-Saharan Africa","authors":"Rohini Janivara, Wenlong C. Chen, Ujani Hazra, Shakuntala Baichoo, Ilir Agalliu, Paidamoyo Kachambwa, Corrine N. Simonti, Lyda M. Brown, Saanika P. Tambe, Michelle S. Kim, Maxine Harlemon, Mohamed Jalloh, Dillon Muzondiwa, Daphne Naidoo, Olabode O. Ajayi, Nana Yaa Snyper, Lamine Niang, Halimatou Diop, Medina Ndoye, James E. Mensah, Afua O. D. Abrahams, Richard Biritwum, Andrew A. Adjei, Akindele O. Adebiyi, Olayiwola Shittu, Olufemi Ogunbiyi, Sikiru Adebayo, Maxwell M. Nwegbu, Hafees O. Ajibola, Olabode P. Oluwole, Mustapha A. Jamda, Audrey Pentz, Christopher A. Haiman, Petrus V. Spies, André van der Merwe, Michael B. Cook, Stephen J. Chanock, Sonja I. Berndt, Stephen Watya, Alexander Lubwama, Mazvita Muchengeti, Sean Doherty, Natalie Smyth, David Lounsbury, Brian Fortier, Thomas E. Rohan, Judith S. Jacobson, Alfred I. Neugut, Ann W. Hsing, Alexander Gusev, Oseremen I. Aisuodionoe-Shadrach, Maureen Joffe, Ben Adusei, Serigne M. Gueye, Pedro W. Fernandez, Jo McBride, Caroline Andrews, Lindsay N. Petersen, Joseph Lachance, Timothy R. Rebbeck","doi":"10.1038/s41588-024-01931-3","DOIUrl":"10.1038/s41588-024-01931-3","url":null,"abstract":"Men of African descent have the highest prostate cancer incidence and mortality rates, yet the genetic basis of prostate cancer in African men has been understudied. We used genomic data from 3,963 cases and 3,509 controls from Ghana, Nigeria, Senegal, South Africa and Uganda to infer ancestry-specific genetic architectures and fine-map disease associations. Fifteen independent associations at 8q24.21, 6q22.1 and 11q13.3 reached genome-wide significance, including four new associations. Intriguingly, multiple lead associations are private alleles, a pattern arising from recent mutations and the out-of-Africa bottleneck. These African-specific alleles contribute to haplotypes with odds ratios above 2.4. We found that the genetic architecture of prostate cancer differs across Africa, with effect size differences contributing more to this heterogeneity than allele frequency differences. Population genetic analyses reveal that African prostate cancer associations are largely governed by neutral evolution. Collectively, our findings emphasize the utility of conducting genetic studies that use diverse populations. Genome-wide association analyses of prostate cancer in men from sub-Saharan Africa identify population-specific risk variants and regional differences in effect sizes. Founder effects contribute to continental differences in the genetic architecture of prostate cancer.","PeriodicalId":18985,"journal":{"name":"Nature genetics","volume":"56 10","pages":"2093-2103"},"PeriodicalIF":31.7,"publicationDate":"2024-10-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142362867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}