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Li JL, McClellan JC, Zhang H, Gao G, Huo D. Multi-tissue transcriptome-wide association studies identified 235 genes for intrinsic subtypes of breast cancer. J Natl Cancer Inst 2024; 116:1105-1115. [PMID: 38400758 PMCID: PMC11223833 DOI: 10.1093/jnci/djae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/25/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
BACKGROUND Although genome-wide association studies (GWAS) of breast cancer (BC) identified common variants which differ between intrinsic subtypes, genes through which these variants act to impact BC risk have not been fully established. Transcriptome-wide association studies (TWAS) have identified genes associated with overall BC risk, but subtype-specific differences are largely unknown. METHODS We performed two multi-tissue TWAS for each BC intrinsic subtype, including an expression-based approach that collated TWAS signals from expression quantitative trait loci (eQTLs) across multiple tissues and a novel splicing-based approach that collated signals from splicing QTLs (sQTLs) across intron clusters and subsequently across tissues. We used summary statistics for five intrinsic subtypes including Luminal A-like, Luminal B-like, Luminal B/HER2-negative-like, HER2-enriched-like, and triple-negative BC, generated from 106 278 BC cases and 91 477 controls in the Breast Cancer Association Consortium. RESULTS Overall, we identified 235 genes in 88 loci that were associated with at least one of the five intrinsic subtypes. Most genes were subtype-specific, and many have not been reported in previous TWAS. We discovered common variants that modulate expression of CHEK2 confer increased risk to Luminal A-like BC, in contrast to the viewpoint that CHEK2 primarily harbors rare, penetrant mutations. Additionally, our splicing-based TWAS provided population-level support for MDM4 splice variants that increased the risk of triple-negative BC. CONCLUSION Our comprehensive, multi-tissue TWAS corroborated previous GWAS loci for overall BC risk and intrinsic subtypes, while underscoring how common variation that impacts expression and splicing of genes in multiple tissue types can be used to further elucidate the etiology of BC.
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Affiliation(s)
- James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Julian C McClellan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Haoyu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, IL, USA
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2
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Gao G, McClellan J, Barbeira AN, Fiorica PN, Li JL, Mu Z, Olopade OI, Huo D, Im HK. A multi-tissue, splicing-based joint transcriptome-wide association study identifies susceptibility genes for breast cancer. Am J Hum Genet 2024; 111:1100-1113. [PMID: 38733992 PMCID: PMC11179262 DOI: 10.1016/j.ajhg.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/13/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024] Open
Abstract
Splicing-based transcriptome-wide association studies (splicing-TWASs) of breast cancer have the potential to identify susceptibility genes. However, existing splicing-TWASs test the association of individual excised introns in breast tissue only and thus have limited power to detect susceptibility genes. In this study, we performed a multi-tissue joint splicing-TWAS that integrated splicing-TWAS signals of multiple excised introns in each gene across 11 tissues that are potentially relevant to breast cancer risk. We utilized summary statistics from a meta-analysis that combined genome-wide association study (GWAS) results of 424,650 women of European ancestry. Splicing-level prediction models were trained in GTEx (v.8) data. We identified 240 genes by the multi-tissue joint splicing-TWAS at the Bonferroni-corrected significance level; in the tissue-specific splicing-TWAS that combined TWAS signals of excised introns in genes in breast tissue only, we identified nine additional significant genes. Of these 249 genes, 88 genes in 62 loci have not been reported by previous TWASs, and 17 genes in seven loci are at least 1 Mb away from published GWAS index variants. By comparing the results of our splicing-TWASs with previous gene-expression-based TWASs that used the same summary statistics and expression prediction models trained in the same reference panel, we found that 110 genes in 70 loci that are identified only by the splicing-TWASs. Our results showed that for many genes, expression quantitative trait loci (eQTL) did not show a significant impact on breast cancer risk, whereas splicing quantitative trait loci (sQTL) showed a strong impact through intron excision events.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Julian McClellan
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Zepeng Mu
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Olufunmilayo I Olopade
- Section of Hematology and Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
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3
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Head ST, Dezem F, Todor A, Yang J, Plummer J, Gayther S, Kar S, Schildkraut J, Epstein MP. Cis- and trans-eQTL TWASs of breast and ovarian cancer identify more than 100 susceptibility genes in the BCAC and OCAC consortia. Am J Hum Genet 2024; 111:1084-1099. [PMID: 38723630 PMCID: PMC11179407 DOI: 10.1016/j.ajhg.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/11/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Transcriptome-wide association studies (TWASs) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have focused on the regulatory effects of risk-associated SNPs thought to act in cis on a nearby target gene. With growing evidence for distal (trans) regulatory effects of variants on gene expression, we performed TWASs of breast and ovarian cancer using a Bayesian genome-wide TWAS method (BGW-TWAS) that considers effects of both cis- and trans-expression quantitative trait loci (eQTLs). We applied BGW-TWAS to whole-genome and RNA sequencing data in breast and ovarian tissues from the Genotype-Tissue Expression project to train expression imputation models. We applied these models to large-scale GWAS summary statistic data from the Breast Cancer and Ovarian Cancer Association Consortia to identify genes associated with risk of overall breast cancer, non-mucinous epithelial ovarian cancer, and 10 cancer subtypes. We identified 101 genes significantly associated with risk with breast cancer phenotypes and 8 with ovarian phenotypes. These loci include established risk genes and several novel candidate risk loci, such as ACAP3, whose associations are predominantly driven by trans-eQTLs. We replicated several associations using summary statistics from an independent GWAS of these cancer phenotypes. We further used genotype and expression data in normal and tumor breast tissue from the Cancer Genome Atlas to examine the performance of our trained expression imputation models. This work represents an in-depth look into the role of trans eQTLs in the complex molecular mechanisms underlying these diseases.
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Affiliation(s)
- S Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Felipe Dezem
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andrei Todor
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jasmine Plummer
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Simon Gayther
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Siddhartha Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA.
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Ping J, Jia G, Cai Q, Guo X, Tao R, Ambrosone C, Huo D, Ambs S, Barnard ME, Chen Y, Garcia-Closas M, Gu J, Hu JJ, John EM, Li CI, Nathanson K, Nemesure B, Olopade OI, Pal T, Press MF, Sanderson M, Sandler DP, Yoshimatsu T, Adejumo PO, Ahearn T, Brewster AM, Hennis AJM, Makumbi T, Ndom P, O'Brien KM, Olshan AF, Oluwasanu MM, Reid S, Yao S, Butler EN, Huang M, Ntekim A, Li B, Troester MA, Palmer JR, Haiman CA, Long J, Zheng W. Using genome and transcriptome data from African-ancestry female participants to identify putative breast cancer susceptibility genes. Nat Commun 2024; 15:3718. [PMID: 38697998 PMCID: PMC11065893 DOI: 10.1038/s41467-024-47650-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 04/08/2024] [Indexed: 05/05/2024] Open
Abstract
African-ancestry (AA) participants are underrepresented in genetics research. Here, we conducted a transcriptome-wide association study (TWAS) in AA female participants to identify putative breast cancer susceptibility genes. We built genetic models to predict levels of gene expression, exon junction, and 3' UTR alternative polyadenylation using genomic and transcriptomic data generated in normal breast tissues from 150 AA participants and then used these models to perform association analyses using genomic data from 18,034 cases and 22,104 controls. At Bonferroni-corrected P < 0.05, we identified six genes associated with breast cancer risk, including four genes not previously reported (CTD-3080P12.3, EN1, LINC01956 and NUP210L). Most of these genes showed a stronger association with risk of estrogen-receptor (ER) negative or triple-negative than ER-positive breast cancer. We also replicated the associations with 29 genes reported in previous TWAS at P < 0.05 (one-sided), providing further support for an association of these genes with breast cancer risk. Our study sheds new light on the genetic basis of breast cancer and highlights the value of conducting research in AA populations.
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Affiliation(s)
- Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Guochong Jia
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christine Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, USA
| | - Dezheng Huo
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, Center of Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Yu Chen
- Division of Epidemiology, Department of Population Health, NYU Grossman School of Medicine, New York, NY, USA
| | | | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami School of Medicine, Miami, FL, USA
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Christopher I Li
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Katherine Nathanson
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Tuya Pal
- Division of Genetic Medicine, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Michael F Press
- Department of Pathology, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Maureen Sanderson
- Department of Family and Community Medicine, Meharry Medical College, Nashville, TN, USA
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Toshio Yoshimatsu
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Prisca O Adejumo
- Department of Nursing, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Abenaa M Brewster
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anselm J M Hennis
- George Alleyne Chronic Disease Research Centre, University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Paul Ndom
- Yaounde General Hospital, Yaounde, Cameroon
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Andrew F Olshan
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mojisola M Oluwasanu
- Department of Health Promotion and Education, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Sonya Reid
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Elm & Carlton Streets, Buffalo, NY, USA
| | - Ebonee N Butler
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Atara Ntekim
- Department of Radiation Oncology, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
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McClellan JC, Li JL, Gao G, Huo D. Expression- and splicing-based multi-tissue transcriptome-wide association studies identified multiple genes for breast cancer by estrogen-receptor status. Breast Cancer Res 2024; 26:51. [PMID: 38515142 PMCID: PMC10958972 DOI: 10.1186/s13058-024-01809-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Although several transcriptome-wide association studies (TWASs) have been performed to identify genes associated with overall breast cancer (BC) risk, only a few TWAS have explored the differences in estrogen receptor-positive (ER+) and estrogen receptor-negative (ER-) breast cancer. Additionally, these studies were based on gene expression prediction models trained primarily in breast tissue, and they did not account for alternative splicing of genes. METHODS In this study, we utilized two approaches to perform multi-tissue TWASs of breast cancer by ER subtype: (1) an expression-based TWAS that combined TWAS signals for each gene across multiple tissues and (2) a splicing-based TWAS that combined TWAS signals of all excised introns for each gene across tissues. To perform this TWAS, we utilized summary statistics for ER + BC from the Breast Cancer Association Consortium (BCAC) and for ER- BC from a meta-analysis of BCAC and the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA). RESULTS In total, we identified 230 genes in 86 loci that were associated with ER + BC and 66 genes in 29 loci that were associated with ER- BC at a Bonferroni threshold of significance. Of these genes, 2 genes associated with ER + BC at the 1q21.1 locus were located at least 1 Mb from published GWAS hits. For several well-studied tumor suppressor genes such as TP53 and CHEK2 which have historically been thought to impact BC risk through rare, penetrant mutations, we discovered that common variants, which modulate gene expression, may additionally contribute to ER + or ER- etiology. CONCLUSIONS Our study comprehensively examined how differences in common variation contribute to molecular differences between ER + and ER- BC and introduces a novel, splicing-based framework that can be used in future TWAS studies.
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Affiliation(s)
- Julian C McClellan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
- Section of Hematology & Oncology, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
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Zhang Z, Fang T, Chen L, Ji F, Chen J. Multi-omics Mendelian randomization integrating GWAS, eQTL, and mQTL data identified genes associated with breast cancer. Am J Cancer Res 2024; 14:1433-1445. [PMID: 38590415 PMCID: PMC10998764 DOI: 10.62347/bczw1355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 03/02/2024] [Indexed: 04/10/2024] Open
Abstract
Breast cancer (BC) remains a major disease posing a threat to women's health, but the underlying biological interpretation remains largely unknown. Here, we aimed to identify genes associated with breast cancer and analyze their pathophysiological mechanisms based on multi-omics Mendelian randomization (MR). Summary-data-based MR (SMR) was performed to estimate the causal effects of blood and breast mammary tissue expression quantitative trait loci (eQTLs) on BC. External validation analysis was used to validate the identified genes. Integration analyses BC GWAS summaries with eQTLs and DNA methylation QTLs (mQTLs) from the blood were conducted using SMR to prioritize putative blood genes and their regulatory elements associated with BC risk. Finally, two prior genes (ATG10 and RCCD1) from blood tissue reached significant levels in both BCAC (ATG10: ORBRCR = 0.91, PBRCR = 1.29 × 10-11; RCCD1: ORBRCR = 0.90, PBRCR = 3.72 × 10-15) and FinnGen cohorts (ATG10: ORFinnGen = 0.89, PFinnGen = 8.55 × 10-5; RCCD1: ORFinnGen = 0.89, PFinnGen = 2.38 × 10-8). Additionally, those two genes from breast tissues also replicated in both BCAC (ATG10: ORBRCR = 0.95, PBRCR = 1.02 × 10-9; RCCD1: ORBRCR = 0.87, PBRCR = 4.70 × 10-10) and FinnGen cohorts (ATG10: ORFinnGen = 0.93, PFinnGen = 2.38 × 10-4; RCCD1: ORFinnGen = 0.85, PFinnGen = 3.81 × 10-6). Sensitive analysis and external validation analysis validated those two identified genes. Multi-omics MR analysis showed that the SNP signals associated with ATG10 and RCCD1 were significant across the data from BC Genome-wide association study (GWAS), eQTL, and mQTL studies. In conclusion, we identified two priority genes that are potentially associated with BC. These findings improve our limited understanding of the mechanism of BC and shed light on the development of therapeutic agents for treating BC.
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Affiliation(s)
- Zhihao Zhang
- Breast Center, Department of General Surgery, West China Hospital, Sichuan UniversityNo. 37 Guo Xue Alley, Chengdu 610041, Sichuan, P. R. China
| | - Tian Fang
- Department of Medical Oncology, Cancer Center, West China Hospital, Sichuan UniversityNo. 37 Guo Xue Alley, Chengdu 610041, Sichuan, P. R. China
| | - Lanlan Chen
- Department of Hepatobiliary and Pancreatic Surgery, The First Hospital of Jilin UniversityChangchun 130021, Jilin, P. R. China
| | - Fuqing Ji
- Department of Thyroid Breast Surgery, Xi’an No. 3 Hospital, The Affiliated Hospital of Northwest UniversityXi’an 710018, Shaanxi, P. R. China
| | - Jie Chen
- Breast Center, Department of General Surgery, West China Hospital, Sichuan UniversityNo. 37 Guo Xue Alley, Chengdu 610041, Sichuan, P. R. China
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Devadoss D, Akkaoui J, Nair M, Lakshmana MK. LRRC25 expression during physiological aging and in mouse models of Alzheimer's disease and iPSC-derived neurons. Front Mol Neurosci 2024; 17:1365752. [PMID: 38476461 PMCID: PMC10929014 DOI: 10.3389/fnmol.2024.1365752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
The leucine-rich repeat-containing protein 25 (LRRC25) is relatively a novel protein with no information on its role in neuronal or brain function. A recent study suggested LRRC25 is a potential risk factor for Alzheimer's disease (AD). As a first step to understanding LRRC25's role in the brain and AD, we found LRRC25 is expressed in both cell membranes and cytoplasm in a punctuate appearance in astrocytes, microglia, and neurons in cell lines as well as mouse brain. We also found that LRRC25 expression is both age- and brain region-dependent and that 1-day-old (1D) pups expressed the least amount of LRRC25 protein compared to adult ages. In the APΔE9 mice, immunoblot quantified LRRC25 protein levels were increased by 166% (**p < 0.01) in the cortex (CX) and by 215% (***p < 0.001) in the hippocampus (HP) relative to wild-type (WT) controls. Both the brainstem (BS) and cerebellum (CB) showed no significant alterations. In the 3xTg mice, only CX showed an increase of LRRC25 protein by 91% (*p < 0.05) when compared to WT controls although the increased trend was noted in the other brain regions. In the AD patient brains also LRRC25 protein levels were increased by 153% (***p < 0.001) when compared to normal control (NC) subjects. Finally, LRRC25 expression in the iPSC-derived neurons quantified by immunofluorescence was increased by 181% (**p < 0.01) in AD-derived neurons when compared to NC-derived neurons. Thus increased LRRC25 protein in multiple models of AD suggests that LRRC25 may play a pathogenic role in either Aβ or tau pathology in AD. The mechanism for the increased levels of LRRC25 in AD is unknown at present, but a previous study showed that LRRC25 levels also increase during neonatal hypoxic-ischemia neuronal damage. Based on the evidence that autophagy is highly dysregulated in AD, the increased LRRC25 levels may be due to decreased autophagic degradation of LRRC25. Increased LRRC25 in turn may regulate the stability or activity of key enzymes involved in either Aβ or hyperphosphorylated tau generation and thus may contribute to increased plaques and neurofibrillary tangles.
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Affiliation(s)
| | | | | | - Madepalli K. Lakshmana
- Department of Cellular and Molecular Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, United States
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Evans P, Nagai T, Konkashbaev A, Zhou D, Knapik EW, Gamazon ER. Transcriptome-Wide Association Studies (TWAS): Methodologies, Applications, and Challenges. Curr Protoc 2024; 4:e981. [PMID: 38314955 PMCID: PMC10846672 DOI: 10.1002/cpz1.981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Transcriptome-wide association study (TWAS) methodologies aim to identify genetic effects on phenotypes through the mediation of gene transcription. In TWAS, in silico models of gene expression are trained as functions of genetic variants and then applied to genome-wide association study (GWAS) data. This post-GWAS analysis identifies gene-trait associations with high interpretability, enabling follow-up functional genomics studies and the development of genetics-anchored resources. We provide an overview of commonly used TWAS approaches, their advantages and limitations, and some widely used applications. © 2024 Wiley Periodicals LLC.
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Affiliation(s)
- Patrick Evans
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Taylor Nagai
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Anuar Konkashbaev
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan Zhou
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ela W Knapik
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Eric R Gamazon
- Division of Genetic Medicine and Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
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Head ST, Dezem F, Todor A, Yang J, Plummer J, Gayther S, Kar S, Schildkraut J, Epstein MP. Cis- and trans-eQTL TWAS of breast and ovarian cancer identify more than 100 risk associated genes in the BCAC and OCAC consortia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566218. [PMID: 38014246 PMCID: PMC10680675 DOI: 10.1101/2023.11.09.566218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Transcriptome-wide association studies (TWAS) have investigated the role of genetically regulated transcriptional activity in the etiologies of breast and ovarian cancer. However, methods performed to date have only considered regulatory effects of risk associated SNPs thought to act in cis on a nearby target gene. With growing evidence for distal (trans) regulatory effects of variants on gene expression, we performed TWAS of breast and ovarian cancer using a Bayesian genome-wide TWAS method (BGW-TWAS) that considers effects of both cis- and trans-expression quantitative trait loci (eQTLs). We applied BGW-TWAS to whole genome and RNA sequencing data in breast and ovarian tissues from the Genotype-Tissue Expression project to train expression imputation models. We applied these models to large-scale GWAS summary statistic data from the Breast Cancer and Ovarian Cancer Association Consortia to identify genes associated with risk of overall breast cancer, non-mucinous epithelial ovarian cancer, and 10 cancer subtypes. We identified 101 genes significantly associated with risk with breast cancer phenotypes and 8 with ovarian phenotypes. These loci include established risk genes and several novel candidate risk loci, such as ACAP3, whose associations are predominantly driven by trans-eQTLs. We replicated several associations using summary statistics from an independent GWAS of these cancer phenotypes. We further used genotype and expression data in normal and tumor breast tissue from the Cancer Genome Atlas to examine the performance of our trained expression imputation models. This work represents a first look into the role of trans-eQTLs in the complex molecular mechanisms underlying these diseases.
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Affiliation(s)
- S. Taylor Head
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Felipe Dezem
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Andrei Todor
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Jasmine Plummer
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Simon Gayther
- Department of Biomedical Sciences, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Siddhartha Kar
- Early Cancer Institute, Department of Oncology, University of Cambridge, Cambridge CB2 0XZ, UK
| | - Joellen Schildkraut
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Michael P. Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA 30322, USA
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10
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Corradi C, Lencioni G, Gentiluomo M, Felici A, Latiano A, Kiudelis G, van Eijck CHJ, Marta K, Lawlor RT, Tavano F, Boggi U, Dijk F, Cavestro GM, Vermeulen RCH, Hackert T, Petrone MC, Uzunoğlu FG, Archibugi L, Izbicki JR, Morelli L, Zerbi A, Landi S, Stocker H, Talar-Wojnarowska R, Di Franco G, Hegyi P, Sperti C, Carrara S, Capurso G, Gazouli M, Brenner H, Bunduc S, Busch O, Perri F, Oliverius M, Hegyi PJ, Goetz M, Scognamiglio P, Mambrini A, Arcidiacono PG, Kreivenaite E, Kupcinskas J, Hussein T, Ermini S, Milanetto AC, Vodicka P, Kiudelis V, Hlaváč V, Soucek P, Theodoropoulos GE, Basso D, Neoptolemos JP, Nóbrega Aoki M, Pezzilli R, Pasquali C, Chammas R, Testoni SGG, Mohelnikova-Duchonova B, Lucchesi M, Rizzato C, Canzian F, Campa D. Polymorphic variants involved in methylation regulation: a strategy to discover risk loci for pancreatic ductal adenocarcinoma. J Med Genet 2023; 60:980-986. [PMID: 37130759 DOI: 10.1136/jmg-2022-108910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 04/04/2023] [Indexed: 05/04/2023]
Abstract
INTRODUCTION Only a small number of risk factors for pancreatic ductal adenocarcinoma (PDAC) has been established. Several studies identified a role of epigenetics and of deregulation of DNA methylation. DNA methylation is variable across a lifetime and in different tissues; nevertheless, its levels can be regulated by genetic variants like methylation quantitative trait loci (mQTLs), which can be used as a surrogate. MATERIALS AND METHODS We scanned the whole genome for mQTLs and performed an association study in 14 705 PDAC cases and 246 921 controls. The methylation data were obtained from whole blood and pancreatic cancer tissue through online databases. We used the Pancreatic Cancer Cohort Consortium and the Pancreatic Cancer Case-Control Consortium genome-wide association study (GWAS) data as discovery phase and the Pancreatic Disease Research consortium, the FinnGen project and the Japan Pancreatic Cancer Research consortium GWAS as replication phase. RESULTS The C allele of 15q26.1-rs12905855 showed an association with a decreased risk of PDAC (OR=0.90, 95% CI 0.87 to 0.94, p=4.93×10-8 in the overall meta-analysis), reaching genome-level statistical significance. 15q26.1-rs12905855 decreases the methylation of a 'C-phosphate-G' (CpG) site located in the promoter region of the RCCD1 antisense (RCCD1-AS1) gene which, when expressed, decreases the expression of the RCC1 domain-containing (RCCD1) gene (part of a histone demethylase complex). Thus, it is possible that the rs12905855 C-allele has a protective role in PDAC development through an increase of RCCD1 gene expression, made possible by the inactivity of RCCD1-AS1. CONCLUSION We identified a novel PDAC risk locus which modulates cancer risk by controlling gene expression through DNA methylation.
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Affiliation(s)
| | | | | | | | - Anna Latiano
- Division of Gastroenterology and Research Laboratory, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Gediminas Kiudelis
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Casper H J van Eijck
- Department of Surgery, Erasmus Medical Center, Erasmus University, Rotterdam, Netherlands
| | - Katalin Marta
- Center for Traslational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Disease, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Rita T Lawlor
- ARC-NET, Centre for Applied Research on Cancer, University and Hospital Trust of Verona, Verona, Italy
| | - Francesca Tavano
- Division of Gastroenterology and Research Laboratory, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Ugo Boggi
- Division of General and Transplant Surgery, Pisa University Hospital, Pisa, Italy
| | - Frederike Dijk
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Giulia Martina Cavestro
- Division of Experimental Oncology, Gastroenterology and Gastrointestinal Endoscopy Unit, Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | | | - Thilo Hackert
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Maria Chiara Petrone
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - Faik Güntac Uzunoğlu
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Livia Archibugi
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Roma, Italy
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Luca Morelli
- General Surgery, Department of Translational Research and New Technologies in Medicine and Surgery, Università di Pisa, Pisa, Italy
| | - Alessandro Zerbi
- Pancreatic Unit, IRCCS Humanitas Research Hospital, Rozzano, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Stefano Landi
- Department of Biology, University of Pisa, Pisa, Italy
| | - Hannah Stocker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Network Aging Research (NAR), Heidelberg University, Heidelberg, Germany
| | | | - Gregorio Di Franco
- General Surgery, Department of Translational Research and New Technologies in Medicine and Surgery, Università di Pisa, Pisa, Italy
| | - Péter Hegyi
- Center for Traslational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Disease, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Institute for Translational Medicine, Medical School, University of Pécs, Pecs, Hungary
- Janos Szentagothai Research Center, University of Pecs, Pecs, Hungary
| | - Cosimo Sperti
- Department of Surgery-DiSCOG, Padua University Hospital, Padova, Italy
| | - Silvia Carrara
- Endoscopic Unit, Department of Gastroenterology, IRCCS Humanitas Research Hospital, Rozzano, Italy
| | - Gabriele Capurso
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
- Digestive and Liver Disease Unit, Sant'Andrea Hospital, Roma, Italy
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefania Bunduc
- Center for Traslational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Disease, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
- Carol Davila University of Medicine and Pharmacy, Bucarest, Romania
| | - Olivier Busch
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Francesco Perri
- Division of Gastroenterology and Research Laboratory, IRCCS Ospedale Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Martin Oliverius
- Department of Surgery, Third Faculty of Medicine, University Hospital Kralovske Vinohrady, Charles University, Prague, Czech Republic
| | - Péter Jeno Hegyi
- Center for Traslational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Disease, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Mara Goetz
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pasquale Scognamiglio
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrea Mambrini
- Oncology of Massa Carrara, Oncological Department, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Paolo Giorgio Arcidiacono
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | - Edita Kreivenaite
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Tamas Hussein
- Center for Traslational Medicine, Semmelweis University, Budapest, Hungary
- Division of Pancreatic Disease, Heart and Vascular Center, Semmelweis University, Budapest, Hungary
| | - Stefano Ermini
- Blood Transfusion Service, Azienda Ospedaliero Universitaria Meyer, Firenze, Italy
| | | | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine Czech Academy of Sciences, Prague, Czech Republic
- Biomedical Centre and Department of Surgery, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
- First Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University, Prague, Czech Republic
| | - Vytautas Kiudelis
- Department of Gastroenterology, Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Viktor Hlaváč
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - Pavel Soucek
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Pilsen, Czech Republic
| | - George E Theodoropoulos
- First Propaedeutic University Surgery Clinic, Hippocratio General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Daniela Basso
- Department of Medicine-DIMED, Padua University Hospital, Padova, Italy
| | - John P Neoptolemos
- Department of General Surgery, University of Heidelberg, Heidelberg, Germany
| | - Mateus Nóbrega Aoki
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Brazil
| | | | - Claudio Pasquali
- Department of Surgery-DiSCOG, Padua University Hospital, Padova, Italy
| | - Roger Chammas
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, Oswaldo Cruz Foundation (Fiocruz), Curitiba, Brazil
| | - Sabrina Gloria Giulia Testoni
- Pancreato-Biliary Endoscopy and Endoscopic Ultrasound, Pancreas Translational and Clinical Research Center, IRSSC San Raffaele Scientific Institute, Milan, Italy
| | | | - Maurizio Lucchesi
- Oncology of Massa Carrara, Oncological Department, Azienda USL Toscana Nord Ovest, Pisa, Italy
| | - Cosmeri Rizzato
- Department of Translational Research and new Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Daniele Campa
- Department of Biology, University of Pisa, Pisa, Italy
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11
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Gao G, Fiorica PN, McClellan J, Barbeira AN, Li JL, Olopade OI, Im HK, Huo D. A joint transcriptome-wide association study across multiple tissues identifies candidate breast cancer susceptibility genes. Am J Hum Genet 2023; 110:950-962. [PMID: 37164006 PMCID: PMC10257003 DOI: 10.1016/j.ajhg.2023.04.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/14/2023] [Indexed: 05/12/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified more than 200 genomic loci for breast cancer risk, but specific causal genes in most of these loci have not been identified. In fact, transcriptome-wide association studies (TWASs) of breast cancer performed using gene expression prediction models trained in breast tissue have yet to clearly identify most target genes. To identify candidate genes, we performed a GWAS analysis in a breast cancer dataset from UK Biobank (UKB) and combined the results with the GWAS results of the Breast Cancer Association Consortium (BCAC) by a meta-analysis. Using the summary statistics from the meta-analysis, we performed a joint TWAS analysis that combined TWAS signals from multiple tissues. We used expression prediction models trained in 11 tissues that are potentially relevant to breast cancer from the Genotype-Tissue Expression (GTEx) data. In the GWAS analysis, we identified eight loci distinct from those reported previously. In the TWAS analysis, we identified 309 genes at 108 genomic loci to be significantly associated with breast cancer at the Bonferroni threshold. Of these, 17 genes were located in eight regions that were at least 1 Mb away from published GWAS hits. The remaining TWAS-significant genes were located in 100 known genomic loci from previous GWASs of breast cancer. We found that 21 genes located in known GWAS loci remained statistically significant after conditioning on previous GWAS index variants. Our study provides insights into breast cancer genetics through mapping candidate target genes in a large proportion of known GWAS loci and discovering multiple new loci.
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Affiliation(s)
- Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Julian McClellan
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA
| | - Olufunmilayo I Olopade
- Section of Hematology & Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Hae Kyung Im
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL 60637, USA; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA.
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12
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Dai Q, Zhou G, Zhao H, Võsa U, Franke L, Battle A, Teumer A, Lehtimäki T, Raitakari OT, Esko T, Epstein MP, Yang J. OTTERS: a powerful TWAS framework leveraging summary-level reference data. Nat Commun 2023; 14:1271. [PMID: 36882394 PMCID: PMC9992663 DOI: 10.1038/s41467-023-36862-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 02/20/2023] [Indexed: 03/09/2023] Open
Abstract
Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.
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Affiliation(s)
- Qile Dai
- Department of Biostatistics and Bioinformatics, Emory University School of Public Health, Atlanta, GA, 30322, USA
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Geyu Zhou
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
| | - Hongyu Zhao
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06511, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Urmo Võsa
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB, Groningen, The Netherlands
- Oncode Institute, 3521 AL, Utrecht, The Netherlands
| | - Alexis Battle
- Department of Computer Science, and Departments of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17489, Greifswald, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Centre for Cardiovascular Disease Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33520, Finland
| | - Olli T Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, 20520, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, 20520, Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, 20521, Turku, Finland
| | - Tõnu Esko
- Estonian Genome Centre, Institute of Genomics, University of Tartu, 50090, Tartu, Estonia
| | - Michael P Epstein
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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13
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Przanowski P, Przanowska RK, Guertin MJ. ANKLE1 cleaves mitochondrial DNA and contributes to cancer risk by promoting apoptosis resistance and metabolic dysregulation. Commun Biol 2023; 6:231. [PMID: 36859531 PMCID: PMC9977882 DOI: 10.1038/s42003-023-04611-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 02/20/2023] [Indexed: 03/03/2023] Open
Abstract
Alleles within the chr19p13.1 locus are associated with increased risk of both ovarian and breast cancer and increased expression of the ANKLE1 gene. ANKLE1 is molecularly characterized as an endonuclease that efficiently cuts branched DNA and shuttles between the nucleus and cytoplasm. However, the role of ANKLE1 in mammalian development and homeostasis remains unknown. In normal development ANKLE1 expression is limited to the erythroblast lineage and we found that ANKLE1's role is to cleave the mitochondrial genome during erythropoiesis. We show that ectopic expression of ANKLE1 in breast epithelial-derived cells leads to genome instability and mitochondrial DNA (mtDNA) cleavage. mtDNA degradation then leads to mitophagy and causes a shift from oxidative phosphorylation to glycolysis (Warburg effect). Moreover, mtDNA degradation activates STAT1 and expression of epithelial-mesenchymal transition (EMT) genes. Reduction in mitochondrial content contributes to apoptosis resistance, which may allow precancerous cells to avoid apoptotic checkpoints and proliferate. These findings provide evidence that ANKLE1 is the causal cancer susceptibility gene in the chr19p13.1 locus and describe mechanisms by which higher ANKLE1 expression promotes cancer risk.
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Affiliation(s)
- Piotr Przanowski
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA, USA.
| | - Róża K Przanowska
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Michael J Guertin
- Center for Cell Analysis and Modeling, University of Connecticut, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, University of Connecticut, Farmington, CT, USA.
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14
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Song X, Ji J, Rothstein JH, Alexeeff SE, Sakoda LC, Sistig A, Achacoso N, Jorgenson E, Whittemore AS, Klein RJ, Habel LA, Wang P, Sieh W. MiXcan: a framework for cell-type-aware transcriptome-wide association studies with an application to breast cancer. Nat Commun 2023; 14:377. [PMID: 36690614 PMCID: PMC9871010 DOI: 10.1038/s41467-023-35888-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 01/05/2023] [Indexed: 01/25/2023] Open
Abstract
Human bulk tissue samples comprise multiple cell types with diverse roles in disease etiology. Conventional transcriptome-wide association study approaches predict genetically regulated gene expression at the tissue level, without considering cell-type heterogeneity, and test associations of predicted tissue-level expression with disease. Here we develop MiXcan, a cell-type-aware transcriptome-wide association study approach that predicts cell-type-level expression, identifies disease-associated genes via combination of cell-type-level association signals for multiple cell types, and provides insight into the disease-critical cell type. As a proof of concept, we conducted cell-type-aware analyses of breast cancer in 58,648 women and identified 12 transcriptome-wide significant genes using MiXcan compared with only eight genes using conventional approaches. Importantly, MiXcan identified genes with distinct associations in mammary epithelial versus stromal cells, including three new breast cancer susceptibility genes. These findings demonstrate that cell-type-aware transcriptome-wide analyses can reveal new insights into the genetic and cellular etiology of breast cancer and other diseases.
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Affiliation(s)
- Xiaoyu Song
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Jiayi Ji
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph H Rothstein
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey E Alexeeff
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Adriana Sistig
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ninah Achacoso
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Alice S Whittemore
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA
| | - Robert J Klein
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laurel A Habel
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Pei Wang
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Weiva Sieh
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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15
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Mehmood S, Aslam S, Dilshad E, Ismail H, Khan AN. Transforming Diagnosis and Therapeutics Using Cancer Genomics. Cancer Treat Res 2023; 185:15-47. [PMID: 37306902 DOI: 10.1007/978-3-031-27156-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In past quarter of the century, much has been understood about the genetic variation and abnormal genes that activate cancer in humans. All the cancers somehow possess alterations in the DNA sequence of cancer cell's genome. In present, we are heading toward the era where it is possible to obtain complete genome of the cancer cells for their better diagnosis, categorization and to explore treatment options.
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Affiliation(s)
- Sabba Mehmood
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan.
| | - Shaista Aslam
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Rawalpindi, Pakistan
| | - Erum Dilshad
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
| | - Hammad Ismail
- Departments of Biochemistry and Biotechnology, University of Gujrat (UOG) Gujrat, Gujrat, Pakistan
| | - Amna Naheed Khan
- Department of Bioinformatics and Biosciences, Faculty of Health and Life Sciences, Capital University of Science and Technology (CUST) Islamabad, Islamabad, Pakistan
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16
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Downregulation of LRRC19 Is Associated with Poor Prognosis in Colorectal Cancer. JOURNAL OF ONCOLOGY 2022; 2022:5848823. [PMID: 35794979 PMCID: PMC9251150 DOI: 10.1155/2022/5848823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/25/2022] [Indexed: 11/18/2022]
Abstract
Objective. Colorectal cancer (CRC) is globally one of the most often diagnosed cancers with high mortality rates. This study aimed to explore novel biomarkers for the diagnosis and prognosis of CRC. Methods. We collected 4 datasets about CRC in GEO and sought differentially expressed genes (DEGs) with GEO2R. Leucine-rich repeat-containing protein 19 (LRRC19) expression was assessed through the Oncomine and TIMER database analyses, which was further confirmed by qRT-PCR of CRC samples. We used online survival analysis tools (GEPIA, PrognoScan, and Kaplan–Meier plotter) to examine the prognostic value of LRRC19 in CRC and other malignancies. GO and KEGG enrichment analyses were employed to explore the biological functions of LRRC19. Finally, we conducted network prediction by STRING and further validation on the GEPIA to discover other molecules that might interact with LRRC19. Results. A total of 21 upregulated and 46 downregulated DEGs were identified from the 4 datasets. The TIMER and Oncomine online analyses showed lower mRNA of LRRC19 in CRC tissues compared with adjacent normal tissues, which was validated by qRT-PCR in CRC patient samples. The survival analysis through the GEPIA and PrognoScan websites revealed that low LRRC19 expression was significantly correlated with poor prognosis in CRC patients. The Kaplan–Meier plotter survival analysis indicated that low LRRC19 expression was significantly associated with the disease progression of patients with ovarian cancer, gastric cancer, breast cancer, and lung cancer. The enrichment analysis suggested that low expression of LRRC19 could be involved in the retinol metabolism and the zymogen granule membrane. Through STRING and GEPIA, it was found that LRRC19 is clearly associated with ZCCHC10, MOB3B, IMMP2L, and TRMT11. Conclusion. LRRC19 mRNA was prominently decreased in human CRC tissues and was significantly associated with shorter survival in CRC patients. LRRC19 might serve as a possible target for early diagnosis and prognosis assessment in CRC.
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Mehmood S, Faheem M, Ismail H, Farhat SM, Ali M, Younis S, Asghar MN. ‘Breast Cancer Resistance Likelihood and Personalized Treatment Through Integrated Multiomics’. Front Mol Biosci 2022; 9:783494. [PMID: 35495618 PMCID: PMC9048735 DOI: 10.3389/fmolb.2022.783494] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/14/2022] [Indexed: 12/24/2022] Open
Abstract
In recent times, enormous progress has been made in improving the diagnosis and therapeutic strategies for breast carcinoma, yet it remains the most prevalent cancer and second highest contributor to cancer-related deaths in women. Breast cancer (BC) affects one in eight females globally. In 2018 alone, 1.4 million cases were identified worldwide in postmenopausal women and 645,000 cases in premenopausal females, and this burden is constantly increasing. This shows that still a lot of efforts are required to discover therapeutic remedies for this disease. One of the major clinical complications associated with the treatment of breast carcinoma is the development of therapeutic resistance. Multidrug resistance (MDR) and consequent relapse on therapy are prevalent issues related to breast carcinoma; it is due to our incomplete understanding of the molecular mechanisms of breast carcinoma disease. Therefore, elucidating the molecular mechanisms involved in drug resistance is critical. For management of breast carcinoma, the treatment decision not only depends on the assessment of prognosis factors but also on the evaluation of pathological and clinical factors. Integrated data assessments of these multiple factors of breast carcinoma through multiomics can provide significant insight and hope for making therapeutic decisions. This omics approach is particularly helpful since it identifies the biomarkers of disease progression and treatment progress by collective characterization and quantification of pools of biological molecules within and among the cancerous cells. The scrupulous understanding of cancer and its treatment at the molecular level led to the concept of a personalized approach, which is one of the most significant advancements in modern oncology. Likewise, there are certain genetic and non-genetic tests available for BC which can help in personalized therapy. Genetically inherited risks can be screened for personal predisposition to BC, and genetic changes or variations (mutations) can also be identified to decide on the best treatment. Ultimately, further understanding of BC at the molecular level (multiomics) will define more precise choices in personalized medicine. In this review, we have summarized therapeutic resistance associated with BC and the techniques used for its management.
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Affiliation(s)
- Sabba Mehmood
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
- *Correspondence: Sabba Mehmood, ; Muhammad Nadeem Asghar,
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Hammad Ismail
- Department of Biochemistry & Biotechnology University of Gujrat, Gujrat, Pakistan
| | - Syeda Mehpara Farhat
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Mahwish Ali
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Sidra Younis
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Muhammad Nadeem Asghar
- Department of Medical Biology, University of Québec at Trois-Rivieres, Trois-Rivieres, QC, Canada
- *Correspondence: Sabba Mehmood, ; Muhammad Nadeem Asghar,
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18
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Functional annotation of breast cancer risk loci: current progress and future directions. Br J Cancer 2022; 126:981-993. [PMID: 34741135 PMCID: PMC8980003 DOI: 10.1038/s41416-021-01612-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 11/20/2022] Open
Abstract
Genome-wide association studies coupled with large-scale replication and fine-scale mapping studies have identified more than 150 genomic regions that are associated with breast cancer risk. Here, we review efforts to translate these findings into a greater understanding of disease mechanism. Our review comes in the context of a recently published fine-scale mapping analysis of these regions, which reported 352 independent signals and a total of 13,367 credible causal variants. The vast majority of credible causal variants map to noncoding DNA, implicating regulation of gene expression as the mechanism by which functional variants influence risk. Accordingly, we review methods for defining candidate-regulatory sequences, methods for identifying putative target genes and methods for linking candidate-regulatory sequences to putative target genes. We provide a summary of available data resources and identify gaps in these resources. We conclude that while much work has been done, there is still much to do. There are, however, grounds for optimism; combining statistical data from fine-scale mapping with functional data that are more representative of the normal "at risk" breast, generated using new technologies, should lead to a greater understanding of the mechanisms that influence an individual woman's risk of breast cancer.
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Marino N, German R, Podicheti R, Rusch DB, Rockey P, Huang J, Sandusky GE, Temm CJ, Althouse S, Nephew KP, Nakshatri H, Liu J, Vode A, Cao S, Storniolo AMV. Aberrant epigenetic and transcriptional events associated with breast cancer risk. Clin Epigenetics 2022; 14:21. [PMID: 35139887 PMCID: PMC8830042 DOI: 10.1186/s13148-022-01239-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/25/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Genome-wide association studies have identified several breast cancer susceptibility loci. However, biomarkers for risk assessment are still missing. Here, we investigated cancer-related molecular changes detected in tissues from women at high risk for breast cancer prior to disease manifestation. Disease-free breast tissue cores donated by healthy women (N = 146, median age = 39 years) were processed for both methylome (MethylCap) and transcriptome (Illumina's HiSeq4000) sequencing. Analysis of tissue microarray and primary breast epithelial cells was used to confirm gene expression dysregulation. RESULTS Transcriptomic analysis identified 69 differentially expressed genes between women at high and those at average risk of breast cancer (Tyrer-Cuzick model) at FDR < 0.05 and fold change ≥ 2. Majority of the identified genes were involved in DNA damage checkpoint, cell cycle, and cell adhesion. Two genes, FAM83A and NEK2, were overexpressed in tissue sections (FDR < 0.01) and primary epithelial cells (p < 0.05) from high-risk breasts. Moreover, 1698 DNA methylation changes were identified in high-risk breast tissues (FDR < 0.05), partially overlapped with cancer-related signatures, and correlated with transcriptional changes (p < 0.05, r ≤ 0.5). Finally, among the participants, 35 women donated breast biopsies at two time points, and age-related molecular alterations enhanced in high-risk subjects were identified. CONCLUSIONS Normal breast tissue from women at high risk of breast cancer bears molecular aberrations that may contribute to breast cancer susceptibility. This study is the first molecular characterization of the true normal breast tissues, and provides an opportunity to investigate molecular markers of breast cancer risk, which may lead to new preventive approaches.
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Affiliation(s)
- Natascia Marino
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA. .,Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| | - Rana German
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Pam Rockey
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Jie Huang
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - George E Sandusky
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Constance J Temm
- Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Sandra Althouse
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Kenneth P Nephew
- Department of Anatomy, Cell Biology, & Physiology, Indiana University, Bloomington, IN, 47405, USA
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Jun Liu
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, 47405, USA
| | - Ashley Vode
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA
| | - Sha Cao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Anna Maria V Storniolo
- Susan G. Komen Tissue Bank at the IU Simon Comprehensive Cancer Center, Indianapolis, IN, 46202, USA.,Department of Medicine, Hematology/Oncology Division, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
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20
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Parrish RL, Gibson GC, Epstein MP, Yang J. TIGAR-V2: Efficient TWAS tool with nonparametric Bayesian eQTL weights of 49 tissue types from GTEx V8. HGG ADVANCES 2022; 3:100068. [PMID: 35047855 PMCID: PMC8756507 DOI: 10.1016/j.xhgg.2021.100068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/01/2021] [Indexed: 01/12/2023] Open
Abstract
Standard transcriptome-wide association study (TWAS) methods first train gene expression prediction models using reference transcriptomic data and then test the association between the predicted genetically regulated gene expression and phenotype of interest. Most existing TWAS tools require cumbersome preparation of genotype input files and extra coding to enable parallel computation. To improve the efficiency of TWAS tools, we developed Transcriptome-Integrated Genetic Association Resource V2 (TIGAR-V2), which directly reads Variant Call Format (VCF) files, enables parallel computation, and reduces up to 90% of computation cost (mainly due to loading genotype data) compared to the original version. TIGAR-V2 can train gene expression imputation models using either nonparametric Bayesian Dirichlet process regression (DPR) or Elastic-Net (as used by PrediXcan), perform TWASs using either individual-level or summary-level genome-wide association study (GWAS) data, and implement both burden and variance-component statistics for gene-based association tests. We trained gene expression prediction models by DPR for 49 tissues using Genotype-Tissue Expression (GTEx) V8 by TIGAR-V2 and illustrated the usefulness of these Bayesian cis-expression quantitative trait locus (eQTL) weights through TWASs of breast and ovarian cancer utilizing public GWAS summary statistics. We identified 88 and 37 risk genes, respectively, for breast and ovarian cancer, most of which are either known or near previously identified GWAS (∼95%) or TWAS (∼40%) risk genes and three novel independent TWAS risk genes with known functions in carcinogenesis. These findings suggest that TWASs can provide biological insight into the transcriptional regulation of complex diseases. The TIGAR-V2 tool, trained Bayesian cis-eQTL weights, and linkage disequilibrium (LD) information from GTEx V8 are publicly available, providing a useful resource for mapping risk genes of complex diseases.
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Affiliation(s)
- Randy L. Parrish
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Greg C. Gibson
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Michael P. Epstein
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jingjing Yang
- Center for Computational and Quantitative Genetics, Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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21
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Wang Y, Guo P, Zhang Y, Liu L, Yan R, Yuan Z, Song Y. Joint Analysis of Genetic Correlation, Mendelian Randomization and Colocalization Highlights the Bi-Directional Causal Association Between Hypothyroidism and Primary Biliary Cirrhosis. Front Genet 2021; 12:753352. [PMID: 34671386 PMCID: PMC8521021 DOI: 10.3389/fgene.2021.753352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022] Open
Abstract
Background: Hypothyroidism and primary biliary cirrhosis (PBC) are often co-existed in observational epidemiological studies. However, the causal relationship between them remains unclear. Methods: Genetic correlation, Mendelian randomization (MR) and colocalization analysis were combined to assess the potential causal association between hypothyroidism and PBC by using summary statistics from large-scale genome-wide association studies. Various sensitivity analyses had been conducted to assess the robustness and the consistency of the findings. Results: The linkage disequilibrium score regression demonstrated significant evidence of shared genetic architecture between hypothyroidism and PBC, with the genetic correlation estimated to be 0.117 (p = 0.006). The OR of hypothyroidism on PBC was 1.223 (95% CI, 1.072–1.396; p = 2.76 × 10−3) in MR analysis with inverse variance weighted (IVW) method. More importantly, the results from other 7MR methods with different model assumptions, were almost identical with that of IVW, suggesting the findings were robust and convincing. On the other hand, PBC was also causally associated with hypothyroidism (OR, 1.049; 95% CI, 1.010–1.089; p = 0.012), and, again, similar results can also be obtained from other MR methods. Various sensitivity analyses regarding the outlier detection and leave-one-out analysis were also performed. Besides, colocalization analysis suggested that there existed shared causal variants between hypothyroidism and PBC, further highlighting the robustness of the results. Conclusion: Our results suggest evidence for the bi-directional causal association between hypothyroidism and PBC, which may provide insights into the etiology of hypothyroidism and PBC as well as inform prevention and intervention strategies directed toward both diseases.
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Affiliation(s)
- Yanjun Wang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ping Guo
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanan Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lu Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ran Yan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhongshang Yuan
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yongfeng Song
- Department of Endocrinology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China.,Shandong Provincial Key Laboratory of Endocrinology and Lipid Metabolism, Jinan, China.,Institute of Endocrinology and Metabolism, Shandong Academy of Clinical Medicine, Jinan, China
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22
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Hussein S, Khanna P, Yunus N, Gatza ML. Nuclear Receptor-Mediated Metabolic Reprogramming and the Impact on HR+ Breast Cancer. Cancers (Basel) 2021; 13:cancers13194808. [PMID: 34638293 PMCID: PMC8508306 DOI: 10.3390/cancers13194808] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 09/22/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Breast cancer is the most commonly diagnosed and second leading cause of cancer-related deaths in women in the United States, with hormone receptor positive (HR+) tumors representing more than two-thirds of new cases. Recent evidence has indicated that dysregulation of multiple metabolic programs, which can be driven through nuclear receptor activity, is essential for tumor genesis, progression, therapeutic resistance and metastasis. This study will review the current advances in our understanding of the impact and implication of altered metabolic processes driven by nuclear receptors, including hormone-dependent signaling, on HR+ breast cancer. Abstract Metabolic reprogramming enables cancer cells to adapt to the changing microenvironment in order to maintain metabolic energy and to provide the necessary biological macromolecules required for cell growth and tumor progression. While changes in tumor metabolism have been long recognized as a hallmark of cancer, recent advances have begun to delineate the mechanisms that modulate metabolic pathways and the consequence of altered signaling on tumorigenesis. This is particularly evident in hormone receptor positive (HR+) breast cancers which account for approximately 70% of breast cancer cases. Emerging evidence indicates that HR+ breast tumors are dependent on multiple metabolic processes for tumor progression, metastasis, and therapeutic resistance and that changes in metabolic programs are driven, in part, by a number of key nuclear receptors including hormone-dependent signaling. In this review, we discuss the mechanisms and impact of hormone receptor mediated metabolic reprogramming on HR+ breast cancer genesis and progression as well as the therapeutic implications of these metabolic processes in this disease.
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Affiliation(s)
- Shaimaa Hussein
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; (S.H.); (P.K.)
- Department of Radiation Oncology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Pooja Khanna
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; (S.H.); (P.K.)
- Department of Radiation Oncology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- School of Arts and Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA;
| | - Neha Yunus
- School of Arts and Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA;
| | - Michael L. Gatza
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; (S.H.); (P.K.)
- Department of Radiation Oncology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA
- School of Arts and Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA;
- Correspondence: ; Tel.: +1-732-235-8751
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23
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Jiang D, Li W, Wang Z, Fang M. Genome-Wide Identification of Cis-acting Expression QTLs in Large Yellow Croaker. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:225-232. [PMID: 33507423 DOI: 10.1007/s10126-020-10017-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
The large yellow croaker is one of the largest marine economic fish in China with the farming yield about 30 tons per year. The genetic selection for growth and disease resistance has been performed in recent years. The identification of trait-associated molecular makers, causative variants, and causative genes is helpful for genetic selection in large yellow croaker. It has been discovered that most of polygenic traits are controlled with multiple genes via regulatory variant, and GWAS-identified loci are enriched in the regulatory variant. Cis-acting eQTL is a widespread regulatory variant that controls the expression of nearby gene. We herein take advantage of RNA-seq and whole genome sequencing technique to identify genome-wide eQTLs in liver tissue for large yellow croaker; a forward selection routine is applied for identification of multiple eQTLs. To fine map causative mutation for each eQTL, a credible set is built to confine causative variants. Totally, 2427 eQTLs have been identified, 69.7% (1,691/2,427) of them are primary eQTL signals, and the remaining are secondary signals, many functional important target genes have been discovered. We highlight several functional pivotal genes including SMC3, TUSC3, TITIN, MCPH1, and MDHC, in which the expression of MCPH1 is regulated by two eQTLs; the distance of these eQTLs from target genes is symmetrically distributed, 25.5% of them are within 1 Mb region from target genes, whereas 74.5% of them are between 1 and 2 Mb regions; most of the identified eQTL has been well resolved, and 19.3 (469/2427) of eQTL have the size of credible set (the number of variants in credible set) less than 50.
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Affiliation(s)
- Dan Jiang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Wanbo Li
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Ming Fang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
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24
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Yuan Y, Bao J, Chen Z, Villanueva AD, Wen W, Wang F, Zhao D, Fu X, Cai Q, Long J, Shu XO, Zheng D, Moreno V, Zheng W, Lin W, Guo X. Multi-omics analysis to identify susceptibility genes for colorectal cancer. Hum Mol Genet 2021; 30:321-330. [PMID: 33481017 DOI: 10.1093/hmg/ddab021] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 02/05/2023] Open
Abstract
Most genetic variants for colorectal cancer (CRC) identified in genome-wide association studies (GWAS) are located in intergenic regions, implying pathogenic dysregulations of gene expression. However, comprehensive assessments of target genes in CRC remain to be explored. We conducted a multi-omics analysis using transcriptome and/or DNA methylation data from the Genotype-Tissue Expression, The Cancer Genome Atlas and the Colonomics projects. We identified 116 putative target genes for 45 GWAS-identified variants. Using summary-data-based Mendelian randomization approach (SMR), we demonstrated that the CRC susceptibility for 29 out of the 45 CRC variants may be mediated by cis-effects on gene regulation. At a cutoff of the Bonferroni-corrected PSMR < 0.05, we determined 66 putative susceptibility genes, including 39 genes that have not been previously reported. We further performed in vitro assays for two selected genes, DIP2B and SFMBT1, and provide functional evidence that they play a vital role in colorectal carcinogenesis via disrupting cell behavior, including migration, invasion and epithelial-mesenchymal transition. Our study reveals a large number of putative novel susceptibility genes and provides additional insight into the underlying mechanisms for CRC genetic risk loci.
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Affiliation(s)
- Yuan Yuan
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 322000, China
| | - Jiandong Bao
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.,College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhishan Chen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Anna Díez Villanueva
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO); Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL); Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP); Faculty of Medicine, Department of Clinical Sciences, University of Barcelona, Barcelona 08908, Spain
| | - Wanqing Wen
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Fangqin Wang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 322000, China
| | - Dejian Zhao
- Departments of Genetics, Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Xianghui Fu
- Division of Endocrinology and Metabolism, State Key Laboratory of Biotherapy, West China Hospital, Chengdu, Sichuan 610041, China
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Deyou Zheng
- Departments of Genetics, Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program, Catalan Institute of Oncology (ICO); Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL); Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP); Faculty of Medicine, Department of Clinical Sciences, University of Barcelona, Barcelona 08908, Spain
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
| | - Weiqiang Lin
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Jinhua, Zhejiang 322000, China
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.,Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA
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25
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Xie Y, Shan N, Zhao H, Hou L. Transcriptome wide association studies: general framework and methods. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-020-0228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Yang J, Yu X, Zhu G, Wang R, Lou S, Zhu W, Fu C, Liu J, Fan L, Li D, Shao Q, Ma L, Wang L, Wang Z, Pan Y. Integrating GWAS and eQTL to predict genes and pathways for non-syndromic cleft lip with or without palate. Oral Dis 2020; 27:1747-1754. [PMID: 33128317 DOI: 10.1111/odi.13699] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/14/2020] [Accepted: 10/16/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To explore susceptibility genes and pathways for non-syndromic cleft lip with or without cleft palate (NSCL/P). MATERIALS AND METHODS Two genome-wide association studies (GWAS) datasets, including 858 NSCL/P cases and 1,248 controls, were integrated with expression quantitative trait loci (eQTL) dataset identified by Genotype-Tissue Expression (GTEx) project in whole-blood samples. The expression of the candidate genes in mouse orofacial development was inquired from FaceBase. Protein-protein interaction (PPI) network was visualized to identify protein functions. Go and KEGG pathway analyses were performed to explore the underlying risk pathways. RESULTS A total of 233 eQTL single-nucleotide polymorphisms (SNPs) in 432 candidate genes were identified to be associated with the risk of NSCL/P. One hundred and eighty-three susceptible genes were expressed in mouse orofacial development according to FaceBase. PPI network analysis highlighted that these genes involved in ubiquitin-mediated proteolysis (KCTD7, ASB1, UBOX5, ANAPC4) and DNA synthesis (XRCC3, RFC3, KAT5, RHNO1) were associated with the risk of NSCL/P. GO and KEGG pathway analyses revealed that the fatty acid metabolism pathway (ACADL, HSD17B12, ACSL5, PPT1, MCAT) played an important role in the development of NSCL/P. CONCLUSIONS Our results identified novel susceptibility genes and pathways associated with the development of NSCL/P.
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Affiliation(s)
- Jing Yang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Xin Yu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Guirong Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Ruimin Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Shu Lou
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Weihao Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Chengyi Fu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Jinsuo Liu
- Yifangming (Beijing) Technology Co., Ltd, Beijing, China
| | - Liwen Fan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Dandan Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Qinghua Shao
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Lan Ma
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China
| | - Lin Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Zhendong Wang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China
| | - Yongchu Pan
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, China.,Department of Orthodontics, Affiliated Hospital of Stomatology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
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27
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Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, Zhang M, Song L, Chung CC, Zhang T, Xiao W, Albanes D, Andreotti G, Arslan AA, Babic A, Bamlet WR, Beane-Freeman L, Berndt S, Borgida A, Bracci PM, Brais L, Brennan P, Bueno-de-Mesquita B, Buring J, Canzian F, Childs EJ, Cotterchio M, Du M, Duell EJ, Fuchs C, Gallinger S, Gaziano JM, Giles GG, Giovannucci E, Goggins M, Goodman GE, Goodman PJ, Haiman C, Hartge P, Hasan M, Helzlsouer KJ, Holly EA, Klein EA, Kogevinas M, Kurtz RJ, LeMarchand L, Malats N, Männistö S, Milne R, Neale RE, Ng K, Obazee O, Oberg AL, Orlow I, Patel AV, Peters U, Porta M, Rothman N, Scelo G, Sesso HD, Severi G, Sieri S, Silverman D, Sund M, Tjønneland A, Thornquist MD, Tobias GS, Trichopoulou A, Van Den Eeden SK, Visvanathan K, Wactawski-Wende J, Wentzensen N, White E, Yu H, Yuan C, Zeleniuch-Jacquotte A, Hoover R, Brown K, Kooperberg C, Risch HA, Jacobs EJ, Li D, Yu K, Shu XO, Chanock SJ, Wolpin BM, Stolzenberg-Solomon RZ, Chatterjee N, Klein AP, Smith JP, Kraft P, Shi J, Petersen GM, Zheng W, Amundadottir LT. A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer. J Natl Cancer Inst 2020; 112:1003-1012. [PMID: 31917448 PMCID: PMC7566474 DOI: 10.1093/jnci/djz246] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 09/12/2019] [Accepted: 12/30/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Although 20 pancreatic cancer susceptibility loci have been identified through genome-wide association studies in individuals of European ancestry, much of its heritability remains unexplained and the genes responsible largely unknown. METHODS To discover novel pancreatic cancer risk loci and possible causal genes, we performed a pancreatic cancer transcriptome-wide association study in Europeans using three approaches: FUSION, MetaXcan, and Summary-MulTiXcan. We integrated genome-wide association studies summary statistics from 9040 pancreatic cancer cases and 12 496 controls, with gene expression prediction models built using transcriptome data from histologically normal pancreatic tissue samples (NCI Laboratory of Translational Genomics [n = 95] and Genotype-Tissue Expression v7 [n = 174] datasets) and data from 48 different tissues (Genotype-Tissue Expression v7, n = 74-421 samples). RESULTS We identified 25 genes whose genetically predicted expression was statistically significantly associated with pancreatic cancer risk (false discovery rate < .05), including 14 candidate genes at 11 novel loci (1p36.12: CELA3B; 9q31.1: SMC2, SMC2-AS1; 10q23.31: RP11-80H5.9; 12q13.13: SMUG1; 14q32.33: BTBD6; 15q23: HEXA; 15q26.1: RCCD1; 17q12: PNMT, CDK12, PGAP3; 17q22: SUPT4H1; 18q11.22: RP11-888D10.3; and 19p13.11: PGPEP1) and 11 at six known risk loci (5p15.33: TERT, CLPTM1L, ZDHHC11B; 7p14.1: INHBA; 9q34.2: ABO; 13q12.2: PDX1; 13q22.1: KLF5; and 16q23.1: WDR59, CFDP1, BCAR1, TMEM170A). The association for 12 of these genes (CELA3B, SMC2, and PNMT at novel risk loci and TERT, CLPTM1L, INHBA, ABO, PDX1, KLF5, WDR59, CFDP1, and BCAR1 at known loci) remained statistically significant after Bonferroni correction. CONCLUSIONS By integrating gene expression and genotype data, we identified novel pancreatic cancer risk loci and candidate functional genes that warrant further investigation.
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Affiliation(s)
- Jun Zhong
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ashley Jermusyk
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jason W Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evelina Mocci
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- US Food and Drug Administration, Silver Spring, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles C Chung
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wenming Xiao
- National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
- Division of Molecular Genetics and Pathology, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gabriella Andreotti
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan A Arslan
- Department of Obstetrics and Gynecology, New York University School of Medicine, New York, NY, USA
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - Ana Babic
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - William R Bamlet
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Laura Beane-Freeman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ayelet Borgida
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Paige M Bracci
- Department of Epidemiology and Biostatistics, University of California, CA, USA
| | - Lauren Brais
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Paul Brennan
- International Agency for Research on Cancer, Lyon, France
| | - Bas Bueno-de-Mesquita
- Department for Determinants of Chronic Diseases, National Institute for Public Health and the Environment, BA, Bilthoven, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Utrecht, The Netherlands
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Department of Social and Preventive Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Julie Buring
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Erica J Childs
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Michelle Cotterchio
- Cancer Care Ontario, University of Toronto, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Bellvitge Biomedical Research Institute, Catalan Institute of Oncology, Barcelona, Spain
| | | | - Steven Gallinger
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - J Michael Gaziano
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Aging, Brigham and Women’s Hospital, Boston, MA, USA
- Boston VA Healthcare System, Boston, MA, USA
| | - Graham G Giles
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Edward Giovannucci
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Michael Goggins
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Gary E Goodman
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Phyllis J Goodman
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Christopher Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Patricia Hartge
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Manal Hasan
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kathy J Helzlsouer
- Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Elizabeth A Holly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Eric A Klein
- Glickman Urological and Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology, Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Barcelona, Spain
- Hospital del Mar Institute of Medical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Robert J Kurtz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Loic LeMarchand
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Núria Malats
- Genetic and Molecular Epidemiology Group, Spanish National Cancer Research Center, Madrid, Spain
| | - Satu Männistö
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Roger Milne
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Melbourne, VIC, Australia
| | - Rachel E Neale
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Kimmie Ng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ofure Obazee
- Genomic Epidemiology Group, German Cancer Research Center, Heidelberg, Germany
| | - Ann L Oberg
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Irene Orlow
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alpa V Patel
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Miquel Porta
- CIBER Epidemiología y Salud Pública, Barcelona, Spain
- Hospital del Mar Institute of Medical Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ghislaine Scelo
- International Agency for Research on Cancer, Lyon, France
- Cancer Epidemiology and Intelligence Division, Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, VIC, Australia
| | - Howard D Sesso
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Gianluca Severi
- Centre de Recherche en Épidémiologie et Santé des Populations (CESP, Inserm U1018), Facultés de Medicine, Université Paris-Saclay, UPS, UVSQ, Gustave Roussy, Villejuif, France
| | - Sabina Sieri
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Debra Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Malin Sund
- Department of Surgical and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Anne Tjønneland
- Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Hellenic Health Foundation, Athens, Greece
| | - Mark D Thornquist
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Geoffrey S Tobias
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Kala Visvanathan
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, University at Buffalo, Buffalo, NY, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Emily White
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Herbert Yu
- Cancer Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Chen Yuan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anne Zeleniuch-Jacquotte
- Department of Population Health, New York University School of Medicine, New York, NY, USA
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Robert Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Eric J Jacobs
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Rachael Z Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Biostatistics, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jill P Smith
- Department of Medicine, Georgetown University, Washington, DC, USA
| | - Peter Kraft
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Laufey T Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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28
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Evans P, Cox NJ, Gamazon ER. The regulatory genome constrains protein sequence evolution: implications for the search for disease-associated genes. PeerJ 2020; 8:e9554. [PMID: 32765967 PMCID: PMC7380284 DOI: 10.7717/peerj.9554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 06/24/2020] [Indexed: 11/20/2022] Open
Abstract
The development of explanatory models of protein sequence evolution has broad implications for our understanding of cellular biology, population history, and disease etiology. Here we analyze the GTEx transcriptome resource to quantify the effect of the transcriptome on protein sequence evolution in a multi-tissue framework. We find substantial variation among the central nervous system tissues in the effect of expression variance on evolutionary rate, with highly variable genes in the cortex showing significantly greater purifying selection than highly variable genes in subcortical regions (Mann-Whitney U p = 1.4 × 10-4). The remaining tissues cluster in observed expression correlation with evolutionary rate, enabling evolutionary analysis of genes in diverse physiological systems, including digestive, reproductive, and immune systems. Importantly, the tissue in which a gene attains its maximum expression variance significantly varies (p = 5.55 × 10-284) with evolutionary rate, suggesting a tissue-anchored model of protein sequence evolution. Using a large-scale reference resource, we show that the tissue-anchored model provides a transcriptome-based approach to predicting the primary affected tissue of developmental disorders. Using gradient boosted regression trees to model evolutionary rate under a range of model parameters, selected features explain up to 62% of the variation in evolutionary rate and provide additional support for the tissue model. Finally, we investigate several methodological implications, including the importance of evolutionary-rate-aware gene expression imputation models using genetic data for improved search for disease-associated genes in transcriptome-wide association studies. Collectively, this study presents a comprehensive transcriptome-based analysis of a range of factors that may constrain molecular evolution and proposes a novel framework for the study of gene function and disease mechanism.
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Affiliation(s)
- Patrick Evans
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Nancy J Cox
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America
| | - Eric R Gamazon
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, United States of America.,Clare Hall, University of Cambridge, Cambridge, United Kingdom.,MRC Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom.,Data Science Institute, Vanderbilt University, Nashville, TN, United States of America
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Feng H, Gusev A, Pasaniuc B, Wu L, Long J, Abu-full Z, Aittomäki K, Andrulis IL, Anton-Culver H, Antoniou AC, Arason A, Arndt V, Aronson KJ, Arun BK, Asseryanis E, Auer PL, Azzollini J, Balmaña J, Barkardottir RB, Barnes DR, Barrowdale D, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Białkowska K, Blanco A, Blomqvist C, Boeckx B, Bogdanova NV, Bojesen SE, Bolla MK, Bonanni B, Borg A, Brauch H, Brenner H, Briceno I, Broeks A, Brüning T, Burwinkel B, Cai Q, Caldés T, Caligo MA, Campbell I, Canisius S, Campa D, Carter BD, Carter J, Castelao JE, Chang-Claude J, Chanock SJ, Christiansen H, Chung WK, Claes KBM, Clarke CL, Couch FJ, Cox A, Cross SS, Cybulski C, Czene K, Daly MB, de la Hoya M, De Leeneer K, Dennis J, Devilee P, Diez O, Domchek SM, Dörk T, dos-Santos-Silva I, Dunning AM, Dwek M, Eccles DM, Ejlertsen B, Ellberg C, Engel C, Eriksson M, Fasching PA, Fletcher O, Flyger H, Fostira F, Friedman E, Fritschi L, Frost D, Gabrielson M, Ganz PA, Gapstur SM, Garber J, García-Closas M, García-Sáenz JA, Gaudet MM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Gronwald J, Guénel P, Haiman CA, Hall P, Hamann U, Hake C, He W, Heyworth J, Hogervorst FB, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Huang G, Hulick PJ, Humphreys K, Imyanitov EN, Isaacs C, Jakimovska M, Jakubowska A, James P, Janavicius R, Jankowitz RC, John EM, Johnson N, Joseph V, Jung A, Karlan BY, Khusnutdinova E, Kiiski JI, Konstantopoulou I, Kristensen VN, Laitman Y, Lambrechts D, Lazaro C, Leroux D, Leslie G, Lester J, Lesueur F, Lindor N, Lindström S, Lo WY, Loud JT, Lubiński J, Makalic E, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martens JW, Martinez ME, Matricardi L, Maurer T, Mavroudis D, McGuffog L, Meindl A, Menon U, Michailidou K, Kapoor PM, Miller A, Montagna M, Moreno F, Moserle L, Mulligan AM, Muranen TA, Nathanson KL, Neuhausen SL, Nevanlinna H, Nevelsteen I, Nielsen FC, Nikitina-Zake L, Offit K, Olah E, Olopade OI, Olsson H, Osorio A, Papp J, Park-Simon TW, Parsons MT, Pedersen IS, Peixoto A, Peterlongo P, Peto J, Pharoah PD, Phillips KA, Plaseska-Karanfilska D, Poppe B, Pradhan N, Prajzendanc K, Presneau N, Punie K, Pylkäs K, Radice P, Rantala J, Rashid MU, Rennert G, Risch HA, Robson M, Romero A, Saloustros E, Sandler DP, Santos C, Sawyer EJ, Schmidt MK, Schmidt DF, Schmutzler RK, Schoemaker MJ, Scott RJ, Sharma P, Shu XO, Simard J, Singer CF, Skytte AB, Soucy P, Southey MC, Spinelli JJ, Spurdle AB, Stone J, Swerdlow AJ, Tapper WJ, Taylor JA, Teixeira MR, Terry MB, Teulé A, Thomassen M, Thöne K, Thull DL, Tischkowitz M, Toland AE, Tollenaar RAEM, Torres D, Truong T, Tung N, Vachon CM, van Asperen CJ, van den Ouweland AMW, van Rensburg EJ, Vega A, Viel A, Vieiro-Balo P, Wang Q, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Winqvist R, Yang XR, Yannoukakos D, Ziogas A, Milne RL, Easton DF, Chenevix-Trench G, Zheng W, Kraft P, Jiang X. Transcriptome-wide association study of breast cancer risk by estrogen-receptor status. Genet Epidemiol 2020; 44:442-468. [PMID: 32115800 PMCID: PMC7987299 DOI: 10.1002/gepi.22288] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/13/2020] [Accepted: 02/13/2020] [Indexed: 12/24/2022]
Abstract
Previous transcriptome-wide association studies (TWAS) have identified breast cancer risk genes by integrating data from expression quantitative loci and genome-wide association studies (GWAS), but analyses of breast cancer subtype-specific associations have been limited. In this study, we conducted a TWAS using gene expression data from GTEx and summary statistics from the hitherto largest GWAS meta-analysis conducted for breast cancer overall, and by estrogen receptor subtypes (ER+ and ER-). We further compared associations with ER+ and ER- subtypes, using a case-only TWAS approach. We also conducted multigene conditional analyses in regions with multiple TWAS associations. Two genes, STXBP4 and HIST2H2BA, were specifically associated with ER+ but not with ER- breast cancer. We further identified 30 TWAS-significant genes associated with overall breast cancer risk, including four that were not identified in previous studies. Conditional analyses identified single independent breast-cancer gene in three of six regions harboring multiple TWAS-significant genes. Our study provides new information on breast cancer genetics and biology, particularly about genomic differences between ER+ and ER- breast cancer.
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Affiliation(s)
- Helian Feng
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | | | - Lang Wu
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Zomoroda Abu-full
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Irene L. Andrulis
- Fred A, Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, California
| | - Antonis C. Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J. Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen’s University, Kingston, Ontario, Canada
| | - Banu K. Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ella Asseryanis
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Paul L. Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, Vall d’Hebron Institute of Oncology, Barcelona, Spain
| | - Rosa B. Barkardottir
- Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Daniel R. Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias W. Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Javier Benitez
- Centro de Investigaci—n en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Ana Blanco
- Centro de Investigaci—n en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundaci—n Pœblica Galega Medicina Xen—mica, Santiago De Compostela, Spain
- Instituto de Investigacion Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, University Hospital, Karolinska Institute, Stockholm, Sweden
| | - Bram Boeckx
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Natalia V. Bogdanova
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- NN Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E. Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bernardo Bonanni
- Division of Cancer Prevention and Genetics, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, Lund, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence, University of Tuebingen, Tuebingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Ignacio Briceno
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Medical Faculty, Universidad de La Sabana, Bogota, Colombia
| | - Annegien Broeks
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr University Bochum (IPA), Bochum, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, Heidelberg, Germany
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Trinidad Caldés
- Medical Oncology Department, Hospital Cl’nico San Carlos, Instituto de Investigaci—n Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maria A. Caligo
- Section of Molecular Genetics, Dept, of Laboratory Medicine, University Hospital of Pisa, Pisa, Italy
| | - Ian Campbell
- Research Department, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute—Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Daniele Campa
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brian D. Carter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Jonathan Carter
- Department of Gynaecological Oncology, Chris OÕBrien Lifehouse and The University of Sydney, Camperdown, New South Wales, Australia
| | - Jose E. Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hans Christiansen
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Wendy K. Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, New York
| | | | - Christine L. Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - GEMO Study Collaborators
- Department of Tumour Biology, INSERM U830, Paris, France
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
| | - EMBRACE Collaborators
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - GC-HBOC study Collaborators
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Angela Cox
- Department of Oncology and Metabolism, Sheffield Institute for Nucleic Acids (SInFoNiA), University of Sheffield, Sheffield, UK
| | - Simon S. Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Cezary Cybulski
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B. Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Miguel de la Hoya
- Medical Oncology Department, Hospital Cl’nico San Carlos, Instituto de Investigaci—n Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Kim De Leeneer
- Centre for Medical Genetics, Ghent University, Gent, Belgium
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Orland Diez
- Hereditary Cancer Genetics Group, Area of Clinical and Molecular Genetics, Vall dHebron Institute of Oncology (VHIO), University Hospital Vall d’Hebron, Barcelona, Spain
- Clinical and Molecular Genetics Area, University Hospital Vall dHebron, Barcelona, Spain
| | - Susan M. Domchek
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Diana M. Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Carolina Ellberg
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE - Leipzig Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter A. Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, California
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Lin Fritschi
- School of Public Health, Curtin University, Perth, Western Australia, Australia
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Patricia A. Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Centre, UCLA, Los Angeles, California
| | - Susan M. Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
| | - José A. García-Sáenz
- Medical Oncology Department, Hospital Cl’nico San Carlos, Instituto de Investigaci—n Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Mia M. Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Graham G. Giles
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Gord Glendon
- Fred A, Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Andrew K. Godwin
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, Kanas
| | - Mark S. Goldberg
- Department of Medicine, McGill University, Montreal, Quebec, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montreal, Quebec, Canada
| | - David E. Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Mark H. Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Sšdersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christopher Hake
- City of Hope Clinical Cancer Genetics Community Research Network, Duarte, California
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jane Heyworth
- School of Population and Global Health, The University of Western Australia, Perth, Western Australia, Australia
| | - Frans B.L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Robert N. Hoover
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Guanmengqian Huang
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter J. Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, Illinois
- The University of Chicago Pritzker School of Medicine, Chicago, Illinois
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - ABCTB Investigators
- Australian Breast Cancer Tissue Bank, Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - HEBON Investigators
- The Hereditary Breast and Ovarian Cancer Research Group Netherlands (HEBON), Coordinating Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - BCFR Investigators
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - OCGN Investigators
- Ontario Cancer Genetics Network, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia
| | - Milena Jakimovska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D, Efremov’, Macedonian Academy of Sciences and Arts, Skopje Republic of North Macedonia, North Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
| | | | - Rachel C. Jankowitz
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Esther M. John
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Vijai Joseph
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Beth Y. Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, California
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, Ufa, Russia
| | - Johanna I. Kiiski
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | - Vessela N. Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, ICO-IDIBELL (Bellvitge Biomedical Research Institute, Catalan Institute of Oncology), CIBERONC, Barcelona, Spain
| | | | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California, Los Angeles, California
| | - Fabienne Lesueur
- Institut Curie, Paris, France
- Mines ParisTech, Fontainebleau, France
- Genetic Epidemiology of Cancer Team, Inserm U900, Paris, France
| | - Noralane Lindor
- Department of Health Sciences Research, Mayo Clinic, Scottsdale, Arizona
| | - Sara Lindström
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- iFIT-Cluster of Excellence, University of Tuebingen, Tuebingen, Germany
| | - Jennifer T. Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Sara Margolin
- Department of Oncology, Sšdersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Sšdersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - John W.M. Martens
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Maria E. Martinez
- Moores Cancer Center, University of California San Diego, La Jolla, California
- Department of Family Medicine and Public Health, University of California San Diego, La Jolla, California
| | - Laura Matricardi
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology ÊIOV—IRCCS, Padua, Italy
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology and The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Pooja M. Kapoor
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, New York
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology ÊIOV—IRCCS, Padua, Italy
| | - Fernando Moreno
- Medical Oncology Department, Hospital Cl’nico San Carlos, Instituto de Investigaci—n Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Lidia Moserle
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology ÊIOV—IRCCS, Padua, Italy
| | - Anna M. Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Taru A. Muranen
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Katherine L. Nathanson
- Department of Medicine, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Ines Nevelsteen
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Finn C. Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Ana Osorio
- Centro de Investigaci—n en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | | | - Michael T. Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Inge S. Pedersen
- Section of Molecular Diagnostics, Clinical Biochemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM—The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Paul D.P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kelly-Anne Phillips
- Research Department, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Medicine Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology ‘Georgi D, Efremov’, Macedonian Academy of Sciences and Arts, Skopje Republic of North Macedonia, North Macedonia
| | - Bruce Poppe
- Centre for Medical Genetics, Ghent University, Gent, Belgium
| | - Nisha Pradhan
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Karolina Prajzendanc
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
| | - Nadege Presneau
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Kevin Punie
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, Italy
| | | | - Muhammad Usman Rashid
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Basic Sciences, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH & RC), Lahore, Pakistan
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Atocha Romero
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Catarina Santos
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Elinor J. Sawyer
- Research Oncology, GuyÕs Hospital, King’s College London, London, UK
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Daniel F. Schmidt
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Faculty of Information Technology, Monash University, Melbourne, Victoria, Australia
| | - Rita K. Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | | | - Rodney J Scott
- Division of Molecular Medicine, Pathology North, John Hunter Hospital, Newcastle, New South Wales, Australia
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Callaghan, New South Wales, Australia
- Hunter Medical Research Institute, John Hunter Hospital, Newcastle, New South Wales, Australia
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology, University of Kansas Medical Center, Westwood, Kanas
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Quebec–Universite Laval, Research Center, Quebec City, Qubec, Canada
| | - Christian F. Singer
- Department of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Anne-Bine Skytte
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus N, Denmark
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Quebec–Universite Laval, Research Center, Quebec City, Qubec, Canada
| | - Melissa C. Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - John J. Spinelli
- Population Oncology, BC Cancer, Vancouver, British of Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British of Columbia, Canada
| | - Amanda B. Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, Western Australia, Australia
| | - Anthony J. Swerdlow
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | | | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Manuel R. Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Alex Teulé
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence C, Denmark
| | - Kathrin Thöne
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Darcy L. Thull
- Department of Medicine, Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montreal, Quebec, Canada
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Amanda E. Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio
| | | | - Diana Torres
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Celine M. Vachon
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, Minnesota
| | - Christi J. van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Ana Vega
- Centro de Investigaci—n en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Fundaci—n Pœblica Galega Medicina Xen—mica, Santiago De Compostela, Spain
- Instituto de Investigacion Sanitaria de Santiago de Compostela, Santiago de Compostela, Spain
| | - Alessandra Viel
- Division of Functional Onco-genomics and Genetics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Paula Vieiro-Balo
- Hospital Clínico Universitario (SERGAS), Universidad de Santiago de Compostela, CIMUS, Santiago de Compostela, España
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Clarice R. Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | | | - Camilla Wendt
- Department of Clinical Science and Education, Sšdersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research ‘Demokritos’, Athens, Greece
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, California
| | - Roger L. Milne
- Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Xia Jiang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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Tian J, Ying P, Ke J, Zhu Y, Yang Y, Gong Y, Zou D, Peng X, Yang N, Wang X, Mei S, Zhang Y, Wang C, Zhong R, Chang J, Miao X. ANKLE1 N 6 -Methyladenosine-related variant is associated with colorectal cancer risk by maintaining the genomic stability. Int J Cancer 2020; 146:3281-3293. [PMID: 31509622 DOI: 10.1002/ijc.32677] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Accepted: 09/05/2019] [Indexed: 12/21/2022]
Abstract
The N6 -Methyladenosine (m6 A) modification plays an important role in many biological processes, especially tumor development. However, little is still known about how it affects colorectal cancer (CRC) carcinogenesis. Here, we first systematically investigate the association of variants related to m6 A modification with the CRC risk in 1,062 CRC cases and 2,184 controls by using our exome-wide association data and followed by two replication sets including 7,341 CRC cases and 7,902 controls. The variant rs8100241 located in ANKLE1 was significantly associated with CRC risk (odds ratio = 0.88, 95% confidence interval = 0.84-0.92, p = 4.85 × 10-8 ) in 8,403 cases and 10,086 controls. This variant was previously identified to be associated with the susceptibility of breast cancer with BRCA1 mutation triple negative breast cancer. Further functional analysis indicated that overexpression of the rs8100241[A] allele significantly increased the ANKLE1 m6 A level and facilitated the ANKLE1 protein expression compared to that of rs8100241[G] allele. We further found the ANKLE1 m6 A modification was catalyzed by the "writer" complex (METTL3, METTL14, or WTAP) and recognized by the "reader" YTHDF1. Mechanistically, we found that the ANKLE1 functions as a potential tumor suppressor that inhibits cell proliferation and facilitates the genomic stability. An elevated frequency of micronucleated cells, increased cell proliferation, and colony formation ability were observed when ANKLE1 knockdown. Our study illustrated that the germline missense variant can increase CRC risk by influencing ANKLE1 m6 A level, highlighting a clinical potential of variants-associated m6 A modification as a risk marker for CRC prevention.
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Affiliation(s)
- Jianbo Tian
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Pingting Ying
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Juntao Ke
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Ying Zhu
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yang Yang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yajie Gong
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Danyi Zou
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Xiating Peng
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Nan Yang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Xiaoyang Wang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Shufang Mei
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yuxing Zhang
- Department of Colorectal Surgery, The Eighth Hospital of Wuhan City, Wuhan, China
| | - Changyi Wang
- Department of Non-Communicable Disease Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Rong Zhong
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Jiang Chang
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Xiaoping Miao
- Key Laboratory for Environment and Health (Ministry of Education), Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
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Zhang M, Wang X, Chen X, Guo F, Hong J. Prognostic Value of a Stemness Index-Associated Signature in Primary Lower-Grade Glioma. Front Genet 2020; 11:441. [PMID: 32431729 PMCID: PMC7216823 DOI: 10.3389/fgene.2020.00441] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/09/2020] [Indexed: 12/20/2022] Open
Abstract
Objective As a prevalent and infiltrative cancer type of the central nervous system, the prognosis of lower-grade glioma (LGG) in adults is highly heterogeneous. Recent evidence has demonstrated the prognostic value of the mRNA expression-based stemness index (mRNAsi) in LGG. Our aim was to develop a stemness index-based signature (SI-signature) for risk stratification and survival prediction. Methods Differentially expressed genes (DEGs) between LGG in the Cancer Genome Atlas (TCGA) and normal brain tissue samples from the Genotype-Tissue Expression (GTEx) project were screened out, and the weighted gene correlation network analysis (WGCNA) was employed to identify the mRNAsi-related gene sets. Meanwhile, the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed for the functional annotation of the key genes. ESTIMATE was used to calculate tumor purity for acquiring the correct mRNAsi. Differences in overall survival (OS) between the high and low mRNAsi (corrected mRNAsi) groups were compared using the Kaplan Meier analysis. By combining the Lasso regression with univariate and multivariate Cox regression, the SI-signature was constructed and validated using the Chinese Glioma Genome Atlas (CGGA). Results There was a significant difference in OS between the high and low mRNAsi groups, which was also observed in the two corrected mRNAsi groups. Based on threshold limits, 86 DEGs were most significantly associated with mRNAsi via WGCNA. Seven genes (ADAP2, ALOX5AP, APOBEC3C, FCGRT, GNG5, LRRC25, and SP100) were selected to establish a risk signature for primary LGG. The ROC curves showed a fair performance in survival prediction in both the TCGA and the CGGA validation cohorts. Univariate and multivariate Cox regression revealed that the risk group was an independent prognostic factor in primary LGG. The nomogram was developed based on clinical parameters integrated with the risk signature, and its accuracy for predicting 3- and 5-years survival was assessed by the concordance index, the area under the curve of the time-dependent receiver operating characteristics curve, and calibration curves. Conclusion The SI-signature with seven genes could serve as an independent predictor, and suggests the importance of stemness features in risk stratification and survival prediction in primary LGG.
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Affiliation(s)
- Mingwei Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.,Institute of Immunotherapy, Fujian Medical University, Fuzhou, China.,Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou, China.,Fujian Key Laboratory of Individualized Active Immunotherapy, Fuzhou, China.,Fujian Medical University Union Hospital, Fuzhou, China
| | - Xuezhen Wang
- Department of Radiation Oncology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Xiaoping Chen
- Department of Statistics, College of Mathematics and Informatics & FJKLMAA, Fujian Normal University, Fuzhou, China
| | - Feibao Guo
- Department of Radiation Oncology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jinsheng Hong
- Department of Radiation Oncology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China.,Key Laboratory of Radiation Biology (Fujian Medical University), Fujian Province University, Fuzhou, China.,Fujian Key Laboratory of Individualized Active Immunotherapy, Fuzhou, China
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Bhattacharya A, García-Closas M, Olshan AF, Perou CM, Troester MA, Love MI. A framework for transcriptome-wide association studies in breast cancer in diverse study populations. Genome Biol 2020; 21:42. [PMID: 32079541 PMCID: PMC7033948 DOI: 10.1186/s13059-020-1942-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/21/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The relationship between germline genetic variation and breast cancer survival is largely unknown, especially in understudied minority populations who often have poorer survival. Genome-wide association studies (GWAS) have interrogated breast cancer survival but often are underpowered due to subtype heterogeneity and clinical covariates and detect loci in non-coding regions that are difficult to interpret. Transcriptome-wide association studies (TWAS) show increased power in detecting functionally relevant loci by leveraging expression quantitative trait loci (eQTLs) from external reference panels in relevant tissues. However, ancestry- or race-specific reference panels may be needed to draw correct inference in ancestrally diverse cohorts. Such panels for breast cancer are lacking. RESULTS We provide a framework for TWAS for breast cancer in diverse populations, using data from the Carolina Breast Cancer Study (CBCS), a population-based cohort that oversampled black women. We perform eQTL analysis for 406 breast cancer-related genes to train race-stratified predictive models of tumor expression from germline genotypes. Using these models, we impute expression in independent data from CBCS and TCGA, accounting for sampling variability in assessing performance. These models are not applicable across race, and their predictive performance varies across tumor subtype. Within CBCS (N = 3,828), at a false discovery-adjusted significance of 0.10 and stratifying for race, we identify associations in black women near AURKA, CAPN13, PIK3CA, and SERPINB5 via TWAS that are underpowered in GWAS. CONCLUSIONS We show that carefully implemented and thoroughly validated TWAS is an efficient approach for understanding the genetics underpinning breast cancer outcomes in diverse populations.
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Affiliation(s)
- Arjun Bhattacharya
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Andrew F. Olshan
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Charles M. Perou
- Lineberger Comprehensive Cancer Center, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Melissa A. Troester
- Department of Epidemiology, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Pathology and Laboratory Medicine, University of North Carolina-Chapel Hill, Chapel Hill, USA
| | - Michael I. Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, USA
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, USA
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Bioinformatic profiling of prognosis-related genes in the breast cancer immune microenvironment. Aging (Albany NY) 2019; 11:9328-9347. [PMID: 31715586 PMCID: PMC6874454 DOI: 10.18632/aging.102373] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/12/2019] [Indexed: 02/07/2023]
Abstract
In the microenvironment of breast cancer, immune cell infiltration is associated with an improved prognosis. To identify immune-related prognostic markers and therapeutic targets, we determined the lymphocyte-specific kinase (LCK) metagene scores of samples from breast cancer patients in The Cancer Genome Atlas. The LCK metagene score correlated highly with other immune-related scores, as well as with the clinical stage, prognosis and tumor suppressor gene mutation status (BRCA2, TP53, PTEN) of patients in the four breast cancer subtypes. A weighted gene co-expression network analysis was performed to detect representative genes from LCK metagene-related gene modules. In two of these modules, the levels of the co-expressed genes correlated highly with LCK metagene levels, so we conducted an enrichment analysis to discover their functions. We also identified differentially expressed genes in samples with high and low LCK metagene scores. By examining the overlapping results from these analyses, we obtained 115 genes, and found that 22 of them were independent predictors of overall survival in breast cancer patients. These genes were validated for their prognostic and diagnostic value with external data sets and paired tumor and non-tumor tissues. The genes identified herein could serve as diagnostic/prognostic markers and immune-related therapeutic targets in breast cancer.
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Cheng Z, Hou S, Wu Y, Wang X, Sun Y, Liu B, Yuan M. LINC01419 promotes cell proliferation and metastasis in lung adenocarcinoma via sponging miR-519b-3p to up-regulate RCCD1. Biochem Biophys Res Commun 2019; 520:107-114. [PMID: 31582214 DOI: 10.1016/j.bbrc.2019.09.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/21/2019] [Indexed: 12/19/2022]
Abstract
Lung adenocarcinoma (LUAD) is one of the most common type of lung cancer notorious for the high incidence and mortality around the world. Long non-coding RNAs (LncRNAs) are defined as a class of RNAs with length more than 200 nucleotides. Mounting studies have proved that lncRNAs are related closely to incidence of diseases and play crucial roles in cancer progression. Although LINC01419 has been studied in several cancers, the function and mechanism of LINC01419 in LUAD remains a mystery. Our findings showed that LINC01419 level was high in LUAD cells, and LINC01419 knockdown inhibited carcinogenesis via suppressing cell proliferation, migration as well as invasion. Moreover, bioinformatics prediction, luciferase reporter experiments and RIP assay were used to confirm miR-519-3p was sequestered and negatively regulated by LINC01419. Subsequently, RCCD1 was identified as a miR-519b-3p target and had inverse relationship with miR-519b-3p. LINC01419 was positively related to RCCD1. Furthermore, rescue assays confirmed that miR-519b-3p inhibitor or RCCD1 overexpression could neutralize the effect of LINC01419 silenced in cell proliferation, migration and invasion. Taken together, all the results indicated that LINC01419 exhibited oncogenic behaviors LUAD via binding to miR-519b-3p to enhance the expression of RCCD1, manifesting the underlying therapy values of LINC01419 in LUAD.
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Affiliation(s)
- Ziming Cheng
- Department of Thoracic Surgery, Linyi Central Hospital. No.17, Health Road, Linyi, Shandong, 276400, China
| | - Shizhen Hou
- Department of Thoracic Surgery, Linyi Central Hospital. No.17, Health Road, Linyi, Shandong, 276400, China.
| | - Yubing Wu
- Department of Thoracic Surgery, Linyi Central Hospital. No.17, Health Road, Linyi, Shandong, 276400, China
| | - Xiangdong Wang
- Department of Thoracic Surgery, Linyi Central Hospital. No.17, Health Road, Linyi, Shandong, 276400, China
| | - Yi Sun
- Department of Thoracic Surgery, Linyi Central Hospital. No.17, Health Road, Linyi, Shandong, 276400, China
| | - Bing Liu
- Department of Thoracic Surgery, Linyi Central Hospital. No.17, Health Road, Linyi, Shandong, 276400, China
| | - Maoxi Yuan
- Department of Thoracic Surgery, Linyi Central Hospital. No.17, Health Road, Linyi, Shandong, 276400, China
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Olivier M, Asmis R, Hawkins GA, Howard TD, Cox LA. The Need for Multi-Omics Biomarker Signatures in Precision Medicine. Int J Mol Sci 2019; 20:ijms20194781. [PMID: 31561483 PMCID: PMC6801754 DOI: 10.3390/ijms20194781] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/11/2019] [Accepted: 09/25/2019] [Indexed: 12/12/2022] Open
Abstract
Recent advances in omics technologies have led to unprecedented efforts characterizing the molecular changes that underlie the development and progression of a wide array of complex human diseases, including cancer. As a result, multi-omics analyses—which take advantage of these technologies in genomics, transcriptomics, epigenomics, proteomics, metabolomics, and other omics areas—have been proposed and heralded as the key to advancing precision medicine in the clinic. In the field of precision oncology, genomics approaches, and, more recently, other omics analyses have helped reveal several key mechanisms in cancer development, treatment resistance, and recurrence risk, and several of these findings have been implemented in clinical oncology to help guide treatment decisions. However, truly integrated multi-omics analyses have not been applied widely, preventing further advances in precision medicine. Additional efforts are needed to develop the analytical infrastructure necessary to generate, analyze, and annotate multi-omics data effectively to inform precision medicine-based decision-making.
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Affiliation(s)
- Michael Olivier
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Reto Asmis
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Gregory A Hawkins
- Center for Precision Medicine, Department of Biochemistry, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Timothy D Howard
- Center for Precision Medicine, Department of Biochemistry, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
| | - Laura A Cox
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest Baptist Health Comprehensive Cancer Center, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA.
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36
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Ferreira MA, Gamazon ER, Al-Ejeh F, Aittomäki K, Andrulis IL, Anton-Culver H, Arason A, Arndt V, Aronson KJ, Arun BK, Asseryanis E, Azzollini J, Balmaña J, Barnes DR, Barrowdale D, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Białkowska K, Blomqvist C, Bogdanova NV, Bojesen SE, Bolla MK, Borg A, Brauch H, Brenner H, Broeks A, Burwinkel B, Caldés T, Caligo MA, Campa D, Campbell I, Canzian F, Carter J, Carter BD, Castelao JE, Chang-Claude J, Chanock SJ, Christiansen H, Chung WK, Claes KBM, Clarke CL, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, de la Hoya M, Dennis J, Devilee P, Diez O, Dörk T, Dunning AM, Dwek M, Eccles DM, Ejlertsen B, Ellberg C, Engel C, Eriksson M, Fasching PA, Fletcher O, Flyger H, Friedman E, Frost D, Gabrielson M, Gago-Dominguez M, Ganz PA, Gapstur SM, Garber J, García-Closas M, García-Sáenz JA, Gaudet MM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Gronwald J, Guénel P, Haiman CA, Hall P, Hamann U, He W, Heyworth J, Hogervorst FBL, Hollestelle A, Hoover RN, Hopper JL, Hulick PJ, Humphreys K, Imyanitov EN, Isaacs C, Jakimovska M, Jakubowska A, James PA, Janavicius R, Jankowitz RC, John EM, Johnson N, Joseph V, Karlan BY, Khusnutdinova E, Kiiski JI, Ko YD, Jones ME, Konstantopoulou I, Kristensen VN, Laitman Y, Lambrechts D, Lazaro C, Leslie G, Lester J, Lesueur F, Lindström S, Long J, Loud JT, Lubiński J, Makalic E, Mannermaa A, Manoochehri M, Margolin S, Maurer T, Mavroudis D, McGuffog L, Meindl A, Menon U, Michailidou K, Miller A, Montagna M, Moreno F, Moserle L, Mulligan AM, Nathanson KL, Neuhausen SL, Nevanlinna H, Nevelsteen I, Nielsen FC, Nikitina-Zake L, Nussbaum RL, Offit K, Olah E, Olopade OI, Olsson H, Osorio A, Papp J, Park-Simon TW, Parsons MT, Pedersen IS, Peixoto A, Peterlongo P, Pharoah PDP, Plaseska-Karanfilska D, Poppe B, Presneau N, Radice P, Rantala J, Rennert G, Risch HA, Saloustros E, Sanden K, Sawyer EJ, Schmidt MK, Schmutzler RK, Sharma P, Shu XO, Simard J, Singer CF, Soucy P, Southey MC, Spinelli JJ, Spurdle AB, Stone J, Swerdlow AJ, Tapper WJ, Taylor JA, Teixeira MR, Terry MB, Teulé A, Thomassen M, Thöne K, Thull DL, Tischkowitz M, Toland AE, Torres D, Truong T, Tung N, Vachon CM, van Asperen CJ, van den Ouweland AMW, van Rensburg EJ, Vega A, Viel A, Wang Q, Wappenschmidt B, Weitzel JN, Wendt C, Winqvist R, Yang XR, Yannoukakos D, Ziogas A, Kraft P, Antoniou AC, Zheng W, Easton DF, Milne RL, Beesley J, Chenevix-Trench G. Genome-wide association and transcriptome studies identify target genes and risk loci for breast cancer. Nat Commun 2019; 10:1741. [PMID: 30988301 PMCID: PMC6465407 DOI: 10.1038/s41467-018-08053-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 12/14/2018] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 170 breast cancer susceptibility loci. Here we hypothesize that some risk-associated variants might act in non-breast tissues, specifically adipose tissue and immune cells from blood and spleen. Using expression quantitative trait loci (eQTL) reported in these tissues, we identify 26 previously unreported, likely target genes of overall breast cancer risk variants, and 17 for estrogen receptor (ER)-negative breast cancer, several with a known immune function. We determine the directional effect of gene expression on disease risk measured based on single and multiple eQTL. In addition, using a gene-based test of association that considers eQTL from multiple tissues, we identify seven (and four) regions with variants associated with overall (and ER-negative) breast cancer risk, which were not reported in previous GWAS. Further investigation of the function of the implicated genes in breast and immune cells may provide insights into the etiology of breast cancer.
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Affiliation(s)
- Manuel A Ferreira
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
| | - Eric R Gamazon
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN, 37235, USA
- Clare Hall, University of Cambridge, Cambridge, CB3 9AL, UK
| | - Fares Al-Ejeh
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, 00290, Helsinki, Finland
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA, 92617
| | - Adalgeir Arason
- Department of Pathology, Landspitali University Hospital, 101, Reykjavik, Iceland
- BMC (Biomedical Centre), Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, C070, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ella Asseryanis
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), 20133, Milan, Italy
| | - Judith Balmaña
- Oncogenetics Group, Vall dHebron Institute of Oncology (VHIO), 8035, Barcelona, Spain
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology (VHIO), University Hospital, Vall d'Hebron, 08035, Barcelona, Spain
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, 91054, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Javier Benitez
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), 46010, Valencia, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of Russian Academy of Sciences, 450054, Ufa, Russia
| | - Katarzyna Białkowska
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, 00290, Finland
- Department of Oncology, Örebro University Hospital, 70185, Örebro, Sweden
| | - Natalia V Bogdanova
- Department of Radiation Oncology, Hannover Medical School, 30625, Hannover, Germany
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, 223040, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Ake Borg
- Department of Oncology, Lund University and Skåne University Hospital, 222 41, Lund, Sweden
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, 70376, Stuttgart, Germany
- University of Tübingen, 72074, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, C070, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), 69120, Heidelberg, Germany
| | - Annegien Broeks
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, 1066 CX, Amsterdam, The Netherlands
| | - Barbara Burwinkel
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg, University of Heidelberg, 69120, Heidelberg, Germany
| | - Trinidad Caldés
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040, Madrid, Spain
| | - Maria A Caligo
- Section of Molecular Genetics, Dept. of Laboratory Medicine, University Hospital of Pisa, 56126, Pisa, Italy
| | - Daniele Campa
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Department of Biology, University of Pisa, 56126, Pisa, Italy
| | - Ian Campbell
- Research Department, Peter MacCallum Cancer Center, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3000, Australia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Jonathan Carter
- Department of Gynaecological Oncology, Chris O'Brien Lifehouse and The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Brian D Carter
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA, 30303
| | - Jose E Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, 36312, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20850, USA
| | - Hans Christiansen
- Department of Radiation Oncology, Hannover Medical School, 30625, Hannover, Germany
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, 10032, USA
| | | | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, NSW, 2145, Australia
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Angela Cox
- Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, S10 2TN, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, S10 2TN, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Miguel de la Hoya
- Molecular Oncology Laboratory, CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), 28040, Madrid, Spain
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, 2333 ZA, Leiden, The Netherlands
| | - Orland Diez
- Oncogenetics Group, Vall dHebron Institute of Oncology (VHIO), 8035, Barcelona, Spain
- Clinical and Molecular Genetics Area, University Hospital Vall dHebron, Barcelona, 08035, Spain
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, 30625, Hannover, Germany
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Miriam Dwek
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, W1B 2HW, UK
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Bent Ejlertsen
- Department of Oncology, Rigshospitalet, Copenhagen University Hospital, DK-2100, Copenhagen, Denmark
| | - Carolina Ellberg
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, 222 42, Lund, Sweden
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107, Leipzig, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, 91054, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, 2730, Herlev, Denmark
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, 52621, Ramat Gan, Israel
- Sackler Faculty of Medicine, Tel Aviv University, 69978, Ramat Aviv, Israel
| | - Debra Frost
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, 15706, Santiago de Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, 92037, USA
| | - Patricia A Ganz
- Schools of Medicine and Public Health, Division of Cancer Prevention & Control Research, Jonsson Comprehensive Cancer Centre, UCLA, Los Angeles, CA, 90096-6900, USA
| | - Susan M Gapstur
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA, 30303
| | - Judy Garber
- Cancer Risk and Prevention Clinic, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20850, USA
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, SM2 5NG, UK
| | - José A García-Sáenz
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), 28040, Madrid, Spain
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, GA, USA, 30303
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, VIC, 3004, Australia
| | - Gord Glendon
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, ON, M5G 1X5, Canada
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS, 66160, USA
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, QC, H4A 3J1, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, QC, H4A 3J1, Canada
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Anna González-Neira
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20850-9772, USA
| | - Jacek Gronwald
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, 94805, Villejuif, France
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, 118 83, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | - Jane Heyworth
- School of Population and Global Health, The University of Western Australia, Perth, WA, 6009, Australia
| | - Frans B L Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, 1066 CX, The Netherlands
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, 3015 CN, The Netherlands
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20850, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Peter J Hulick
- Center for Medical Genetics, NorthShore University HealthSystem, Evanston, IL, 60201, USA
- The University of Chicago Pritzker School of Medicine, Chicago, IL, 60637, USA
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 65, Stockholm, Sweden
| | | | - Claudine Isaacs
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, 20007, USA
| | - Milena Jakimovska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, 1000, Republic of Macedonia
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, 71-252, Poland
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3000, Australia
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Center, Melbourne, VIC, 3000, Australia
| | - Ramunas Janavicius
- Hematology, oncology and transfusion medicine center, Dept. of Molecular and Regenerative Medicine, Vilnius University Hospital Santariskiu Clinics, Vilnius, 08410, Lithuania
| | - Rachel C Jankowitz
- Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15232, USA
| | - Esther M John
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94304, USA
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Vijai Joseph
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of Russian Academy of Sciences, 450054, Ufa, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State Medical University, 450076, Ufa, Russia
| | - Johanna I Kiiski
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, 00290, Finland
| | - Yon-Dschun Ko
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH, Johanniter Krankenhaus, Bonn, 53177, Germany
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, 0379, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, 0450, Norway
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Chaim Sheba Medical Center, 52621, Ramat Gan, Israel
| | - Diether Lambrechts
- VIB Center for Cancer Biology, VIB, Leuven, 3001, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, University of Leuven, Leuven, 3000, Belgium
| | - Conxi Lazaro
- Molecular Diagnostic Unit, Hereditary Cancer Program, ICO-IDIBELL (Bellvitge Biomedical Research Institute, Catalan Institute of Oncology), CIBERONC, Barcelona, 08908, Spain
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, 90095, USA
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Inserm U900, Paris, 75005, France
- Institut Curie, Paris, 75005, France
- Mines ParisTech, Fontainebleau, 77305, France
| | - Sara Lindström
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, 98195, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, 20850-9772, USA
| | - Jan Lubiński
- Department of Genetics and Pathology, Pomeranian Medical University, 71-252, Szczecin, Poland
| | - Enes Makalic
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, 70210, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, 70210, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, 70210, Finland
| | - Mehdi Manoochehri
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Sara Margolin
- Department of Oncology, Södersjukhuset, 118 83, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, 118 83, Sweden
| | - Tabea Maurer
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, 711 10, Greece
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alfons Meindl
- Department of Gynecology and Obstetrics, University of Munich, Campus Großhadern, Munich, 81377, Germany
| | - Usha Menon
- MRC Clinical Trials Unit at UCL, Institute of Clinical Trials & Methodology, University College London, London, WC1V 6LJ, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Electron Microscopy/Molecular Pathology and The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology & Genetics, Nicosia, 1683, Cyprus
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center, Roswell Park Cancer Institute, Buffalo, NY, 14263, USA
| | - Marco Montagna
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, 35128, Italy
| | - Fernando Moreno
- Medical Oncology Department, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), 28040, Madrid, Spain
| | - Lidia Moserle
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV - IRCCS, Padua, 35128, Italy
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
- Laboratory Medicine Program, University Health Network, Toronto, ON, M5G 2C4, Canada
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19066, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, 00290, Finland
| | - Ines Nevelsteen
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Finn C Nielsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, DK-2100, Denmark
| | | | - Robert L Nussbaum
- Cancer Genetics and Prevention Program, University of California San Francisco, San Francisco, CA, 94143-1714, USA
| | - Kenneth Offit
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
- Clinical Genetics Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Edith Olah
- Department of Molecular Genetics, National Institute of Oncology, Budapest, 1122, Hungary
| | | | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, 222 42, Lund, Sweden
| | - Ana Osorio
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), 46010, Valencia, Spain
- Human Cancer Genetics Programme, Spanish National Cancer Research Centre (CNIO), 28029, Madrid, Spain
| | - Janos Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, 1122, Hungary
| | | | - Michael T Parsons
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Inge Sokilde Pedersen
- Molecular Diagnostics, Aalborg University Hospital, Aalborg, 9000, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, 9000, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, 9000, Denmark
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute, Porto, 4220-072, Portugal
| | - Paolo Peterlongo
- Genome Diagnostics Program, IFOM - the FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, 20139, Italy
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology 'Georgi D. Efremov', Macedonian Academy of Sciences and Arts, Skopje, 1000, Republic of Macedonia
| | - Bruce Poppe
- Centre for Medical Genetics, Ghent University, Gent, 9000, Belgium
| | - Nadege Presneau
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, W1B 2HW, UK
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori (INT), Milan, 20133, Italy
| | - Johanna Rantala
- Clinical Genetics, Karolinska Institutet, Stockholm, 171 76, Sweden
| | - Gad Rennert
- Clalit National Cancer Control Center, Carmel Medical Center and Technion Faculty of Medicine, Haifa, 35254, Israel
| | - Harvey A Risch
- Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, 06510, USA
| | | | - Kristin Sanden
- City of Hope Clinical Cancer Genetics Community Research Network, Duarte, CA, 91010, USA
| | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, 1066 CX, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, 1066 CX, The Netherlands
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Oncology, University of Kansas Medical Center, Westwood, KS, 66205, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval, Research Center, Québec City, QC, G1V 4G2, Canada
| | - Christian F Singer
- Dept of OB/GYN and Comprehensive Cancer Center, Medical University of Vienna, 1090, Vienna, Austria
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval, Research Center, Québec City, QC, G1V 4G2, Canada
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
- Department of Clinical Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - John J Spinelli
- Population Oncology, BC Cancer, Vancouver, BC, V5Z 1G1, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, WA, 6000, Australia
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - William J Tapper
- Faculty of Medicine, University of Southampton, Southampton, SO17 1BJ, UK
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, 27709, USA
| | - Manuel R Teixeira
- Department of Genetics, Portuguese Oncology Institute, Porto, 4220-072, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto, Porto, 4050-013, Portugal
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Alex Teulé
- Genetic Counseling Unit, Hereditary Cancer Program, IDIBELL (Bellvitge Biomedical Research Institute),Catalan Institute of Oncology, CIBERONC, Barcelona, 08908, Spain
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odence C, 5000, Denmark
| | - Kathrin Thöne
- Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Darcy L Thull
- Department of Medicine, Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology, McGill University, Montréal, QC, H4A 3J1, Canada
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, 110231, Colombia
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, 94805, Villejuif, France
| | - Nadine Tung
- Department of Medical Oncology, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Celine M Vachon
- Department of Health Science Research, Division of Epidemiology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Christi J van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, 2333 ZA, The Netherlands
| | - Ans M W van den Ouweland
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | | | - Ana Vega
- Fundación Pública galega Medicina Xenómica-SERGAS, Grupo de Medicina Xenómica-USC, CIBERER, IDIS, Santiago de Compostela, Spain
| | - Alessandra Viel
- Division of Functional onco-genomics and genetics, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, 33081, Italy
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Barbara Wappenschmidt
- Center for Hereditary Breast and Ovarian Cancer, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50937, Germany
- Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937, Cologne, Germany
| | | | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, 118 83, Sweden
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, 90570, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, 90570, Finland
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, 20850, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Centre for Scientific Research 'Demokritos', Athens, 15310, Greece
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA, 92617
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, 02115, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Roger L Milne
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, VIC, 3004, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC, 3168, Australia
| | - Jonathan Beesley
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
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Jones CC, Bradford Y, Amos CI, Blot WJ, Chanock SJ, Harris CC, Schwartz AG, Spitz MR, Wiencke JK, Wrensch MR, Wu X, Aldrich MC. Cross-Cancer Pleiotropic Associations with Lung Cancer Risk in African Americans. Cancer Epidemiol Biomarkers Prev 2019; 28:715-723. [PMID: 30894353 PMCID: PMC6449205 DOI: 10.1158/1055-9965.epi-18-0935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/02/2018] [Accepted: 12/31/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Identifying genetic variants with pleiotropic associations across multiple cancers can reveal shared biologic pathways. Prior pleiotropic studies have primarily focused on European-descent individuals. Yet population-specific genetic variation can occur, and potential pleiotropic associations among diverse racial/ethnic populations could be missed. We examined cross-cancer pleiotropic associations with lung cancer risk in African Americans. METHODS We conducted a pleiotropic analysis among 1,410 African American lung cancer cases and 2,843 controls. We examined 36,958 variants previously associated (or in linkage disequilibrium) with cancer in prior genome-wide association studies. Logistic regression analyses were conducted, adjusting for age, sex, global ancestry, study site, and smoking status. RESULTS We identified three novel genomic regions significantly associated (FDR-corrected P <0.10) with lung cancer risk (rs336958 on 5q14.3, rs7186207 on 16q22.2, and rs11658063 on 17q12). On chromosome16q22.2, rs7186207 was significantly associated with reduced risk [OR = 0.43; 95% confidence interval (CI), 0.73-0.89], and functional annotation using GTEx showed rs7186207 modifies DHODH gene expression. The minor allele at rs336958 on 5q14.3 was associated with increased lung cancer risk (OR = 1.47; 95% CI, 1.22-1.78), whereas the minor allele at rs11658063 on 17q12 was associated with reduced risk (OR = 0.80; 95% CI, 0.72-0.90). CONCLUSIONS We identified novel associations on chromosomes 5q14.3, 16q22.2, and 17q12, which contain HNF1B, DHODH, and HAPLN1 genes, respectively. SNPs within these regions have been previously associated with multiple cancers. This is the first study to examine cross-cancer pleiotropic associations for lung cancer in African Americans. IMPACT Our findings demonstrate novel cross-cancer pleiotropic associations with lung cancer risk in African Americans.
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Affiliation(s)
- Carissa C Jones
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Yuki Bradford
- School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | | | - Ann G Schwartz
- Karmanos Cancer Institute, Wayne State University, Detroit, Michigan
| | - Margaret R Spitz
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - John K Wiencke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
- Institute of Human Genetics, University of California San Francisco, San Francisco, California
| | - Xifeng Wu
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Melinda C Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee.
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee
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Hu Y, Li M, Lu Q, Weng H, Wang J, Zekavat SM, Yu Z, Li B, Gu J, Muchnik S, Shi Y, Kunkle BW, Mukherjee S, Natarajan P, Naj A, Kuzma A, Zhao Y, Crane PK, Lu H, Zhao H. A statistical framework for cross-tissue transcriptome-wide association analysis. Nat Genet 2019; 51:568-576. [PMID: 30804563 PMCID: PMC6788740 DOI: 10.1038/s41588-019-0345-7] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 01/09/2019] [Indexed: 12/12/2022]
Abstract
Transcriptome-wide association analysis is a powerful approach to studying the genetic architecture of complex traits. A key component of this approach is to build a model to impute gene expression levels from genotypes by using samples with matched genotypes and gene expression data in a given tissue. However, it is challenging to develop robust and accurate imputation models with a limited sample size for any single tissue. Here, we first introduce a multi-task learning method to jointly impute gene expression in 44 human tissues. Compared with single-tissue methods, our approach achieved an average of 39% improvement in imputation accuracy and generated effective imputation models for an average of 120% more genes. We describe a summary-statistic-based testing framework that combines multiple single-tissue associations into a powerful metric to quantify the overall gene-trait association. We applied our method, called UTMOST (unified test for molecular signatures), to multiple genome-wide-association results and demonstrate its advantages over single-tissue strategies.
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Affiliation(s)
- Yiming Hu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Mo Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Qiongshi Lu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Haoyi Weng
- Division of Biostatistics, The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Jiawei Wang
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Seyedeh M Zekavat
- Yale School of Medicine, New Haven, CT, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Zhaolong Yu
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
| | - Boyang Li
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Jianlei Gu
- SJTU-Yale Joint Center for Biostatistics, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Sydney Muchnik
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Yu Shi
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | - Pradeep Natarajan
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Adam Naj
- Center for Clinical Epidemiology and Biostatistic, and the Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amanda Kuzma
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yi Zhao
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hui Lu
- SJTU-Yale Joint Center for Biostatistics, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA.
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
- SJTU-Yale Joint Center for Biostatistics, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China.
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
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Geeleher P, Nath A, Wang F, Zhang Z, Barbeira AN, Fessler J, Grossman RL, Seoighe C, Stephanie Huang R. Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. Genome Biol 2018; 19:130. [PMID: 30205839 PMCID: PMC6131897 DOI: 10.1186/s13059-018-1507-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/14/2018] [Indexed: 02/06/2023] Open
Abstract
Expression quantitative trait loci (eQTLs) identified using tumor gene expression data could affect gene expression in cancer cells, tumor-associated normal cells, or both. Here, we have demonstrated a method to identify eQTLs affecting expression in cancer cells by modeling the statistical interaction between genotype and tumor purity. Only one third of breast cancer risk variants, identified as eQTLs from a conventional analysis, could be confidently attributed to cancer cells. The remaining variants could affect cells of the tumor microenvironment, such as immune cells and fibroblasts. Deconvolution of tumor eQTLs will help determine how inherited polymorphisms influence cancer risk, development, and treatment response.
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Affiliation(s)
- Paul Geeleher
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Aritro Nath
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Fan Wang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Zhenyu Zhang
- Center for Data Intensive Science, University of Chicago, Chicago, IL, USA
| | - Alvaro N Barbeira
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jessica Fessler
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Robert L Grossman
- Center for Data Intensive Science, University of Chicago, Chicago, IL, USA
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, Galway, Ireland
| | - R Stephanie Huang
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN, USA.
- Department of Experimental and Clinical Pharmacology, College of Pharmacy, Room 5-130 WDH, 1332A, 308 Harvard St SE, Minneapolis, MN, 55455, USA.
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Rivandi M, Martens JWM, Hollestelle A. Elucidating the Underlying Functional Mechanisms of Breast Cancer Susceptibility Through Post-GWAS Analyses. Front Genet 2018; 9:280. [PMID: 30116257 PMCID: PMC6082943 DOI: 10.3389/fgene.2018.00280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/09/2018] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 170 single nucleotide polymorphisms (SNPs) associated with the susceptibility to breast cancer. Together, these SNPs explain 18% of the familial relative risk, which is estimated to be nearly half of the total familial breast cancer risk that is collectively explained by low-risk susceptibility alleles. An important aspect of this success has been the access to large sample sizes through collaborative efforts within the Breast Cancer Association Consortium (BCAC), but also collaborations between cancer association consortia. Despite these achievements, however, understanding of each variant's underlying mechanism and how these SNPs predispose women to breast cancer remains limited and represents a major challenge in the field, particularly since the vast majority of the GWAS-identified SNPs are located in non-coding regions of the genome and are merely tags for the causal variants. In recent years, fine-scale mapping studies followed by functional evaluation of putative causal variants have begun to elucidate the biological function of several GWAS-identified variants. In this review, we discuss the findings and lessons learned from these post-GWAS analyses of 22 risk loci. Identifying the true causal variants underlying breast cancer susceptibility and their function not only provides better estimates of the explained familial relative risk thereby improving polygenetic risk scores (PRSs), it also increases our understanding of the biological mechanisms responsible for causing susceptibility to breast cancer. This will facilitate the identification of further breast cancer risk alleles and the development of preventive medicine for those women at increased risk for developing the disease.
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Affiliation(s)
- Mahdi Rivandi
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands.,Department of Modern Sciences and Technologies, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, Netherlands.,Cancer Genomics Centre, Utrecht, Netherlands
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Wittkowski KM, Dadurian C, Seybold MP, Kim HS, Hoshino A, Lyden D. Complex polymorphisms in endocytosis genes suggest alpha-cyclodextrin as a treatment for breast cancer. PLoS One 2018; 13:e0199012. [PMID: 29965997 PMCID: PMC6028090 DOI: 10.1371/journal.pone.0199012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 05/17/2018] [Indexed: 02/06/2023] Open
Abstract
Most breast cancer deaths are caused by metastasis and treatment options beyond radiation and cytotoxic drugs, which have severe side effects, and hormonal treatments, which are or become ineffective for many patients, are urgently needed. This study reanalyzed existing data from three genome-wide association studies (GWAS) using a novel computational biostatistics approach (muGWAS), which had been validated in studies of 600-2000 subjects in epilepsy and autism. MuGWAS jointly analyzes several neighboring single nucleotide polymorphisms while incorporating knowledge about genetics of heritable diseases into the statistical method and about GWAS into the rules for determining adaptive genome-wide significance. Results from three independent GWAS of 1000-2000 subjects each, which were made available under the National Institute of Health's "Up For A Challenge" (U4C) project, not only confirmed cell-cycle control and receptor/AKT signaling, but, for the first time in breast cancer GWAS, also consistently identified many genes involved in endo-/exocytosis (EEC), most of which had already been observed in functional and expression studies of breast cancer. In particular, the findings include genes that translocate (ATP8A1, ATP8B1, ANO4, ABCA1) and metabolize (AGPAT3, AGPAT4, DGKQ, LPPR1) phospholipids entering the phosphatidylinositol cycle, which controls EEC. These novel findings suggest scavenging phospholipids as a novel intervention to control local spread of cancer, packaging of exosomes (which prepare distant microenvironment for organ-specific metastases), and endocytosis of β1 integrins (which are required for spread of metastatic phenotype and mesenchymal migration of tumor cells). Beta-cyclodextrins (βCD) have already been shown to be effective in in vitro and animal studies of breast cancer, but exhibits cholesterol-related ototoxicity. The smaller alpha-cyclodextrins (αCD) also scavenges phospholipids, but cannot fit cholesterol. An in-vitro study presented here confirms hydroxypropyl (HP)-αCD to be twice as effective as HPβCD against migration of human cells of both receptor negative and estrogen-receptor positive breast cancer. If the previous successful animal studies with βCDs are replicated with the safer and more effective αCDs, clinical trials of adjuvant treatment with αCDs are warranted. Ultimately, all breast cancer are expected to benefit from treatment with HPαCD, but women with triple-negative breast cancer (TNBC) will benefit most, because they have fewer treatment options and their cancer advances more aggressively.
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Affiliation(s)
- Knut M. Wittkowski
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, United States of America
| | - Christina Dadurian
- Center for Clinical and Translational Science, The Rockefeller University, New York, New York, United States of America
| | - Martin P. Seybold
- Institut für Formale Methoden der Informatik, Universität Stuttgart, Stuttgart, Germany
| | - Han Sang Kim
- Department of Pediatrics, and Cell and Developmental Biology Weill Medical College of Cornell University, New York, New York, United States of America
| | - Ayuko Hoshino
- Department of Pediatrics, and Cell and Developmental Biology Weill Medical College of Cornell University, New York, New York, United States of America
| | - David Lyden
- Department of Pediatrics, and Cell and Developmental Biology Weill Medical College of Cornell University, New York, New York, United States of America
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42
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Wu L, Shi W, Long J, Guo X, Michailidou K, Beesley J, Bolla MK, Shu XO, Lu Y, Cai Q, Al-Ejeh F, Rozali E, Wang Q, Dennis J, Li B, Zeng C, Feng H, Gusev A, Barfield RT, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Auer PL, Barrdahl M, Baynes C, Beckmann MW, Benitez J, Bermisheva M, Blomqvist C, Bogdanova NV, Bojesen SE, Brauch H, Brenner H, Brinton L, Broberg P, Brucker SY, Burwinkel B, Caldés T, Canzian F, Carter BD, Castelao JE, Chang-Claude J, Chen X, Cheng TYD, Christiansen H, Clarke CL, Collée M, Cornelissen S, Couch FJ, Cox D, Cox A, Cross SS, Cunningham JM, Czene K, Daly MB, Devilee P, Doheny KF, Dörk T, Dos-Santos-Silva I, Dumont M, Dwek M, Eccles DM, Eilber U, Eliassen AH, Engel C, Eriksson M, Fachal L, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fritschi L, Gabrielson M, Gago-Dominguez M, Gapstur SM, García-Closas M, Gaudet MM, Ghoussaini M, Giles GG, Goldberg MS, Goldgar DE, González-Neira A, Guénel P, Hahnen E, Haiman CA, Håkansson N, Hall P, Hallberg E, Hamann U, Harrington P, Hein A, Hicks B, Hillemanns P, Hollestelle A, Hoover RN, Hopper JL, Huang G, Humphreys K, Hunter DJ, Jakubowska A, Janni W, John EM, Johnson N, Jones K, Jones ME, Jung A, Kaaks R, Kerin MJ, Khusnutdinova E, Kosma VM, Kristensen VN, Lambrechts D, Le Marchand L, Li J, Lindström S, Lissowska J, Lo WY, Loibl S, Lubinski J, Luccarini C, Lux MP, MacInnis RJ, Maishman T, Kostovska IM, Mannermaa A, Manson JE, Margolin S, Mavroudis D, Meijers-Heijboer H, Meindl A, Menon U, Meyer J, Mulligan AM, Neuhausen SL, Nevanlinna H, Neven P, Nielsen SF, Nordestgaard BG, Olopade OI, Olson JE, Olsson H, Peterlongo P, Peto J, Plaseska-Karanfilska D, Prentice R, Presneau N, Pylkäs K, Rack B, Radice P, Rahman N, Rennert G, Rennert HS, Rhenius V, Romero A, Romm J, Rudolph A, Saloustros E, Sandler DP, Sawyer EJ, Schmidt MK, Schmutzler RK, Schneeweiss A, Scott RJ, Scott CG, Seal S, Shah M, Shrubsole MJ, Smeets A, Southey MC, Spinelli JJ, Stone J, Surowy H, Swerdlow AJ, Tamimi RM, Tapper W, Taylor JA, Terry MB, Tessier DC, Thomas A, Thöne K, Tollenaar RAEM, Torres D, Truong T, Untch M, Vachon C, Van Den Berg D, Vincent D, Waisfisz Q, Weinberg CR, Wendt C, Whittemore AS, Wildiers H, Willett WC, Winqvist R, Wolk A, Xia L, Yang XR, Ziogas A, Ziv E, Dunning AM, Pharoah PDP, Simard J, Milne RL, Edwards SL, Kraft P, Easton DF, Chenevix-Trench G, Zheng W. A transcriptome-wide association study of 229,000 women identifies new candidate susceptibility genes for breast cancer. Nat Genet 2018; 50:968-978. [PMID: 29915430 PMCID: PMC6314198 DOI: 10.1038/s41588-018-0132-x] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/17/2018] [Indexed: 01/17/2023]
Abstract
The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study evaluating associations of genetically predicted gene expression with breast cancer risk in 122,977 cases and 105,974 controls of European ancestry. We used data from the Genotype-Tissue Expression Project to establish genetic models to predict gene expression in breast tissue and evaluated model performance using data from The Cancer Genome Atlas. Of the 8,597 genes evaluated, significant associations were identified for 48 at a Bonferroni-corrected threshold of P < 5.82 × 10-6, including 14 genes at loci not yet reported for breast cancer. We silenced 13 genes and showed an effect for 11 on cell proliferation and/or colony-forming efficiency. Our study provides new insights into breast cancer genetics and biology.
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Affiliation(s)
- Lang Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wei Shi
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jirong Long
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yingchang Lu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Fares Al-Ejeh
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Esdy Rozali
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bingshan Li
- Department of Molecular Physiology & Biophysics, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Chenjie Zeng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Helian Feng
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alexander Gusev
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
| | - Richard T Barfield
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Irene L Andrulis
- Fred A. Litwin Center for Cancer Genetics, Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute, Queen's University, Kingston, Ontario, Canada
| | - Paul L Auer
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Myrto Barrdahl
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Matthias W Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Javier Benitez
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Valencia, Spain
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics, Ufa Scientific Center of Russian Academy of Sciences, Ufa, Russia
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, University of Örebro, Örebro, Sweden
| | - Natalia V Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
- N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus
| | - Stig E Bojesen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Louise Brinton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Per Broberg
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Sara Y Brucker
- Department of Gynecology and Obstetrics, University of Tübingen, Tübingen, Germany
| | - Barbara Burwinkel
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Trinidad Caldés
- Medical Oncology Department, CIBERONC Hospital Clínico San Carlos, Madrid, Spain
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brian D Carter
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - J Esteban Castelao
- Oncology and Genetics Unit, Instituto de Investigacion Biomedica Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Vigo, Spain
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Xiaoqing Chen
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Hans Christiansen
- Department of Radiation Oncology, Hannover Medical School, Hannover, Germany
| | - Christine L Clarke
- Westmead Institute for Medical Research, University of Sydney, Sydney, New South Wales, Australia
| | - Margriet Collée
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David Cox
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- INSERM U1052, Cancer Research Center of Lyon, Lyon, France
| | - Angela Cox
- Sheffield Institute for Nucleic Acids, Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK
| | - Simon S Cross
- Academic Unit of Pathology, Department of Neuroscience, University of Sheffield, Sheffield, UK
| | - Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Peter Devilee
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Kimberly F Doheny
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Isabel Dos-Santos-Silva
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Martine Dumont
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Miriam Dwek
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Diana M Eccles
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ursula Eilber
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - A Heather Eliassen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
| | - Mikael Eriksson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laura Fachal
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Peter A Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
| | - Dieter Flesch-Janys
- Institute for Medical Biometrics and Epidemiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Cancer Epidemiology, Clinical Cancer Registry, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Lin Fritschi
- School of Public Health, Curtin University, Perth, Western Australia, Australia
| | - Marike Gabrielson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Manuela Gago-Dominguez
- Genomic Medicine Group, Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Complejo Hospitalario Universitario de Santiago, SERGAS, Santiago De Compostela, Spain
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | | | - Mia M Gaudet
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Maya Ghoussaini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Graham G Giles
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, Quebec, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital, McGill University, Montréal, Quebec, Canada
| | - David E Goldgar
- Department of Dermatology, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Anna González-Neira
- Human Cancer Genetics Program, Spanish National Cancer Research Centre, Madrid, Spain
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Niclas Håkansson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Alexander Hein
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Peter Hillemanns
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Antoinette Hollestelle
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Robert N Hoover
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Guanmengqian Huang
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith Humphreys
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - David J Hunter
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Nuffield Department of Population Health, University of Oxford, Big Data Institute, Oxford, UK
| | - Anna Jakubowska
- Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics, Pomeranian Medical University, Szczecin, Poland
| | - Wolfgang Janni
- Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Esther M John
- Department of Epidemiology, Cancer Prevention Institute of California, Fremont, CA, USA
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Nichola Johnson
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Audrey Jung
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael J Kerin
- School of Medicine, National University of Ireland, Galway, Ireland
| | - Elza Khusnutdinova
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russia
| | - Veli-Matti Kosma
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Vessela N Kristensen
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Biology, Oslo University Hospital, University of Oslo, Oslo, Norway
| | - Diether Lambrechts
- VIB KULeuven Center for Cancer Biology, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Sara Lindström
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jolanta Lissowska
- Department of Cancer Epidemiology and Prevention, M. Sklodowska-Curie Institute - Oncology Center, Warsaw, Poland
| | - Wing-Yee Lo
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
| | | | - Jan Lubinski
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Michael P Lux
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Robert J MacInnis
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Tom Maishman
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Ivana Maleva Kostovska
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Arto Mannermaa
- Translational Cancer Research Area, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - JoAnn E Manson
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sara Margolin
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Dimitrios Mavroudis
- Department of Medical Oncology, University Hospital of Heraklion, Heraklion, Greece
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Technische Universität München, Munich, Germany
| | - Usha Menon
- Gynaecological Cancer Research Centre, Women's Cancer, Institute for Women's Health, University College London, London, UK
| | - Jeffery Meyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Anna Marie Mulligan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Laboratory Medicine Program, University Health Network, Toronto, Ontario, Canada
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Patrick Neven
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Sune F Nielsen
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
| | - Børge G Nordestgaard
- Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Herlev, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, The University of Chicago, Chicago, IL, USA
| | - Janet E Olson
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Håkan Olsson
- Department of Cancer Epidemiology, Clinical Sciences, Lund University, Lund, Sweden
| | - Paolo Peterlongo
- IFOM, The FIRC (Italian Foundation for Cancer Research) Institute of Molecular Oncology, Milan, Italy
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Skopje, Macedonia
| | - Ross Prentice
- Cancer Prevention Program, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nadege Presneau
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Katri Pylkäs
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Brigitte Rack
- Department of Gynecology and Obstetrics, University Hospital Ulm, Ulm, Germany
| | - Paolo Radice
- Unit of Molecular Bases of Genetic Risk and Genetic Testing, Department of Research, Fondazione IRCCS (Istituto Di Ricovero e Cura a Carattere Scientifico) Istituto Nazionale dei Tumori (INT), Milan, Italy
| | - Nazneen Rahman
- Section of Cancer Genetics, The Institute of Cancer Research, London, UK
| | - Gad Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology and Clalit National Cancer Control Center, Haifa, Israel
| | - Hedy S Rennert
- Department of Community Medicine and Epidemiology, Carmel Medical Center, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology and Clalit National Cancer Control Center, Haifa, Israel
| | - Valerie Rhenius
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Atocha Romero
- Medical Oncology Department, CIBERONC Hospital Clínico San Carlos, Madrid, Spain
- Medical Oncology Department, Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Jane Romm
- Center for Inherited Disease Research (CIDR), Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Anja Rudolph
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Elinor J Sawyer
- Research Oncology, Guy's Hospital, King's College London, London, UK
| | - Marjanka K Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO), University Hospital of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Andreas Schneeweiss
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- National Center for Tumor Diseases, University of Heidelberg, Heidelberg, Germany
| | - Rodney J Scott
- Division of Molecular Medicine, Pathology North, John Hunter Hospital, Newcastle, New South Wales, Australia
- Discipline of Medical Genetics, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Newcastle, New South Wales, Australia
| | | | - Sheila Seal
- Section of Cancer Genetics, The Institute of Cancer Research, London, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Martha J Shrubsole
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Ann Smeets
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Melissa C Southey
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - John J Spinelli
- Cancer Control Research, BC Cancer Agency, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Stone
- The Curtin UWA Centre for Genetic Origins of Health and Disease, Curtin University and University of Western Australia, Perth, Western Australia, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne and the Royal Women's Hospital, Melbourne, Victoria, Australia
| | - Harald Surowy
- Department of Obstetrics and Gynecology, University of Heidelberg, Heidelberg, Germany
- Molecular Epidemiology Group, C080, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anthony J Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Rulla M Tamimi
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - William Tapper
- Cancer Sciences Academic Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
- Epigenetic and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Daniel C Tessier
- McGill University and Génome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Abigail Thomas
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Kathrin Thöne
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Rob A E M Tollenaar
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Diana Torres
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics, Pontificia Universidad Javeriana, Bogota, Colombia
| | - Thérèse Truong
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP), INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Michael Untch
- Department of Gynecology and Obstetrics, Helios Clinics Berlin-Buch, Berlin, Germany
| | - Celine Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - David Van Den Berg
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Daniel Vincent
- McGill University and Génome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Quinten Waisfisz
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Clarice R Weinberg
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Camilla Wendt
- Department of Oncology - Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Alice S Whittemore
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Hans Wildiers
- Leuven Multidisciplinary Breast Center, Department of Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - Walter C Willett
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Robert Winqvist
- Laboratory of Cancer Genetics and Tumor Biology, Cancer and Translational Medicine Research Unit, Biocenter Oulu, University of Oulu, Oulu, Finland
- Laboratory of Cancer Genetics and Tumor Biology, Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | - Alicja Wolk
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lucy Xia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Argyrios Ziogas
- Department of Epidemiology, University of California Irvine, Irvine, CA, USA
| | - Elad Ziv
- Department of Medicine, Institute for Human Genetics, UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Jacques Simard
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Roger L Milne
- Cancer Epidemiology & Intelligence Division, Cancer Council Victoria, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stacey L Edwards
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Georgia Chenevix-Trench
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
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Lilyquist J, Ruddy KJ, Vachon CM, Couch FJ. Common Genetic Variation and Breast Cancer Risk-Past, Present, and Future. Cancer Epidemiol Biomarkers Prev 2018; 27:380-394. [PMID: 29382703 PMCID: PMC5884707 DOI: 10.1158/1055-9965.epi-17-1144] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/05/2018] [Accepted: 01/11/2018] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most common cancer among women in the United States, with up to 30% of those diagnosed displaying a family history of breast cancer. To date, 18% of the familial risk of breast cancer can be explained by SNPs. This review summarizes the discovery of risk-associated SNPs using candidate gene and genome-wide association studies (GWAS), including discovery and replication in large collaborative efforts such as The Collaborative Oncologic Gene-environment Study and OncoArray. We discuss the evolution of GWAS studies, efforts to discover additional SNPs, and methods for identifying causal variants. We summarize findings associated with overall breast cancer, pathologic subtypes, and mutation carriers (BRCA1, BRCA2, and CHEK2). In addition, we summarize the development of polygenic risk scores (PRS) using the risk-associated SNPs and show how PRS can contribute to estimation of individual risks for developing breast cancer. Cancer Epidemiol Biomarkers Prev; 27(4); 380-94. ©2018 AACRSee all articles in this CEBP Focus section, "Genome-Wide Association Studies in Cancer."
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Affiliation(s)
- Jenna Lilyquist
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | | | - Celine M Vachon
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Fergus J Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
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44
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Riahi A, Radmanesh H, Schürmann P, Bogdanova N, Geffers R, Meddeb R, Kharrat M, Dörk T. Exome sequencing and case-control analyses identify RCC1 as a candidate breast cancer susceptibility gene. Int J Cancer 2018; 142:2512-2517. [PMID: 29363114 DOI: 10.1002/ijc.31273] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/29/2017] [Accepted: 01/05/2018] [Indexed: 01/03/2023]
Abstract
Breast cancer is a genetic disease but the known genes explain a minority of cases. To elucidate the molecular basis of breast cancer in the Tunisian population, we performed exome sequencing on six BRCA1/BRCA2 mutation-negative patients with familial breast cancer and identified a novel frameshift mutation in RCC1, encoding the Regulator of Chromosome Condensation 1. Subsequent genotyping detected the 19-bp deletion in additional 5 out of 153 (3%) breast cancer patients but in none of 400 female controls (p = 0.0015). The deletion was enriched in patients with a positive family history (5%, p = 0.0009) and co-segregated with breast cancer in the initial pedigree. The mutant allele was lost in 4/6 breast tumors from mutation carriers which may be consistent with the hypothesis that RCC1 dysfunction provides a selective disadvantage at the stage of tumor progression. In summary, we propose RCC1 as a likely breast cancer susceptibility gene in the Tunisian population.
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Affiliation(s)
- Aouatef Riahi
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Laboratoire Génétique Humaine, Faculté de Médecine de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Hoda Radmanesh
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Medical Genetic Research Center (MGRC), School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Peter Schürmann
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Natalia Bogdanova
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.,Hannover Medical School, Radiation Oncology Research Unit, Hannover, Germany
| | - Robert Geffers
- Genome Analytics Unit, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Rym Meddeb
- Laboratoire Génétique Humaine, Faculté de Médecine de Tunis, University Tunis El Manar, Tunis, Tunisia.,Department of Hereditary and Congenital Disorders, Charles Nicolle Hospital, Tunis, Tunisia
| | - Maher Kharrat
- Laboratoire Génétique Humaine, Faculté de Médecine de Tunis, University Tunis El Manar, Tunis, Tunisia
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
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45
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Mechanic LE, Lindström S, Daily KM, Sieberts SK, Amos CI, Chen HS, Cox NJ, Dathe M, Feuer EJ, Guertin MJ, Hoffman J, Liu Y, Moore JH, Myers CL, Ritchie MD, Schildkraut J, Schumacher F, Witte JS, Wang W, Williams SM, Gillanders EM. Up For A Challenge (U4C): Stimulating innovation in breast cancer genetic epidemiology. PLoS Genet 2017; 13:e1006945. [PMID: 28957327 PMCID: PMC5619686 DOI: 10.1371/journal.pgen.1006945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Affiliation(s)
- Leah E. Mechanic
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Sara Lindström
- Department of Epidemiology, University of Washington School of Public Health, Seattle, Washington, United States of America
| | | | | | - Christopher I. Amos
- Department of Biomedical Data Sciences, Dartmouth College, Lebanon, New Hampshire, United States of America
| | - Huann-Sheng Chen
- Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nancy J. Cox
- Division of Genetic Medicine, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Marina Dathe
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eric J. Feuer
- Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael J. Guertin
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Joshua Hoffman
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Yunxian Liu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Jason H. Moore
- Division of Informatics, Department of Biostatistics and Epidemiology, Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota, United States of America
| | - Marylyn D. Ritchie
- Department of Biochemistry and Molecular Biology, Center for Systems Genomics, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Biomedical and Translational Informatics, Geisinger Health System, Danville, Pennsylvania, United States of America
| | - Joellen Schildkraut
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
| | - Fredrick Schumacher
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | - John S. Witte
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Wen Wang
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, Minneapolis, Minnesota, United States of America
| | - Scott M. Williams
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America
| | | | | | - Elizabeth M. Gillanders
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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