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He J, Perera D, Wen W, Ping J, Li Q, Lyu L, Chen Z, Shu X, Long J, Cai Q, Shu XO, Zheng W, Long Q, Guo X. Enhancing Disease Risk Gene Discovery by Integrating Transcription Factor-Linked Trans-located Variants into Transcriptome-Wide Association Analyses. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.10.10.23295443. [PMID: 37873299 PMCID: PMC10593059 DOI: 10.1101/2023.10.10.23295443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Transcriptome-wide association studies (TWAS) have been successful in identifying disease susceptibility genes by integrating cis-variants predicted gene expression with genome-wide association studies (GWAS) data. However, trans-located variants for predicting gene expression remain largely unexplored. Here, we introduce transTF-TWAS, which incorporates transcription factor (TF)-linked trans-located variants to enhance model building. Using data from the Genotype-Tissue Expression project, we predict gene expression and alternative splicing and applied these models to large GWAS datasets for breast, prostate, and lung cancers. We demonstrate that transTF-TWAS outperforms other existing TWAS approaches in both constructing gene prediction models and identifying disease-associated genes, as evidenced by simulations and real data analysis. Our transTF-TWAS approach significantly contributes to the discovery of disease risk genes. Findings from this study have shed new light on several genetically driven key regulators and their associated regulatory networks underlying disease susceptibility.
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2
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Joosten SEP, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Yavuz K, Donaldson Collier M, Morova T, Altintaş UB, Kim Y, Canisius S, Moelans CB, van Diest PJ, Korkmaz G, Lack NA, Vermeulen M, Linn SC, Zwart W. Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions. Genome Res 2024; 34:539-555. [PMID: 38719469 PMCID: PMC11146591 DOI: 10.1101/gr.278680.123] [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: 10/30/2023] [Accepted: 04/11/2024] [Indexed: 06/05/2024]
Abstract
Estrogen Receptor 1 (ESR1; also known as ERα, encoded by ESR1 gene) is the main driver and prime drug target in luminal breast cancer. ESR1 chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ESR1 chromatin action, along with its biological implications. Here, we use a large set of ESR1 ChIP-seq data from 70 ESR1+ breast cancers to explore inter-patient heterogeneity in ESR1 DNA binding to reveal a striking inter-tumor heterogeneity of ESR1 action. Of note, commonly shared ESR1 sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1 and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we can confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ESR1-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ESR1 landscape, with the most common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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Affiliation(s)
- Stacey E P Joosten
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Sebastian Gregoricchio
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Suzan Stelloo
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
| | - Elif Yapıcı
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Chia-Chi Flora Huang
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Kerim Yavuz
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Maria Donaldson Collier
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Oncode Institute, The Netherlands
| | - Tunç Morova
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Umut Berkay Altintaş
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Yongsoo Kim
- Department of Pathology, Amsterdam University Medical Center, Cancer Center Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Sander Canisius
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Cathy B Moelans
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Paul J van Diest
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
| | - Gozde Korkmaz
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
| | - Nathan A Lack
- Koç University School of Medicine, 34450 Istanbul, Turkey
- Koç University Research Center for Translational Medicine (KUTTAM), 34450 Istanbul, Turkey
- Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, V6H 3Z6 Canada
| | - Michiel Vermeulen
- Oncode Institute, The Netherlands
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6500HB Nijmegen, The Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Sabine C Linn
- Division of Molecular Pathology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
- Department of Pathology, Utrecht University Medical Centre, 3584 CX Utrecht, The Netherlands
- Department of Medical Oncology, Antoni van Leeuwenhoek Hospital, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Wilbert Zwart
- Division of Oncogenomics, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands;
- Oncode Institute, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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3
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Guo X, Ping J, Yang Y, Su X, Shu XO, Wen W, Chen Z, Zhang Y, Tao R, Jia G, He J, Cai Q, Zhang Q, Giles GG, Pearlman R, Rennert G, Vodicka P, Phipps A, Gruber SB, Casey G, Peters U, Long J, Lin W, Zheng W. Large-scale alternative polyadenylation (APA)-wide association studies to identify putative susceptibility genes in human common cancers. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.05.23298125. [PMID: 37986797 PMCID: PMC10659493 DOI: 10.1101/2023.11.05.23298125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Alternative polyadenylation (APA) modulates mRNA processing in the 3' untranslated regions (3'UTR), which affect mRNA stability and translation efficiency. Here, we build genetic models to predict APA levels in multiple tissues using sequencing data of 1,337 samples from the Genotype-Tissue Expression, and apply these models to assess associations between genetically predicted APA levels and cancer risk with data from large genome-wide association studies of six common cancers, including breast, ovary, prostate, colorectum, lung, and pancreas among European-ancestry populations. At a Bonferroni-corrected P □<□0.05, we identify 58 risk genes, including seven in newly identified loci. Using luciferase reporter assays, we demonstrate that risk alleles of 3'UTR variants, rs324015 ( STAT6 ), rs2280503 ( DIP2B ), rs1128450 ( FBXO38 ) and rs145220637 ( LDAH ), could significantly increase post-transcriptional activities of their target genes compared to reference alleles. Further gene knockdown experiments confirm their oncogenic roles. Our study provides additional insight into the genetic susceptibility of these common cancers.
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4
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Joosten SE, Gregoricchio S, Stelloo S, Yapıcı E, Huang CCF, Collier MD, Morova T, Altintas B, Kim Y, Canisius S, Korkmaz G, Lack N, Vermeulen M, Linn SC, Zwart W. Breast cancer risk SNPs converge on estrogen receptor binding sites commonly shared between breast tumors to locally alter estrogen signalling output. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564691. [PMID: 37961147 PMCID: PMC10634999 DOI: 10.1101/2023.10.30.564691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Estrogen Receptor alpha (ERα) is the main driver and prime drug target in luminal breast. ERα chromatin binding is extensively studied in cell lines and a limited number of human tumors, using consensi of peaks shared among samples. However, little is known about inter-tumor heterogeneity of ERα chromatin action, along with its biological implications. Here, we use a large set of ERα ChIP-seq data from 70 ERα+ breast cancers to explore inter-patient heterogeneity in ERα DNA binding, to reveal a striking inter-tumor heterogeneity of ERα action. Interestingly, commonly-shared ERα sites showed the highest estrogen-driven enhancer activity and were most-engaged in long-range chromatin interactions. In addition, the most-commonly shared ERα-occupied enhancers were enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ERα and its pioneer factor FOXA1. Finally, in the TCGA breast cancer cohort, we could confirm these variations to associate with differences in expression for the target gene. Cumulatively, we reveal a natural hierarchy of ERα-chromatin interactions in breast cancers within a highly heterogeneous inter-tumor ERα landscape, with the most-common shared regions being most active and affected by germline functional risk SNPs for breast cancer development.
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5
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Ying P, Chen C, Lu Z, Chen S, Zhang M, Cai Y, Zhang F, Huang J, Fan L, Ning C, Li Y, Wang W, Geng H, Liu Y, Tian W, Yang Z, Liu J, Huang C, Yang X, Xu B, Li H, Zhu X, Li N, Li B, Wei Y, Zhu Y, Tian J, Miao X. Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk. Nat Commun 2023; 14:5958. [PMID: 37749132 PMCID: PMC10520073 DOI: 10.1038/s41467-023-41690-z] [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: 12/20/2022] [Accepted: 09/14/2023] [Indexed: 09/27/2023] Open
Abstract
Genome-wide association studies have identified numerous variants associated with human complex traits, most of which reside in the non-coding regions, but biological mechanisms remain unclear. However, assigning function to the non-coding elements is still challenging. Here we apply Activity-by-Contact (ABC) model to evaluate enhancer-gene regulation effect by integrating multi-omics data and identified 544,849 connections across 20 cancer types. ABC model outperforms previous approaches in linking regulatory variants to target genes. Furthermore, we identify over 30,000 enhancer-gene connections in colorectal cancer (CRC) tissues. By integrating large-scale population cohorts (23,813 cases and 29,973 controls) and multipronged functional assays, we demonstrate an ABC regulatory variant rs4810856 associated with CRC risk (Odds Ratio = 1.11, 95%CI = 1.05-1.16, P = 4.02 × 10-5) by acting as an allele-specific enhancer to distally facilitate PREX1, CSE1L and STAU1 expression, which synergistically activate p-AKT signaling. Our study provides comprehensive regulation maps and illuminates a single variant regulating multiple genes, providing insights into cancer etiology.
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Grants
- Distinguished Young Scholars of China (NSFC-81925032), Key Program of National Natural Science Foundation of China (NSFC-82130098), the Fundamental Research Funds for the Central Universities (2042022rc0026, 2042023kf1005),Knowledge Innovation Program of Wuhan (2023020201010060).
- Youth Program of National Natural Science Foundation of China (NSFC-82003547), Program of Health Commission of Hubei Province (WJ2023M045) and Fundamental Research Funds for the Central Universities (WHU: 2042022kf1031).
- The National Science Fund for Excellent Young Scholars (NSFC-82322058), Program of National Natural Science Foundation of China (NSFC-82103929, NSFC-82273713), Young Elite Scientists Sponsorship Program by cst(2022QNRC001), National Science Fund for Distinguished Young Scholars of Hubei Province of China (2023AFA046), Fundamental Research Funds for the Central Universities (WHU:2042022kf1205) and Knowledge Innovation Program of Wuhan (whkxjsj011, 2023020201010073).
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Affiliation(s)
- Pingting Ying
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Can Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Shuoni Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Fuwei Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Jinyu Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Linyun Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Caibo Ning
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yanmin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Wenzhuo Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Hui Geng
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yizhuo Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Wen Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Zhiyong Yang
- Department of Hepatobiliary and Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Jiuyang Liu
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Chaoqun Huang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Xiaojun Yang
- Department of Gastrointestinal Surgery, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Bin Xu
- Cancer Center, Renmin Hospital of Wuhan University, Wuhan University, Wuhan, 430060, China
| | - Heng Li
- Department of Urology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xu Zhu
- Department of Gastrointestinal Surgery, Renmin Hospital of Wuhan University, Wuhan, 430071, China
| | - Ni Li
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Yongchang Wei
- Department of Gastrointestinal Oncology, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Wuhan University, Wuhan, 430071, China.
- Department of Gastrointestinal Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Radiation Oncology, Renmin Hospital of Wuhan University, Wuhan, 430071, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, 430030, China.
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6
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Ding YC, Song H, Adamson AW, Schmolze D, Hu D, Huntsman S, Steele L, Patrick CS, Tao S, Hernandez N, Adams CD, Fejerman L, Gardner K, Nápoles AM, Pérez-Stable EJ, Weitzel JN, Bengtsson H, Huang FW, Neuhausen SL, Ziv E. Profiling the Somatic Mutational Landscape of Breast Tumors from Hispanic/Latina Women Reveals Conserved and Unique Characteristics. Cancer Res 2023; 83:2600-2613. [PMID: 37145128 PMCID: PMC10390863 DOI: 10.1158/0008-5472.can-22-2510] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 02/16/2023] [Accepted: 05/02/2023] [Indexed: 05/06/2023]
Abstract
Somatic mutational profiling is increasingly being used to identify potential targets for breast cancer. However, limited tumor-sequencing data from Hispanic/Latinas (H/L) are available to guide treatment. To address this gap, we performed whole-exome sequencing (WES) and RNA sequencing on 146 tumors and WES of matched germline DNA from 140 H/L women in California. Tumor intrinsic subtype, somatic mutations, copy-number alterations, and expression profiles of the tumors were characterized and compared with data from tumors of non-Hispanic White (White) women in The Cancer Genome Atlas (TCGA). Eight genes were significantly mutated in the H/L tumors including PIK3CA, TP53, GATA3, MAP3K1, CDH1, CBFB, PTEN, and RUNX1; the prevalence of mutations in these genes was similar to that observed in White women in TCGA. Four previously reported Catalogue of Somatic Mutations in Cancer (COSMIC) mutation signatures (1, 2, 3, 13) were found in the H/L dataset, along with signature 16 that has not been previously reported in other breast cancer datasets. Recurrent amplifications were observed in breast cancer drivers including MYC, FGFR1, CCND1, and ERBB2, as well as a recurrent amplification in 17q11.2 associated with high KIAA0100 gene expression that has been implicated in breast cancer aggressiveness. In conclusion, this study identified a higher prevalence of COSMIC signature 16 and a recurrent copy-number amplification affecting expression of KIAA0100 in breast tumors from H/L compared with White women. These results highlight the necessity of studying underrepresented populations. SIGNIFICANCE Comprehensive characterization of genomic and transcriptomic alterations in breast tumors from Hispanic/Latina patients reveals distinct genetic alterations and signatures, demonstrating the importance of inclusive studies to ensure equitable care for patients. See related commentary by Schmit et al., p. 2443.
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Affiliation(s)
- Yuan Chun Ding
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Hanbing Song
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Aaron W. Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Daniel Schmolze
- Department of Pathology, City of Hope Medical Center, Duarte, California
| | - Donglei Hu
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Scott Huntsman
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Carmina S. Patrick
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Shu Tao
- Integrative Genomics Shared Resource, Beckman Research Institute of City of Hope, Duarte, California
| | - Natalie Hernandez
- Western University of Health Sciences College of Graduate Nursing, Pomona, California
| | | | - Laura Fejerman
- Department of Public Health Sciences and Comprehensive Cancer Center, University of California Davis, Davis, California
| | - Kevin Gardner
- Department of Pathology and Cell Biology, Columbia University Irvine Medical Center, New York, New York
| | - Anna María Nápoles
- Division of Intramural Research, National Institute on Minority and Health Disparities, National Institutes of Health, Bethesda, Maryland
| | | | | | - Henrik Bengtsson
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
| | - Franklin W. Huang
- Division of Hematology/Oncology, Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Bakar Computational Health Sciences Institute, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
- Chan Zuckerberg Biohub, San Francisco, California
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, California
| | - Susan L. Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California
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7
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van Amerongen R, Bentires-Alj M, van Boxtel AL, Clarke RB, Fre S, Suarez EG, Iggo R, Jechlinger M, Jonkers J, Mikkola ML, Koledova ZS, Sørlie T, Vivanco MDM. Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research. J Mammary Gland Biol Neoplasia 2023; 28:17. [PMID: 37450065 PMCID: PMC10349020 DOI: 10.1007/s10911-023-09544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/25/2023] [Indexed: 07/18/2023] Open
Abstract
On 8 December 2022 the organizing committee of the European Network for Breast Development and Cancer labs (ENBDC) held its fifth annual Think Tank meeting in Amsterdam, the Netherlands. Here, we embraced the opportunity to look back to identify the most prominent breakthroughs of the past ten years and to reflect on the main challenges that lie ahead for our field in the years to come. The outcomes of these discussions are presented in this position paper, in the hope that it will serve as a summary of the current state of affairs in mammary gland biology and breast cancer research for early career researchers and other newcomers in the field, and as inspiration for scientists and clinicians to move the field forward.
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Affiliation(s)
- Renée van Amerongen
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands.
| | - Mohamed Bentires-Alj
- Laboratory of Tumor Heterogeneity, Metastasis and Resistance, Department of Biomedicine, University of Basel and University Hospital of Basel, Basel, Switzerland
| | - Antonius L van Boxtel
- Developmental, Stem Cell and Cancer Biology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands
| | - Robert B Clarke
- Manchester Breast Centre, Division of Cancer Sciences, School of Medical Sciences, University of Manchester, Manchester, UK
| | - Silvia Fre
- Institut Curie, Genetics and Developmental Biology Department, PSL Research University, CNRS UMR3215, U93475248, InsermParis, France
| | - Eva Gonzalez Suarez
- Transformation and Metastasis Laboratory, Molecular Oncology, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Oncobell, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Richard Iggo
- INSERM U1312, University of Bordeaux, 33076, Bordeaux, France
| | - Martin Jechlinger
- Cell Biology and Biophysics Department, EMBL, Heidelberg, Germany
- Molit Institute of Personalized Medicine, Heilbronn, Germany
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX, Amsterdam, The Netherlands
| | - Marja L Mikkola
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, P.O.B. 56, 00014, Helsinki, Finland
| | - Zuzana Sumbalova Koledova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Therese Sørlie
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Maria dM Vivanco
- Cancer Heterogeneity Lab, CIC bioGUNE, Basque Research and Technology Alliance, BRTA, Technological Park Bizkaia, 48160, Derio, Spain
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8
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Wang S, Qin S, Cai B, Zhan J, Chen Q. Promising therapeutic mechanism for Chinese herbal medicine in ameliorating renal fibrosis in diabetic nephropathy. Front Endocrinol (Lausanne) 2023; 14:932649. [PMID: 37522131 PMCID: PMC10376707 DOI: 10.3389/fendo.2023.932649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Diabetic nephropathy (DN) is one of the most serious chronic microvascular abnormalities of diabetes mellitus and the major cause of uremia. Accumulating evidence has confirmed that fibrosis is a significant pathological feature that contributes to the development of chronic kidney disease in DN. However, the exact mechanism of renal fibrosis in DN is still unclear, which greatly hinders the treatment of DN. Chinese herbal medicine (CHM) has shown efficacy and safety in ameliorating inflammation and albuminuria in diabetic patients. In this review, we outline the underlying mechanisms of renal fibrosis in DN, including oxidative stress (OS) generation and OS-elicited ASK1-p38/JNK activation. Also, we briefly summarize the current status of CHM treating DN by improving renal fibrosis. The treatment of DN by inhibiting ASK1 activation to alleviate renal fibrosis in DN with CHM will promote the discovery of novel therapeutic targets for DN and provide a beneficial therapeutic method for DN.
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Affiliation(s)
- Shengju Wang
- Department of Nephrology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Shuai Qin
- Department of Nephrology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Baochao Cai
- Diabetes Department, Jiaxing Hospital of Traditional Chinese Medicine, Jiaxing, Zhejiang, China
| | - Jihong Zhan
- Department of Nephrology, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Qiu Chen
- Department of Endocrinology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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9
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Vízkeleti L, Spisák S. Rewired Metabolism Caused by the Oncogenic Deregulation of MYC as an Attractive Therapeutic Target in Cancers. Cells 2023; 12:1745. [PMID: 37443779 PMCID: PMC10341379 DOI: 10.3390/cells12131745] [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: 04/10/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
MYC is one of the most deregulated oncogenes on multiple levels in cancer. As a node transcription factor, MYC plays a diverse regulatory role in many cellular processes, including cell cycle and metabolism, both in physiological and pathological conditions. The relentless growth and proliferation of tumor cells lead to an insatiable demand for energy and nutrients, which requires the rewiring of cellular metabolism. As MYC can orchestrate all aspects of cellular metabolism, its altered regulation plays a central role in these processes, such as the Warburg effect, and is a well-established hallmark of cancer development. However, our current knowledge of MYC suggests that its spatial- and concentration-dependent contribution to tumorigenesis depends more on changes in the global or relative expression of target genes. As the direct targeting of MYC is proven to be challenging due to its relatively high toxicity, understanding its underlying regulatory mechanisms is essential for the development of tumor-selective targeted therapies. The aim of this review is to comprehensively summarize the diverse forms of MYC oncogenic deregulation, including DNA-, transcriptional- and post-translational level alterations, and their consequences for cellular metabolism. Furthermore, we also review the currently available and potentially attractive therapeutic options that exploit the vulnerability arising from the metabolic rearrangement of MYC-driven tumors.
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Affiliation(s)
- Laura Vízkeleti
- Department of Bioinformatics, Faculty of Medicine, Semmelweis University, 1094 Budapest, Hungary;
| | - Sándor Spisák
- Institute of Enzymology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, 1117 Budapest, Hungary
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10
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Zhong C, Wu C, Lin Y, Lin D. Refined expression quantitative trait locus analysis on adenocarcinoma at the gastroesophageal junction reveals susceptibility and prognostic markers. Front Genet 2023; 14:1180500. [PMID: 37265963 PMCID: PMC10230079 DOI: 10.3389/fgene.2023.1180500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/03/2023] [Indexed: 06/03/2023] Open
Abstract
Objectives: This study aimed to explore cell type level expression quantitative trait loci (eQTL) in adenocarcinoma at the gastroesophageal junction (ACGEJ) and identify susceptibility and prognosis markers. Methods: Whole-genome sequencing (WGS) was performed on 120 paired samples from Chinese ACGEJ patients. Germline mutations were detected by GATK tools. RNA sequencing (RNA-seq) data on ACGEJ samples were taken from our previous studies. Public single-cell RNA sequencing (scRNA-seq) data were used to produce the proportion of epithelial cells. Matrix eQTL and a linear mixed model were used to identify condition-specific cis-eQTLs. The R package coloc was used to perform co-localization analysis with the public data of genome-wide association studies (GWASs). Log-rank and Cox regression tests were used to identify survival-associated eQTL and genes. Functions of candidate risk loci were explored by experimental validation. Results: Refined eQTL analyses of paired ACGEJ samples were performed and 2,036 potential ACGEJ-specific eQTLs with East Asian specificity were identified in total. ACGEJ-gain eQTLs were enriched at promoter regions more than ACGEJ-loss eQTLs. rs658524 was identified as the top eQTL close to the transcription start site of its paired gene (CTSW). rs2240191-RASAL1, rs4236599-FOXP2, rs4947311-PSORS1C1, rs13134812-LOC391674, and rs17508585-CDK13-DT were identified as ACGEJ-specific susceptibility eQTLs. rs309483-LINC01355 was associated with the overall survival of ACGEJ patients. We explored functions of candidate eQTLs such as rs658524, rs309483, rs2240191, and rs4947311 by experimental validation. Conclusion: This study provides new risk loci for ACGEJ susceptibility and effective disease prognosis biomarkers.
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Affiliation(s)
- Ce Zhong
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chen Wu
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuan Lin
- Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, China
| | - Dongxin Lin
- Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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11
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Ji X, Wang E, Cui Q. Deciphering gene contributions and etiologies of somatic mutational signatures of cancer. Brief Bioinform 2023; 24:6995381. [PMID: 36682004 DOI: 10.1093/bib/bbad017] [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: 07/27/2022] [Revised: 12/15/2022] [Accepted: 01/04/2023] [Indexed: 01/23/2023] Open
Abstract
Somatic mutational signatures (MSs) identified by genome sequencing play important roles in exploring the cause and development of cancer. Thus far, many such signatures have been identified, and some of them do imply causes of cancer. However, a major bottleneck is that we do not know the potential meanings (i.e. carcinogenesis or biological functions) and contributing genes for most of them. Here, we presented a computational framework, Gene Somatic Genome Pattern (GSGP), which can decipher the molecular mechanisms of the MSs. More importantly, it is the first time that the GSGP is able to process MSs from ribonucleic acid (RNA) sequencing, which greatly extended the applications of both MS analysis and RNA sequencing (RNAseq). As a result, GSGP analyses match consistently with previous reports and identify the etiologies for a number of novel signatures. Notably, we applied GSGP to RNAseq data and revealed an RNA-derived MS involved in deficient deoxyribonucleic acid mismatch repair and microsatellite instability in colorectal cancer. Researchers can perform customized GSGP analysis using the web tools or scripts we provide.
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Affiliation(s)
- Xiangwen Ji
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
| | - Edwin Wang
- Department of Biochemistry and Molecular Biology, Medical Genetics, and Oncology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Qinghua Cui
- Department of Biomedical Informatics, School of Basic Medical Science, Peking University Health Science Center, Beijing, China
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12
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An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. Nat Commun 2023; 14:1208. [PMID: 36869052 PMCID: PMC9984425 DOI: 10.1038/s41467-023-36897-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/22/2023] [Indexed: 03/05/2023] Open
Abstract
Genetic sharing is extensively observed for autoimmune diseases, but the causal variants and their underlying molecular mechanisms remain largely unknown. Through systematic investigation of autoimmune disease pleiotropic loci, we found most of these shared genetic effects are transmitted from regulatory code. We used an evidence-based strategy to functionally prioritize causal pleiotropic variants and identify their target genes. A top-ranked pleiotropic variant, rs4728142, yielded many lines of evidence as being causal. Mechanistically, the rs4728142-containing region interacts with the IRF5 alternative promoter in an allele-specific manner and orchestrates its upstream enhancer to regulate IRF5 alternative promoter usage through chromatin looping. A putative structural regulator, ZBTB3, mediates the allele-specific loop to promote IRF5-short transcript expression at the rs4728142 risk allele, resulting in IRF5 overactivation and M1 macrophage polarization. Together, our findings establish a causal mechanism between the regulatory variant and fine-scale molecular phenotype underlying the dysfunction of pleiotropic genes in human autoimmunity.
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13
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Association of the Estrogen Receptor 1 Polymorphisms rs2046210 and rs9383590 with the Risk, Age at Onset and Prognosis of Breast Cancer. Cells 2023; 12:cells12040515. [PMID: 36831182 PMCID: PMC9953811 DOI: 10.3390/cells12040515] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/16/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Estrogen receptor α (ERα), encoded by the ESR1 gene, is a key prognostic and predictive biomarker firmly established in routine diagnostics and as a therapeutic target of breast cancer, and it has a central function in breast cancer biology. Genetic variants at 6q25.1, containing the ESR1 gene, were found to be associated with breast cancer susceptibility. The rs2046210 and rs9383590 single nucleotide variants (SNVs) are located in the same putative enhancer region upstream of ESR1 and were separately identified as candidate causal variants responsible for these associations. Here, both SNVs were genotyped in a hospital-based case-control study of 409 female breast cancer patients and 422 female controls of a Central European (Austrian) study population. We analyzed the association of both SNVs with the risk, age at onset, clinically and molecularly relevant characteristics and prognosis of breast cancer. We also assessed the concordances between both SNVs and the associations of each SNV conditional on the other SNV. The minor alleles of both SNVs were found to be non-significantly associated with an increased breast cancer risk. Significant associations were found in specific subpopulations, particularly in patients with an age younger than 55 years. The minor homozygotes of rs2046210 and the minor homozygotes plus heterozygotes of rs9383590 exhibited a several-years-younger age at onset than the common homozygotes, which was more pronounced in ER-positive and luminal patients. Importantly, the observed associations of each SNV were not consistently nullified upon correction for the other SNV nor upon analyses in common homozygotes for the other SNV. We conclude that both SNVs remain independent candidate causal variants.
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14
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Zhu L, Liu K, Bao B, Li F, Liang W, Jiang Z, Hao X, Wang J. A nomogram based on genotypic and clinicopathologic factors to predict the non-sentinel lymph node metastasis in Chinese women breast cancer patients. Front Oncol 2023; 13:1028830. [PMID: 37152050 PMCID: PMC10154525 DOI: 10.3389/fonc.2023.1028830] [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: 08/26/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023] Open
Abstract
Background Sentinel lymph node biopsy (SLNB) is the standard treatment for breast cancer patients with clinically negative axilla. However, axillary lymph node dissection (ALND) is still the standard care for sentinel lymph node (SLN) positive patients. Clinical data reveals about 40-75% of patients without non-sentinel lymph node (NSLN) metastasis after ALND. Unnecessary ALND increases the risk of complications and detracts from quality of life. In this study, we expect to develop a nomogram based on genotypic and clinicopathologic factors to predict the risk of NSLN metastasis in SLN-positive Chinese women breast cancer patients. Methods This retrospective study collected data from 1,879 women breast cancer patients enrolled from multiple centers. Genotypic features contain 96 single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility, therapy and prognosis. SNP genotyping was identified by the quantitative PCR detection platform. The genetic features were divided into two clusters by the mutational stability. The normalized polygenic risk score (PRS) was used to evaluate the combined effect of each SNP cluster. Recursive feature elimination (RFE) based on linear discriminant analysis (LDA) was adopted to select the most useful predictive features, and RFE based on support vector machine (SVM) was used to reduce the number of SNPs. Multivariable logistic regression models (i.e., nomogram) were built for predicting NSLN metastasis. The predictive abilities of three types of model (based on only clinicopathologic information, the integrated clinicopathologic and all SNPs information, and integrated clinicopathologic and significant SNPs information) were compared. Internal and external validations were performed and the area under ROC curves (AUCs) as well as a series of evaluation indicators were assessed. Results 229 patients underwent SLNB followed by ALND and without any neo-adjuvant therapy, 79 among them (34%) had a positive axillary NSLN metastasis. The LDA-RFE identified the characteristics including lymphovascular invasion, number of positive SLNs, number of negative SLNs and two SNP clusters as significant predictors of NSLN metastasis. Furthermore, the SVM-RFE selected 29 significant SNPs in the prediction of NSLN metastasis. In internal validation, the median AUCs of the clinical and all SNPs combining model, the clinical and 29 significant SNPs combining model, and the clinical model were 0.837, 0.795 and 0.708 respectively. Meanwhile, in external validation, the AUCs of the three models were 0.817, 0.815 and 0.745 respectively. Conclusion We present a new nomogram by combining genotypic and clinicopathologic factors to achieve higher sensitivity and specificity comparing with traditional clinicopathologic factors to predict NSLN metastasis in Chinese women breast cancer. It is recommended that more validations are required in prospective studies among different patient populations.
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Affiliation(s)
- Liling Zhu
- Department of Breast Surgery, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Liling Zhu, ; Xiaopeng Hao, ; Jiandong Wang,
| | - Ke Liu
- Academic Department of Breast Cancer Education Association, Beijing, China
| | - Baoshi Bao
- Department of General Surgery, The First Medical Center of the General Hospital of the People’s Liberation Army of China, Beijing, China
| | - Fengyun Li
- Academic Department of Breast Cancer Education Association, Beijing, China
| | - Wentao Liang
- Academic Department of Beijing Centragene Technology Co., Ltd., Beijing, China
| | - Zhaoyun Jiang
- Academic Department of Breast Cancer Education Association, Beijing, China
| | - Xiaopeng Hao
- Department of General Surgery, The First Medical Center of the General Hospital of the People’s Liberation Army of China, Beijing, China
- *Correspondence: Liling Zhu, ; Xiaopeng Hao, ; Jiandong Wang,
| | - Jiandong Wang
- Department of General Surgery, The First Medical Center of the General Hospital of the People’s Liberation Army of China, Beijing, China
- *Correspondence: Liling Zhu, ; Xiaopeng Hao, ; Jiandong Wang,
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He J, Wen W, Beeghly A, Chen Z, Cao C, Shu XO, Zheng W, Long Q, Guo X. Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers. Nat Commun 2022; 13:7118. [PMID: 36402776 PMCID: PMC9675749 DOI: 10.1038/s41467-022-34888-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
Transcriptome-wide association studies (TWAS) have successfully discovered many putative disease susceptibility genes. However, TWAS may suffer from inaccuracy of gene expression predictions due to inclusion of non-regulatory variants. By integrating prior knowledge of susceptible transcription factor occupied elements, we develop sTF-TWAS and demonstrate that it outperforms existing TWAS approaches in both simulation and real data analyses. Under the sTF-TWAS framework, we build genetic models to predict alternative splicing and gene expression in normal breast, prostate and lung tissues from the Genotype-Tissue Expression project and apply these models to data from large genome-wide association studies (GWAS) conducted among European-ancestry populations. At Bonferroni-corrected P < 0.05, we identify 354 putative susceptibility genes for these cancers, including 189 previously unreported in GWAS loci and 45 in loci unreported by GWAS. These findings provide additional insight into the genetic susceptibility of human cancers. Additionally, we show the generalizability of the sTF-TWAS on non-cancer diseases.
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Affiliation(s)
- Jingni He
- grid.22072.350000 0004 1936 7697Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada ,grid.452223.00000 0004 1757 7615Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Wanqing Wen
- grid.152326.10000 0001 2264 7217Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Alicia Beeghly
- grid.152326.10000 0001 2264 7217Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Zhishan Chen
- grid.152326.10000 0001 2264 7217Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Chen Cao
- grid.22072.350000 0004 1936 7697Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada
| | - Xiao-Ou Shu
- grid.152326.10000 0001 2264 7217Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Wei Zheng
- grid.152326.10000 0001 2264 7217Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN USA
| | - Quan Long
- grid.22072.350000 0004 1936 7697Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, Canada ,grid.22072.350000 0004 1936 7697Department of Medical Genetics, University of Calgary, Calgary, Canada ,grid.22072.350000 0004 1936 7697Department of Mathematics & Statistics, University of Calgary, Calgary, Canada ,grid.22072.350000 0004 1936 7697Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada ,grid.22072.350000 0004 1936 7697Hotchkiss Brain Institute, University of Calgary, Calgary, Canada
| | - Xingyi Guo
- grid.152326.10000 0001 2264 7217Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA
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16
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Pathak AK, Husain N, Kant S, Bala L. Reflection of p53 phenotype in tumor tissue by genotypic variants in glutathione S-transferases: An association with DNA damage in lung adenocarcinoma. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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17
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Xi E, Bai J, Zhang K, Yu H, Guo Y. Genomic variants disrupt miRNA-mRNA regulation. Chem Biodivers 2022; 19:e202200623. [PMID: 35985010 DOI: 10.1002/cbdv.202200623] [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: 06/29/2022] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
Micro RNA (miRNA) and its regulatory effect on messenger RNA (mRNA) gene expression are a major focus in cancer research. Disruption in the normal miRNA-mRNA regulation network can result in serious cascading biological repercussions. In this study, we curated miRNA-related variants from major genomic consortiums and thoroughly evaluated how these variants could exert their effects by cross-validating with independent functional knowledge bases. Nearly all known variants (more than 664 million) categorized by type (germline, somatic, epigenetic) were mapped to the genomic regions involved in miRNA-mRNA binding (miRNA seeds and miRNA-mRNA 3'-UTR binding sequence). Subsets of miRNA-related variants supported by additional functional evidence, such as expression Quantitative Trait Loci (eQTL) and Genome-Wide Association Study (GWAS), were identified and scrutinized. Our results show that variants in miRNA seeds can substantially alter the composition of an miRNA's target mRNA set. Various functional analyses converged to reveal a post-transcriptional complex regulatory network where miRNA, eQTL, and RNA-binding protein intertwined to disseminate the impact of genomic variants. These results may potentially explain how certain variants affect disease/trait risks in genome wide association studies.
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Affiliation(s)
- Ellie Xi
- University of New Mexico - Albuquerque: The University of New Mexico, Internal Medicine, 100A Cancer Research Facility, 100A Cancer Research Facility, 87131, Albuquerque, UNITED STATES
| | - Judy Bai
- University of New Mexico - Albuquerque: The University of New Mexico, Internal Medicine, 100A Cancer Research Facility, 100A Cancer Research Facility, 87131, Albuquerque, UNITED STATES
| | - Klaira Zhang
- University of New Mexico - Albuquerque: The University of New Mexico, Internal Medicine, 100A Cancer Research Facility, 100A Cancer Research Facility, 87131, Albuquerque, UNITED STATES
| | - Hui Yu
- University of New Mexico - Albuquerque: The University of New Mexico, Internal Medicine, 100A Cancer Research Facility, Albuquerque, UNITED STATES
| | - Yan Guo
- University of New Mexico, Cancer Research Facility 100A, 87131, Albuquerque, UNITED STATES
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18
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Zafar A, Shafiq M, Ali B, Sadee W, Shakoori AR, Shakoori FR. Association of IRGM promoter region polymorphisms and haplotype with pulmonary tuberculosis in Pakistani (Punjab) population. Tuberculosis (Edinb) 2022; 136:102233. [DOI: 10.1016/j.tube.2022.102233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 06/03/2022] [Accepted: 07/13/2022] [Indexed: 10/17/2022]
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19
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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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20
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Allelic imbalance of HLA-B expression in human lung cells infected with coronavirus and other respiratory viruses. Eur J Hum Genet 2022; 30:922-929. [PMID: 35322240 PMCID: PMC8940983 DOI: 10.1038/s41431-022-01070-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/09/2022] [Accepted: 02/09/2022] [Indexed: 01/01/2023] Open
Abstract
The human leucocyte antigen (HLA) loci have been widely characterized to be associated with viral infectious diseases using either HLA allele frequency-based association or in silico predicted studies. However, there is less experimental evidence to link the HLA alleles with COVID-19 and other respiratory infectious diseases, particularly in the lung cells. To examine the role of HLA alleles in response to coronavirus and other respiratory viral infections in disease-relevant cells, we designed a two-stage study by integrating publicly accessible RNA-seq data sets, and performed allelic expression (AE) analysis on heterozygous HLA genotypes. We discovered an increased AE pattern accompanied with overexpression of HLA-B gene in SARS-CoV-2-infected human lung epithelial cells. Analysis of independent data sets verified the respiratory virus-induced AE of HLA-B gene in lung cells and tissues. The results were further experimentally validated in cultured lung cells infected with SARS-CoV-2. We further uncovered that the antiviral cytokine IFNβ contribute to AE of the HLA-B gene in lung cells. Our analyses provide a new insight into allelic influence on the HLA expression in association with SARS-CoV-2 and other common viral infectious diseases.
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21
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Zhang Y, Day K, Absher DM. STAT3-mediated allelic imbalance of novel genetic variant Rs1047643 and B-cell-specific super-enhancer in association with systemic lupus erythematosus. eLife 2022; 11:72837. [PMID: 35188103 PMCID: PMC8884724 DOI: 10.7554/elife.72837] [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: 08/06/2021] [Accepted: 02/18/2022] [Indexed: 11/24/2022] Open
Abstract
Mapping of allelic imbalance (AI) at heterozygous loci has the potential to establish links between genetic risk for disease and biological function. Leveraging multi-omics data for AI analysis and functional annotation, we discovered a novel functional risk variant rs1047643 at 8p23 in association with systemic lupus erythematosus (SLE). This variant displays dynamic AI of chromatin accessibility and allelic expression on FDFT1 gene in B cells with SLE. We further found a B-cell restricted super-enhancer (SE) that physically contacts with this SNP-residing locus, an interaction that also appears specifically in B cells. Quantitative analysis of chromatin accessibility and DNA methylation profiles further demonstrated that the SE exhibits aberrant activity in B cell development with SLE. Functional studies identified that STAT3, a master factor associated with autoimmune diseases, directly regulates both the AI of risk variant and the activity of SE in cultured B cells. Our study reveals that STAT3-mediated SE activity and cis-regulatory effects of SNP rs1047643 at 8p23 locus are associated with B cell deregulation in SLE.
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Affiliation(s)
- Yanfeng Zhang
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | | | - Devin M Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
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22
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Du F, Peng L, Wang Q, Dong K, Pei W, Zhuo H, Xu T, Jing C, Li L, Zhang J. CCDC12 promotes tumor development and invasion through the Snail pathway in colon adenocarcinoma. Cell Death Dis 2022; 13:187. [PMID: 35217636 PMCID: PMC8881494 DOI: 10.1038/s41419-022-04617-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/10/2022] [Accepted: 02/09/2022] [Indexed: 12/02/2022]
Abstract
Integrative expression Quantitative Trait Loci (eQTL) analysis found that rs8180040 was significantly associated with Coiled-coil domain containing 12 (CCDC12) in colon adenocarcinoma (COAD) patients. Immunohistochemical staining and western blotting confirmed CCDC12 was highly expressed in COAD tissues, which was consistent with RNA-Seq data from the TCGA database. Knockdown of CCDC12 could significantly reduce proliferation, migration, invasion, and tumorigenicity of colon cancer cells, while exogenous overexpression of CCDC12 had the opposite effect. Four plex Isobaric Tags for Relative and Absolute Quantitation assays were performed to determine its function and potential regulatory mechanism and demonstrated that overexpression of CCDC12 would change proteins on the adherens junction pathway. Overexpressed Snail and knocked down CCDC12 subsequently in SW480 cells, and we found that overexpression of Snail did not significantly change CCDC12 levels in SW480 cells, while knockdown of CCDC12 reduced that of Snail. CCDC12 plays a significant role in tumorigenesis, development, and invasion of COAD and may affect the epithelial to mesenchymal transformation process of colon cancer cells by regulating the Snail pathway.
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The Expression Quantitative Trait Loci in Immune Response Genes Impact the Characteristics and Survival of Colorectal Cancer. Diagnostics (Basel) 2022; 12:diagnostics12020315. [PMID: 35204406 PMCID: PMC8871427 DOI: 10.3390/diagnostics12020315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 02/05/2023] Open
Abstract
The impact of germline variants on the regulation of the expression of tumor microenvironment (TME)-based immune response genes remains unclear. Expression quantitative trait loci (eQTL) provide insight into the effect of downstream target genes (eGenes) regulated by germline-associated variants (eVariants). Through eQTL analyses, we illustrated the relationships between germline eVariants, TME-based immune response eGenes, and clinical outcomes. In this study, both RNA sequencing data from primary tumor and germline whole-genome sequencing data were collected from patients with stage III colorectal cancer (CRC). Ninety-nine high-risk subjects were subjected to immune response gene expression analyses. Seventy-seven subjects remained for further analysis after quality control, of which twenty-two patients (28.5%) experienced tumor recurrence. We found that 65 eQTL, including 60 germline eVariants and 22 TME-based eGenes, impacted the survival of cancer patients. For the recurrence prediction model, 41 differentially expressed genes (DEGs) achieved the best area under the receiver operating characteristic curve of 0.93. In total, 19 survival-associated eGenes were identified among the DEGs. Most of these genes were related to the regulation of lymphocytes and cytokines. A high expression of HGF, CCR5, IL18, FCER1G, TDO2, IFITM2, and LAPTM5 was significantly associated with a poor prognosis. In addition, the FCER1G eGene was associated with tumor invasion, tumor nodal stage, and tumor site. The eVariants that regulate the TME-based expression of FCER1G, including rs2118867 and rs12124509, were determined to influence survival and chromatin binding preferences. We also demonstrated that FCER1G and co-expressed genes in TME were related to the aggregation of leukocytes via pathway analysis. By analyzing the eQTL from the cancer genome using germline variants and TME-based RNA sequencing, we identified the eQTL in immune response genes that impact colorectal cancer characteristics and survival.
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Dai H, Chu X, Liang Q, Wang M, Li L, Zhou Y, Zheng Z, Wang W, Wang Z, Li H, Wang J, Zheng H, Zhao Y, Liu L, Yao H, Luo M, Wang Q, Kang S, Li Y, Wang K, Song F, Zhang R, Wu X, Cheng X, Zhang W, Wei Q, Li MJ, Chen K. Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women. Cell Discov 2021; 7:121. [PMID: 34930913 PMCID: PMC8688503 DOI: 10.1038/s41421-021-00342-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/23/2021] [Indexed: 12/03/2022] Open
Abstract
Ovarian cancer survival varies considerably among patients, to which germline variation may also contribute in addition to mutational signatures. To identify genetic markers modulating ovarian cancer outcome, we performed a genome-wide association study in 2130 Chinese ovarian cancer patients and found a hitherto unrecognized locus at 3p26.1 to be associated with the overall survival (Pcombined = 8.90 × 10−10). Subsequent statistical fine-mapping, functional annotation, and eQTL mapping prioritized a likely casual SNP rs9311399 in the non-coding regulatory region. Mechanistically, rs9311399 altered its enhancer activity through an allele-specific transcription factor binding and a long-range interaction with the promoter of a lncRNA BHLHE40-AS1. Deletion of the rs9311399-associated enhancer resulted in expression changes in several oncogenic signaling pathway genes and a decrease in tumor growth. Thus, we have identified a novel genetic locus that is associated with ovarian cancer survival possibly through a long-range gene regulation of oncogenic pathways.
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Affiliation(s)
- Hongji Dai
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Xinlei Chu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Qian Liang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Mengyun Wang
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lian Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yao Zhou
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhanye Zheng
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Zhao Wang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Haixin Li
- Cancer Biobank, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Jianhua Wang
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Yanrui Zhao
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Luyang Liu
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Hongcheng Yao
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Menghan Luo
- Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qiong Wang
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Shan Kang
- Department of Obstetrics and Gynaecology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Yan Li
- Department of Molecular Biology, Hebei Medical University, Fourth Hospital, Shijiazhuang, China
| | - Ke Wang
- Department of Gynecologic Oncology, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Fengju Song
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China
| | - Ruoxin Zhang
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaohua Wu
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Cheng
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wei Zhang
- Center for Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Wake Forest Baptist Medical Center, Winston-Salem, NC, USA.,Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China. .,Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA. .,Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, USA.
| | - Mulin Jun Li
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China. .,Department of Pharmacology, the Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Molecular Cancer Epidemiology of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin, China.
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25
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Ren N, Li B, Liu Q, Yang L, Liu X, Huang Q. Dinucleotide tag-based parallel reporter gene assay method enables efficient identification of regulatory mutations. Biotechnol J 2021; 17:e2100341. [PMID: 34894203 DOI: 10.1002/biot.202100341] [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: 07/01/2021] [Revised: 12/07/2021] [Accepted: 12/09/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND The causal single nucleotide polymorphisms (SNPs) leading to increased cancer predisposition mainly function as gene regulatory elements, the evaluation of which largely relies on the parallel reporter gene assay system. However, the common DNA barcodes used in parallel reporter gene assay systems typically because nucleotide composition bias, and many barcodes must be allocated for each sequence to reduce the bias effect. MAIN METHODS AND MAJOR RESULTS Here, a versatile dinucleotide-tag reporter system (DiR) that enables parallel analysis of regulatory elements with minimized bias based on next-generation sequencing is described. The DiR system is more robust than the classical luciferase assay method, particularly for the investigation of moderate-level regulatory elements. The authors applied the DiR-seq assay in the functional evaluation of SNPs with prostate cancer risk and nominated two and six regulatory SNPs in PC-3 and LNCaP cells, respectively. CONCLUSIONS AND IMPLICATIONS The DiR system has great potential to advance the functional study of SNPs associated with polygenic disease risks.
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Affiliation(s)
- Naixia Ren
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Bo Li
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Qingqing Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Lele Yang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Xiaodan Liu
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao, China
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26
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Ren N, Li Y, Xiong Y, Li P, Ren Y, Huang Q. Functional Screenings Identify Regulatory Variants Associated with Breast Cancer Susceptibility. Curr Issues Mol Biol 2021; 43:1756-1777. [PMID: 34889888 PMCID: PMC8928974 DOI: 10.3390/cimb43030124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/12/2021] [Accepted: 10/15/2021] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified more than 2000 single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility, most of which are located in the non-coding region. However, the causal SNPs functioning as gene regulatory elements still remain largely undisclosed. Here, we applied a Dinucleotide Parallel Reporter sequencing (DiR-seq) assay to evaluate 288 breast cancer risk SNPs in nine different breast cancer cell lines. Further multi-omics analysis with the ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing), DNase-seq (DNase I hypersensitive sites sequencing) and histone modification ChIP-seq (Chromatin Immunoprecipitation sequencing) nominated seven functional SNPs in breast cancer cells. Functional investigations show that rs4808611 affects breast cancer progression by altering the gene expression of NR2F6. For the other site, rs2236007, the alteration promotes the binding of the suppressive transcription factor EGR1 and results in the downregulation of PAX9 expression. The downregulated expression of PAX9 causes cancer malignancies and is associated with the poor prognosis of breast cancer patients. Our findings contribute to defining the functional risk SNPs and the related genes for breast cancer risk prediction.
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27
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FOXA1 of regulatory variant associated with risk of breast cancer through allele-specific enhancer in the Chinese population. Breast Cancer 2021; 29:247-259. [PMID: 34635981 DOI: 10.1007/s12282-021-01305-1] [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: 05/18/2021] [Accepted: 10/07/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND FOXA1 is a pioneer transcription factor which has been established as a carcinogenic factor and can regulate the expression of downstream target genes in breast cancer. We hypothesized that genetic variants modulating FOXA1 expression might play a role in the risk of breast cancer. METHODS Physical interaction predicted by PreSTIGE analysis and CHIA-PET data integration with cis-expression quantitative trait loci (cis-eQTL) based SNP-FOXA1 analysis were used to identify potentially regulatory variants modulating the expression of FOXA1. Then, we utilized a case-control study consisting of 855 new diagnosed breast cancer cases and 920 controls in the Chinese population to identify breast cancer associated variants. Biological assays were conducted in breast cancer cell lines to illustrate the effects of associated variants on breast cancer risk. RESULTS We identified that rs7160774 G > A variant was associated with lower risk of breast cancer (OR = 0.77, 95% confidence interval = 0.62-0.96, P = 0.022). Biological experiments indicated that rs7160774[A] allele down-regulated the expression of FOXA1 compared to the G allele by influencing transcription factor binding affinity, thus playing an important role in the development of breast cancer. CONCLUSION Our study suggested that the regulatory variant rs7160774 was associated with risk of breast cancer by long-range modulating FOXA1 expression and provided critical insights into pinpoint causal genetic variants.
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28
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Jiang L, Guo F, Tang J, Yu H, Ness S, Duan M, Mao P, Zhao YY, Guo Y. SBSA: an online service for somatic binding sequence annotation. Nucleic Acids Res 2021; 50:e4. [PMID: 34606615 PMCID: PMC8500130 DOI: 10.1093/nar/gkab877] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/10/2021] [Accepted: 09/17/2021] [Indexed: 12/11/2022] Open
Abstract
Efficient annotation of alterations in binding sequences of molecular regulators can help identify novel candidates for mechanisms study and offer original therapeutic hypotheses. In this work, we developed Somatic Binding Sequence Annotator (SBSA) as a full-capacity online tool to annotate altered binding motifs/sequences, addressing diverse types of genomic variants and molecular regulators. The genomic variants can be somatic mutation, single nucleotide polymorphism, RNA editing, etc. The binding motifs/sequences involve transcription factors (TFs), RNA-binding proteins, miRNA seeds, miRNA-mRNA 3′-UTR binding target, or can be any custom motifs/sequences. Compared to similar tools, SBSA is the first to support miRNA seeds and miRNA-mRNA 3′-UTR binding target, and it unprecedentedly implements a personalized genome approach that accommodates joint adjacent variants. SBSA is empowered to support an indefinite species, including preloaded reference genomes for SARS-Cov-2 and 25 other common organisms. We demonstrated SBSA by annotating multi-omics data from over 30,890 human subjects. Of the millions of somatic binding sequences identified, many are with known severe biological repercussions, such as the somatic mutation in TERT promoter region which causes a gained binding sequence for E26 transformation-specific factor (ETS1). We further validated the function of this TERT mutation using experimental data in cancer cells. Availability:http://innovebioinfo.com/Annotation/SBSA/SBSA.php.
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Affiliation(s)
- Limin Jiang
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an 710069, China.,School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Fei Guo
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Hui Yu
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Scott Ness
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Mingrui Duan
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Peng Mao
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Ying-Yong Zhao
- Faculty of Life Science & Medicine, Northwest University, No. 229 Taibai North Road, Xi'an 710069, China
| | - Yan Guo
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
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29
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Yu QY, Lu TP, Hsiao TH, Lin CH, Wu CY, Tzeng JY, Hsiao CK. An Integrative Co-localization (INCO) Analysis for SNV and CNV Genomic Features With an Application to Taiwan Biobank Data. Front Genet 2021; 12:709555. [PMID: 34567069 PMCID: PMC8456116 DOI: 10.3389/fgene.2021.709555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/23/2021] [Indexed: 11/13/2022] Open
Abstract
Genomic studies have been a major approach to elucidating disease etiology and to exploring potential targets for treatments of many complex diseases. Statistical analyses in these studies often face the challenges of multiplicity, weak signals, and the nature of dependence among genetic markers. This situation becomes even more complicated when multi-omics data are available. To integrate the data from different platforms, various integrative analyses have been adopted, ranging from the direct union or intersection operation on sets derived from different single-platform analysis to complex hierarchical multi-level models. The former ignores the biological relationship between molecules while the latter can be hard to interpret. We propose in this study an integrative approach that combines both single nucleotide variants (SNVs) and copy number variations (CNVs) in the same genomic unit to co-localize the concurrent effect and to deal with the sparsity due to rare variants. This approach is illustrated with simulation studies to evaluate its performance and is applied to low-density lipoprotein cholesterol and triglyceride measurements from Taiwan Biobank. The results show that the proposed method can more effectively detect the collective effect from both SNVs and CNVs compared to traditional methods. For the biobank analysis, the identified genetic regions including the gene VNN2 could be novel and deserve further investigation.
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Affiliation(s)
- Qi-You Yu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Ching-Heng Lin
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Yun Wu
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, United States.,Department of Statistics, University of Pennsylvania, Philadelphia, PA, United States
| | - Jung-Ying Tzeng
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Statistics and Bioinformatics Research Center, North Carolina State University, Raleigh, NC, United States
| | - Chuhsing Kate Hsiao
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan.,Department of Public Health, National Taiwan University, Taipei, Taiwan
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Genetic variations of DNA bindings of FOXA1 and co-factors in breast cancer susceptibility. Nat Commun 2021; 12:5318. [PMID: 34518541 PMCID: PMC8438084 DOI: 10.1038/s41467-021-25670-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/25/2021] [Indexed: 11/21/2022] Open
Abstract
Identifying transcription factors (TFs) whose DNA bindings are altered by genetic variants that regulate susceptibility genes is imperative to understand transcriptional dysregulation in disease etiology. Here, we develop a statistical framework to analyze extensive ChIP-seq and GWAS data and identify 22 breast cancer risk-associated TFs. We find that, by analyzing genetic variations of TF-DNA bindings, the interaction of FOXA1 with co-factors such as ESR1 and E2F1, and the interaction of TFs with chromatin features (i.e., enhancers) play a key role in breast cancer susceptibility. Using genetic variants occupied by the 22 TFs, transcriptome-wide association analyses identify 52 previously unreported breast cancer susceptibility genes, including seven with evidence of essentiality from functional screens in breast relevant cell lines. We show that FOXA1 and co-factors form a core TF-transcriptional network regulating the susceptibility genes. Our findings provide additional insights into genetic variations of TF-DNA bindings (particularly for FOXA1) underlying breast cancer susceptibility. The identification of transcription factors (TFs) whose binding sites are affected by risk genetic variants remains crucial. Here, the authors develop a statistical framework to analyse ChIP-seq and GWAS data, identify 22 breast cancer risk-associated TFs and a core TF-transcriptional network for FOXA1 and co-factors.
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31
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Spirko-Burns L, Devarajan K. Supervised Dimension Reduction for Large-Scale "Omics" Data With Censored Survival Outcomes Under Possible Non-Proportional Hazards. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2032-2044. [PMID: 31940547 DOI: 10.1109/tcbb.2020.2965934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The past two decades have witnessed significant advances in high-throughput "omics" technologies such as genomics, proteomics, metabolomics, transcriptomics and radiomics. These technologies have enabled simultaneous measurement of the expression levels of tens of thousands of features from individual patient samples and have generated enormous amounts of data that require analysis and interpretation. One specific area of interest has been in studying the relationship between these features and patient outcomes, such as overall and recurrence-free survival, with the goal of developing a predictive "omics" profile. Large-scale studies often suffer from the presence of a large fraction of censored observations and potential time-varying effects of features, and methods for handling them have been lacking. In this paper, we propose supervised methods for feature selection and survival prediction that simultaneously deal with both issues. Our approach utilizes continuum power regression (CPR) - a framework that includes a variety of regression methods - in conjunction with the parametric or semi-parametric accelerated failure time (AFT) model. Both CPR and AFT fall within the linear models framework and, unlike black-box models, the proposed prognostic index has a simple yet useful interpretation. We demonstrate the utility of our methods using simulated and publicly available cancer genomics data.
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32
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Ren N, Liu Q, Yan L, Huang Q. Parallel Reporter Assays Identify Altered Regulatory Role of rs684232 in Leading to Prostate Cancer Predisposition. Int J Mol Sci 2021; 22:8792. [PMID: 34445492 PMCID: PMC8395720 DOI: 10.3390/ijms22168792] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/07/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
Functional characterization of cancer risk-associated single nucleotide polymorphism (SNP) identified by genome-wide association studies (GWAS) has become a big challenge. To identify the regulatory risk SNPs that can lead to transcriptional misregulation, we performed parallel reporter gene assays with both alleles of 213 prostate cancer risk-associated GWAS SNPs in 22Rv1 cells. We disclosed 32 regulatory SNPs that exhibited different regulatory activities with two alleles. For one of the regulatory SNPs, rs684232, we found that the variation altered chromatin binding of transcription factor FOXA1 on the DNA region and led to aberrant gene expression of VPS53, FAM57A, and GEMIN4, which play vital roles in prostate cancer malignancy. Our findings reveal the roles and underlying mechanism of rs684232 in prostate cancer progression and hold great promise in benefiting prostate cancer patients with prognostic prediction and target therapies.
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Affiliation(s)
| | | | | | - Qilai Huang
- Shandong Provincial Key Laboratory of Animal Cell and Developmental Biology, School of Life Sciences, Shandong University, Qingdao 266237, China; (N.R.); (Q.L.); (L.Y.)
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33
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Margalit S, Abramson Y, Sharim H, Manber Z, Bhattacharya S, Chen YW, Vilain E, Barseghyan H, Elkon R, Sharan R, Ebenstein Y. Long reads capture simultaneous enhancer-promoter methylation status for cell-type deconvolution. Bioinformatics 2021; 37:i327-i333. [PMID: 34252972 PMCID: PMC8275347 DOI: 10.1093/bioinformatics/btab306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2021] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION While promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long reads that report on the methylation status of enhancer-promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer-promoter methylation profiles. RESULTS To evaluate our hypothesis we examine long-read optical methylome data for the GM12878 cell line and myoblast cell lines from two donors. We identified over 100 000 enhancer-promoter pairs that co-exist on at least 30 individual DNA molecules. We developed a detailed methodology for mixture deconvolution and applied it to estimate the proportional cell compositions in synthetic mixtures. Analysis of promoter methylation, as well as enhancer-promoter pairwise methylation, resulted in very accurate estimates. In addition, we show that pairwise methylation analysis can be generalized from deconvolving different cell types to subtle scenarios where one wishes to resolve different cell populations of the same cell-type. AVAILABILITY AND IMPLEMENTATION The code used in this work to analyze single-molecule Bionano Genomics optical maps is available via the GitHub repository https://github.com/ebensteinLab/Single_molecule_methylation_in_EP.
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Affiliation(s)
- Sapir Margalit
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yotam Abramson
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Hila Sharim
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Zohar Manber
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Surajit Bhattacharya
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Eric Vilain
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Hayk Barseghyan
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC 20010, USA.,Department of Genomics and Precision Medicine, George Washington University, Washington, DC 20052, USA
| | - Ran Elkon
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Roded Sharan
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel.,School of Computer Science, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Yuval Ebenstein
- Department of Physical Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv 6997801, Israel
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Senda N, Kawaguchi-Sakita N, Kawashima M, Inagaki-Kawata Y, Yoshida K, Takada M, Kataoka M, Torii M, Nishimura T, Kawaguchi K, Suzuki E, Kataoka Y, Matsumoto Y, Yoshibayashi H, Yamagami K, Tsuyuki S, Takahara S, Yamauchi A, Shinkura N, Kato H, Moriguchi Y, Okamura R, Kan N, Suwa H, Sakata S, Mashima S, Yotsumoto F, Tachibana T, Tanaka M, Togashi K, Haga H, Yamada T, Kosugi S, Inamoto T, Sugimoto M, Ogawa S, Toi M. Optimization of prediction methods for risk assessment of pathogenic germline variants in the Japanese population. Cancer Sci 2021; 112:3338-3348. [PMID: 34036661 PMCID: PMC8353892 DOI: 10.1111/cas.14986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Predicting pathogenic germline variants (PGVs) in breast cancer patients is important for selecting optimal therapeutics and implementing risk reduction strategies. However, PGV risk factors and the performance of prediction methods in the Japanese population remain unclear. We investigated clinicopathological risk factors using the Tyrer‐Cuzick (TC) breast cancer risk evaluation tool to predict BRCA PGVs in unselected Japanese breast cancer patients (n = 1,995). Eleven breast cancer susceptibility genes were analyzed using target‐capture sequencing in a previous study; the PGV prevalence in BRCA1, BRCA2, and PALB2 was 0.75%, 3.1%, and 0.45%, respectively. Significant associations were found between the presence of BRCA PGVs and early disease onset, number of familial cancer cases (up to third‐degree relatives), triple‐negative breast cancer patients under the age of 60, and ovarian cancer history (all P < .0001). In total, 816 patients (40.9%) satisfied the National Comprehensive Cancer Network (NCCN) guidelines for recommending multigene testing. The sensitivity and specificity of the NCCN criteria for discriminating PGV carriers from noncarriers were 71.3% and 60.7%, respectively. The TC model showed good discrimination for predicting BRCA PGVs (area under the curve, 0.75; 95% confidence interval, 0.69‐0.81). Furthermore, use of the TC model with an optimized cutoff of TC score ≥0.16% in addition to the NCCN guidelines improved the predictive efficiency for high‐risk groups (sensitivity, 77.2%; specificity, 54.8%; about 11 genes). Given the influence of ethnic differences on prediction, we consider that further studies are warranted to elucidate the role of environmental and genetic factors for realizing precise prediction.
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Affiliation(s)
- Noriko Senda
- Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | | | | | | | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Masahiro Takada
- Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | - Masako Kataoka
- Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Kyoto, Japan
| | - Masae Torii
- Department of Breast Surgery, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan
| | | | | | - Eiji Suzuki
- Department of Breast Surgery, Kyoto University, Kyoto, Japan
| | - Yuki Kataoka
- Department of Healthcare Epidemiology, School of Public Health, in the Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Hiroshi Yoshibayashi
- Department of Breast Surgery, Japanese Red Cross Wakayama Medical Center, Wakayama, Japan
| | - Kazuhiko Yamagami
- Department of Breast Surgery and Oncology, Shinko Hospital, Kobe, Japan
| | - Shigeru Tsuyuki
- Department of Breast Surgery, Osaka Red Cross Hospital, Osaka, Japan
| | | | - Akira Yamauchi
- Department of Breast Surgery, Kitano Hospital, Osaka, Japan
| | - Nobuhiko Shinkura
- Department of Surgery, Ijinkai Takeda General Hospital, Kyoto, Japan
| | - Hironori Kato
- Department of Breast Surgery, Kobe City Medical Center General Hospital, Kobe, Japan
| | | | - Ryuji Okamura
- Department of Breast Surgery, Yamatotakada Municipal Hospital, Yamatotakada, Japan
| | | | - Hirofumi Suwa
- Department of Breast Surgery, Hyogo Prefectural Amagasaki General Medical Center, Amagasaki, Japan
| | - Shingo Sakata
- Department of Breast Surgery, Rakuwakai Otowa Hospital, Kyoto, Japan
| | - Susumu Mashima
- Department of Surgery, Japan Community Health Care Organization, Yamato Koriyama Hospital, Yamato Koriyama, Japan
| | - Fumiaki Yotsumoto
- Department of Breast Surgery, Shiga General Hospital, Moriyama, Japan
| | | | - Mitsuru Tanaka
- Department of Surgery, Hirakata Kohsai Hospital, Hirakata, Japan
| | - Kaori Togashi
- Department of Diagnostic Imaging and Nuclear Medicine, Kyoto University, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Takahiro Yamada
- Department of Medical Ethics/Medical Genetics, Kyoto University, Kyoto, Japan
| | - Shinji Kosugi
- Department of Medical Ethics/Medical Genetics, Kyoto University, Kyoto, Japan
| | - Takashi Inamoto
- Faculty of Health Care, Tenri Health Care University, Tenri, Japan
| | - Masahiro Sugimoto
- Health Promotion and Preemptive Medicine, Research and Development Center for Minimally Invasive Therapies, Tokyo Medical University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
| | - Masakazu Toi
- Department of Breast Surgery, Kyoto University, Kyoto, Japan
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35
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Rong Y, Dong SS, Hu WX, Guo Y, Chen YX, Chen JB, Zhu DL, Chen H, Yang TL. DDRS: Detection of drug response SNPs specifically in patients receiving drug treatment. Comput Struct Biotechnol J 2021; 19:3650-3657. [PMID: 34257842 PMCID: PMC8254081 DOI: 10.1016/j.csbj.2021.06.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/16/2021] [Accepted: 06/16/2021] [Indexed: 12/15/2022] Open
Abstract
Detecting SNPs associated with drug efficacy or toxicity is helpful to facilitate personalized medicine. Previous studies usually find SNPs associated with clinical outcome only in patients received a specific treatment. However, without information from patients without drug treatment, it is possible that the detected SNPs are associated with patients' clinical outcome even without drug treatment. Here we aimed to detect drug response SNPs based on data from patients with and without drug treatment through combing the cox proportional-hazards model and pairwise Kaplan-Meier survival analysis. A pipeline named Detection of Drug Response SNPs (DDRS) was built and applied to TCGA breast cancer data including 363 patients with doxorubicin treatment and 321 patients without any drug treatment. We identified 548 doxorubicin associated SNPs. Drug response score derived from these SNPs were associated with drug-resistant level (indicated by IC50) of breast cancer cell lines. Enrichment analyses showed that these SNPs were enriched in active epigenetic regulation markers (e.g., H3K27ac). Compared with random genes, the cis-eQTL genes of these SNPs had a shorter protein-protein interaction distance to doxorubicin associated genes. In addition, linear discriminant analysis showed that the eQTL gene expression levels could be used to predict clinical outcome for patients with doxorubicin treatment (AUC = 0.738). Specifically, we identified rs2817101 as a drug response SNP for doxorubicin treatment. Higher expression level of its cis-eQTL gene GSTA1 is associated with poorer survival. This approach can also be applied to identify new drug associated SNPs in other cancers.
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Affiliation(s)
- Yu Rong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Shan-Shan Dong
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Wei-Xin Hu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Yan Guo
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Yi-Xiao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Jia-Bin Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Dong-Li Zhu
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Hao Chen
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Tie-Lin Yang
- Biomedical Informatics & Genomics Center, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China.,National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy, The Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, PR China
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36
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Deng Y, Xie K, Logothetis CJ, Thompson TC, Kim J, Huang M, Chang DW, Gu J, Wu X, Ye Y. Genetic variants in epithelial-mesenchymal transition genes as predictors of clinical outcomes in localized prostate cancer. Carcinogenesis 2021; 41:1057-1064. [PMID: 32215555 DOI: 10.1093/carcin/bgaa026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 03/13/2020] [Accepted: 03/24/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Epithelial-mesenchymal transition (EMT) plays a pivotal role in the progression of prostate cancer (PCa). However, little is known about genetic variants in the EMT pathway as predictors of aggressiveness, biochemical recurrence (BCR) and disease reclassification in localized PCa. PATIENTS AND METHODS In this multistage study, we evaluated 5186 single nucleotide polymorphisms (SNPs) from 264 genes related to EMT pathway to identify SNPs associated with PCa aggressiveness and BCR in the MD Anderson PCa (MDA-PCa) patient cohort (N = 1762), followed by assessment of the identified SNPs with disease reclassification in the active surveillance (AS) cohort (N = 392). RESULTS In the MDA-PCa cohort, 312 SNPs were associated with high D'Amico risk (P < 0.05), among which, 14 SNPs in 10 genes were linked to BCR risk. In the AS cohort, 2 of 14 identified SNPs (rs76779889 and rs7083961) in C-terminal Binding Proteins 2 gene were associated with reclassification risk. The associations of rs76779889 with different endpoints were: D'Amico high versus low, odds ratio [95% confidence interval (CI)] = 2.89 (1.32-6.34), P = 0.008; BCR, hazard ratio (HR) (95% CI) = 2.88 (1.42-5.85), P = 0.003; and reclassification, HR (95% CI) = 2.83 (1.40-5.74), P = 0.004. For rs7083961, the corresponding risk estimates were: D'Amico high versus low, odds ratio (95% CI) = 1.69 (1.12-2.57), P = 0.013; BCR, HR (95% CI) = 1.87 (1.15-3.02), P = 0.011 and reclassification, HR (95% CI) = 1.72 (1.09-2.72), P = 0.020. There were cumulative effects of these two SNPs on modulating these endpoints. CONCLUSION Genetic variants in EMT pathway may influence the risks of localized PCa's aggressiveness, BCR and disease reclassification, suggesting their potential role in the assessment and management of localized PCa.
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Affiliation(s)
- Yang Deng
- Department of Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kunlin Xie
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Liver Surgery and Liver Transplantation, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Christopher J Logothetis
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Timothy C Thompson
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeri Kim
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for Biostatistics, Bioinformatics, and Big Data, Second Affiliated Hospital and Department of Epidemiology and Health Statistics School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Big Data in Health Science, School of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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37
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Rare variants regulate expression of nearby individual genes in multiple tissues. PLoS Genet 2021; 17:e1009596. [PMID: 34061836 PMCID: PMC8195400 DOI: 10.1371/journal.pgen.1009596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 06/11/2021] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
The rapid decrease in sequencing cost has enabled genetic studies to discover rare variants associated with complex diseases and traits. Once this association is identified, the next step is to understand the genetic mechanism of rare variants on how the variants influence diseases. Similar to the hypothesis of common variants, rare variants may affect diseases by regulating gene expression, and recently, several studies have identified the effects of rare variants on gene expression using heritability and expression outlier analyses. However, identifying individual genes whose expression is regulated by rare variants has been challenging due to the relatively small sample size of expression quantitative trait loci studies and statistical approaches not optimized to detect the effects of rare variants. In this study, we analyze whole-genome sequencing and RNA-seq data of 681 European individuals collected for the Genotype-Tissue Expression (GTEx) project (v8) to identify individual genes in 49 human tissues whose expression is regulated by rare variants. To improve statistical power, we develop an approach based on a likelihood ratio test that combines effects of multiple rare variants in a nonlinear manner and has higher power than previous approaches. Using GTEx data, we identify many genes regulated by rare variants, and some of them are only regulated by rare variants and not by common variants. We also find that genes regulated by rare variants are enriched for expression outliers and disease-causing genes. These results suggest the regulatory effects of rare variants, which would be important in interpreting associations of rare variants with complex traits. It has been shown that rare variants may affect many diseases including both rare and common diseases with the advent of next-generation sequencing technology. An important question is how rare variants affect diseases or traits, especially whether or how they regulate gene expression as they may affect diseases through gene regulation. However, it is challenging to identify the regulatory effects of rare variants because it often requires large sample sizes and the existing statistical approaches are not optimized for it. Here, we develop a novel method, LRT-q, based on a likelihood ratio test that aggregates the effects of multiple rare variants nonlinearly to achieve higher statistical power than previous rare variant association methods. We apply LRT-q to the latest GTEx v8 dataset and identify regulatory effect of rare variants on individual genes. We also observe that genes regulated by rare variants are likely to be disease-causing genes. These results demonstrate the functional effects of rare variants, especially on gene expression, which provides important biological insights in understanding the genetic mechanism of rare variants in complex traits and diseases.
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38
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Zhan J, Sun S, Chen Y, Xu C, Chen Q, Li M, Pei Y, Li Q. MiR-3130-5p is an intermediate modulator of 2q33 and influences the invasiveness of lung adenocarcinoma by targeting NDUFS1. Cancer Med 2021; 10:3700-3714. [PMID: 33978320 PMCID: PMC8178510 DOI: 10.1002/cam4.3885] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/11/2021] [Accepted: 03/13/2021] [Indexed: 12/11/2022] Open
Abstract
Genome‐wide association studies (GWAS) have reported a handful of loci associated with lung cancer risk, of which the pathogenic pathways are largely unknown. We performed cis‐expression quantitative trait loci (eQTL) mapping for 376 lung cancer related GWAS loci in 227 TCGA lung adenocarcinoma (LUAD) and reported two risk loci as eQTL of miRNA. Among the miRNAs in association with lung cancer risk, we further predicted and validated miR‐3130‐5p as an intermediate modulator of risk loci 2q33 and the tumor suppressor NDUFS1. We assessed the phenotypic impacts of the interaction between miR‐3130‐5p and NDUFS1 in both lung cancer cell lines and mice xenograft models. As a result, miR‐3130‐5p directly regulates the expression of NDUFS1 and the corresponding tumor invasiveness, migration and epithelial‐mesenchymal transition (EMT). Our findings provide important clues for the pathogenic mechanism of 2q33 in lung carcinogenesis which informs clinical diagnosis and prognosis of LUAD. We performed a cis‐eQTL analysis for 376 lung cancer risk loci based on the expression profiles of 251 miRNAs in a cohort of 227 TCGA lung adenocarcinoma. We report a novel pathogenic pathway of 2q33 via miR‐3130‐5p and NDUFS1.
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Affiliation(s)
- Juan Zhan
- Department of Pulmonary and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Oncology, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Shenghua Sun
- Department of Pulmonary and Critical Care Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yixing Chen
- Laboratory, Xiamen Cancer Center, The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Chaoqun Xu
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Qinwei Chen
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
| | - Minjie Li
- Department of Thoracic Surgery, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Yihua Pei
- Central Laboratory, Zhongshan Hospital, Xiamen University, Xiamen, China
| | - Qiyuan Li
- National Institute for Data Science in Health and Medicine, School of Medicine, Xiamen University, Xiamen, China
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39
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Wang J, Ma X, Zhang Q, Chen Y, Wu D, Zhao P, Yu Y. The Interaction Analysis of SNP Variants and DNA Methylation Identifies Novel Methylated Pathogenesis Genes in Congenital Heart Diseases. Front Cell Dev Biol 2021; 9:665514. [PMID: 34041244 PMCID: PMC8143053 DOI: 10.3389/fcell.2021.665514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Congenital heart defect (CHD) is a rare and complicated disease with a high mortality rate. Its etiology remains unclear and includes many aspects. DNA methylation has been indicated to be involved in heart development in the early stage of life, and aberrant methylation level was related to CHDs. This study provides the first evidence of the cross talk of SNP variants and DNA methylation in clarifying CHD underlying genomic cause. We gathered whole exome sequencing (WES) data for Group 1 consisting of patients with PA (n = 78), TOF (n = 20), TAPVC (n = 78), and PDA (n = 40), and 100 healthy children as control group. Rare non-synonymous mutations and novel genes were found and highlighted. Meanwhile, we carried out the second analysis of DNA methylation data from patients with PA (n = 3), TAPVC (n = 3), TOF (n = 3), and PDA (n = 2), and five healthy controls using 850 K array in Group 2. DNA methylation was linked to WES data, and we explored an obvious overlap of hyper/hypomethylated genes. Next, we identified some candidate genes by Fisher’s exact test and Burden analysis; then, those methylated genes were figured out by the criteria of the mutation located in the CpG islands of the genome, differential methylation sites (DMS), and DNA methylation quantitative trait loci (meQTLs) in the database, respectively. Also, the interaction of differentially methylated candidate genes with known CHD pathogenetic genes was depicted in a molecular network. Taken together, our findings show that nine novel genes (ANGPTL4, VEGFA, PAX3, MUC4, HLA-DRB1, TJP2, BCR, PKD1, and HK2) in methylation level are critical to CHD and reveal a new insight into the molecular pathogenesis of CHD.
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Affiliation(s)
- Jing Wang
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China.,Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoqin Ma
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China
| | - Qi Zhang
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yinghui Chen
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dan Wu
- Department of Pediatric, Yangpu District Shidong Hospital, Shanghai, China
| | - Pengjun Zhao
- Department of Pediatric Cardiology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Yu
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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40
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Maguire S, Perraki E, Tomczyk K, Jones ME, Fletcher O, Pugh M, Winter T, Thompson K, Cooke R, Trainer A, James P, Bojesen S, Flyger H, Nevanlinna H, Mattson J, Friedman E, Laitman Y, Palli D, Masala G, Zanna I, Ottini L, Silvestri V, Hollestelle A, Hooning MJ, Novaković S, Krajc M, Gago-Dominguez M, Castelao JE, Olsson H, Hedenfalk I, Saloustros E, Georgoulias V, Easton DF, Pharoah P, Dunning AM, Bishop DT, Neuhausen SL, Steele L, Ashworth A, Garcia Closas M, Houlston R, Swerdlow A, Orr N. Common Susceptibility Loci for Male Breast Cancer. J Natl Cancer Inst 2021; 113:453-461. [PMID: 32785646 PMCID: PMC8023850 DOI: 10.1093/jnci/djaa101] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 05/14/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The etiology of male breast cancer (MBC) is poorly understood. In particular, the extent to which the genetic basis of MBC differs from female breast cancer (FBC) is unknown. A previous genome-wide association study of MBC identified 2 predisposition loci for the disease, both of which were also associated with risk of FBC. METHODS We performed genome-wide single nucleotide polymorphism genotyping of European ancestry MBC case subjects and controls in 3 stages. Associations between directly genotyped and imputed single nucleotide polymorphisms with MBC were assessed using fixed-effects meta-analysis of 1380 cases and 3620 controls. Replication genotyping of 810 cases and 1026 controls was used to validate variants with P values less than 1 × 10-06. Genetic correlation with FBC was evaluated using linkage disequilibrium score regression, by comprehensively examining the associations of published FBC risk loci with risk of MBC and by assessing associations between a FBC polygenic risk score and MBC. All statistical tests were 2-sided. RESULTS The genome-wide association study identified 3 novel MBC susceptibility loci that attained genome-wide statistical significance (P < 5 × 10-08). Genetic correlation analysis revealed a strong shared genetic basis with estrogen receptor-positive FBC. Men in the top quintile of genetic risk had a fourfold increased risk of breast cancer relative to those in the bottom quintile (odds ratio = 3.86, 95% confidence interval = 3.07 to 4.87, P = 2.08 × 10-30). CONCLUSIONS These findings advance our understanding of the genetic basis of MBC, providing support for an overlapping genetic etiology with FBC and identifying a fourfold high-risk group of susceptible men.
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Affiliation(s)
- Sarah Maguire
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Eleni Perraki
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Katarzyna Tomczyk
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Michael E Jones
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Olivia Fletcher
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Matthew Pugh
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Timothy Winter
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Kyle Thompson
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Rosie Cooke
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - kConFab Consortium
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alison Trainer
- Parkville Familial Cancer Clinic, Sir Peter MacCallum Department of Oncology, University of Melbourne and Royal Melbourne Hospital, East Melbourne, Victoria, Australia
| | - Paul James
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Stig Bojesen
- Department of Clinical Biochemistry, Herlev Hospital, Copenhagen University Hospital, Herlev, Denmark
- The Copenhagen General Population Study, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Flyger
- Department of Breast Surgery, Herlev and Gentofte Hospital, Copenhagen University Hospital, Copenhagen, Denmark
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Johanna Mattson
- Department of Oncology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eitan Friedman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Centre, Tel Aviv, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit, Sheba Medical Centre, Tel Aviv, Israel
- The Sackler School of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | - Domenico Palli
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Giovanna Masala
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Ines Zanna
- Cancer Risk Factors and Life-Style Epidemiology Unit, Institute for Cancer Research, Prevention and Clinical Network-ISPRO, Florence, Italy
| | - Laura Ottini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | | | - Antoinette Hollestelle
- Department of Medical Oncology, Familial Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Maartje J Hooning
- Department of Medical Oncology, Familial Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Srdjan Novaković
- Department of Molecular Diagnostics, Institute of Oncology Ljubljana, Ljubljana, Slovenia
| | - Mateja Krajc
- Institute of Oncology Ljubljana, Cancer Genetics Clinic, Epidemiology and Cancer Registry, Ljubljana, Slovenia
| | - 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 (CHUS), Servicio Galego de Saúde (SERGAS), Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria Galicia Sur (IISGS), Xerencia de Xestion Integrada de Vigo-SERGAS, Oncology and Genetics Unit, Vigo, Spain
| | - Jose Esteban Castelao
- Genetic Oncology Unit, Complexo Hospitalario Universitario de Vigo (CHUVI), SERGAS, Vigo, Spain
| | - Hakan Olsson
- Division of Oncology, Department of Clinical Sciences, Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Ingrid Hedenfalk
- Division of Oncology, Department of Clinical Sciences, Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | | | - Vasilios Georgoulias
- Department of Medical Oncology, University General Hospital of Heraklion, Heraklion, Greece
| | - Douglas F Easton
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Paul Pharoah
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Department of Oncology, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - D Timothy Bishop
- Division of Immunology, Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Linda Steele
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Alan Ashworth
- UCSF Helen Diller Family Comprehensive Cancer Centre, San Francisco, CA, USA
| | | | - Richard Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, UK
| | - Nick Orr
- The Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
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41
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Variable expression quantitative trait loci analysis of breast cancer risk variants. Sci Rep 2021; 11:7192. [PMID: 33785833 PMCID: PMC8009949 DOI: 10.1038/s41598-021-86690-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/12/2021] [Indexed: 01/08/2023] Open
Abstract
Genome wide association studies (GWAS) have identified more than 180 variants associated with breast cancer risk, however the underlying functional mechanisms and biological pathways which confer disease susceptibility remain largely unknown. As gene expression traits are under genetic regulation we hypothesise that differences in gene expression variability may identify causal breast cancer susceptibility genes. We performed variable expression quantitative trait loci (veQTL) analysis using tissue-specific expression data from the Genotype-Tissue Expression (GTEx) Common Fund Project. veQTL analysis identified 70 associations (p < 5 × 10–8) consisting of 60 genes and 27 breast cancer risk variants, including 55 veQTL that were observed in breast tissue only. Pathway analysis of genes associated with breast-specific veQTL revealed an enrichment of four genes (CYP11B1, CYP17A1 HSD3B2 and STAR) involved in the C21-steroidal biosynthesis pathway that converts cholesterol to breast-related hormones (e.g. oestrogen). Each of these four genes were significantly more variable in individuals homozygous for rs11075995 (A/A) breast cancer risk allele located in the FTO gene, which encodes an RNA demethylase. The A/A allele was also found associated with reduced expression of FTO, suggesting an epi-transcriptomic mechanism may underlie the dysregulation of genes involved in hormonal biosynthesis leading to an increased risk of breast cancer. These findings provide evidence that genetic variants govern high levels of expression variance in breast tissue, thus building a more comprehensive insight into the underlying biology of breast cancer risk loci.
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42
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Macauda A, Piredda C, Clay-Gilmour AI, Sainz J, Buda G, Markiewicz M, Barington T, Ziv E, Hildebrandt MAT, Belachew AA, Varkonyi J, Prejzner W, Druzd-Sitek A, Spinelli J, Andersen NF, Hofmann JN, Dudziński M, Martinez-Lopez J, Iskierka-Jazdzewska E, Milne RL, Mazur G, Giles GG, Ebbesen LH, Rymko M, Jamroziak K, Subocz E, Reis RM, Garcia-Sanz R, Suska A, Haastrup EK, Zawirska D, Grzasko N, Vangsted AJ, Dumontet C, Kruszewski M, Dutka M, Camp NJ, Waller RG, Tomczak W, Pelosini M, Raźny M, Marques H, Abildgaard N, Wątek M, Jurczyszyn A, Brown EE, Berndt S, Butrym A, Vachon CM, Norman AD, Slager SL, Gemignani F, Canzian F, Campa D. Expression quantitative trait loci of genes predicting outcome are associated with survival of multiple myeloma patients. Int J Cancer 2021; 149:327-336. [PMID: 33675538 DOI: 10.1002/ijc.33547] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 12/24/2022]
Abstract
Gene expression profiling can be used for predicting survival in multiple myeloma (MM) and identifying patients who will benefit from particular types of therapy. Some germline single nucleotide polymorphisms (SNPs) act as expression quantitative trait loci (eQTLs) showing strong associations with gene expression levels. We performed an association study to test whether eQTLs of genes reported to be associated with prognosis of MM patients are directly associated with measures of adverse outcome. Using the genotype-tissue expression portal, we identified a total of 16 candidate genes with at least one eQTL SNP associated with their expression with P < 10-7 either in EBV-transformed B-lymphocytes or whole blood. We genotyped the resulting 22 SNPs in 1327 MM cases from the International Multiple Myeloma rESEarch (IMMEnSE) consortium and examined their association with overall survival (OS) and progression-free survival (PFS), adjusting for age, sex, country of origin and disease stage. Three polymorphisms in two genes (TBRG4-rs1992292, TBRG4-rs2287535 and ENTPD1-rs2153913) showed associations with OS at P < .05, with the former two also associated with PFS. The associations of two polymorphisms in TBRG4 with OS were replicated in 1277 MM cases from the International Lymphoma Epidemiology (InterLymph) Consortium. A meta-analysis of the data from IMMEnSE and InterLymph (2579 cases) showed that TBRG4-rs1992292 is associated with OS (hazard ratio = 1.14, 95% confidence interval 1.04-1.26, P = .007). In conclusion, we found biologically a plausible association between a SNP in TBRG4 and OS of MM patients.
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Affiliation(s)
- Angelica Macauda
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Biology, University of Pisa, Pisa, Italy
| | | | - Alyssa I Clay-Gilmour
- Department of Epidemiology & Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, South Carolina, USA
| | - Juan Sainz
- Genomic Oncology Area, GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada/Andalusian Regional Government, Granada, Spain.,Hematology department, Virgen de las Nieves University Hospital, Granada, Spain
| | - Gabriele Buda
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Miroslaw Markiewicz
- Department of Hematology and Bone Marrow Transplantation, SPSKM Hospital, Katowice, Poland
| | - Torben Barington
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Elad Ziv
- Department of Medicine, Division of General Internal Medicine, Institute for Human Genetics, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Michelle A T Hildebrandt
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Alem A Belachew
- Department of Epidemiology, Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Judit Varkonyi
- Third Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Witold Prejzner
- Department of Hematology and Transplantation, Medical University of Gdansk, Gdansk, Poland
| | - Agnieszka Druzd-Sitek
- Department of Lymphoid Malignacies, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - John 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
| | | | - Jonathan N Hofmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Marek Dudziński
- Department of Hematology, Institute of Medical Sciences, College of Medical Sciences, University of Rzeszow, Rzeszow, Poland
| | | | | | - 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
| | - Grzegorz Mazur
- Department of Internal and Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Graham G Giles
- 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
| | | | - Marcin Rymko
- Department of Hematology, N. Copernicus Town Hospital, Torun, Poland
| | - Krzysztof Jamroziak
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Edyta Subocz
- Department of Haematology, Military Institute of Medicine, Warsaw, Poland
| | - Rui Manuel Reis
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,Molecular Oncology Research Center, Barretos, São Paulo, Brazil
| | - Ramon Garcia-Sanz
- Department of Hematology, University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Anna Suska
- Department of Hematology, Jagiellonian University Medical College, Cracow, Poland
| | - Eva Kannik Haastrup
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Daria Zawirska
- Department of Hematology, University Hospital of Cracow, Cracow, Poland
| | - Norbert Grzasko
- Department of Experimental Hematooncolog, Medical University of Lublin, Lublin, Poland.,Department of Hematology, St. John's Cancer Center, Lublin, Poland
| | - Annette Juul Vangsted
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Charles Dumontet
- Cancer Research Center of Lyon/Hospices Civils de Lyon, Lyon, France
| | - Marcin Kruszewski
- Department of Hematology, University Hospital Bydgoszcz, Bydgoszcz, Poland
| | - Magdalena Dutka
- Department of Hematology and Transplantation, Medical University of Gdansk, Gdansk, Poland
| | | | | | | | - Matteo Pelosini
- Clinical and Experimental Medicine, Section of Hematology, University of Pisa, Pisa, Italy
| | - Małgorzata Raźny
- Department of Hematology, Rydygier Specialistic Hospital, Cracow, Poland
| | | | - Niels Abildgaard
- Department of Hematology, Odense University Hospital, Odense, Denmark
| | - Marzena Wątek
- Hematology Clinic, Holycross Cancer Center, Kielce, Poland
| | - Artur Jurczyszyn
- Department of Hematology, Jagiellonian University Medical College, Cracow, Poland
| | - Elizabeth E Brown
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sonja Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Aleksandra Butrym
- Department of Internal and Occupational Diseases, Hypertension and Clinical Oncology, Wroclaw Medical University, Wroclaw, Poland
| | - Celine M Vachon
- Genetic Epidemiology and Risk Assessment Program, Mayo Clinic Comprehensive Cancer Center, and Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Aaron D Norman
- Genetic Epidemiology and Risk Assessment Program, Mayo Clinic Comprehensive Cancer Center, and Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Susan L Slager
- Genetic Epidemiology and Risk Assessment Program, Mayo Clinic Comprehensive Cancer Center, and Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - 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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43
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Coignard J, Lush M, Beesley J, O'Mara TA, Dennis J, Tyrer JP, Barnes DR, McGuffog L, Leslie G, Bolla MK, Adank MA, Agata S, Ahearn T, Aittomäki K, Andrulis IL, Anton-Culver H, Arndt V, Arnold N, Aronson KJ, Arun BK, Augustinsson A, Azzollini J, Barrowdale D, Baynes C, Becher H, Bermisheva M, Bernstein L, Białkowska K, Blomqvist C, Bojesen SE, Bonanni B, Borg A, Brauch H, Brenner H, Burwinkel B, Buys SS, Caldés T, Caligo MA, Campa D, Carter BD, Castelao JE, Chang-Claude J, Chanock SJ, Chung WK, Claes KBM, Clarke CL, Collée JM, Conroy DM, Czene K, Daly MB, Devilee P, Diez O, Ding YC, Domchek SM, Dörk T, Dos-Santos-Silva I, Dunning AM, Dwek M, Eccles DM, Eliassen AH, Engel C, Eriksson M, Evans DG, Fasching PA, Flyger H, Fostira F, Friedman E, Fritschi L, Frost D, Gago-Dominguez M, Gapstur SM, Garber J, Garcia-Barberan V, García-Closas M, García-Sáenz JA, Gaudet MM, Gayther SA, Gehrig A, Georgoulias V, Giles GG, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Greene MH, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hall P, Hamann U, Harrington PA, Hart SN, He W, Hogervorst FBL, Hollestelle A, Hopper JL, Horcasitas DJ, Hulick PJ, Hunter DJ, Imyanitov EN, Jager A, Jakubowska A, James PA, Jensen UB, John EM, Jones ME, Kaaks R, Kapoor PM, Karlan BY, Keeman R, Khusnutdinova E, Kiiski JI, Ko YD, Kosma VM, Kraft P, Kurian AW, Laitman Y, Lambrechts D, Le Marchand L, Lester J, Lesueur F, Lindstrom T, Lopez-Fernández A, Loud JT, Luccarini C, Mannermaa A, Manoukian S, Margolin S, Martens JWM, Mebirouk N, Meindl A, Miller A, Milne RL, Montagna M, Nathanson KL, Neuhausen SL, Nevanlinna H, Nielsen FC, O'Brien KM, Olopade OI, Olson JE, Olsson H, Osorio A, Ottini L, Park-Simon TW, Parsons MT, Pedersen IS, Peshkin B, Peterlongo P, Peto J, Pharoah PDP, Phillips KA, Polley EC, Poppe B, Presneau N, Pujana MA, Punie K, Radice P, Rantala J, Rashid MU, Rennert G, Rennert HS, Robson M, Romero A, Rossing M, Saloustros E, Sandler DP, Santella R, Scheuner MT, Schmidt MK, Schmidt G, Scott C, Sharma P, Soucy P, Southey MC, Spinelli JJ, Steinsnyder Z, Stone J, Stoppa-Lyonnet D, Swerdlow A, Tamimi RM, Tapper WJ, Taylor JA, Terry MB, Teulé A, Thull DL, Tischkowitz M, Toland AE, Torres D, Trainer AH, Truong T, Tung N, Vachon CM, Vega A, Vijai J, Wang Q, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wolk A, Yadav S, Yang XR, Yannoukakos D, Zheng W, Ziogas A, Zorn KK, Park SK, Thomassen M, Offit K, Schmutzler RK, Couch FJ, Simard J, Chenevix-Trench G, Easton DF, Andrieu N, Antoniou AC. A case-only study to identify genetic modifiers of breast cancer risk for BRCA1/BRCA2 mutation carriers. Nat Commun 2021; 12:1078. [PMID: 33597508 PMCID: PMC7890067 DOI: 10.1038/s41467-020-20496-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 11/19/2020] [Indexed: 02/02/2023] Open
Abstract
Breast cancer (BC) risk for BRCA1 and BRCA2 mutation carriers varies by genetic and familial factors. About 50 common variants have been shown to modify BC risk for mutation carriers. All but three, were identified in general population studies. Other mutation carrier-specific susceptibility variants may exist but studies of mutation carriers have so far been underpowered. We conduct a novel case-only genome-wide association study comparing genotype frequencies between 60,212 general population BC cases and 13,007 cases with BRCA1 or BRCA2 mutations. We identify robust novel associations for 2 variants with BC for BRCA1 and 3 for BRCA2 mutation carriers, P < 10-8, at 5 loci, which are not associated with risk in the general population. They include rs60882887 at 11p11.2 where MADD, SP11 and EIF1, genes previously implicated in BC biology, are predicted as potential targets. These findings will contribute towards customising BC polygenic risk scores for BRCA1 and BRCA2 mutation carriers.
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Affiliation(s)
- Juliette Coignard
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France
- Institut Curie Paris, Paris, France
- Mines ParisTech Fontainebleau, Paris, France
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- PSL University Paris, Paris, France
- Paris Sud University, Orsay, France
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan Beesley
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Tracy A O'Mara
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jonathan P Tyrer
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Daniel R Barnes
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Lesley McGuffog
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Goska Leslie
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Muriel A Adank
- Family Cancer Clinic, The Netherlands Cancer Institute, Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Simona Agata
- Immunology and Molecular Oncology, Unit Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Thomas Ahearn
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - 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, ON, Canada
- Department of Molecular Genetics University of Toronto, Toronto, ON, Canada
| | - Hoda Anton-Culver
- Department of Epidemiology, Genetic Epidemiology Research Institute University of California Irvine, Irvine, CA, USA
| | - Volker Arndt
- Division of Clinical Epidemiology and Aging Research German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Norbert Arnold
- Department of Gynaecology and Obstetrics University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
- Institute of Clinical Molecular Biology University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, Kiel, Germany
| | - Kristan J Aronson
- Department of Public Health Sciences, and Cancer Research Institute Queen's University, Kingston, ON, Canada
| | - Banu K Arun
- Department of Breast Medical Oncology University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Annelie Augustinsson
- Department of Cancer Epidemiology, Clinical Sciences Lund University, Lund, 22242, Sweden
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Daniel Barrowdale
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Caroline Baynes
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Heiko Becher
- Institute for Medical Biometrics and Epidemiology University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marina Bermisheva
- Institute of Biochemistry and Genetics Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
| | - Leslie Bernstein
- Department of Population Sciences Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Katarzyna Białkowska
- Department of Genetics and Pathology Pomeranian Medical University Szczecin, Szczecin, Poland
| | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital University of Helsinki, Helsinki, Finland
- Department of Oncology Örebro University Hospital, Örebro, Sweden
| | - 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
| | - 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 Tübingen, Tübingen, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research 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
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology Group, C080 German Cancer Research Center (DKFZ), Heidelberg, Germany
- Molecular Biology of Breast Cancer, University Womens Clinic Heidelberg University of Heidelberg, Heidelberg, Germany
| | - Saundra S Buys
- Department of Medicine Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Trinidad Caldés
- Molecular Oncology Laboratory CIBERONC, Hospital Clinico San Carlos, IdISSC (Instituto de Investigación Sanitaria del Hospital Clínico San Carlos), Madrid, Spain
| | - Maria A Caligo
- SOD Genetica Molecolare University Hospital, Pisa, Italy
| | - Daniele Campa
- Department of Biology University of Pisa, Pisa, Italy
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Brian D Carter
- Behavioral and Epidemiology Research Group American Cancer Society Atlanta, Atlanta, GA, USA
| | - 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 National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | | | - Christine L Clarke
- Westmead Institute for Medical Research University of Sydney, Sydney, NSW, Australia
| | - J Margriet Collée
- Department of Clinical Genetics Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Don M Conroy
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mary B Daly
- Department of Clinical Genetics Fox Chase Cancer Center Philadelphia, 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
| | - Orland Diez
- Oncogenetics Group Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain
- Clinical and Molecular Genetics Area University Hospital Vall d'Hebron, Barcelona, Spain
| | - Yuan Chun Ding
- Department of Population Sciences Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan M Domchek
- Basser Center for BRCA, Abramson Cancer Center University of Pennsylvania, Philadelphia, PA, 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
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Miriam Dwek
- School of Life Sciences University of Westminster, London, UK
| | - Diana M Eccles
- Faculty of Medicine University of Southampton, Southampton, UK
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology Harvard TH Chan School of Public Health, 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
| | - D Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences The University of Manchester, Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St Mary's Hospital, Manchester, UK
- Genomic Medicine, North West Genomics hub Manchester Academic Health Science Centre, Manchester Universities Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Peter A Fasching
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology University of California at Los Angeles, Los Angeles, CA, USA
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN University Hospital Erlangen, Friedrich-Alexander-University, Erlangen-Nuremberg, Erlangen, Germany
| | - 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 íDemokritosí, 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
| | - 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
- Behavioral and Epidemiology Research Group American Cancer Society Atlanta, Atlanta, GA, USA
| | - Judy Garber
- Division of Cancer Genetics and Prevention, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Vanesa Garcia-Barberan
- Medical Oncology Department, Hospital Clínico San Carlos Instituto de Investigación Sanitaria San Carlos (IdISSC), Centro Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Montserrat García-Closas
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - 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), Madrid, Spain
| | - Mia M Gaudet
- Behavioral and Epidemiology Research Group American Cancer Society Atlanta, Atlanta, GA, USA
| | - Simon A Gayther
- Center for Bioinformatics and Functional Genomics and the Cedars Sinai Genomics Core Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Andrea Gehrig
- Department of Human Genetics University Würzburg, Würzburg, Germany
| | | | - Graham G Giles
- Cancer Epidemiology Division Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health Monash University, Clayton, VIC, Australia
| | - Andrew K Godwin
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mark S Goldberg
- Department of Medicine, McGill University, Montréal, QC, Canada
- Division of Clinical Epidemiology, Royal Victoria Hospital McGill University Montréal, Montréal, QC, Canada
| | - David E Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - 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, MD, USA
| | - Pascal Guénel
- Cancer & Environment Group, Center for Research in Epidemiology and Population Health (CESP) INSERM, University Paris-Sud, University Paris-Saclay, Villejuif, France
| | - Lothar Haeberle
- Department of Gynaecology and Obstetrics, University Hospital Erlangen Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Eric Hahnen
- Center for Hereditary Breast and Ovarian Cancer Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO) Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Christopher A Haiman
- Department of Preventive Medicine, Keck School of Medicine University of Southern California, Los Angeles, CA, USA
| | | | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Oncology, Södersjukhuset, Stockholm, Sweden
| | - Ute Hamann
- Molecular Genetics of Breast Cancer German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patricia A Harrington
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Wei He
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - 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
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Darling J Horcasitas
- New Mexico Oncology Hematology Consultants, University of New Mexico, Albuquerque, NM, USA
| | - Peter J Hulick
- Center for Medical Genetics NorthShore University HealthSystem, Evanston, IL, USA
- The University of Chicago Pritzker School of Medicine Chicago, Chicago, IL, USA
| | - David J Hunter
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics Harvard TH Chan School of Public Health Boston, Boston, MA, USA
- Nuffield Department of Population Health University of Oxford, Oxford, UK
| | | | - Agnes Jager
- Department of Medical Oncology, Family Cancer Clinic Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Anna Jakubowska
- Department of Genetics and Pathology Pomeranian Medical University Szczecin, Szczecin, Poland
- Independent Laboratory of Molecular Biology and Genetic Diagnostics Pomeranian Medical University, Szczecin, Poland
| | - Paul A James
- Sir Peter MacCallum Department of Oncology The University of Melbourne, Melbourne, VIC, Australia
- Parkville Familial Cancer Centre Peter MacCallum Cancer Center, Melbourne, VIC, Australia
| | - Uffe Birk Jensen
- Department of Clinical Genetics Aarhus, University Hospital, Aarhus, Denmark
| | - Esther M John
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael E Jones
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Rudolf Kaaks
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pooja Middha Kapoor
- Division of Cancer Epidemiology German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Genetics and Epidemiology The Institute of Cancer Research, London, UK
| | - Beth Y Karlan
- Faculty of Medicine University of Heidelberg, Heidelberg, Germany
- David Geffen School of Medicine, Department of Obstetrics and Gynecology University of California at Los Angeles, Los Angeles, CA, USA
| | - Renske Keeman
- Womenís Cancer Program at the Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia
- Division of Molecular Pathology The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Johanna I Kiiski
- Department of Genetics and Fundamental Medicine Bashkir State Medical University, Ufa, Russia
| | - Yon-Dschun Ko
- Department of Obstetrics and Gynecology, Helsinki University Hospital University of Helsinki, Helsinki, Finland
| | - Veli-Matti Kosma
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH Johanniter Krankenhaus, Bonn, Germany
- Translational Cancer Research Area University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine University of Eastern Finland, Kuopio, Finland
| | - Peter Kraft
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics Harvard TH Chan School of Public Health Boston, Boston, MA, USA
| | - Allison W Kurian
- Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Yael Laitman
- The Susanne Levy Gertner Oncogenetics Unit Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Diether Lambrechts
- VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics University of Leuven, Leuven, Belgium
| | - Loic Le Marchand
- Epidemiology Program University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Jenny Lester
- Faculty of Medicine University of Heidelberg, Heidelberg, Germany
- David Geffen School of Medicine, Department of Obstetrics and Gynecology University of California at Los Angeles, Los Angeles, CA, USA
| | - Fabienne Lesueur
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France
- Institut Curie Paris, Paris, France
- Mines ParisTech Fontainebleau, Paris, France
- PSL University Paris, Paris, France
| | - Tricia Lindstrom
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Adria Lopez-Fernández
- High Risk and Cancer Prevention Group Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Jennifer T Loud
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics National Cancer Institute, Bethesda, MD, USA
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology University of Cambridge, Cambridge, UK
| | - Arto Mannermaa
- Department of Internal Medicine, Evangelische Kliniken Bonn gGmbH Johanniter Krankenhaus, Bonn, Germany
- Translational Cancer Research Area University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine University of Eastern Finland, Kuopio, Finland
| | - 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, Södersjukhuset, Stockholm, Sweden
- Department of Clinical Science and Education, Södersjukhuset Karolinska Institutet, Stockholm, Sweden
| | - John W M Martens
- Department of Medical Oncology, Family Cancer Clinic Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Noura Mebirouk
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France
- Institut Curie Paris, Paris, France
- Mines ParisTech Fontainebleau, Paris, France
- PSL University Paris, Paris, France
| | - Alfons Meindl
- Department of Gynecology and Obstetrics University of Munich, Campus Grosshadern, Munich, Germany
| | - Austin Miller
- NRG Oncology, Statistics and Data Management Center Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Roger L Milne
- Cancer Epidemiology Division Cancer Council Victoria, Melbourne, VIC, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Precision Medicine, School of Clinical Sciences at Monash Health Monash University, Clayton, VIC, Australia
| | - Marco Montagna
- Immunology and Molecular Oncology, Unit Veneto Institute of Oncology IOV - IRCCS, Padua, Italy
| | - Katherine L Nathanson
- Basser Center for BRCA, Abramson Cancer Center University of Pennsylvania, Philadelphia, PA, USA
| | - Susan L Neuhausen
- Department of Population Sciences Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Heli Nevanlinna
- Department of Genetics and Fundamental Medicine Bashkir State Medical University, Ufa, Russia
| | - Finn C Nielsen
- Center for Genomic Medicine Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Katie M O'Brien
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, 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, 22242, Sweden
| | - Ana Osorio
- Human Cancer Genetics Programme Spanish National Cancer Research Centre (CNIO), Madrid, Spain
- Centro de Investigación en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Laura Ottini
- Department of Molecular Medicine University La Sapienza, Rome, Italy
| | | | - Michael T Parsons
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Inge Sokilde Pedersen
- Molecular Diagnostics Aalborg University Hospital, Aalborg, Denmark
- Clinical Cancer Research Center Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine Aalborg University, Aalborg, Denmark
| | - Beth Peshkin
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - 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
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology The University of Melbourne, Melbourne, VIC, Australia
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Bruce Poppe
- Centre for Medical Genetics Ghent University, Gent, Belgium
| | - Nadege Presneau
- School of Life Sciences University of Westminster, London, UK
| | - Miquel Angel Pujana
- Translational Research Laboratory IDIBELL (Bellvitge Biomedical Research Institute), Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Kevin Punie
- Leuven Multidisciplinary Breast Center, Department of Oncology Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
| | - 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 U 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
| | - Hedy S Rennert
- Clalit National Cancer Control Center Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Atocha Romero
- Medical Oncology Department Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Maria Rossing
- Center for Genomic Medicine Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Dale P Sandler
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
| | - Regina Santella
- Department of Epidemiology, Mailman School of Public Health Columbia University, New York, NY, USA
| | - Maren T Scheuner
- Cancer Genetics and Prevention Program University of California San Francisco, San Francisco, CA, USA
| | - Marjanka K Schmidt
- Womenís Cancer Program at the Samuel Oschin Comprehensive Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Division of Psychosocial Research and Epidemiology The Netherlands Cancer Institute - Antoni van Leeuwenhoek hospital, Amsterdam, The Netherlands
| | - Gunnar Schmidt
- Institute of Human Genetics Hannover Medical School, Hannover, Germany
| | - Christopher Scott
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Priyanka Sharma
- Department of Internal Medicine, Division of Medical Oncology University of Kansas Medical Center, Westwood, KS, USA
| | - Penny Soucy
- Genomics Center, Centre Hospitalier Universitaire de Québec - Université Laval Research Center, Québec City, QC, Canada
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health Monash University, Clayton, VIC, Australia
- Department of Clinical Pathology The University of Melbourne, Melbourne, VIC, Australia
| | - John J Spinelli
- Population Oncology BC Cancer, Vancouver, BC, Canada
- School of Population and Public Health University of British Columbia, Vancouver, BC, Canada
| | - Zoe Steinsnyder
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Jennifer Stone
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
- The Curtin UWA Centre for Genetic Origins of Health and Disease Curtin University and University of Western Australia, Perth, Western Australia, Australia
| | - Dominique Stoppa-Lyonnet
- Service de Génétique Institut Curie, Paris, France
- Department of Tumour Biology INSERM U830, Paris, France
- Université Paris Descartes, Paris, France
| | - Anthony Swerdlow
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Division of Breast Cancer Research Institute of Cancer Research, London, UK
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology Harvard TH Chan School of Public Health, Boston, MA, USA
- Program in Genetic Epidemiology and Statistical Genetics Harvard TH Chan School of Public Health Boston, Boston, MA, USA
| | | | - Jack A Taylor
- Epidemiology Branch National Institute of Environmental Health Sciences, NIH Research Triangle Park, Durham, NC, USA
- Epigenetic and Stem Cell Biology Laboratory National Institute of Environmental Health Sciences, NIH Research Triangle Park, Triangle Park, NC, USA
| | - Mary Beth Terry
- Department of Epidemiology, Mailman School of Public Health Columbia University, New York, NY, USA
| | - Alex Teulé
- Hereditary Cancer Program ONCOBELL-IDIBELL-IDIBGI-IGTP, Catalan Institute of Oncology, CIBERONC, Barcelona, Spain
| | - Darcy L Thull
- Department of Medicine Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Marc Tischkowitz
- Program in Cancer Genetics, Departments of Human Genetics and Oncology McGill University, Montréal, QC, Canada
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Center, University of Cambridge, Cambridge, UK
| | - Amanda E Toland
- Department of Cancer Biology and Genetics The Ohio State University, Columbus, OH, USA
| | - Diana Torres
- Molecular Genetics of Breast Cancer German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Human Genetics Pontificia Universidad Javeriana, Bogota, Colombia
| | - Alison H Trainer
- Parkville Familial Cancer Centre Peter MacCallum Cancer Center, Melbourne, VIC, Australia
- Department of medicine University Of Melbourne, Melbourne, VIC, Australia
| | - 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, MA, USA
| | - Celine M Vachon
- Department of Health Science Research, Division of Epidemiology Mayo Clinic, Rochester, MN, USA
| | - Ana Vega
- Fundación Pública Galega Medicina Xenómica-SERGAS, Instituto de Investigación Sanitaria Santiago de Compostela (IDIS); CIBERER, Santiago de Compostela, Spain
| | - Joseph Vijai
- Clinical Genetics Service, Department of Medicine Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - 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 Integrated Oncology (CIO) 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, Triangle Park, NC, USA
| | | | - Camilla Wendt
- Department of Clinical Science and Education, Södersjukhuset Karolinska Institutet, Stockholm, Sweden
| | - Alicja Wolk
- Institute of Environmental Medicine Karolinska Institutet, Stockholm, Sweden
- Department of Surgical Sciences Uppsala University, Uppsala, Sweden
| | | | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD, USA
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES National Centre for Scientific Research íDemokritosí, Athens, Greece
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Argyrios Ziogas
- Department of Epidemiology, Genetic Epidemiology Research Institute University of California Irvine, Irvine, CA, USA
| | - Kristin K Zorn
- Magee-Womens Hospital, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sue K Park
- Department of Preventive Medicine Seoul National University College of Medicine, Seoul, Korea
- Department of Biomedical Sciences Seoul National University Graduate School, Seoul, Korea
- Cancer Research Institute Seoul National University, Seoul, Korea
| | - Mads Thomassen
- Department of Clinical Genetics Odense University Hospital, Odence C, Denmark
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine Memorial Sloan-Kettering Cancer Center, New York, NY, USA
- Clinical Genetics Research Lab, Department of Cancer Biology and Genetics Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Rita K Schmutzler
- Center for Hereditary Breast and Ovarian Cancer Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Center for Integrated Oncology (CIO) Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology Mayo Clinic, Rochester, MN, USA
| | - Jacques Simard
- Department of Epidemiology, Genetic Epidemiology Research Institute University of California Irvine, Irvine, CA, USA
| | - Georgia Chenevix-Trench
- Department of Genetics and Computational Biology QIMR Berghofer Medical Research Institute, Brisbane, QLD, 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
| | - Nadine Andrieu
- Genetic Epidemiology of Cancer team, Inserm, U900, Paris, France.
- Institut Curie Paris, Paris, France.
- Mines ParisTech Fontainebleau, Paris, France.
- PSL University Paris, Paris, France.
| | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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Fuady AM, van Roon-Mom WMC, Kiełbasa SM, Uh HW, Houwing-Duistermaat JJ. Statistical method for modeling sequencing data from different technologies in longitudinal studies with application to Huntington disease. Biom J 2020; 63:745-760. [PMID: 33350510 PMCID: PMC8049011 DOI: 10.1002/bimj.201900235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 01/13/2023]
Abstract
Advancement of gene expression measurements in longitudinal studies enables the identification of genes associated with disease severity over time. However, problems arise when the technology used to measure gene expression differs between time points. Observed differences between the results obtained at different time points can be caused by technical differences. Modeling the two measurements jointly over time might provide insight into the causes of these different results. Our work is motivated by a study of gene expression data of blood samples from Huntington disease patients, which were obtained using two different sequencing technologies. At time point 1, DeepSAGE technology was used to measure the gene expression, with a subsample also measured using RNA‐Seq technology. At time point 2, all samples were measured using RNA‐Seq technology. Significant associations between gene expression measured by DeepSAGE and disease severity using data from the first time point could not be replicated by the RNA‐Seq data from the second time point. We modeled the relationship between the two sequencing technologies using the data from the overlapping samples. We used linear mixed models with either DeepSAGE or RNA‐Seq measurements as the dependent variable and disease severity as the independent variable. In conclusion, (1) for one out of 14 genes, the initial significant result could be replicated with both technologies using data from both time points; (2) statistical efficiency is lost due to disagreement between the two technologies, measurement error when predicting gene expressions, and the need to include additional parameters to account for possible differences.
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Affiliation(s)
- Angga M Fuady
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.,Department of Biostatistics and Research Support, Div. Julius Centrum, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Szymon M Kiełbasa
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands
| | - Hae-Won Uh
- Department of Biostatistics and Research Support, Div. Julius Centrum, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jeanine J Houwing-Duistermaat
- Department of Biostatistics and Research Support, Div. Julius Centrum, University Medical Center Utrecht, Utrecht, the Netherlands.,Department of Statistics and Alan Turing Institute, University of Leeds, Leeds, United Kingdom
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Porta‐Pardo E, Valencia A, Godzik A. Understanding oncogenicity of cancer driver genes and mutations in the cancer genomics era. FEBS Lett 2020; 594:4233-4246. [PMID: 32239503 PMCID: PMC7529711 DOI: 10.1002/1873-3468.13781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 01/23/2020] [Accepted: 02/09/2020] [Indexed: 12/12/2022]
Abstract
One of the key challenges of cancer biology is to catalogue and understand the somatic genomic alterations leading to cancer. Although alternative definitions and search methods have been developed to identify cancer driver genes and mutations, analyses of thousands of cancer genomes return a remarkably similar catalogue of around 300 genes that are mutated in at least one cancer type. Yet, many features of these genes and their role in cancer remain unclear, first and foremost when a somatic mutation is truly oncogenic. In this review, we first summarize some of the recent efforts in completing the catalogue of cancer driver genes. Then, we give an overview of different aspects that influence the oncogenicity of somatic mutations in the core cancer driver genes, including their interactions with the germline genome, other cancer driver mutations, the immune system, or their potential role in healthy tissues. In the coming years, this research holds promise to illuminate how, when, and why cancer driver genes and mutations are really drivers, and thereby move personalized cancer medicine and targeted therapies forward.
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Affiliation(s)
- Eduard Porta‐Pardo
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
- Josep Carreras Leukaemia Research Institute (IJC)BadalonaSpain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC)BarcelonaSpain
- Institucio Catalana de Recerca I Estudis Avançats (ICREA)BarcelonaSpain
| | - Adam Godzik
- Division of Biomedical SciencesUniversity of California Riverside School of MedicineRiversideCAUSA
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46
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Zhou Z, Huang F, Shrivastava I, Zhu R, Luo A, Hottiger M, Bahar I, Liu Z, Cristofanilli M, Wan Y. New insight into the significance of KLF4 PARylation in genome stability, carcinogenesis, and therapy. EMBO Mol Med 2020; 12:e12391. [PMID: 33231937 PMCID: PMC7721363 DOI: 10.15252/emmm.202012391] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 10/01/2020] [Accepted: 10/19/2020] [Indexed: 01/17/2023] Open
Abstract
KLF4 plays a critical role in determining cell fate responding to various stresses or oncogenic signaling. Here, we demonstrated that KLF4 is tightly regulated by poly(ADP‐ribosyl)ation (PARylation). We revealed the subcellular compartmentation for KLF4 is orchestrated by PARP1‐mediated PARylation. We identified that PARylation of KLF4 is critical to govern KLF4 transcriptional activity through recruiting KLF4 from soluble nucleus to the chromatin. We mapped molecular motifs on KLF4 and PARP1 that facilitate their interaction and unveiled the pivotal role of the PBZ domain YYR motif (Y430, Y451 and R452) on KLF4 in enabling PARP1‐mediated PARylation of KLF4. Disruption of KLF4 PARylation results in failure in DNA damage response. Depletion of KLF4 by RNA interference or interference with PARP1 function by KLF4YYR/AAA (a PARylation‐deficient mutant) significantly sensitizes breast cancer cells to PARP inhibitors. We further demonstrated the role of KLF4 in modulating homologous recombination through regulating BRCA1 transcription. Our work points to the synergism between KLF4 and PARP1 in tumorigenesis and cancer therapy, which provides a potential new therapeutic strategy for killing BRCA1‐proficient triple‐negative breast cancer cells.
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Affiliation(s)
- Zhuan Zhou
- Department of Obstetrics and Gynecology, Department of Pharmacology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Furong Huang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Indira Shrivastava
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Rui Zhu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Aiping Luo
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Michael Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Ivet Bahar
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Zhihua Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Massimo Cristofanilli
- Lynn Sage Breast Cancer Program, Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yong Wan
- Department of Obstetrics and Gynecology, Department of Pharmacology, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Nameki R, Chang H, Reddy J, Corona RI, Lawrenson K. Transcription factors in epithelial ovarian cancer: histotype-specific drivers and novel therapeutic targets. Pharmacol Ther 2020; 220:107722. [PMID: 33137377 DOI: 10.1016/j.pharmthera.2020.107722] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) are major contributors to cancer risk and somatic development. In preclinical and clinical studies, direct or indirect inhibition of TF-mediated oncogenic gene expression profiles have proven to be effective in many tumor types, highlighting this group of proteins as valuable therapeutic targets. In spite of this, our understanding of TFs in epithelial ovarian cancer (EOC) is relatively limited. EOC is a heterogeneous disease composed of five major histologic subtypes; high-grade serous, low-grade serous, endometrioid, clear cell and mucinous. Each histology is associated with unique clinical etiologies, sensitivity to therapies, and molecular signatures - including diverse transcriptional regulatory programs. While some TFs are shared across EOC subtypes, a set of TFs are expressed in a histotype-specific manner and likely explain part of the histologic diversity of EOC subtypes. Targeting TFs present with unique opportunities for development of novel precision medicine strategies for ovarian cancer. This article reviews the critical TFs in EOC subtypes and highlights the potential of exploiting TFs as biomarkers and therapeutic targets.
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Affiliation(s)
- Robbin Nameki
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Heidi Chang
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jessica Reddy
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Rosario I Corona
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Kate Lawrenson
- Women's Cancer Research Program at the Samuel Oschin Comprehensive Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, USA; Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Liu S, Harmston N, Glaser TL, Wong Y, Zhong Z, Madan B, Virshup DM, Petretto E. Wnt-regulated lncRNA discovery enhanced by in vivo identification and CRISPRi functional validation. Genome Med 2020; 12:89. [PMID: 33092630 PMCID: PMC7580003 DOI: 10.1186/s13073-020-00788-5] [Citation(s) in RCA: 13] [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: 02/13/2020] [Accepted: 10/02/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Wnt signaling is an evolutionarily conserved developmental pathway that is frequently hyperactivated in cancer. While multiple protein-coding genes regulated by Wnt signaling are known, the functional lncRNAs regulated by Wnt signaling have not been systematically characterized. METHODS We comprehensively mapped Wnt-regulated lncRNAs from an orthotopic Wnt-addicted pancreatic cancer model and examined the response of lncRNAs to Wnt inhibition between in vivo and in vitro cancer models. We further annotated and characterized these Wnt-regulated lncRNAs using existing genomic classifications (using data from FANTOM5) in the context of Wnt signaling and inferred their role in cancer pathogenesis (using GWAS and expression data from the TCGA). To functionally validate Wnt-regulated lncRNAs, we performed CRISPRi screens to assess their role in cancer cell proliferation both in vivo and in vitro. RESULTS We identified 3633 lncRNAs, of which 1503 were regulated by Wnt signaling in an orthotopic Wnt-addicted pancreatic cancer model. These lncRNAs were much more sensitive to changes in Wnt signaling in xenografts than in cultured cells. Our analysis suggested that Wnt signaling inhibition could influence the co-expression relationship of Wnt-regulated lncRNAs and their eQTL-linked protein-coding genes. Wnt-regulated lncRNAs were also implicated in specific gene networks involved in distinct biological processes that contribute to the pathogenesis of cancers. Consistent with previous genome-wide lncRNA CRISPRi screens, around 1% (13/1503) of the Wnt-regulated lncRNAs were found to modify cancer cell growth in vitro. This included CCAT1 and LINC00263, previously reported to regulate cancer growth. Using an in vivo CRISPRi screen, we doubled the discovery rate, identifying twice as many Wnt-regulated lncRNAs (25/1503) that had a functional effect on cancer cell growth. CONCLUSIONS Our study demonstrates the value of studying lncRNA functions in vivo, provides a valuable resource of lncRNAs regulated by Wnt signaling, and establishes a framework for systematic discovery of functional lncRNAs.
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Affiliation(s)
- Shiyang Liu
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore
| | | | - Trudy Lee Glaser
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Yunka Wong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Zheng Zhong
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Babita Madan
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - David M Virshup
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore.
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina, USA.
| | - Enrico Petretto
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore, Singapore.
- MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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Li W, Xu C, Guo J, Liu K, Hu Y, Wu D, Fang H, Zou Y, Wei Z, Wang Z, Zhou Y, Li Q. Cis- and Trans-Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential Clinical and Therapeutic Implications. Front Oncol 2020; 10:602104. [PMID: 33194770 PMCID: PMC7604522 DOI: 10.3389/fonc.2020.602104] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/28/2020] [Indexed: 11/13/2022] Open
Abstract
Many cancer risk loci act as expression quantitative trait loci (eQTLs) of transcripts including non-coding RNA. Long non-coding RNAs (lncRNAs) are implicated in various human cancers. However, the pathological and clinical impacts of the genetic determinants of lncRNAs in cancers remain largely unknown. In this study, we performed eQTL mapping of lncRNA expression (elncRNA) in 11 TCGA cancer types and characterized the biological processes of elncRNAs in the setting of genomic location, cancer treatment responses, and immune microenvironment. As a result, 10.86% of the cis-eQTLs and 1.67% of the trans-eQTLs of lncRNA were related to known genome-wide association studies (GWAS) cancer risk loci. The elncRNAs are significantly enriched for those which are previously annotated as predictive of drug sensitivities in cancer cell lines. We further revealed the downstream transcriptomic effectors of eQTL-elncRNA pairs. Our data specifically suggested that the genes affected by eQTL-elncRNA associations are enriched in the immune system processes and eQTL-elncRNA associations influence the constitution of tumor infiltrating lymphocytes. In ovarian cancer, the "rs34631313-AC092580.4" pair was associated with increased fraction of CD8+ T cells and M1 Macrophage; whereas in KIRC, the "rs9546285-LINC00426" pair was associated with increased fraction of CD8+ T cells and a decreased fraction of M2 macrophages. Our findings provide a systematic view of the transcriptomic impacts of the eQTL landscape of lncRNA in human cancers and suggest its strong potential relevance to cancer immunity and treatment.
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Affiliation(s)
- Wenzhi Li
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chaoqun Xu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Jintao Guo
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Ke Liu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Yudi Hu
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Dan Wu
- Department of Oncology, Xiamen the Fifth Hospital, Xiamen, China
| | - Hongkun Fang
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Yun Zou
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ziwei Wei
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhong Wang
- Department of Urology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhou
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Qiyuan Li
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
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Jiang L, Duan M, Guo F, Tang J, Oybamiji O, Yu H, Ness S, Zhao YY, Mao P, Guo Y. SMDB: pivotal somatic sequence alterations reprogramming regulatory cascades. NAR Cancer 2020; 2:zcaa030. [PMID: 33094288 PMCID: PMC7556404 DOI: 10.1093/narcan/zcaa030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/04/2020] [Accepted: 09/28/2020] [Indexed: 12/27/2022] Open
Abstract
Binding motifs for transcription factors, RNA-binding proteins, microRNAs (miRNAs), etc. are vital for proper gene transcription and translation regulation. Sequence alteration mechanisms including single nucleotide mutations, insertion, deletion, RNA editing and single nucleotide polymorphism can lead to gains and losses of binding motifs; such consequentially emerged or vanished binding motifs are termed ‘somatic motifs’ by us. Somatic motifs have been studied sporadically but have never been curated into a comprehensive resource. By analyzing various types of sequence altering data from large consortiums, we successfully identified millions of somatic motifs, including those for important transcription factors, RNA-binding proteins, miRNA seeds and miRNA–mRNA 3′-UTR target motifs. While a few of these somatic motifs have been well studied, our results contain many novel somatic motifs that occur at high frequency and are thus likely to cause important biological repercussions. Genes targeted by these altered motifs are excellent candidates for further mechanism studies. Here, we present the first database that hosts millions of somatic motifs ascribed to a variety of sequence alteration mechanisms.
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Affiliation(s)
- Limin Jiang
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Mingrui Duan
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Fei Guo
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
| | - Jijun Tang
- Department of Computer Science, University of South Carolina, Columbia, SC 29208, USA
| | - Olufunmilola Oybamiji
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Hui Yu
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Scott Ness
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Peng Mao
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
| | - Yan Guo
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87109, USA
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