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McClellan JC, Li JL, Gao G, Huo D. Expression- and splicing-based multi-tissue transcriptome-wide association studies identified multiple genes for breast cancer by estrogen-receptor status. Breast Cancer Res 2024; 26:51. [PMID: 38515142 PMCID: PMC10958972 DOI: 10.1186/s13058-024-01809-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Although several transcriptome-wide association studies (TWASs) have been performed to identify genes associated with overall breast cancer (BC) risk, only a few TWAS have explored the differences in estrogen receptor-positive (ER+) and estrogen receptor-negative (ER-) breast cancer. Additionally, these studies were based on gene expression prediction models trained primarily in breast tissue, and they did not account for alternative splicing of genes. METHODS In this study, we utilized two approaches to perform multi-tissue TWASs of breast cancer by ER subtype: (1) an expression-based TWAS that combined TWAS signals for each gene across multiple tissues and (2) a splicing-based TWAS that combined TWAS signals of all excised introns for each gene across tissues. To perform this TWAS, we utilized summary statistics for ER + BC from the Breast Cancer Association Consortium (BCAC) and for ER- BC from a meta-analysis of BCAC and the Consortium of Investigators of Modifiers of BRCA1 and BRCA2 (CIMBA). RESULTS In total, we identified 230 genes in 86 loci that were associated with ER + BC and 66 genes in 29 loci that were associated with ER- BC at a Bonferroni threshold of significance. Of these genes, 2 genes associated with ER + BC at the 1q21.1 locus were located at least 1 Mb from published GWAS hits. For several well-studied tumor suppressor genes such as TP53 and CHEK2 which have historically been thought to impact BC risk through rare, penetrant mutations, we discovered that common variants, which modulate gene expression, may additionally contribute to ER + or ER- etiology. CONCLUSIONS Our study comprehensively examined how differences in common variation contribute to molecular differences between ER + and ER- BC and introduces a novel, splicing-based framework that can be used in future TWAS studies.
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Affiliation(s)
- Julian C McClellan
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - James L Li
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
| | - Dezheng Huo
- Department of Public Health Sciences, University of Chicago, Chicago, IL, 60637, USA.
- Section of Hematology & Oncology, Department of Medicine, University of Chicago, Chicago, IL, 60637, USA.
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Li JY, Jing R, Wei H, Wang M, Xiaowei Q, Liu H, Jian L, Ou JH, Jiang WH, Tian FG, Sheng Y, Li HY, Xu H, Zhang RS, Guan AH, Liu K, Jiang HC, Ren Y, He JJ, Huang W, Liao N, Cai X, Ming J, Ling R, Xu Y, Hu CY, Zhang J, Guo B, Ouyang L, Shuai P, Liu Z, Zhong L, Zeng Z, Zhang T, Xuan Z, Tan X, Liang J, Pan Q, Chen L, Zhang F, Fan LJ, Zhang Y, Yang X, BoLi J, Chen C, Jiang J. Germline mutations in 40 cancer susceptibility genes among Chinese patients with high hereditary risk breast cancer. Int J Cancer 2018; 144:281-289. [PMID: 29752822 DOI: 10.1002/ijc.31601] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 04/13/2018] [Accepted: 04/25/2018] [Indexed: 01/08/2023]
Abstract
Multigene panel testing of breast cancer predisposition genes have been extensively conducted in Europe and America, which is relatively rare in Asia however. In this study, we assessed the frequency of germline mutations in 40 cancer predisposition genes, including BRCA1 and BRCA2, among a large cohort of Chinese patients with high hereditary risk of BC. From 2015 to 2016, consecutive BC patients from 26 centers of China with high hereditary risk were recruited (n = 937). Clinical information was collected and next-generation sequencing (NGS) was performed using blood samples of participants to identify germline mutations. In total, we acquired 223 patients with putative germline mutations, including 159 in BRCA1/2, 61 in 15 other BC susceptibility genes and 3 in both BRCA1/2 and non-BRCA1/2 gene. Major mutant non-BRCA1/2 genes were TP53 (n = 18), PALB2 (n = 11), CHEK2 (n = 6), ATM (n = 6) and BARD1 (n = 5). No factors predicted pathologic mutations in non-BRCA1/2 genes when treated as a whole. TP53 mutations were associated with HER-2 positive BC and younger age at diagnosis; and CHEK2 and PALB2 mutations were enriched in patients with luminal BC. Among high hereditary risk Chinese BC patients, 23.8% contained germline mutations, including 6.8% in non-BRCA1/2 genes. TP53 and PALB2 had a relatively high mutation rate (1.9 and 1.2%). Although no factors predicted for detrimental mutations in non-BRCA1/2 genes, some clinical features were associated with mutations of several particular genes.
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Affiliation(s)
- Jun-Yan Li
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Ruilin Jing
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Hongyi Wei
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Minghao Wang
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Qi Xiaowei
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Haoxi Liu
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Liu Jian
- Department of Medical Oncology, Fujian Provincial Cancer Hospital, Fuzhou, Fujian, 350014, China
| | - Jiang-Hua Ou
- Department of Breast Surgery, The Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, China
| | - Wei-Hua Jiang
- Department of Breast Surgery, The Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi, Xinjiang, 830011, China
| | - Fu-Guo Tian
- Department of Breast Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi, 030013, China
| | - Yuan Sheng
- Department of Thyroid and Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Heng-Yu Li
- Department of Thyroid and Breast Surgery, Changhai Hospital, Second Military Medical University, Shanghai, 200433, China
| | - Hong Xu
- Department of Breast Surgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, 110042, China
| | - Rui-Shan Zhang
- Department of Breast Surgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, 110042, China
| | - Ai-Hua Guan
- Department of Breast Surgery, Jilin Cancer Hospital & Institute, Changchun, Jilin, 130000, China
| | - Ke Liu
- Department of Breast Surgery, Jilin Cancer Hospital & Institute, Changchun, Jilin, 130000, China
| | - Hong-Chuan Jiang
- Department of General Surgery, Beijing Chaoyang Hospital Affiliated to Capital Medical University, Beijing, 100020, China
| | - Yu Ren
- Department of Breast Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Jian-Jun He
- Department of Breast Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Weiwei Huang
- Department of Medical Oncology, Fujian Provincial Cancer Hospital, Fuzhou, Fujian, 350014, China
| | - Ning Liao
- Department of Breast, Cancer Center, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, 510080, China
| | - Xiangjun Cai
- Department of Hepatobiliary and General Surgery, PLA No.202 Hospital, Shenyang Liaoning, 110812, China
| | - Jia Ming
- Department of Breast, Thyroid, and Pancreas Surgery, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, China
| | - Rui Ling
- Depatement of Thyroid, Breast and Vascular Surgery, Xijing hospital, Forth Military University, Xi'an, Shaanxi, 710032, China
| | - Yan Xu
- Department of Breast surgery, Daping Hospital, Research Institute of Surgery, Third Military Medical University, Chongqing, 400038, China
| | - Chun-Yan Hu
- Department of Breast surgery, Daping Hospital, Research Institute of Surgery, Third Military Medical University, Chongqing, 400038, China
| | - Jianguo Zhang
- Department of Breast Surgery, the Second Affiliated Hospital of Harbin Medical College, Harbin, Heilongjiang, 150086, China
| | - Baoliang Guo
- Department of Breast Surgery, the Second Affiliated Hospital of Harbin Medical College, Harbin, Heilongjiang, 150086, China
| | - Lizhi Ouyang
- Hunan Cancer Hospital, Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 4100013, China
| | - Ping Shuai
- Health Management Center, Sichuan Provincial People's Hospital, Chengdu, Sichuan, 610072, China
| | - Zhenzhen Liu
- Department of Breast Surgery, Henan Cancer Hospital, Zhengzhou, Henan, 450008, China
| | - Ling Zhong
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Zhen Zeng
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Ting Zhang
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Zhaoling Xuan
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Xuanni Tan
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Junbin Liang
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Qinwen Pan
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Li Chen
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Fan Zhang
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Lin-Jun Fan
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Yi Zhang
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Xinhua Yang
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Jing BoLi
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
| | - Chongjian Chen
- Annoroad Gene Technology (Beijing) Co. Ltd, Beijing, 100176, China
| | - Jun Jiang
- Department of Breast Surgery, Southwest Hospital, the Third Military Medical University, Chongqing, 400038, China
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Jiang C, Yu S, Qian P, Guo R, Zhang R, Ao Z, Li Q, Wu G, Chen Y, Li J, Wang C, Yao W, Xu J, Qian G, Ji F. The breast cancer susceptibility-related polymorphisms at the TOX3/LOC643714 locus associated with lung cancer risk in a Han Chinese population. Oncotarget 2018; 7:59742-59753. [PMID: 27486757 PMCID: PMC5312345 DOI: 10.18632/oncotarget.10874] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 07/09/2016] [Indexed: 11/25/2022] Open
Abstract
It has been well established that besides environmental factors, genetic factors are also associated with lung cancer risk. However, to date, the prior identified genetic variants and loci only explain a small fraction of the familial risk of lung cancer. Hence it is vital to investigate the remaining missing heritability to understand the development and process of lung cancer. In the study, to test our hypothesis that the previously identified breast cancer risk-associated genetic polymorphisms at the TOX3/LOC643714 locus might contribute to lung cancer risk, 16 SNPs at the TOX3/LOC643714 locus were evaluated in a Han Chinese population based on a case-control study. Pearson's chi-square test or Fisher's exact test revealed that rs9933638, rs12443621, and rs3104746 were significantly associated with lung cancer risk (P < 0.001, P < 0.001, and P = 0.005, respectively). Logistic regression analyses displayed that lung cancer risk of individuals with rs9933638(GG+GA) were 1.89 times higher than that of rs9933638AA carriers (OR = 1.893, 95% CI = 1.308-2.741, P = 0.001). Similar findings were manifested for rs12443621 (OR = 1.824, 95% CI = 1.272-2.616, P = 0.001, rs12443621(GG+GA) carriers vs. rs12443621AA carriers) and rs3104746 (OR = 1.665, 95% CI = 1.243-2.230, P = 0.001, rs3104746TT carriers vs. rs3104746(TA+AA) carriers). The study discovered for the first time that three SNPs (rs9933638, rs12443621, and rs3104746) at the TOX3/LOC643714 locus contributed to lung cancer risk, providing new evidences that lung cancer and breast cancer are linked at the molecular and genetic level to a certain extent.
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Affiliation(s)
- Chaowen Jiang
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Shilong Yu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Pin Qian
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Ruiling Guo
- Department of Respiratory Diseases, 324th Hospital of People's Liberation Army (No.324 Hospital of PLA), Chongqing 400020, China
| | - Ruijie Zhang
- Department of Respiratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Zhi Ao
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Qi Li
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Guoming Wu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Yan Chen
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Jin Li
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Changzheng Wang
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Wei Yao
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Jiancheng Xu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Guisheng Qian
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
| | - Fuyun Ji
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Third Military Medical University, Chongqing 400037, China
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