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Buyukcelebi K, Duval AJ, Abdula F, Elkafas H, Seker-Polat F, Adli M. Integrating leiomyoma genetics, epigenomics, and single-cell transcriptomics reveals causal genetic variants, genes, and cell types. Nat Commun 2024; 15:1169. [PMID: 38326302 PMCID: PMC10850163 DOI: 10.1038/s41467-024-45382-0] [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: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/09/2024] Open
Abstract
Uterine fibroids (UF), that can disrupt normal uterine function and cause significant physical and psychological health problems, are observed in nearly 70% of women of reproductive age. Although heritable genetics is a significant risk factor, specific genetic variations and gene targets causally associated with UF are poorly understood. Here, we performed a meta-analysis on existing fibroid genome-wide association studies (GWAS) and integrated the identified risk loci and potentially causal single nucleotide polymorphisms (SNPs) with epigenomics, transcriptomics, 3D chromatin organization from diverse cell types as well as primary UF patient's samples. This integrative analysis identifies 24 UF-associated risk loci that potentially target 394 genes, of which 168 are differentially expressed in UF tumors. Critically, integrating this data with single-cell gene expression data from UF patients reveales the causal cell types with aberrant expression of these target genes. Lastly, CRISPR-based epigenetic repression (dCas9-KRAB) or activation (dCas9-p300) in a UF disease-relevant cell type further refines and narrows down the potential gene targets. Our findings and the methodological approach indicate the effectiveness of integrating multi-omics data with locus-specific epigenetic editing approaches for identifying gene- and celt type-targets of disease-relevant risk loci.
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Affiliation(s)
- Kadir Buyukcelebi
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Alexander J Duval
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Fatih Abdula
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Hoda Elkafas
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Fidan Seker-Polat
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA
| | - Mazhar Adli
- Department of Obstetrics and Gynecology, Robert Lurie Comprehensive Cancer Center, Feinberg School of Medicine at Northwestern University, Chicago, IL, USA.
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4
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Li W, Cai X, Li HJ, Song M, Zhang CY, Yang Y, Zhang L, Zhao L, Liu W, Wang L, Shao M, Zhang Y, Zhang C, Cai J, Zhou DS, Li X, Hui L, Jia QF, Qu N, Zhong BL, Zhang SF, Chen J, Xia B, Li Y, Song X, Fan W, Tang W, Tang W, Tang J, Chen X, Yue W, Zhang D, Fang Y, Xiao X, Li M, Lv L, Chang H. Independent replications and integrative analyses confirm TRANK1 as a susceptibility gene for bipolar disorder. Neuropsychopharmacology 2021; 46:1103-1112. [PMID: 32791513 PMCID: PMC8114920 DOI: 10.1038/s41386-020-00788-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/02/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
Genetic analyses for bipolar disorder (BD) have achieved prominent success in Europeans in recent years, whereas its genetic basis in other populations remains relatively less understood. We herein report that the leading risk locus for BD in European genome-wide association studies (GWAS), the single-nucleotide polymorphism (SNP) rs9834970 near TRANK1 at 3p22 region, is also genome-wide significantly associated with BD in a meta-analysis of four independent East Asian samples including 5748 cases and 65,361 controls (p = 2.27 × 10-8, odds ratio = 1.136). Expression quantitative trait loci (eQTL) analyses and summary data-based Mendelian randomization (SMR) analyses in multiple human brain samples suggest that lower TRANK1 mRNA expression is a principal BD risk factor explaining its genetic risk signals at 3p22. We also identified another SNP rs4789 in the 3' untranslated region (3'UTR) of TRANK1 showing stronger eQTL associations as well as genome-wide significant association with BD. Despite the relatively unclear neuronal function of TRANK1, our mRNA expression analyses in the human brains and in rat primary cortical neurons reveal that genes highly correlated with TRANK1 are significantly enriched in the biological processes related to dendritic spine, synaptic plasticity, axon guidance and circadian entrainment, and are also more likely to exhibit strong associations in psychiatric GWAS (e.g., the CACNA1C gene). Overall, our results support that TRANK1 is a potential BD risk gene. Further studies elucidating its roles in this illness are needed.
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Affiliation(s)
- Wenqiang Li
- grid.412990.70000 0004 1808 322XHenan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,grid.412990.70000 0004 1808 322XHenan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Xin Cai
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Hui-Juan Li
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Meng Song
- grid.412990.70000 0004 1808 322XHenan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,grid.412990.70000 0004 1808 322XHenan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Chu-Yi Zhang
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Yongfeng Yang
- grid.412990.70000 0004 1808 322XHenan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,grid.412990.70000 0004 1808 322XHenan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Luwen Zhang
- grid.412990.70000 0004 1808 322XHenan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,grid.412990.70000 0004 1808 322XHenan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Lijuan Zhao
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Weipeng Liu
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Lu Wang
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China ,grid.410726.60000 0004 1797 8419Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan China
| | - Minglong Shao
- grid.412990.70000 0004 1808 322XHenan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,grid.412990.70000 0004 1808 322XHenan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Yan Zhang
- grid.412990.70000 0004 1808 322XHenan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan China ,grid.412990.70000 0004 1808 322XHenan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan China
| | - Chen Zhang
- grid.16821.3c0000 0004 0368 8293Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Cai
- grid.16821.3c0000 0004 0368 8293Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dong-Sheng Zhou
- grid.452715.00000 0004 1782 599XDepartment of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang China
| | - Xingxing Li
- grid.452715.00000 0004 1782 599XDepartment of Psychiatry, Ningbo Kangning Hospital, Ningbo, Zhejiang China
| | - Li Hui
- grid.263761.70000 0001 0198 0694Suzhou Guangji Hospital, The Affiliated Guangji Hospital of Soochow University, Suzhou, Jiangsu China
| | - Qiu-Fang Jia
- grid.263761.70000 0001 0198 0694Suzhou Guangji Hospital, The Affiliated Guangji Hospital of Soochow University, Suzhou, Jiangsu China
| | - Na Qu
- grid.33199.310000 0004 0368 7223Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China ,grid.503241.10000 0004 1760 9015Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei China
| | - Bao-Liang Zhong
- grid.33199.310000 0004 0368 7223Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China ,grid.503241.10000 0004 1760 9015Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei China
| | - Shu-Fang Zhang
- grid.33199.310000 0004 0368 7223Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China ,grid.503241.10000 0004 1760 9015Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei China
| | - Jing Chen
- grid.33199.310000 0004 0368 7223Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China ,grid.503241.10000 0004 1760 9015Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei China
| | - Bin Xia
- grid.33199.310000 0004 0368 7223Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China ,grid.503241.10000 0004 1760 9015Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei China
| | - Yi Li
- grid.33199.310000 0004 0368 7223Affiliated Wuhan Mental Health Center, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei China ,grid.503241.10000 0004 1760 9015Research Center for Psychological and Health Sciences, China University of Geosciences, Wuhan, Hubei China
| | - Xueqin Song
- grid.412633.1The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Weixing Fan
- Jinhua Second Hospital, Jinhua, Zhejiang China
| | - Wei Tang
- grid.268099.c0000 0001 0348 3990Department of Psychiatry, The Affiliated Kangning Hospital of Wenzhou Medical University, Wenzhou, Zhejiang China
| | - Wenxin Tang
- grid.469604.90000 0004 1765 5222Hangzhou Seventh People’s Hospital, Hangzhou, Zhejiang China
| | - Jinsong Tang
- grid.13402.340000 0004 1759 700XDepartment of Psychiatry, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang China ,Key Laboratory of Medical Neurobiology of Zhejiang Province, Hangzhou, Zhejiang China
| | - Xiaogang Chen
- grid.216417.70000 0001 0379 7164Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan China ,National Clinical Research Center for Mental Disorders, Changsha, Hunan China ,National Technology Institute of Mental Disorders, Changsha, Hunan China ,Hunan Key Laboratory of Psychiatry and Mental Health, Changsha, Hunan China ,grid.489086.bMental Health Institute of Central South University, Changsha, Hunan China ,Hunan Medical Center for Mental Health, Changsha, Hunan China
| | - Weihua Yue
- grid.11135.370000 0001 2256 9319Peking University Sixth Hospital/Institute of Mental Health, Beijing, China ,grid.459847.30000 0004 1798 0615NHC Key Laboratory of Mental Health (Peking University) and National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China ,grid.11135.370000 0001 2256 9319Peking-Tsinghua Joint Center for Life Sciences and PKU IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Dai Zhang
- grid.11135.370000 0001 2256 9319Peking University Sixth Hospital/Institute of Mental Health, Beijing, China ,grid.459847.30000 0004 1798 0615NHC Key Laboratory of Mental Health (Peking University) and National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), Beijing, China ,grid.11135.370000 0001 2256 9319Peking-Tsinghua Joint Center for Life Sciences and PKU IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Yiru Fang
- grid.16821.3c0000 0004 0368 8293Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Xiao
- grid.9227.e0000000119573309Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China. .,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
| | - Luxian Lv
- Henan Mental Hospital, The Second Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China. .,Henan Key Lab of Biological Psychiatry, International Joint Research Laboratory for Psychiatry and Neuroscience of Henan, Xinxiang Medical University, Xinxiang, Henan, China. .,Henan Province People's Hospital, Zhengzhou, Henan, China.
| | - Hong Chang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.
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