1
|
Zhang M, Qin Z, Huang Y, Tian W, Li Y, Wang C, Zhao W, Dai Y, Shi X, Gershwin ME, Ma X, Wang M, Liu X, Chen W, Qiu F. Association of CCR6 functional polymorphisms with Primary Biliary Cholangitis. J Transl Autoimmun 2024; 8:100234. [PMID: 38405661 PMCID: PMC10891324 DOI: 10.1016/j.jtauto.2024.100234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/11/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
The biliary epithelial cells release CC chemokine receptor 6 (CCR6) ligand 20 (CCL20), leading to recruitment of CCR6+ T cells and subsequent infiltration into the biliary epithelium in primary biliary cholangitis patients. Previous genome-wide multi-national meta-analysis, including our Han Chinese cohort, showed significant association of CCR6 and CCL20 single nucleotide polymorphisms (SNP) with PBC. We report here that significantly associated SNPs, identified in the CCR6 locus based on our Han Chinese genome-wide association study, can be separated into "protective" and "risk" groups, but only "risk" SNPs were confirmed using a separate Han Chinese PBC cohort. Only weak association of CCL20 SNPs was observed in Han Chinese PBC cohorts. Fine-mapping and logistical analysis identified a previously defined functional variant that, leads to increased CCR6 expression, which contributed to increased genetic susceptibility to PBC in Han Chinese cohort.
Collapse
Affiliation(s)
- Mingming Zhang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Zhuye Qin
- Department of Laboratory Medicine, Southeast University Hospital, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Yexi Huang
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Wenyan Tian
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - You Li
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, 200001, China
| | - Chan Wang
- Institute of Translational Medicine, Yangzhou University Medical College, Yangzhou, Jiangsu, 225009, China
| | - Weifeng Zhao
- Department of Hepatology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Yaping Dai
- Department of Laboratory Medicine, The Fifth People's Hospital of Wuxi, Wuxi, Jiangsu, 214000, China
| | - Xingjuan Shi
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu, 210096, China
| | - M. Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis School of Medicine, Davis, CA, 95616, USA
| | - Xiong Ma
- Department of Gastroenterology and Hepatology, Shanghai Institute of Digestive Diseases, Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital, Shanghai, 200001, China
| | - Meilin Wang
- Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, Nanjing Medical University School of Public Health, Nanjing, Jiangsu, 210029, China
| | - Xiangdong Liu
- Key Laboratory of Developmental Genes and Human Diseases, School of Life Science and Technology, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Weichang Chen
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, 215006, China
| | - Fang Qiu
- Department of Laboratory Medicine, The Fourth Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210031, China
| |
Collapse
|
2
|
Liu X, Zheng X, Shu Y, Qu X, Wang Q, Liu X, Hu FY, Liu J, Lian Y, He BM, Li C, Zhou D, Qiu W, Sun L, Hong Z. Genome-Wide Association Study Identifies IFIH1 and HLA-DQB1*05:02 Loci Associated With Anti-NMDAR Encephalitis. NEUROLOGY(R) NEUROIMMUNOLOGY & NEUROINFLAMMATION 2024; 11:e200221. [PMID: 38579189 PMCID: PMC11010247 DOI: 10.1212/nxi.0000000000200221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/19/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND AND OBJECTIVES Anti-N-methyl-d-aspartate receptor (NMDAR) encephalitis is a rare autoimmune neurologic disorder, the genetic etiology of which remains poorly understood. Our study aims to investigate the genetic basis of this disease in the Chinese Han population. METHODS We performed a genome-wide association study and fine-mapping study within the major histocompatibility complex (MHC) region of 413 Chinese patients with anti-NMDAR encephalitis recruited from 6 large tertiary hospitals and 7,127 healthy controls. RESULTS Our genome-wide association analysis identified a strong association at the IFIH1 locus on chromosome 2q24.2 (rs3747517, p = 1.06 × 10-8, OR = 1.55, 95% CI, 1.34-1.80), outside of the human leukocyte antigen (HLA) region. Furthermore, through a fine-mapping study of the MHC region, we discovered associations for 3 specific HLA class I and II alleles. Notably, HLA-DQB1*05:02 (p = 1.43 × 10-12; OR, 2.10; 95% CI 1.70-2.59) demonstrates the strongest association among classical HLA alleles, closely followed by HLA-A*11:01 (p = 4.36 × 10-7; OR, 1.52; 95% CI 1.29-1.79) and HLA-A*02:07 (p = 1.28 × 10-8; OR, 1.87; 95% CI 1.50-2.31). In addition, we uncovered 2 main HLA amino acid variation associated with anti-NMDAR encephalitis including HLA-DQβ1-126H (p = 1.43 × 10-12; OR, 2.10; 95% CI 1.70-2.59), exhibiting a predisposing effect, and HLA-B-97R (p = 3.40 × 10-8; OR, 0.63; 95% CI 0.53-0.74), conferring a protective effect. Computational docking analysis suggested a close relationship between the NR1 subunit of NMDAR and DQB1*05:02. DISCUSSION Our findings indicate that genetic variation in IFIH1, involved in the type I interferon signaling pathway and innate immunity, along with variations in the HLA class I and class II genes, has substantial implications for the susceptibility to anti-NMDAR encephalitis in the Chinese Han population.
Collapse
Affiliation(s)
- Xu Liu
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Xiaodong Zheng
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Yaqing Shu
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Xiao Qu
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Qun Wang
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Xiao Liu
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Fa-Yun Hu
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Jie Liu
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Yajun Lian
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Bao-Ming He
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Caihua Li
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Dong Zhou
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Wei Qiu
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Liangdan Sun
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| | - Zhen Hong
- From the Department of Neurology (X. Liu, F.-Y.H., D.Z., Z.H.), West China Hospital, Sichuan University, Chengdu; Department of Dermatology (X.Z., L.S.), the First Affiliated Hospital of Anhui Medical University; Key Laboratory of Dermatology (Anhui Medical University) (X.Z., L.S.), Ministry of Education; Anhui Province Laboratory of Inflammation and Immune Mediated Diseases (X.Z.); Anhui Provincial Institute of Translational Medicine (X.Z.), Hefei; Department of Neurology (Y.S., W.Q.), The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou; Genesky Biotechnologies Inc. (X.Q., C.L.), Shanghai; Department of Neurology (Q.W., X. Liu), Beijing Tiantan Hospital, Capital Medical University; Department of Neurology (J.L., B.-M.H.), Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu; Department of Neurology (Y.L.), First Affiliated Hospital of Zhengzhou University; Institute of Brain Science and Brain-Inspired Technology of West China Hospital (D.Z.), Sichuan University, Chengdu; North China University of Science and Technology Affiliated Hospital (L.S.); Health Science Center (L.S.), North China University of Science and Technology; School of Public Health (L.S.), North China University of Science and Technology, Tangshan; Inflammation and Immune Diseases Laboratory of North China University of Science and Technology (L.S.); and Department of Neurology (Z.H.), Chengdu Shangjin Nanfu Hospital, China
| |
Collapse
|
3
|
Konkwo C, Chowdhury S, Vilarinho S. Genetics of liver disease in adults. Hepatol Commun 2024; 8:e0408. [PMID: 38551385 PMCID: PMC10984672 DOI: 10.1097/hc9.0000000000000408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
Chronic liver disease stands as a significant global health problem with an estimated 2 million annual deaths across the globe. Combining the use of next-generation sequencing technologies with evolving knowledge in the interpretation of genetic variation across the human genome is propelling our understanding, diagnosis, and management of both rare and common liver diseases. Here, we review the contribution of risk and protective alleles to common forms of liver disease, the rising number of monogenic diseases affecting the liver, and the role of somatic genetic variants in the onset and progression of oncological and non-oncological liver diseases. The incorporation of genomic information in the diagnosis and management of patients with liver disease is driving the beginning of a new era of genomics-informed clinical hepatology practice, facilitating personalized medicine, and improving patient care.
Collapse
Affiliation(s)
- Chigoziri Konkwo
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
| | - Shanin Chowdhury
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Silvia Vilarinho
- Department of Internal Medicine, Section of Digestive Diseases, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| |
Collapse
|
4
|
Floreani A, Gabbia D, De Martin S. Current Perspectives on the Molecular and Clinical Relationships between Primary Biliary Cholangitis and Hepatocellular Carcinoma. Int J Mol Sci 2024; 25:2194. [PMID: 38396870 PMCID: PMC10888596 DOI: 10.3390/ijms25042194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Primary biliary cholangitis (PBC) is an autoimmune liver disease characterised by the immune-mediated destruction of small and medium intrahepatic bile ducts, with variable outcomes and progression. This review summarises the state of the art regarding the risk of neoplastic progression in PBC patients, with a particular focus on the molecular alterations present in PBC and in hepatocellular carcinoma (HCC), which is the most frequent liver cancer in these patients. Major risk factors are male gender, viral infections, e.g., HBV and HCV, non-response to UDCA, and high alcohol intake, as well as some metabolic-associated factors. Overall, HCC development is significantly more frequent in patients with advanced histological stages, being related to liver cirrhosis. It seems to be of fundamental importance to unravel eventual dysfunctional molecular pathways in PBC patients that may be used as biomarkers for HCC development. In the near future, this will possibly take advantage of artificial intelligence-designed algorithms.
Collapse
Affiliation(s)
- Annarosa Floreani
- University of Padova, 35122 Padova, Italy;
- Scientific Consultant IRCCS Negrar, 37024 Verona, Italy
| | - Daniela Gabbia
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy;
| | - Sara De Martin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy;
| |
Collapse
|
5
|
Khan T, Ledoux IM, Aziz F, Al Ali F, Chin-Smith E, Ata M, Karim MY, Marr N. Associations between HLA class II alleles and IgE sensitization to allergens in the Qatar Biobank cohort. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2023; 2:100117. [PMID: 37779520 PMCID: PMC10509938 DOI: 10.1016/j.jacig.2023.100117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/16/2023] [Accepted: 02/05/2023] [Indexed: 10/03/2023]
Abstract
Background Allergic disorders are the consequence of IgE sensitization to allergens. Population studies have shown that certain human leukocyte antigen (HLA) alleles are associated with increased or decreased risk of developing allergy. Objective We aimed to characterize the relationship between HLA class II allelic diversity and IgE sensitization in an understudied Arab population. Methods We explored associations between IgE sensitization to 7 allergen mixes and mesquite (comprising 41 food or aeroallergens) and 45 common classical HLA class II alleles in a well-defined cohort of 797 individuals representing the general adult population of Qatari nationals and long-term residents. To do so, we performed HLA calling from whole genome sequencing data at 2-field resolution using 2 independent algorithms. We then applied 3 different regression models to assess either each allergen mix independently, in the context of IgE sensitization to other allergens tested, or polysensitization. Results More than half (n = 447) of the study participants showed IgE sensitization to at least 1 allergen, most of them (n = 400) to aeroallergens (Phadiatop). We identified statistically significant negative and positive associations with 24 HLA class II alleles. These have been reported to confer risk or protection from variety of diseases; however, only a few have previously been associated with allergy in other populations. Conclusions Our study reveals several new risk and protective genetic markers for allergen-specific IgE sensitization. This is a first and essential step toward a better understanding of the origins of allergic diseases in this understudied population.
Collapse
Affiliation(s)
- Taushif Khan
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
- Department of Computational Science, The Jackson Laboratory, Farmington, Conn
| | | | - Ferdousey Aziz
- the Department of Pathology, Sidra Medicine, Doha, Qatar
| | - Fatima Al Ali
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
| | | | - Manar Ata
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
| | - Mohammed Yousuf Karim
- the Department of Pathology, Sidra Medicine, Doha, Qatar
- the College of Medicine, Qatar University, Doha, Qatar
| | - Nico Marr
- Department of Human Immunology, Sidra Medicine, Doha, Qatar
- the College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Institute of Translational Immunology, Brandenburg Medical School, Brandenburg an der Havel, Germany
| |
Collapse
|
6
|
Khor SS, Ueno K, Nishida N, Kawashima M, Kawai Y, Aiba Y, Hitomi Y, Nagasaki M, Nakamura M, Tokunaga K. Novel HLA allele associations with susceptibility, staging, symptomatic state, autoimmune hepatitis and hepatocellular carcinoma events for primary biliary cholangitis in the Japanese population. Front Immunol 2023; 14:1151502. [PMID: 37325616 PMCID: PMC10264690 DOI: 10.3389/fimmu.2023.1151502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/18/2023] [Indexed: 06/17/2023] Open
Abstract
Primary biliary cholangitis (PBC) is a rare autoimmune disease with a clear predisposition for human leukocyte antigen (HLA)-DR/DQ-associated loss of immune tolerance for the E2 component of the pyruvate dehydrogenase complex. Three-field-resolution HLA imputation of 1,670 Japanese PBC patients and 2,328 healthy controls was conducted using Japanese population-specific HLA reference panels. Eighteen previously reported Japanese PBC-associated HLA alleles were confirmed and extended to 3-field-resolution, including HLA-DRB1*08:03 to HLA-DRB1*08:03:02, HLA-DQB1*03:01 to HLA-DQB1*03:01:01, HLA-DQB1*04:01 to HLA-DQB1*04:01:01 and HLA-DQB1*06:04 to HLA-DQB1*06:04:01. In addition, additional significant novel HLA alleles were identified, including 3 novel susceptible HLA-DQA1 alleles: HLA-DQA1*03:03:01, HLA-DQA1*04:01:01, HLA-DQA1*01:04:01 and 1 novel protective HLA-DQA1 allele, HLA-DQA1*05:05:01. In addition, PBC patients carrying HLA-DRB1*15:01:01 and HLA-DQA1*03:03:01 would have a higher predisposition toward developing concomitant autoimmune hepatitis (AIH). Further, late-stage and symptomatic PBC shared the same susceptible HLA alleles of HLA-A*26:01:01, HLA-DRB1*09:01:02 and HLA-DQB1*03:03:02. Lastly, HLA-DPB1*05:01:01 was identified as a potential risk HLA allele for development of hepatocellular carcinoma (HCC) in PBC patients. In conclusion, we have extended the current knowledge of HLA allele associations to 3-field resolution and identified novel HLA allele associations with predisposition risk, staging, symptomatic state, and AIH and HCC events for Japanese PBC patients.
Collapse
Affiliation(s)
- Seik-Soon Khor
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kazuko Ueno
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nao Nishida
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
- The Research Center for Hepatitis and Immunology, Research Institute, National Center for Global Health and Medicine, Ichikawa, Japan
| | - Minae Kawashima
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems, Chiba, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Yoshihiro Aiba
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Masao Nagasaki
- Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, Omura, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, Omura, Japan
- Headquarters of Primary Biliary Cholangitis (PBC) Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, NHO Nagasaki Medical Center, Omura, Japan
| | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| |
Collapse
|
7
|
Hitomi Y, Nakamura M. The Genetics of Primary Biliary Cholangitis: A GWAS and Post-GWAS Update. Genes (Basel) 2023; 14:405. [PMID: 36833332 PMCID: PMC9957238 DOI: 10.3390/genes14020405] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Primary biliary cholangitis (PBC) is a chronic, progressive cholestatic liver disease in which the small intrahepatic bile ducts are destroyed by autoimmune reactions. Among autoimmune diseases, which are polygenic complex traits caused by the combined contribution of genetic and environmental factors, PBC exhibits the strongest involvement of genetic heritability in disease development. As at December 2022, genome-wide association studies (GWASs) and associated meta-analyses identified approximately 70 PBC susceptibility gene loci in various populations, including those of European and East Asian descent. However, the molecular mechanisms through which these susceptibility loci affect the pathogenesis of PBC are not fully understood. This study provides an overview of current data regarding the genetic factors of PBC as well as post-GWAS approaches to identifying primary functional variants and effector genes in disease-susceptibility loci. Possible mechanisms of these genetic factors in the development of PBC are also discussed, focusing on four major disease pathways identified by in silico gene set analyses, namely, (1) antigen presentation by human leukocyte antigens, (2) interleukin-12-related pathways, (3) cellular responses to tumor necrosis factor, and (4) B cell activation, maturation, and differentiation pathways.
Collapse
Affiliation(s)
- Yuki Hitomi
- Department of Human Genetics, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan
| | - Minoru Nakamura
- Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
- Department of Hepatology, Nagasaki University Graduate School of Biomedical Sciences, 2-1001-1 Kubara, Omura 856-8562, Japan
- Headquarters of PBC Research in NHO Study Group for Liver Disease in Japan (NHOSLJ), Clinical Research Center, National Hospital Organization (NHO) Nagasaki Medical Center, 2-1001-1 Kubara, Omura 856-8562, Japan
| |
Collapse
|
8
|
Huang CY, Zhang HP, Han WJ, Zhao DT, Liao HY, Ma YX, Xu B, Li LJ, Han Y, Liu XH, Wang Q, Lou JL, Zhang XD, Zhao J, Li WJ, Liu YM, Yan HP. Disease predisposition of human leukocyte antigen class II genes influences the gut microbiota composition in patients with primary biliary cholangitis. Front Immunol 2022; 13:984697. [PMID: 36203614 PMCID: PMC9531677 DOI: 10.3389/fimmu.2022.984697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe human leukocyte antigen (HLA) susceptibility gene is the main genetic risk factor for primary biliary cholangitis (PBC). The prognosis of patients with PBC is linked to gut microbiota dysbiosis. However, whether the HLA alleles are associated with the gut microbiota distribution and disease severity remains unknown.MethodsA cohort of 964 Chinese patients with PBC was enrolled at Beijing YouAn Hospital, Beijing, China. High-resolution genotyping of the HLA class I and class II loci from 151 of these patients was performed using sequence-based PCR. Stool samples were collected from 43 of the 151 fully HLA-typed patients to analyze their microbiota compositions via 16S RNA gene sequencing.ResultsOf the 964 patients, the male:female ratio was 114:850, and 342 of these patients (35.5%) had already developed liver cirrhosis (LC) before enrollment. Patients with PBC showed a significantly higher frequency of HLA DRB1*08:03 than did the controls (21.2% vs. 9.0%, P=0.0001). HLA-DRB1*03:01, DRB1*07:01, DRB1*14:05, and DRB1*14:54 frequencies were also increased but did not reach significance after Bonferroni’s correction. Conversely, the DQB1*03:01 frequency was significantly lower in patients with PBC than in the controls (24.5% vs. 39.2%, P=0.0010). The patients’ gut microbiota were analyzed from four perspectives. The microbial community abundances were significantly lower in FHRAC-positive patients (patients with a combination of five HLA DRB1 high-risk alleles) than in FHRAC-negative patients (P<0.05). Of the top 10 microbial genera, Lachnospiraceae_incertae_sedis was higher in the FHRAC-positive patients than in the FHRAC-negative patients (P<0.05). linear discriminant analysis (LDA) effect-size (LEfSe) analysis showed different microbes at different levels in the FHRAC-negative patients but not in the FHRAC-positive patients. DQB1*03:01-positive patients contained mostly Lactobacillaceae at the family level. A comparison of the FHRAC-positive patients with and without liver cirrhosis showed that the abundances of Veillonella were significantly higher in patients with cirrhosis and FHRAC than in those without cirrhosis and are FHRAC-negative.ConclusionThe HLA class II genes may influence the gut microbiota compositions in patients with PBC. Differential gut microbiota were expressed at different taxonomic levels. Some bacterial abundances may be increased in FHRAC-positive patients with PBC and cirrhosis.
Collapse
Affiliation(s)
- Chun-Yang Huang
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Hai-Ping Zhang
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Wei-Jia Han
- Department of Gastroenterology, Integrated Clinical Microecology Center, Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Dan-Tong Zhao
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Hui-Yu Liao
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Yin-Xue Ma
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Bin Xu
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Li-Juan Li
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Xiu-Hong Liu
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Qi Wang
- Institute of Hepatology, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Jin-Li Lou
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Xiao-Dan Zhang
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Juan Zhao
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Wen-Juan Li
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
| | - Yan-Min Liu
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
- *Correspondence: Hui-Ping Yan, , ; Yan-Min Liu,
| | - Hui-Ping Yan
- Second Department of Liver Disease Center, Beijing YouAn Hospital, Capital Medical University, Beijing, China
- Clinical Laboratory Center and Clinical Research Center for Autoimmune Liver Disease, Beijing YouAn Hospital, Capital Medical University, Beijing, China
- *Correspondence: Hui-Ping Yan, , ; Yan-Min Liu,
| |
Collapse
|
9
|
Mulinacci G, Palermo A, Gerussi A, Asselta R, Gershwin ME, Invernizzi P. New insights on the role of human leukocyte antigen complex in primary biliary cholangitis. Front Immunol 2022; 13:975115. [PMID: 36119102 PMCID: PMC9471323 DOI: 10.3389/fimmu.2022.975115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/11/2022] [Indexed: 01/04/2023] Open
Abstract
Primary Biliary Cholangitis (PBC) is a rare autoimmune cholangiopathy. Genetic studies have shown that the strongest statistical association with PBC has been mapped in the human leukocyte antigen (HLA) locus, a highly polymorphic area that mostly contribute to the genetic variance of the disease. Furthermore, PBC presents high variability throughout different population groups, which may explain the different geoepidemiology of the disease. A major role in defining HLA genetic contribution has been given by genome-wide association studies (GWAS) studies; more recently, new technologies have been developed to allow a deeper understanding. The study of the altered peptides transcribed by genetic alterations also allowed the development of novel therapeutic strategies in the context of immunotolerance. This review summarizes what is known about the immunogenetics of PBC with a focus on the HLA locus, the different distribution of HLA alleles worldwide, and how HLA modifications are associated with the pathogenesis of PBC. Novel therapeutic strategies are also outlined.
Collapse
Affiliation(s)
- Giacomo Mulinacci
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Andrea Palermo
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Alessio Gerussi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Istituti di Ricovero e Cura a Carattere Scientifico (IRCCS) Humanitas Research Hospital, Milan, Italy
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Merrill Eric Gershwin
- Division of Rheumatology, Allergy and Clinical Immunology, University of California, Davis, Davis, CA, United States
| | - Pietro Invernizzi
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy
- *Correspondence: Pietro Invernizzi,
| |
Collapse
|
10
|
Terziroli Beretta-Piccoli B, Mieli-Vergani G, Vergani D. HLA, gut microbiome and hepatic autoimmunity. Front Immunol 2022; 13:980768. [PMID: 36059527 PMCID: PMC9433828 DOI: 10.3389/fimmu.2022.980768] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/25/2022] [Indexed: 12/12/2022] Open
Abstract
Genetic susceptibility to autoimmune liver diseases is conferred mainly by polymorphisms of genes encoding for the human leukocyte antigens (HLA). The strongest predisposition to autoimmune hepatitis type 1 (AIH-1) is linked to the allele DRB1*03:01, possession of which is associated with earlier disease onset and more severe course. In populations where this allele is very rare, such as in Asia, and in DRB1*03-negative patients, risk of AIH-1 is conferred by DRB1*04, which is associated with later disease onset and milder phenotype. AIH type 2 (AIH-2) is associated with DRB1*07. The pediatric condition referred to as autoimmune sclerosing cholangitis (ASC), is associated with the DRB1*13 in populations of Northern European ancestry. DRB1*1501 is protective from AIH-1, AIH-2 and ASC in Northern European populations. Possession of the DRB1*08 allele is associated with an increased risk of primary biliary cholangitis (PBC) across different populations. DRB1*03:01 and B*08:01 confer susceptibility to primary sclerosing cholangitis (PSC), as well as DRB1*13 and DRB1*15 in Europe. The hepatic blood supply is largely derived from the splanchnic circulation, suggesting a pathophysiological role of the gut microbiome. AIH appears to be associated with dysbiosis, increased gut permeability, and translocation of intestinal microbial products into the circulation; molecular mimicry between microbial and host antigens may trigger an autoaggressive response in genetically-predisposed individuals. In PBC an altered enteric microbiome may affect intestinal motility, immunological function and bile secretion. Patients with PSC have a gut microbial profile different from health as well as from patients with inflammatory bowel disease without PSC.
Collapse
Affiliation(s)
- Benedetta Terziroli Beretta-Piccoli
- Faculty of Biomedical Sciences, Epatocentro Ticino and Università della Svizzera Italiana, Lugano, Switzerland
- MowatLabs, Faculty of Life Sciences and Medicine, King’s College London, King’s College Hospital, London, United Kingdom
- *Correspondence: Benedetta Terziroli Beretta-Piccoli,
| | - Giorgina Mieli-Vergani
- MowatLabs, Faculty of Life Sciences and Medicine, King’s College London, King’s College Hospital, London, United Kingdom
| | - Diego Vergani
- MowatLabs, Faculty of Life Sciences and Medicine, King’s College London, King’s College Hospital, London, United Kingdom
| |
Collapse
|
11
|
How genetic risk contributes to autoimmune liver disease. Semin Immunopathol 2022; 44:397-410. [PMID: 35650446 PMCID: PMC9256578 DOI: 10.1007/s00281-022-00950-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/06/2022] [Indexed: 12/16/2022]
Abstract
Genome-wide association studies (GWAS) for autoimmune hepatitis (AIH) and GWAS/genome-wide meta-analyses (GWMA) for primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) have been successful over the past decade, identifying about 100 susceptibility loci in the human genome, with strong associations with the HLA locus and many susceptibility variants outside the HLA locus with relatively low risk. However, identifying causative variants and genes and determining their effects on liver cells and their immunological microenvironment is far from trivial. Polygenic risk scores (PRSs) based on current genome-wide data have limited potential to predict individual disease risk. Interestingly, results of mediated expression score regression analysis provide evidence that a substantial portion of gene expression at susceptibility loci is mediated by genetic risk variants, in contrast to many other complex diseases. Genome- and transcriptome-wide comparisons between AIH, PBC, and PSC could help to better delineate the shared inherited component of autoimmune liver diseases (AILDs), and statistical fine-mapping, chromosome X-wide association testing, and genome-wide in silico drug screening approaches recently applied to GWMA data from PBC could potentially be successfully applied to AIH and PSC. Initial successes through single-cell RNA sequencing (scRNA-seq) experiments in PBC and PSC now raise high hopes for understanding the impact of genetic risk variants in the context of liver-resident immune cells and liver cell subpopulations, and for bridging the gap between genetics and disease.
Collapse
|
12
|
Li Y, Liu X, Wang Y, Zhou Y, Hu S, Yang H, Zhong W, Zhao J, Wang X, Chu H, Zheng Y, Zhang J, Zhou L, Wang B. Novel HLA-DRB1 alleles contribute risk for disease susceptibility in primary biliary cholangitis. Dig Liver Dis 2022; 54:228-236. [PMID: 34016546 DOI: 10.1016/j.dld.2021.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Primary biliary cholangitis (PBC) is a complex disease with high heritability. We investigated the association between human leukocyte antigen (HLA)-DRB1 alleles and PBC in families and sporadic cases to evaluate the genetic components of the disease. METHODS We performed whole exome sequencing in three PBC families. We genotyped HLA-DRB1 and calculated the association between HLA-DRB1 alleles and the encoding amino acid sequences with the clinical features. RESULTS Ten variants harboured the HLA-DRB1 gene associated with PBC. DRB1×07:01, 14:01 and 14:05 were highly increased in PBC. Ten coding region polymorphisms were associated with PBC that encode the amino acid variants of HLA-DR β54, β59 and β66 located in the peptide-binding site of the MHC molecule. Glutamine at position 54 was confirmed as a risk amino acid, verifying the results of familial aggregation analysis of PBC families. DISCUSSION Familial aggregation analysis indicated that HLA-DRB1 is a candidate gene for the risk of disease course. Considering that amino acid variations are critical to peptide-binding properties, they underlie the major component of MHC association with PBC.
Collapse
Affiliation(s)
- Yanni Li
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China; Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Xin Liu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yi Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China; Department of General Surgery, YouAn Hospital, Capital Medical University, Beijing, China
| | - Yi Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Shixian Hu
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Hui Yang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Weilong Zhong
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jingwen Zhao
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaoyi Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongyu Chu
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Yanping Zheng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Jie Zhang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Lu Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China; Department of Gastroenterology and Hepatology, People's Hospital of Hetian District, Xinjiang Uygur Autonomous Region, China.
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China.
| |
Collapse
|
13
|
Naito T, Okada Y. HLA imputation and its application to genetic and molecular fine-mapping of the MHC region in autoimmune diseases. Semin Immunopathol 2021; 44:15-28. [PMID: 34786601 PMCID: PMC8837514 DOI: 10.1007/s00281-021-00901-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022]
Abstract
Variations of human leukocyte antigen (HLA) genes in the major histocompatibility complex region (MHC) significantly affect the risk of various diseases, especially autoimmune diseases. Fine-mapping of causal variants in this region was challenging due to the difficulty in sequencing and its inapplicability to large cohorts. Thus, HLA imputation, a method to infer HLA types from regional single nucleotide polymorphisms, has been developed and has successfully contributed to MHC fine-mapping of various diseases. Different HLA imputation methods have been developed, each with its own advantages, and recent methods have been improved in terms of accuracy and computational performance. Additionally, advances in HLA reference panels by next-generation sequencing technologies have enabled higher resolution and a more reliable imputation, allowing a finer-grained evaluation of the association between sequence variations and disease risk. Risk-associated variants in the MHC region would affect disease susceptibility through complicated mechanisms including alterations in peripheral responses and central thymic selection of T cells. The cooperation of reliable HLA imputation methods, informative fine-mapping, and experimental validation of the functional significance of MHC variations would be essential for further understanding of the role of the MHC in the immunopathology of autoimmune diseases.
Collapse
Affiliation(s)
- Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan.
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Osaka, Suita, 565-0871, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| |
Collapse
|
14
|
Mai H, Chen J, Chen H, Liu Z, Huang G, Wang J, Xiao Q, Ren W, Zhou B, Hou J, Jiang D. Fine Mapping of the MHC Region Identifies Novel Variants Associated with HBV-Related Hepatocellular Carcinoma in Han Chinese. J Hepatocell Carcinoma 2021; 8:951-961. [PMID: 34430511 PMCID: PMC8378933 DOI: 10.2147/jhc.s321919] [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: 05/26/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction Genome-wide association studies identified susceptibility loci in the major histocompatibility complex region for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC). However, the causal variants underlying HBV-related HCC pathogenesis remain elusive. Methods With a total of 1,161 HBV-related HCC cases and 1,353 chronic HBV carriers without HCC, we imputed human leukocyte antigen (HLA) variants based on a Chinese HLA reference panel and evaluated the associations of these variants with the risk of HBV-related HCC. Conditional analyses were used to identify independent signals associated with the risk of HBV-related HCC (P false-discovery rate (FDR) <0.20). A total of 14,930 variants within the MHC region were genotyped or imputed. Results We identified two variants, rs114401688 (P = 1.05 × 10−6, PFDR = 2.43 × 10−3) and rs115126566 (P = 9.04 × 10−5, PFDR = 1.77 × 10−1), that are independently associated with the risk of HBV-related HCC. Single nucleotide polymorphism (SNP) rs114401688 is in linkage disequilibrium with a previously reported SNP rs9275319. In the current study, we found that its association with HCC could be explained by HLA-DQB1*04 and HLA-DRB1*04. SNP rs115126566 is a novel risk variant and may function by regulating transcriptions of HLA-DPA1/DPB1 through enhancer-mediated mechanisms. HLA zygosity analysis showed that homozygosity at HLA-DQB1 gene is suggestively associated with a higher risk of HCC (P = 0.10) and the risk was more pronounced in the older age group (age ≥50, P = 0.03). Discussion Our findings further the understanding of the genetic basis for HBV-related HCC predisposition in chronic HBV carriers.
Collapse
Affiliation(s)
- Haoming Mai
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jiaxuan Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Haitao Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China.,School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, 518107, People's Republic of China
| | - Zhiwei Liu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Guanlin Huang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jialin Wang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Qianyi Xiao
- School of Public Health, Fudan University, Shanghai, 200032, People's Republic of China
| | - Weihua Ren
- Central Laboratory, First Affiliated Hospital, Henan University of Science and Technology, Luoyang, Henan Province, 471009, People's Republic of China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Deke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| |
Collapse
|
15
|
The genetic architecture of primary biliary cholangitis. Eur J Med Genet 2021; 64:104292. [PMID: 34303876 DOI: 10.1016/j.ejmg.2021.104292] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/03/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022]
Abstract
Primary biliary cholangitis (PBC) is a rare autoimmune disease of the liver affecting the small bile ducts. From a genetic point of view, PBC is a complex trait and several genetic and environmental factors have been called in action to explain its etiopathogenesis. Similarly to other complex traits, PBC has benefited from the introduction of genome-wide association studies (GWAS), which identified many variants predisposing or protecting toward the development of the disease. While a progressive endeavour toward the characterization of candidate loci and downstream pathways is currently ongoing, there is still a relatively large portion of heritability of PBC to be revealed. In addition, genetic variation behind progression of the disease and therapeutic response are mostly to be investigated yet. This review outlines the state-of-the-art regarding the genetic architecture of PBC and provides some hints for future investigations, focusing on the study of gene-gene interactions, the application of whole-genome sequencing techniques, and the investigation of X chromosome that can be helpful to cover the missing heritability gap in PBC.
Collapse
|
16
|
Ramírez-Marín Y, Abad-Contreras DE, Ustarroz-Cano M, Pérez-Gallardo NS, Villafuerte-García L, Puente-Guzmán DM, del Villar-Velasco JL, Rodríguez-López LA, Torres-Villalobos G, Mercado MÁ, Tapia-Jurado J, Martínez-García FD, Harmsen MC, Piña-Barba MC, Giraldo-Gomez DM. Perfusion Decellularization of Extrahepatic Bile Duct Allows Tissue-Engineered Scaffold Generation by Preserving Matrix Architecture and Cytocompatibility. MATERIALS 2021; 14:ma14113099. [PMID: 34198787 PMCID: PMC8201334 DOI: 10.3390/ma14113099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 12/19/2022]
Abstract
Reconstruction of bile ducts damaged remains a vexing medical problem. Surgeons have few options when it comes to a long segment reconstruction of the bile duct. Biological scaffolds of decellularized biliary origin may offer an approach to support the replace of bile ducts. Our objective was to obtain an extracellular matrix scaffold derived from porcine extrahepatic bile ducts (dECM-BD) and to analyze its biological and biochemical properties. The efficiency of the tailored perfusion decellularization process was assessed through histology stainings. Results from 4'-6-diamidino-2-phenylindole (DAPI), Hematoxylin and Eosin (H&E) stainings, and deoxyribonucleic acid (DNA) quantification showed proper extracellular matrix (ECM) decellularization with an effectiveness of 98%. Immunohistochemistry results indicate an effective decrease in immunogenic marker as human leukocyte antigens (HLA-A) and Cytokeratin 7 (CK7) proteins. The ECM of the bile duct was preserved according to Masson and Herovici stainings. Data derived from scanning electron microscopy (SEM) and thermogravimetric analysis (TGA) showed the preservation of the dECM-BD hierarchical structures. Cytotoxicity of dECM-BD was null, with cells able to infiltrate the scaffold. In this work, we standardized a decellularization method that allows one to obtain a natural bile duct scaffold with hierarchical ultrastructure preservation and adequate cytocompatibility.
Collapse
Affiliation(s)
- Yolik Ramírez-Marín
- Program of Medical Specialization General Surgery, Division of Posgraduate Studies, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito de Posgrados, Unidad de Posgrado Edificio “E” 2° piso, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico;
- National Institute of Medical Sciences and Nutrition of Mexico Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc. 16, Tlalpan, Ciudad de México 14080, Mexico; (L.A.R.-L.); (G.T.-V.); (M.Á.M.)
| | - David Eduardo Abad-Contreras
- Laboratory for Biomaterials, Materials Research Institute, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico; (D.E.A.-C.); (M.C.P.-B.)
| | - Martha Ustarroz-Cano
- Department of Cell and Tissue Biology, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Interior, Edificio “A” 3° piso, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico;
| | - Norma S. Pérez-Gallardo
- Surgical Training Section, Faculty of Veterinary Medicine and Animal Husbandry, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico; (N.S.P.-G.); (L.V.-G.); (D.M.P.-G.); (J.L.d.V.-V.)
| | - Lorena Villafuerte-García
- Surgical Training Section, Faculty of Veterinary Medicine and Animal Husbandry, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico; (N.S.P.-G.); (L.V.-G.); (D.M.P.-G.); (J.L.d.V.-V.)
| | - Dulce Maria Puente-Guzmán
- Surgical Training Section, Faculty of Veterinary Medicine and Animal Husbandry, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico; (N.S.P.-G.); (L.V.-G.); (D.M.P.-G.); (J.L.d.V.-V.)
| | - Jorge Luna del Villar-Velasco
- Surgical Training Section, Faculty of Veterinary Medicine and Animal Husbandry, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico; (N.S.P.-G.); (L.V.-G.); (D.M.P.-G.); (J.L.d.V.-V.)
| | - Leonardo Alejandro Rodríguez-López
- National Institute of Medical Sciences and Nutrition of Mexico Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc. 16, Tlalpan, Ciudad de México 14080, Mexico; (L.A.R.-L.); (G.T.-V.); (M.Á.M.)
| | - Gonzalo Torres-Villalobos
- National Institute of Medical Sciences and Nutrition of Mexico Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc. 16, Tlalpan, Ciudad de México 14080, Mexico; (L.A.R.-L.); (G.T.-V.); (M.Á.M.)
| | - Miguel Ángel Mercado
- National Institute of Medical Sciences and Nutrition of Mexico Salvador Zubirán, Vasco de Quiroga 15, Belisario Domínguez Secc. 16, Tlalpan, Ciudad de México 14080, Mexico; (L.A.R.-L.); (G.T.-V.); (M.Á.M.)
| | - Jesús Tapia-Jurado
- Unit of Advanced Medical Simulation, Division of Posgraduate Studies, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito de Posgrados, Unidad de Posgrado Edificio “B” 2° piso, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico;
| | - Francisco Drusso Martínez-García
- Department of Pathology and Medical Biology, University Medical Center Groningen University of Groningen, Hanzeplein 1, 9713 Groningen, The Netherlands; (F.D.M.-G.); (M.C.H.)
| | - Martin Conrad Harmsen
- Department of Pathology and Medical Biology, University Medical Center Groningen University of Groningen, Hanzeplein 1, 9713 Groningen, The Netherlands; (F.D.M.-G.); (M.C.H.)
| | - M. Cristina Piña-Barba
- Laboratory for Biomaterials, Materials Research Institute, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Exterior, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico; (D.E.A.-C.); (M.C.P.-B.)
| | - David M. Giraldo-Gomez
- Department of Cell and Tissue Biology, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Interior, Edificio “A” 3° piso, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico;
- Microscopy Core Facility, Faculty of Medicine, National Autonomous University of Mexico (UNAM), Avenida Universidad 3000, Circuito Interior, Edificio “A” planta baja, Ciudad Universitaria, Coyoacán, Ciudad de México 04510, Mexico
- Correspondence:
| |
Collapse
|
17
|
Kling D, Phillips C, Kennett D, Tillmar A. Investigative genetic genealogy: Current methods, knowledge and practice. Forensic Sci Int Genet 2021; 52:102474. [PMID: 33592389 DOI: 10.1016/j.fsigen.2021.102474] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/12/2021] [Accepted: 01/27/2021] [Indexed: 12/15/2022]
Abstract
Investigative genetic genealogy (IGG) has emerged as a new, rapidly growing field of forensic science. We describe the process whereby dense SNP data, commonly comprising more than half a million markers, are employed to infer distant relationships. By distant we refer to degrees of relatedness exceeding that of first cousins. We review how methods of relationship matching and SNP analysis on an enlarged scale are used in a forensic setting to identify a suspect in a criminal investigation or a missing person. There is currently a strong need in forensic genetics not only to understand the underlying models to infer relatedness but also to fully explore the DNA technologies and data used in IGG. This review brings together many of the topics and examines their effectiveness and operational limits, while suggesting future directions for their forensic validation. We further investigated the methods used by the major direct-to-consumer (DTC) genetic ancestry testing companies as well as submitting a questionnaire where providers of forensic genetic genealogy summarized their operation/services. Although most of the DTC market, and genetic genealogy in general, has undisclosed, proprietary algorithms we review the current knowledge where information has been discussed and published more openly.
Collapse
Affiliation(s)
- Daniel Kling
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Forensic Sciences, Oslo University Hospital, Oslo, Norway.
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain.
| | - Debbie Kennett
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Andreas Tillmar
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping, Sweden; Department of Biomedical and Clinical Sciences, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| |
Collapse
|
18
|
Teng JL, Chen X, Chen J, Zeng T, He L, Li M, Luo CN, Liu S, Ding TT, Yimaiti K, Li X, Ding Y, Cheng XB, Zhou J, Ye JN, Ji J, Su YT, Shi H, Sun Y, Gao C, Hu QY, Chi HH, Yuan X, Zhou ZC, Wang D, Wang K, Feng D, Li C, Sun Y, Niu Y, Xu X, Chen LJ, Xu J, Wu LJ, Zhou Z, Pan D, Niu H, Yang CD, Yongyong Shi, Li Z, Liu HL. The amino acid variants in HLA II molecules explain the major association with adult-onset Still's disease in the Han Chinese population. J Autoimmun 2020; 116:102562. [PMID: 33168359 DOI: 10.1016/j.jaut.2020.102562] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 10/23/2022]
Abstract
Adult-onset Still's disease (AOSD) is a rare autoinflammatory disease with systemic involvement, and its pathophysiology remains unclear. Genome-wide association studies (GWAS) in the Chinese population have revealed an association between AOSD and the major histocompatibility complex (MHC) locus; however, causal variants in the MHC remain undetermined. In the present study, we identified independent amino-acid polymorphisms in human leukocyte antigen (HLA) molecules that are associated with Han Chinese patients with AOSD by fine-mapping the MHC locus. Through conditional analyses, we identified position 34 in HLA-DQα1 (p = 1.44 × 10-14) and Asn in HLA-DRβ1 position 37 (p = 5.12 × 10-11) as the major determinants for AOSD. Moreover, we identified the associations for three main HLA class II alleles: HLA-DQB1*06:02 (OR = 2.70, p = 3.02 × 10-14), HLA-DRB1*15:01 (OR = 2.44, p = 3.66 × 10-13), and HLA-DQA1*01:02 (OR = 1.97, p = 1.09 × 10-9). This study reveals the relationship between functional variations in the class II HLA region and AOSD, implicating the MHC locus in the pathogenesis of AOSD.
Collapse
Affiliation(s)
- Jia-Lin Teng
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Xia Chen
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Jianhua Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ting Zeng
- Xinhua Hospital Chongming Branch Affiliated to Shanghai Jiao Tong University School of Medicine, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Meihang Li
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Cai-Nan Luo
- Department of Rheumatology and Immunology, People's Hospital of Xinjiang Ugyur Autonomous Region, Urumqi, 830001, China
| | - Shuang Liu
- Department of Rheumatology and Immunology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Ting-Ting Ding
- Department of Rheumatology and Immunology, First Affiliated Hospital of Bengbu Medical College, 233000, China
| | - Kuerbanjiang Yimaiti
- Department of Rheumatology and Immunology, People's Hospital of Xinjiang Ugyur Autonomous Region, Urumqi, 830001, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yonghe Ding
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Xiao-Bing Cheng
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Juan Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Jun-Na Ye
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Jue Ji
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Yu-Tong Su
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Hui Shi
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Yue Sun
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Chengwen Gao
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Qiong-Yi Hu
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Hui-Hui Chi
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Xuan Yuan
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Zhuo-Chao Zhou
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Dong Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Dong Feng
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Changgui Li
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Yuanchao Sun
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Yujuan Niu
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Xiaolei Xu
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China
| | - Lin-Jie Chen
- Department of Rheumatology and Immunology, First Affiliated Hospital of Bengbu Medical College, 233000, China
| | - Jian Xu
- Department of Rheumatology and Immunology, First Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Li-Jun Wu
- Department of Rheumatology and Immunology, People's Hospital of Xinjiang Ugyur Autonomous Region, Urumqi, 830001, China
| | - Zhaowei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Dun Pan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China
| | - Haitao Niu
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Department of Urology, The Affiliated Hospital of Qingdao University, Qingdao, China; Key Laboratory, Department of Urology and Andrology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Cheng-de Yang
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China
| | - Yongyong Shi
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Psychiatry, The First Teaching Hospital of Xinjiang Medical University, Urumqi, China; Changning Mental Health Center, Shanghai, China
| | - Zhiqiang Li
- The Affiliated Hospital of Qingdao University & the Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, China; Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai, China; Institute of Social Cognitive and Behavioral Sciences, Shanghai Jiao Tong University, Shanghai, China; Institute of Neuropsychiatric Science and Systems Biological Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Hong-Lei Liu
- Department of Rheumatology and Immunology, Shanghai Jiao Tong University School of Medicine Affiliated Ruijin Hospital, Shanghai, China.
| |
Collapse
|
19
|
Kunst RF, Niemeijer M, van der Laan LJW, Spee B, van de Graaf SFJ. From fatty hepatocytes to impaired bile flow: Matching model systems for liver biology and disease. Biochem Pharmacol 2020; 180:114173. [PMID: 32717228 DOI: 10.1016/j.bcp.2020.114173] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 02/08/2023]
Abstract
A large variety of model systems are used in hepatobiliary research. In this review, we aim to provide an overview of established and emerging models for specific research questions. We specifically discuss the value and limitations of these models for research on metabolic associated fatty liver disease (MAFLD), (previously named non-alcoholic fatty liver diseases/non-alcoholic steatohepatitis (NAFLD/NASH)) and cholestasis-related diseases such as primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC). The entire range of models is discussed varying from immortalized cell lines, mature or pluripotent stem cell-based models including organoids/spheroids, to animal models and human ex vivo models such as normothermic machine perfusion of livers and living liver slices. Finally, the pros and cons of each model are discussed as well as the need in the scientific community for continuous innovation in model development to better mimic the human (patho)physiology.
Collapse
Affiliation(s)
- Roni F Kunst
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands
| | - Marije Niemeijer
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, the Netherlands; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, the Netherlands
| | - Luc J W van der Laan
- Department of Surgery, Erasmus MC-University Medical Center, Rotterdam, the Netherlands
| | - Bart Spee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, the Netherlands
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|