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Zöllner J, Finer S, Linton KJ, van Heel DA, Williamson C, Dixon PH. Rare variant contribution to cholestatic liver disease in a South Asian population in the United Kingdom. Sci Rep 2023; 13:8120. [PMID: 37208429 PMCID: PMC10199085 DOI: 10.1038/s41598-023-33391-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/12/2023] [Indexed: 05/21/2023] Open
Abstract
This study assessed the contribution of five genes previously known to be involved in cholestatic liver disease in British Bangladeshi and Pakistani people. Five genes (ABCB4, ABCB11, ATP8B1, NR1H4, TJP2) were interrogated by exome sequencing data of 5236 volunteers. Included were non-synonymous or loss of function (LoF) variants with a minor allele frequency < 5%. Variants were filtered, and annotated to perform rare variant burden analysis, protein structure, and modelling analysis in-silico. Out of 314 non-synonymous variants, 180 fulfilled the inclusion criteria and were mostly heterozygous unless specified. 90 were novel and of those variants, 22 were considered likely pathogenic and 9 pathogenic. We identified variants in volunteers with gallstone disease (n = 31), intrahepatic cholestasis of pregnancy (ICP, n = 16), cholangiocarcinoma and cirrhosis (n = 2). Fourteen novel LoF variants were identified: 7 frameshift, 5 introduction of premature stop codon and 2 splice acceptor variants. The rare variant burden was significantly increased in ABCB11. Protein modelling demonstrated variants that appeared to likely cause significant structural alterations. This study highlights the significant genetic burden contributing to cholestatic liver disease. Novel likely pathogenic and pathogenic variants were identified addressing the underrepresentation of diverse ancestry groups in genomic research.
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Affiliation(s)
| | - Sarah Finer
- Institute for Population Health Sciences, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Kenneth J Linton
- Centre for Cell Biology and Cutaneous Research, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Catherine Williamson
- Department of Women and Children's Health, School of Life Course Sciences, FOLSM, King's College London, 2.30W Hodgkin Building, Guy's Campus, London, SE1 1UL, UK.
| | - Peter H Dixon
- Department of Women and Children's Health, School of Life Course Sciences, FOLSM, King's College London, 2.30W Hodgkin Building, Guy's Campus, London, SE1 1UL, UK
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Cheng J, Gong L, Mi X, Wu X, Zheng J, Yang W. Case series of progressive familial intrahepatic cholestasis type 3: Characterization of variants in ABCB4 in China. Front Med (Lausanne) 2022; 9:962408. [PMID: 36569137 PMCID: PMC9774490 DOI: 10.3389/fmed.2022.962408] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
Objective To improve the accuracy of the diagnosis of familial progressive intrahepatic cholestasis type 3 (PFIC3, https://www.omim.org/entry/602347). Materials and methods Between September 2019 and March 2021, we recruited four patients with PFIC3 from two liver centers in East China. Molecular genetic findings of ATP-binding cassette subfamily B member 4 [ATP binding cassette transporter A4 (ABCB4), https://www.omim.org/entry/171060] were prospectively examined, and clinical records, laboratory readouts, and macroscopic and microscopic appearances of the liver were analyzed. Results Four patients experienced cholestasis, mild jaundice, and elevated levels of serum direct bilirubin, γ-glutamyltransferase, or total bile acids. All patients had moderate-to-severe liver fibrosis or biliary cirrhosis, and their liver biopsy specimens stained positive with rhodamine. Molecular immunohistochemistry revealed reduced or absent MDR3 expression in all liver specimens. A novel mutation of ABCB4 (c.1560 + 2T > A) was identified in patients with PFIC3, which is of high clinical significance and may help understand mutant ABCB4 pathogenesis. Conclusion MDR3 immunohistochemistry and molecular genetic analyses of ABCB4 are essential for the accurate diagnosis of PFIC3.
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Affiliation(s)
- Jinlin Cheng
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ling Gong
- Department of Infectious Diseases, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xiaoxiao Mi
- Department of Translational Medicine Platform, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xiangyan Wu
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Jun Zheng
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Wenjun Yang
- Department of Pathology, The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China,*Correspondence: Wenjun Yang,
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Progressive Familial Intrahepatic Cholestasis: Need for Genetic Analysis Before Liver Transplantation. J Clin Exp Hepatol 2022; 12:686-688. [PMID: 35535065 PMCID: PMC9077163 DOI: 10.1016/j.jceh.2021.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/08/2021] [Indexed: 12/12/2022] Open
Abstract
The clinical course after liver transplantation (LT) in progressive familial intrahepatic cholestasis type 1 (PFIC1) is complicated by intractable diarrhoea, growth failure, graft steatosis and cirrhosis. Recent evidence from Japan suggests the role of genotype to predict outcome after LT. We report a case with pathogenic frameshift mutation who had failed partial external biliary diversion, underwent LT and his post-LT course has been complicated by intractable diarrhoea, growth failure, steatosis and fibrosis. This case highlights the fact that homozygous frameshift p.Gly197LeufsTer10 mutation in ATP8B1 is associated with poor outcome and genetic evaluation should be mandatory before subjecting the patient to LT.
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Zhou JL, Zhao YZ, Wang SS, Chen MX, Zhou S, Chen C. RNA Splicing: A Versatile Regulatory Mechanism in Pediatric Liver Diseases. Front Mol Biosci 2021; 8:725308. [PMID: 34651015 PMCID: PMC8505697 DOI: 10.3389/fmolb.2021.725308] [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: 06/15/2021] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
With the development of high-throughput sequencing technology, the posttranscriptional mechanism of alternative splicing is becoming better understood. From decades of studies, alternative splicing has been shown to occur in multiple tissues, including the brain, heart, testis, skeletal muscle, and liver. This regulatory mechanism plays an important role in physiological functions in most liver diseases. Currently, due to the absence of symptoms, chronic pediatric liver diseases have a significant impact on public health. Furthermore, the progression of the disease is accelerated in children, leading to severe damage to their liver tissue if no precautions are taken. To this end, this review article summarizes the current knowledge of alternative splicing in pediatric liver diseases, paying special attention to liver damage in the child stage. The discussion of the regulatory role of splicing in liver diseases and its potential as a new therapeutic target is also included.
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Affiliation(s)
- Jian-Li Zhou
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Yu-Zhen Zhao
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Shan-Shan Wang
- School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Shaoming Zhou
- Division of Gastroenterology, Shenzhen Children's Hospital, Shenzhen, China
| | - Chen Chen
- Department of Infectious Disease, Nanjing Second Hospital, Nanjing University of Chinese Medicine, Nanjing, China
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Zhang W, Lin R, Lu Z, Sheng H, Xu Y, Li X, Cheng J, Cai Y, Mao X, Liu L. Phenotypic and Molecular Characteristics of Children with Progressive Familial Intrahepatic Cholestasis in South China. Pediatr Gastroenterol Hepatol Nutr 2020; 23:558-566. [PMID: 33215027 PMCID: PMC7667226 DOI: 10.5223/pghn.2020.23.6.558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/21/2020] [Accepted: 06/23/2020] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Progressive familial intrahepatic cholestasis (PFIC) is a rare genetic autosomal recessive disease caused by mutations in ATP8B1, ABCB11 or ABCB4. Mutational analysis of these genes is a reliable approach to identify the disorder. METHODS We collected and analyzed relevant data related to clinical diagnosis, biological investigation, and molecular determination in nine children carrying these gene mutations, who were from unrelated families in South China. RESULTS Of the nine patients (five males, four females) with PFIC, one case of PFIC1, four cases of PFIC2, and four cases of PFIC3 were diagnosed. Except in patient no. 8, jaundice and severe pruritus were the major clinical signs in all forms. γ-glutamyl transpeptidase was low in patients with PFIC1/PFIC2, and remained mildly elevated in patients with PFIC3. We identified 15 different mutations, including nine novel mutations (p.R470HfsX8, p.Q794X and p.I1170T of ABCB11 gene mutations, p.G319R, p.A1047P, p.G1074R, p.T830NfsX11, p.A1047PfsX8 and p.N1048TfsX of ABCB4 gene mutations) and six known mutations (p.G446R and p.F529del of ATP8B1 gene mutations, p.A588V, p.G1004D and p.R1057X of ABCB11 gene mutations, p.P479L of ABCB4 gene mutations). The results showed that compared with other regions, these three types of PFIC genes had different mutational spectrum in China. CONCLUSION The study expands the genotypic spectrum of PFIC. We identified nine novel mutations of PFIC and our findings could help in the diagnosis and treatment of this disease.
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Affiliation(s)
- Wen Zhang
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ruizhu Lin
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Zhikun Lu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Huiying Sheng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yi Xu
- Department of Infectious Disease, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xiuzhen Li
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jing Cheng
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yanna Cai
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xiaojian Mao
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Li Liu
- Department of Genetics and Endocrinology, Guangzhou Women and Children's Medical Center, Guangzhou, China
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