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Petri BJ, Piell KM, Wahlang B, Head KZ, Rouchka EC, Park JW, Hwang JY, Banerjee M, Cave MC, Klinge CM. Altered splicing factor and alternative splicing events in a mouse model of diet- and polychlorinated biphenyl-induced liver disease. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 103:104260. [PMID: 37683712 PMCID: PMC10591945 DOI: 10.1016/j.etap.2023.104260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is associated with human environmental exposure to polychlorinated biphenyls (PCBs). Alternative splicing (AS) is dysregulated in steatotic liver disease and is regulated by splicing factors (SFs) and N-6 methyladenosine (m6A) modification. Here integrated analysis of hepatic mRNA-sequencing data was used to identify differentially expressed SFs and differential AS events (ASEs) in the livers of high fat diet-fed C57BL/6 J male mice exposed to Aroclor1260, PCB126, Aroclor1260 + PCB126, or vehicle control. Aroclor1260 + PCB126 co-exposure altered 100 SFs and replicate multivariate analysis of transcript splicing (rMATS) identified 449 ASEs in 366 genes associated with NAFLD pathways. These ASEs were similar to those resulting from experimental perturbations in m6A writers, readers, and erasers. These results demonstrate specific hepatic SF and AS regulatory mechanisms are disrupted by HFD and PCB exposures, contributing to the expression of altered isoforms that may play a role in NAFLD progression to NASH.
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Affiliation(s)
- Belinda J Petri
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Kellianne M Piell
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
| | - Banrida Wahlang
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Kimberly Z Head
- University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Eric C Rouchka
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; KY INBRE Bioinformatics Core, University of Louisville, USA
| | - Juw Won Park
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; KY INBRE Bioinformatics Core, University of Louisville, USA; Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292 USA
| | - Jae Yeon Hwang
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Mayukh Banerjee
- University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; Department of Pharmacology and Toxicology, University of Louisville, Louisville, KY 40292 USA
| | - Matthew C Cave
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA; University of Louisville Hepatobiology and Toxicology Center, USA; The University of Louisville Superfund Research Center, USA; Division of Gastroenterology, Hepatology & Nutrition, Department of Medicine, University of Louisville School of Medicine, USA
| | - Carolyn M Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA; University of Louisville Center for Integrative Environmental Health Sciences (CIEHS), USA.
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Asuri S, McIntosh S, Taylor V, Rokeby A, Kelly J, Shumansky K, Field LL, Yoshida EM, Arbour L. Primary Biliary Cholangitis in British Columbia First Nations: Clinical features and discovery of novel genetic susceptibility loci. Liver Int 2018; 38:940-948. [PMID: 29297981 DOI: 10.1111/liv.13686] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/21/2017] [Indexed: 02/13/2023]
Abstract
BACKGROUND & AIMS Primary Biliary Cholangitis (PBC) is a chronic autoimmune liver disease characterized by destruction of intrahepatic bile ducts, portal inflammation and cirrhosis. Although rare in most populations, it is prevalent and often familial in British Columbia First Nations. We hypothesized that major genetic factors increased the risk in First Nations. METHODS In all, 44 individuals with Primary Biliary Cholangitis and 61 unaffected relatives from 32 First Nations families participated. Family history and co-morbidities were documented. Medical records were reviewed and available biopsies were re-reviewed by our team pathologist. Genotyping was performed on DNA from 36 affected persons and 27 unaffected relatives using the Affymetrix Human Mapping 500K Array Set. MERLIN software was used to carry out multipoint parametric and nonparametric linkage analysis. Candidate genes were identified and entered into InnateDB and KEGG software to identify potential pathways affecting pathogenesis. RESULTS In all, 34% of families were multiplex. Fifty per cent of cases and 33% of unaffected relatives reported other autoimmune disease. Three genomic regions (9q21, 17p13 and 19p13) produced LOD scores of 2.3 or greater suggestive of linkage, but no single linkage peak reached statistical significance. Candidate genes identified in the three regions suggested involvement of IL17, NFκB, IL6, JAK-STAT, IFNγ and TGFβ immune signalling pathways. Specifically, four genes-ACT1, PIN1, DNMT1 and NTN1-emerged as having roles in these pathways that may influence Primary Biliary Cholangitis pathogenesis. CONCLUSIONS Our whole genome linkage study results reflect the multifactorial nature of Primary Biliary Cholangitis, support previous studies suggesting signalling pathway involvement and identify new candidate genes for consideration.
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Affiliation(s)
- Sirisha Asuri
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sarah McIntosh
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Valerie Taylor
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Andrew Rokeby
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - James Kelly
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Karey Shumansky
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Lanora Leigh Field
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Eric M Yoshida
- Division of Gastroenterology, University of British Columbia, Vancouver, BC, Canada
| | - Laura Arbour
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.,Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
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Zimmer V, Bohle RM, Weber SN, Lammert F, Jüngst C. Benign recurrent intrahepatic cholestasis (BRIC)-like episode associated with ATP8B1 variation underlying protracted cholestatic course of acute hepatitis E virus infection. Dig Liver Dis 2018; 50:206-207. [PMID: 29191380 DOI: 10.1016/j.dld.2017.10.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/21/2017] [Accepted: 10/28/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Vincent Zimmer
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany.
| | - Rainer M Bohle
- Institute of Pathology, Saarland University Medical Center, Saarland University, Homburg, Germany.
| | - Susanne N Weber
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany.
| | - Frank Lammert
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany.
| | - Christoph Jüngst
- Department of Medicine II, Saarland University Medical Center, Saarland University, Homburg, Germany.
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Paziewska A, Habior A, Rogowska A, Zych W, Goryca K, Karczmarski J, Dabrowska M, Ambrozkiewicz F, Walewska-Zielecka B, Krawczyk M, Cichoz-Lach H, Milkiewicz P, Kowalik A, Mucha K, Raczynska J, Musialik J, Boryczka G, Wasilewicz M, Ciecko-Michalska I, Ferenc M, Janiak M, Kanikowska A, Stankiewicz R, Hartleb M, Mach T, Grzymislawski M, Raszeja-Wyszomirska J, Wunsch E, Bobinski T, Mikula M, Ostrowski J. A novel approach to genome-wide association analysis identifies genetic associations with primary biliary cholangitis and primary sclerosing cholangitis in Polish patients. BMC Med Genomics 2017; 10:2. [PMID: 28056976 PMCID: PMC5217265 DOI: 10.1186/s12920-016-0239-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 12/15/2016] [Indexed: 01/28/2023] Open
Abstract
Background Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are forms of hepatic autoimmunity, and risk for both diseases has a strong genetic component. This study aimed to define the genetic architecture of PBC and PSC within the Polish population. Methods Subjects were 443 women with PBC, 120 patients with PSC, and 934 healthy controls recruited from Gastroenterology Departments in various Polish hospitals. Allelotyping employed a pooled-DNA sample-based genome-wide association study (GWAS) approach, using Illumina Human Omni2.5-Exome BeadChips and the following novel selection criteria for risk loci: blocks of at least 10 single nucleotide polymorphisms (SNPs) in strong linkage disequilibrium, where the distance between each adjacent SNP pair in the block was less than 30 kb, and each SNP was associated with disease at a significance level of P < 0.005. A selected index SNP from each block was validated using TaqMan SNP genotyping assays. Results Nineteen and twenty-one SNPs were verified as associated with PBC and PSC, respectively, by individual genotyping; 19 (10/9, PBC/PSC) SNPs reached a stringent (corrected) significance threshold and a further 21 (9/12, PBC/PSC) reached a nominal level of significance (P < 0.05 with odds ratio (OR) > 1.2 or < 0.83), providing suggestive evidence of association. The SNPs mapped to seven (1p31.3, 3q13, 6p21, 7q32.1, 11q23.3, 17q12, 19q13.33) and one (6p21) chromosome region previously associated with PBC and PSC, respectively. The SNP, rs35730843, mapping to the POLR2G gene promoter (P = 1.2 × 10-5, OR = 0.39) demonstrated the highest effect size, and was protective for PBC, whereas for PSC respective SNPs were: rs13191240 in the intron of ADGRB3 gene (P = 0.0095, OR = 0.2) and rs3822659 (P = 0.0051, OR = 0.236) along with rs9686714 (P = 0.00077, OR = 0.2), both located in the WWC1 gene. Conclusions Our cost-effective GWAS approach followed by individual genotyping confirmed several previously identified associations and discovered new susceptibility loci associated with PBC and/or PSC in Polish patients. However, further functional studies are warranted to understand the roles of these newly identified variants in the development of the two disorders. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0239-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnieszka Paziewska
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Andrzej Habior
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Agnieszka Rogowska
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Włodzimierz Zych
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jakub Karczmarski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Michalina Dabrowska
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Bozena Walewska-Zielecka
- Department of Public Health, Faculty of Health Sciences, Medical University of Warsaw, Warsaw, Poland
| | - Marek Krawczyk
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | | | - Piotr Milkiewicz
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland.,Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | | | - Krzysztof Mucha
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Joanna Raczynska
- Department of Immunology, Transplantology and Internal Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Joanna Musialik
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Grzegorz Boryczka
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Michal Wasilewicz
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Irena Ciecko-Michalska
- Department of Gastroenterology and Infectious Diseases, Collegium Medicum Jagiellonian University, Krakow, Poland
| | - Malgorzata Ferenc
- Department of Gastroenterology, Provincial Hospital, Olsztyn, Poland
| | - Maria Janiak
- Department of Gastroenterology and Hepatology, Medical University of Gdansk, Gdansk, Poland
| | - Alina Kanikowska
- Department of Internal and Metabolic Diseases and Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Rafal Stankiewicz
- Department of General, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Marek Hartleb
- Department of Gastroenterology and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Tomasz Mach
- Department of Gastroenterology and Infectious Diseases, Collegium Medicum Jagiellonian University, Krakow, Poland
| | - Marian Grzymislawski
- Department of Internal and Metabolic Diseases and Dietetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Joanna Raszeja-Wyszomirska
- Department of General, Liver and Internal Medicine Unit, Transplant and Liver Surgery, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Wunsch
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Bobinski
- Department of Gastroenterology, Provincial Hospital, Ostroleka, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Gastroenterology, Hepatology and Oncology, Medical Center for Postgraduate Education, Warsaw, Poland. .,Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Roentgena 5, 02-781, Warsaw, Poland.
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