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Glessner JT, Ningappa MB, Ngo KA, Zahid M, So J, Higgs BW, Sleiman PMA, Narayanan T, Ranganathan S, March M, Prasadan K, Vaccaro C, Reyes-Mugica M, Velazquez J, Salgado CM, Ebrahimkhani MR, Schmitt L, Rajasundaram D, Paul M, Pellegrino R, Gittes GK, Li D, Wang X, Billings J, Squires R, Ashokkumar C, Sharif K, Kelly D, Dhawan A, Horslen S, Lo CW, Shin D, Subramaniam S, Hakonarson H, Sindhi R. Biliary atresia is associated with polygenic susceptibility in ciliogenesis and planar polarity effector genes. J Hepatol 2023; 79:1385-1395. [PMID: 37572794 PMCID: PMC10729795 DOI: 10.1016/j.jhep.2023.07.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
Abstract
BACKGROUND & AIMS Biliary atresia (BA) is poorly understood and leads to liver transplantation (LT), with the requirement for and associated risks of lifelong immunosuppression, in most children. We performed a genome-wide association study (GWAS) to determine the genetic basis of BA. METHODS We performed a GWAS in 811 European BA cases treated with LT in US, Canadian and UK centers, and 4,654 genetically matched controls. Whole-genome sequencing of 100 cases evaluated synthetic association with rare variants. Functional studies included whole liver transcriptome analysis of 64 BA cases and perturbations in experimental models. RESULTS A GWAS of common single nucleotide polymorphisms (SNPs), i.e. allele frequencies >1%, identified intronic SNPs rs6446628 in AFAP1 with genome-wide significance (p = 3.93E-8) and rs34599046 in TUSC3 at sub-threshold genome-wide significance (p = 1.34E-7), both supported by credible peaks of neighboring SNPs. Like other previously reported BA-associated genes, AFAP1 and TUSC3 are ciliogenesis and planar polarity effectors (CPLANE). In gene-set-based GWAS, BA was associated with 6,005 SNPs in 102 CPLANE genes (p = 5.84E-15). Compared with non-CPLANE genes, more CPLANE genes harbored rare variants (allele frequency <1%) that were assigned Human Phenotype Ontology terms related to hepatobiliary anomalies by predictive algorithms, 87% vs. 40%, p <0.0001. Rare variants were present in multiple genes distinct from those with BA-associated common variants in most BA cases. AFAP1 and TUSC3 knockdown blocked ciliogenesis in mouse tracheal cells. Inhibition of ciliogenesis caused biliary dysgenesis in zebrafish. AFAP1 and TUSC3 were expressed in fetal liver organoids, as well as fetal and BA livers, but not in normal or disease-control livers. Integrative analysis of BA-associated variants and liver transcripts revealed abnormal vasculogenesis and epithelial tube formation, explaining portal vein anomalies that co-exist with BA. CONCLUSIONS BA is associated with polygenic susceptibility in CPLANE genes. Rare variants contribute to polygenic risk in vulnerable pathways via unique genes. IMPACT AND IMPLICATIONS Liver transplantation is needed to cure most children born with biliary atresia, a poorly understood rare disease. Transplant immunosuppression increases the likelihood of life-threatening infections and cancers. To improve care by preventing this disease and its progression to transplantation, we examined its genetic basis. We find that this disease is associated with both common and rare mutations in highly specialized genes which maintain normal communication and movement of cells, and their organization into bile ducts and blood vessels during early development of the human embryo. Because defects in these genes also cause other birth defects, our findings could lead to preventive strategies to lower the incidence of biliary atresia and potentially other birth defects.
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Affiliation(s)
- Joseph T Glessner
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mylarappa B Ningappa
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kim A Ngo
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, USA
| | - Maliha Zahid
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Juhoon So
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brandon W Higgs
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Tejaswini Narayanan
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, USA
| | - Sarangarajan Ranganathan
- Division of Pathology and Laboratory Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael March
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Krishna Prasadan
- Rangos Research Center Animal Imaging Core, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Courtney Vaccaro
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Miguel Reyes-Mugica
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Jeremy Velazquez
- Department of Pathology, School of Medicine, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Claudia M Salgado
- Division of Pediatric Pathology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Mo R Ebrahimkhani
- Department of Pathology, School of Medicine, Pittsburgh Liver Research Center, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lori Schmitt
- Histology Core Laboratory Manager, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dhivyaa Rajasundaram
- Department of Pediatrics, Division of Health Informatics, Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Morgan Paul
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Renata Pellegrino
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - George K Gittes
- Surgeon-in-Chief Emeritus, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Dong Li
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiang Wang
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan Billings
- Center for Applied Genomics (CAG), Children's Hospital of Philadelphia, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Robert Squires
- Pediatric Gastroenterology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Chethan Ashokkumar
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Khalid Sharif
- Paediatric Liver Unit Including Intestinal Transplantation, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Deirdre Kelly
- Paediatric Liver Unit Including Intestinal Transplantation, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Anil Dhawan
- Paediatric Liver GI and Nutrition Center and MowatLabs, NHS Foundation Trust, King's College Hospital, London, UK
| | - Simon Horslen
- Pediatric Gastroenterology, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA, USA
| | - Cecilia W Lo
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Donghun Shin
- Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, and Nanoengineering, University of California, San Diego, San Diego, La Jolla, CA, USA.
| | - Hakon Hakonarson
- Divisions of Human Genetics and Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
| | - Rakesh Sindhi
- Hillman Center for Pediatric Transplantation, UPMC-Children's Hospital of Pittsburgh, and Thomas E Starzl Transplant Institute, University of Pittsburgh, Pittsburgh, PA, USA.
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He L, Chung PHY, Lui VCH, Tang CSM, Tam PKH. Current Understanding in the Clinical Characteristics and Molecular Mechanisms in Different Subtypes of Biliary Atresia. Int J Mol Sci 2022; 23:ijms23094841. [PMID: 35563229 PMCID: PMC9103665 DOI: 10.3390/ijms23094841] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/23/2022] [Accepted: 04/24/2022] [Indexed: 02/01/2023] Open
Abstract
Biliary atresia is a severe obliterative cholangiopathy in early infancy that is by far the most common cause of surgical jaundice and the most common indicator for liver transplantation in children. With the advanced knowledge gained from different clinical trials and the development of research models, a more precise clinical classification of BA (i.e., isolated BA (IBA), cystic BA (CBA), syndromic BA (SBA), and cytomegalovirus-associated BA (CMVBA)) is proposed. Different BA subtypes have similar yet distinguishable clinical manifestations. The clinical and etiological heterogeneity leads to dramatically different prognoses; hence, treatment needs to be specific. In this study, we reviewed the clinical characteristics of different BA subtypes and revealed the molecular mechanisms of their developmental contributors. We aimed to highlight the differences among these various subtypes of BA which ultimately contribute to the development of a specific management protocol for each subtype.
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Affiliation(s)
- Lin He
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau SAR, China;
| | - Patrick Ho Yu Chung
- Division of Paediatric Surgery, Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; (V.C.H.L.); (C.S.M.T.); (P.K.H.T.)
- Correspondence: ; Tel.: +852-22554850; Fax: +852-28173155
| | - Vincent Chi Hang Lui
- Division of Paediatric Surgery, Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; (V.C.H.L.); (C.S.M.T.); (P.K.H.T.)
| | - Clara Sze Man Tang
- Division of Paediatric Surgery, Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; (V.C.H.L.); (C.S.M.T.); (P.K.H.T.)
| | - Paul Kwong Hang Tam
- Division of Paediatric Surgery, Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China; (V.C.H.L.); (C.S.M.T.); (P.K.H.T.)
- Faculty of Medicine, Macau University of Science and Technology, Macau SAR, China
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Whole exome sequencing analysis for mutations in isolated type III biliary atresia patients. Clin Exp Hepatol 2020; 6:347-353. [PMID: 33511283 PMCID: PMC7816631 DOI: 10.5114/ceh.2020.102156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
Aim of the study Biliary atresia is an idiopathic, destructive disease that affects both extrahepatic and intrahepatic bile ducts with severe inflammation and manifests as progressive jaundice within the first few months of life. In this study, we aimed to investigate the significance of genetic mutations in the onset of biliary atresia disease. Material and methods With the approval of the ethics committee and parental consent, blood was taken from patients to obtain their DNA, and the study commenced. In this prospective study, we examined the DNA of 10 patients with no disease other than biliary atresia, and an exome sequence analysis was performed with the new-generation DNA sequencing method. The genetic structure of biliary atresia disease was examined by statistical analysis of the mutations, which were determined according to the reference DNA sequencing. Results In the exome sequence analysis, the number of mutations detected among the patients changed significantly; the lowest number was 12,591, and the maximum was 19,863. By examining these mutations, we identified the mutated genes that were common to all patients. Conclusions In this study, the highest mutation rates were detected in the PRIM2 and MAP2K3 genes. These genes have not previously been associated with biliary atresia.
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Asgharzadeh M, Fadaee M, Mahdavipoor B, Sheykhsaran E, Rashedi J, Pourostadi M, Asgharzadeh V, Vegari A, Kafil HS. Polymorphism of the IFN-ɣ gene in the Azeri population of Iran. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Abstract
PURPOSE OF REVIEW Biliary atresia is a poorly understood deadly disease. Genetic predisposition factors are suspected albeit not firmly established. This review summarizes recent evidence of genetic alterations in biliary atresia. RECENT FINDINGS Whole-genome association studies in biliary atresia patients identified four distinct predisposition loci with four different genes potentially involved in the disease occurrence. Variations in these genes were searched for, but none were found in patients with biliary atresia suggesting complex mechanisms. SUMMARY Despite decades since its description and decades of intensive researches, cause of biliary atresia disease remains enigmatic. The inheritance of biliary atresia is not Mendelian. Genetic predisposition factor is one of the explored fields to explain biliary atresia pathogenicity. Biliary atresia has been associated with several inborn syndromes, chromosome anomalies, and gene polymorphisms in specific populations. Four predisposition loci encompassing genes relevant to the disease have been identified, but no pathogenic variations were found in biliary atresia patients. Few reported cases of isolated biliary atresia manifestation in the context of known genetic diseases suggest coincidental findings. Alternatives to classic genetic alterations are proposed to explain genetic predisposition in biliary atresia including noncoding and epigenetic factors. Biliary atresia is most likely related to complex traits making its genetic exploration challenging.
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Chen Y, Gilbert MA, Grochowski CM, McEldrew D, Llewellyn J, Waisbourd-Zinman O, Hakonarson H, Bailey-Wilson JE, Russo P, Wells RG, Loomes KM, Spinner NB, Devoto M. A genome-wide association study identifies a susceptibility locus for biliary atresia on 2p16.1 within the gene EFEMP1. PLoS Genet 2018; 14:e1007532. [PMID: 30102696 PMCID: PMC6107291 DOI: 10.1371/journal.pgen.1007532] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 08/23/2018] [Accepted: 07/04/2018] [Indexed: 02/06/2023] Open
Abstract
Biliary atresia (BA) is a rare pediatric cholangiopathy characterized by fibrosclerosing obliteration of the extrahepatic bile ducts, leading to cholestasis, fibrosis, cirrhosis, and eventual liver failure. The etiology of BA remains unknown, although environmental, inflammatory, infectious, and genetic risk factors have been proposed. We performed a genome-wide association study (GWAS) in a European-American cohort of 343 isolated BA patients and 1716 controls to identify genetic loci associated with BA. A second GWAS was performed in an independent European-American cohort of 156 patients with BA and other extrahepatic anomalies and 212 controls to confirm the identified candidate BA-associated SNPs. Meta-analysis revealed three genome-wide significant BA-associated SNPs on 2p16.1 (rs10865291, rs6761893, and rs727878; P < 5 ×10-8), located within the fifth intron of the EFEMP1 gene, which encodes a secreted extracellular protein implicated in extracellular matrix remodeling, cell proliferation, and organogenesis. RNA expression analysis showed an increase in EFEMP1 transcripts from human liver specimens isolated from patients with either BA or other cholestatic diseases when compared to normal control liver samples. Immunohistochemistry demonstrated that EFEMP1 is expressed in cholangiocytes and vascular smooth muscle cells in liver specimens from patients with BA and other cholestatic diseases, but it is absent from cholangiocytes in normal control liver samples. Efemp1 transcripts had higher expression in cholangiocytes and portal fibroblasts as compared with other cell types in normal rat liver. The identification of a novel BA-associated locus, and implication of EFEMP1 as a new BA candidate susceptibility gene, could provide new insights to understanding the mechanisms underlying this severe pediatric disorder.
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Affiliation(s)
- Ying Chen
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, Department of Pediatrics, at The Children's Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Melissa A. Gilbert
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Christopher M. Grochowski
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Deborah McEldrew
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jessica Llewellyn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Orith Waisbourd-Zinman
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics at The Children's Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Schneider Children's Medical Center of Israel, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Hakon Hakonarson
- Division of Human Genetics, Department of Pediatrics, at The Children's Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joan E. Bailey-Wilson
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Baltimore, Maryland, United States of America
| | - Pierre Russo
- Division of Anatomic Pathology, Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Rebecca G. Wells
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kathleen M. Loomes
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics at The Children's Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Nancy B. Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marcella Devoto
- Division of Human Genetics, Department of Pediatrics, at The Children's Hospital of Philadelphia, and The Perelman School of Medicine at The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Molecular Medicine, Sapienza University, Rome, Italy
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7
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Abstract
To date, the etiology and pathogenic underpinning of the progression of the most prevalent serious neonatal liver disease, biliary atresia, remains elusive. This disease presents as an aggressive form of neonatal cholestasis characterized by the destruction and obliteration of the extrahepatic bile ducts within the first few weeks of life and a rapid progression of biliary fibrosis, likely due to unremitting cholestasis and retention of biliary constituents including bile acids. In ∼5% of patients, biliary atresia is associated with laterality features, suggesting a genetic underpinning to a disease that begins soon after birth. However, biliary atresia does not occur within families and twins are discordant, indicating an absence of strict mendelian inheritance. Despite this, genes related to bile duct dysmorphogenesis/ciliopathies overlapping with features of biliary atresia in both humans and nonhuman model systems have been proposed. Taken together, strict genetic etiologies leading to a common pathway of a neonatal cholangiopathy resulting in biliary atresia remain elusive. Contributions from fibrogenesis- and inflammation-based studies suggest that early engagement of these pathways contributes to disease progression, but a recent double-blind study did not suggest any benefit from early use of corticosteroids. However, there are genetic contributions to the adaptation and response to cholangiopathies and cholestasis that may be present in certain populations that likely impact upon the response to hepatoportoenterostomy and subsequent biliary tract function. Studies utilizing next generation sequencing technologies (e.g., exome analysis) are ongoing in several laboratories around the world; they are expected to provide insights into genetic contributions to biliary atresia outcomes. Altogether, combinations of exome sequencing and large population studies are expected to reveal causative and modifying genes relevant to patients with biliary atresia as a means to provide therapeutic targets and potential opportunities for genetic screening.
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Affiliation(s)
- Anya Mezina
- Emory University School of Medicine, Atlanta, Ga., USA
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Wang D, Zhong X, Huang D, Chen R, Bai G, Li Q, Yu B, Fan Y, Sun X. Functional polymorphisms of interferon-gamma affect pneumonia-induced sepsis. PLoS One 2014; 9:e87049. [PMID: 24475220 PMCID: PMC3901723 DOI: 10.1371/journal.pone.0087049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/17/2013] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE Sepsis is an inflammatory syndrome caused by infection, and both its incidence and mortality are high. Because interferon-gamma (IFN-γ) plays an important role in inflammation, this work assessed IFN-γ single nucleotide polymorphism (SNPs) that may be associated with sepsis. METHODS A total of 196 patients with pneumonia-induced sepsis and 213 age- and sex-matched healthy volunteers participated in our study from July 2012 to July 2013 in Guangzhou, China. Patient clinical information was collected. Clinical pathology was assessed in subgroups defined based on clinical criteria, APACHE II (acute physiology and chronic health evaluation) and SOFA (sepsis-related organ failure assessment) scores and discharge rate. Four functional SNPs, -1616T/C (rs2069705), -764G/C (rs2069707), +874A/T (rs2430561) and +3234C/T (rs2069718), were genotyped by Snapshot in both sepsis patients and healthy controls. Pearson's chi-square test or Fisher's exact test were used to analyze the distribution of the SNPs, and the probability values (P values), odds ratios (OR) and 95% confidence intervals (CIs) were calculated. RESULTS No mutations in the IFN-γ -764G/C SNP were detected among the participants in our study. The +874A/T and +3234C/T SNPs were in strong linkage disequilibrium (LD) (r(2) = 0.894). The -1616 TC+TT, +874 AT+AA genotype and the TAC haplotype were significantly associated with sepsis susceptibility, while the CTT haplotype was associated with protection against sepsis incidence. Genotype of -1616 TT wasn't only protective against severity of sepsis, but also against higher APACHE II and SOFA scores as +874 AA and +3234 CC. The TAC haplotype was was protective against progression to severe sepsis either. CONCLUSION Our results suggest that functional IFN-γ SNPs and their haplotypes are associated with pneumonia-induced sepsis.
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Affiliation(s)
- Ding Wang
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xuan Zhong
- The department of intensive care unit, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Dongjian Huang
- The department of intensive care unit, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Rui Chen
- Reproductive Department, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Guibin Bai
- The department of intensive care unit, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Qing Li
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Bolan Yu
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yong Fan
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiaofang Sun
- Key Laboratory for Major Obstetric Diseases of Guangdong Province, Key Laboratory of Reproduction and Genetics of Guangdong Higher Education Institutes, Experimental Department of Institute of Gynecology and Obstetrics, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Cui S, Leyva-Vega M, Tsai EA, Eauclaire SF, Glessner JT, Hakonarson H, Devoto M, Haber BA, Spinner NB, Matthews RP. Evidence from human and zebrafish that GPC1 is a biliary atresia susceptibility gene. Gastroenterology 2013; 144:1107-1115.e3. [PMID: 23336978 PMCID: PMC3736559 DOI: 10.1053/j.gastro.2013.01.022] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Revised: 01/03/2013] [Accepted: 01/07/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Biliary atresia (BA) is a progressive fibroinflammatory disorder of infants involving the extrahepatic and intrahepatic biliary tree. Its etiology is unclear but is believed to involve exposure of a genetically susceptible individual to certain environmental factors. BA occurs exclusively in the neonatal liver, so variants of genes expressed during hepatobiliary development could affect susceptibility. Genome-wide association studies previously identified a potential region of interest at 2q37. We continued these studies to narrow the region and identify BA susceptibility genes. METHODS We searched for copy number variants that were increased among patients with BA (n = 61) compared with healthy individuals (controls; n = 5088). After identifying a candidate gene, we investigated expression patterns of orthologues in zebrafish liver and the effects of reducing expression, with morpholino antisense oligonucleotides, on biliary development, gene expression, and signal transduction. RESULTS We observed a statistically significant increase in deletions at 2q37.3 in patients with BA that resulted in deletion of one copy of GPC1, which encodes glypican 1, a heparan sulfate proteoglycan that regulates Hedgehog signaling and inflammation. Knockdown of gpc1 in zebrafish led to developmental biliary defects. Exposure of the gpc1 morphants to cyclopamine, a Hedgehog antagonist, partially rescued the gpc1-knockdown phenotype. Injection of zebrafish with recombinant Sonic Hedgehog led to biliary defects similar to those of the gpc1 morphants. Liver samples from patients with BA had reduced levels of apical GPC1 in cholangiocytes compared with samples from controls. CONCLUSIONS Based on genetic analysis of patients with BA and zebrafish, GPC1 appears to be a BA susceptibility gene. These findings also support a role for Hedgehog signaling in the pathogenesis of BA.
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Affiliation(s)
- Shuang Cui
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Melissa Leyva-Vega
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Ellen A. Tsai
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,Genomics and Computational Biology Graduate Group, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Steven F. Eauclaire
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joseph T. Glessner
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,Department of Genetics, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Marcella Devoto
- Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,Department of Biostatistics and Epidemiology, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,Department of Molecular Medicine, University of Rome La Sapienza, Rome, Italy
| | - Barbara A. Haber
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nancy B. Spinner
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Randolph P. Matthews
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,Department of Pediatrics, The Children’s Hospital of Philadelphia Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
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10
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Okamura A, Harada K, Nio M, Nakanuma Y. Participation of natural killer cells in the pathogenesis of bile duct lesions in biliary atresia. J Clin Pathol 2012; 66:99-108. [DOI: 10.1136/jclinpath-2012-201097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
AimsImmunological disturbances including innate immunity after a suspected viral infection are considered important to the pathogenesis of bile duct lesions in cases of biliary atresia (BA). In this study, we tried to evaluate whether natural killer (NK) cells and CX3CL1 (Fractalkine) and its receptor (CX3CR1) are involved in the bile duct injury.MethodsUsing the section of BA (22 cases) and controls, immunohistochemistry for CD56, CD16, CD68, CX3CL1 and CX3CR1 was performed. Moreover, using cultured biliary epithelial cells (BECs) and NK cells, the production of CX3CL1 in BECs and the migration of NK cells were evaluated.ResultsIt was found that CD56(−)CD16(+)CD68(−) NK cells were increased around the damaged small and large bile ducts in BA and hepatitis C virus-related chronic hepatitis in comparison with other controls. CX3CL1 was strongly expressed on the damaged bile ducts in BA, while this expression was relatively weak or absent in the bile ducts of normal liver. The results suggest the CD56(−)CD16(+) NK cells to be involved in the development of bile duct injuries in BA. These CD16(+) NK cells were positive for CX3CR1, and attracted by CX3CL1 expressed on bile ducts. Further study revealed that stimulation with poly(I:C) (a synthetic analogue of viral dsRNA) increased the expression of CX3CL1 on cultured BECs followed by increased migrational activity of cultured NK cells.ConclusionsCD56(−)CD16(+) NK cells with reduced NK activity may be involved in the bile duct damage in BA, and CD16(+) NK cells expressing CX3CR1 may be attracted by and interact with bile ducts expressing CX3CL1.
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11
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Popadic D, Savic E, Spuran Z, Markovic M, Mostarica Stojkovic M, Ramic Z, Pravica V. Distinctive frequencies of +874T/A IFN-γ gene polymorphism in a healthy Serbian population. Clin Transl Sci 2012; 5:461-3. [PMID: 23253667 DOI: 10.1111/cts.12000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
PURPOSE Single nucleotide polymorphism (SNP) in IFN-γ gene (+874T/A) that determines high (TT), low (AA), and intermediate (TA) responder phenotypes has shown associations with susceptibility to infectious and chronic inflammatory diseases, as well as disease outcome. Therefore, the susceptibility to and outcome of certain diseases can vary in different ethnic populations partially due to the notable differences in frequencies of genotypes and alleles between them. The aim of this study was to determine the distribution of +874T/A genotype and allele frequencies in a healthy Serbian population as a reference for further disease association studies. MATERIALS AND METHODS Genomic DNA samples from 166 healthy volunteers were evaluated for IFN-γ SNP at position +874 using TaqMan SNP genotyping assay. RESULTS The frequencies of AA, AT, and TT genotypes were 28.9%, 49.4%, and 21.7%, respectively. The A and T allele frequencies were 53.6% and 46.4%. CONCLUSIONS Analysis of genotype and allele frequencies for IFN-γ+874T/A SNP in healthy subjects revealed, for the first time, the genetic profile for this polymorphism in a Serbian population resembling most European populations, but differing from some Asian and African ethnic groups.
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Affiliation(s)
- Dusan Popadic
- Institute for Microbiology and Immunology, School of Medicine, University of Belgrade, Serbia
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12
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Su Y, Tang LY, Chen LJ, He JR, Su FX, Lin Y, Chen WQ, Xie XM, Ren ZF. Joint effects of febrile acute infection and an interferon-γ polymorphism on breast cancer risk. PLoS One 2012; 7:e37275. [PMID: 22624006 PMCID: PMC3356273 DOI: 10.1371/journal.pone.0037275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/17/2012] [Indexed: 11/18/2022] Open
Abstract
Background There is an inverse relationship between febrile infection and the risk of malignancies. Interferon gamma (IFN-γ) plays an important role in fever induction and its expression increases with incubation at fever-range temperatures. Therefore, the genetic polymorphism of IFN-γ may modify the association of febrile infection with breast cancer risk. Methodology and Principal Findings Information on potential breast cancer risk factors, history of fever during the last 10 years, and blood specimens were collected from 839 incident breast cancer cases and 863 age-matched controls between October 2008 and June 2010 in Guangzhou, China. IFN-γ (rs2069705) was genotyped using a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry platform. Odds ratios (OR) and 95% confidence intervals (CIs) were calculated using multivariate logistic regression. We found that women who had experienced ≥1 fever per year had a decreased risk of breast cancer [ORs and 95% CI: 0.77 (0.61–0.99)] compared to those with less than one fever a year. This association only occurred in women with CT/TT genotypes [0.54 (0.37–0.77)] but not in those with the CC genotype [1.09 (0.77–1.55)]. The association of IFN-γ rs2069705 with the risk of breast cancer was not significant among all participants, while the CT/TT genotypes were significantly related to an elevated risk of breast cancer [1.32 (1.03–1.70)] among the women with <1 fever per year and to a reduced risk of breast cancer [0.63 (0.40–0.99)] among women with ≥1 fever per year compared to the CC genotype. A marked interaction between fever frequencies and the IFN-γ genotypes was observed (P for multiplicative and additive interactions were 0.005 and 0.058, respectively). Conclusions Our findings indicate a possible link between febrile acute infection and a decreased risk of breast cancer, and this association was modified by IFN-γ rs2069705.
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Affiliation(s)
- Yi Su
- The School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Lu-Ying Tang
- The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Li-Juan Chen
- The School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Jian-Rong He
- The School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Feng-Xi Su
- The Second Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ying Lin
- The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Wei-Qing Chen
- The School of Public Health, Sun Yat-Sen University, Guangzhou, China
| | - Xiao-Ming Xie
- Department of Breast Oncology, Sun Yat-Sen University, Guangzhou, China
- * E-mail: (XX); (ZR)
| | - Ze-Fang Ren
- The School of Public Health, Sun Yat-Sen University, Guangzhou, China
- * E-mail: (XX); (ZR)
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Lee HC, Chang TY, Yeung CY, Chan WT, Jiang CB, Chen WF, Chan HW, Yang HW, Lin M, Lee YJ. Genetic variability of interleukin 4 gene in Taiwanese children with biliary atresia. Cytokine 2012; 57:402-5. [PMID: 22227092 DOI: 10.1016/j.cyto.2011.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 12/05/2011] [Accepted: 12/14/2011] [Indexed: 01/28/2023]
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He JR, Chen LJ, Su Y, Cen YL, Tang LY, Yu DD, Chen WQ, Wang SM, Song EW, Ren ZF. Joint effects of Epstein-Barr virus and polymorphisms in interleukin-10 and interferon-γ on breast cancer risk. J Infect Dis 2011; 205:64-71. [PMID: 22095765 DOI: 10.1093/infdis/jir710] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The relationship between Epstein-Barr virus (EBV) and breast cancer (BC) is controversial. Interleukin-10 (IL-10) and interferon-γ (IFN-γ) are believed to play a critical role in the host's responses to EBV infection, and their genetic variations may modify the association of EBV with BC risk. METHODS We examined serum levels of EBV viral capsid antigen (VCA) immunoglobulin A (IgA) and nuclear antigen-1 (EBNA-1) IgA along with the polymorphisms of IL-10 rs1800871 and IFN-γ rs2069705 in 354 incident BC cases and 504 age-matched controls. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using multivariate logistic regression. RESULTS VCA IgA and EBNA-1 IgA levels were positively associated with BC risk. IL-10 rs1800871 (TC/CC) was associated with a reduced BC risk (OR, 0.74 [95% CI, 0.55-1.00]) but had no interaction with EBV infection on BC risk. IFN-γ rs2069705 was not directly associated with BC risk but interacted with EBNA-1 IgA on BC risk. Among women with the CC genotype, EBNA-1 IgA seropositivity significantly increased the risk of BC compared to EBNA-1 IgA seronegativity (OR, 5.14 [95% CI, 1.76-14.98]). CONCLUSIONS These results suggest that EBV may contribute to the risk of BC and that this contribution may be modified by genetic variations in IFN-γ.
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Affiliation(s)
- Jian-Rong He
- The School of Public Health, Sun Yat-sen University, Guangzhou, China.
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