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Lam WY, Tang CSM, So MT, Yue H, Hsu JS, Chung PHY, Nicholls JM, Yeung F, Lee CWD, Ngo DN, Nguyen PAH, Mitchison HM, Jenkins D, O'Callaghan C, Garcia-Barceló MM, Lee SL, Sham PC, Lui VCH, Tam PKH. Identification of a wide spectrum of ciliary gene mutations in nonsyndromic biliary atresia patients implicates ciliary dysfunction as a novel disease mechanism. EBioMedicine 2021; 71:103530. [PMID: 34455394 PMCID: PMC8403738 DOI: 10.1016/j.ebiom.2021.103530] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 07/09/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022] Open
Abstract
Background Biliary atresia (BA) is the most common obstructive cholangiopathy in neonates, often progressing to end-stage cirrhosis. BA pathogenesis is believed to be multifactorial, but the genetic contribution, especially for nonsyndromic BA (common form: > 85%) remains poorly defined. Methods We conducted whole exome sequencing on 89 nonsyndromic BA trios to identify rare variants contributing to BA etiology. Functional evaluation using patients’ liver biopsies, human cell and zebrafish models were performed. Clinical impact on respiratory system was assessed with clinical evaluation, nasal nitric oxide (nNO), high speed video analysis and transmission electron microscopy. Findings We detected rare, deleterious de novo or biallelic variants in liver-expressed ciliary genes in 31.5% (28/89) of the BA patients. Burden test revealed 2.6-fold (odds ratio (OR) [95% confidence intervals (CI)]= 2.58 [1.15–6.07], adjusted p = 0.034) over-representation of rare, deleterious mutations in liver-expressed ciliary gene set in patients compared to controls. Functional analyses further demonstrated absence of cilia in the BA livers with KIF3B and TTC17 mutations, and knockdown of PCNT, KIF3B and TTC17 in human control fibroblasts and cholangiocytes resulted in reduced number of cilia. Additionally, CRISPR/Cas9-engineered zebrafish knockouts of KIF3B, PCNT and TTC17 displayed reduced biliary flow. Abnormally low level of nNO was detected in 80% (8/10) of BA patients carrying deleterious ciliary mutations, implicating the intrinsic ciliary defects. Interpretation Our findings support strong genetic susceptibility for nonsyndromic BA. Ciliary gene mutations leading to cholangiocyte cilia malformation and dysfunction could be a key biological mechanism in BA pathogenesis. Funding The study is supported by General Research Fund, HMRF Commissioned Paediatric Research at HKCH and Li Ka Shing Faculty of Medicine Enhanced New Staff Start-up Fund.
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Affiliation(s)
- Wai-Yee Lam
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China; Dr Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China
| | - Clara Sze-Man Tang
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China; Dr Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China
| | - Man-Ting So
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China
| | - Haibing Yue
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China
| | - Jacob Shujui Hsu
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Patrick Ho-Yu Chung
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China
| | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fanny Yeung
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China
| | - Chun-Wai Davy Lee
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | | | - Hannah M Mitchison
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Dagan Jenkins
- Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Christopher O'Callaghan
- Respiratory, Critical Care & Anaesthesia Section, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Maria-Mercè Garcia-Barceló
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China
| | - So-Lun Lee
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong SAR, China
| | - Pak-Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Vincent Chi-Hang Lui
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China; Dr Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China.
| | - Paul Kwong-Hang Tam
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, LKS Faculty of Medicine Building, 21 Sassoon Road, Hong Kong SAR, China; Dr Li Dak-Sum Research Centre, The University of Hong Kong, Hong Kong SAR, China.
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2
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van de Putte R, Wijers CHW, Reutter H, Vermeulen SH, Marcelis CLM, Brosens E, Broens PMA, Homberg M, Ludwig M, Jenetzky E, Zwink N, Sloots CEJ, de Klein A, Brooks AS, Hofstra RMW, Holsink SAC, van der Zanden LFM, Galesloot TE, Tam PKH, Steehouwer M, Acuna-Hidalgo R, van de Vorst M, Kiemeney LA, Garcia-Barceló MM, de Blaauw I, Brunner HG, Roeleveld N, van Rooij IALM. Exome chip association study excluded the involvement of rare coding variants with large effect sizes in the etiology of anorectal malformations. PLoS One 2019; 14:e0217477. [PMID: 31136621 PMCID: PMC6538182 DOI: 10.1371/journal.pone.0217477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 05/13/2019] [Indexed: 01/09/2023] Open
Abstract
INTRODUCTION Anorectal malformations (ARM) are rare congenital malformations, resulting from disturbed hindgut development. A genetic etiology has been suggested, but evidence for the involvement of specific genes is scarce. We evaluated the contribution of rare and low-frequency coding variants in ARM etiology, assuming a multifactorial model. METHODS We analyzed 568 Caucasian ARM patients and 1,860 population-based controls using the Illumina HumanExome Beadchip array, which contains >240,000 rare and low-frequency coding variants. GenomeStudio clustering and calling was followed by re-calling of 'no-calls' using zCall for patients and controls simultaneously. Single variant and gene-based analyses were performed to identify statistically significant associations, applying Bonferroni correction. Following an extra quality control step, candidate variants were selected for validation using Sanger sequencing. RESULTS When we applied a MAF of ≥1.0%, no variants or genes showed statistically significant associations with ARM. Using a MAF cut-off at 0.4%, 13 variants initially reached statistical significance, but had to be discarded upon further inspection: ten variants represented calling errors of the software, while the minor alleles of the remaining three variants were not confirmed by Sanger sequencing. CONCLUSION Our results show that rare and low-frequency coding variants with large effect sizes, present on the exome chip do not contribute to ARM etiology.
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Affiliation(s)
- Romy van de Putte
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail:
| | - Charlotte H. W. Wijers
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Heiko Reutter
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Neonatology, Children’s Hospital, University of Bonn, Bonn, Germany
| | - Sita H. Vermeulen
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Carlo L. M. Marcelis
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
- Department of Pediatric Surgery, Sophia’s Children’s Hospital—Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Paul M. A. Broens
- Department of Surgery, Division of Pediatric Surgery, University Medical Center Groningen, Groningen, The Netherlands
| | - Markus Homberg
- Department of Child and Adolescent Psychiatry and Psychotherapy, Johannes-Gutenberg University, Mainz, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Ekkehart Jenetzky
- Department of Child and Adolescent Psychiatry and Psychotherapy, Johannes-Gutenberg University, Mainz, Germany
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center, Heidelberg, Germany
| | - Nadine Zwink
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Cornelius E. J. Sloots
- Department of Pediatric Surgery, Sophia’s Children’s Hospital—Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Alice S. Brooks
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Robert M. W. Hofstra
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Sophie A. C. Holsink
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Loes F. M. van der Zanden
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tessel E. Galesloot
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine of the University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development and Growth, Li Ka Shing Faculty of Medicine of the University of Hong Kong, Hong Kong, China
- Department of Psychiatry, Li Ka Shing Faculty of Medicine of the University of Hong Kong, Hong Kong, China
| | - Marloes Steehouwer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maartje van de Vorst
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lambertus A. Kiemeney
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Urology, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Maria-Mercè Garcia-Barceló
- Experimental Cardiology Laboratory, Division Heart and Lungs, University Medical Center Utrecht, Utrecht, the Netherlands
- Image Sciences Institute, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ivo de Blaauw
- Department of Surgery—Pediatric Surgery, Radboudumc Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Nel Roeleveld
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris A. L. M. van Rooij
- Department for Health Evidence, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Surgery—Pediatric Surgery, Radboudumc Amalia Children’s Hospital, Radboud University Medical Center, Nijmegen, The Netherlands
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3
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Qian C, Wu Z, Ng RCL, Garcia-Barceló MM, Yuan ZW, Wong KKY, Tam PKH, Lui VCH. Conditional deletion of platelet derived growth factor receptor alpha (Pdgfra) in urorectal mesenchyme causes mesenchyme apoptosis and urorectal developmental anomalies in mice. Cell Death Differ 2018; 26:1396-1410. [PMID: 30323271 DOI: 10.1038/s41418-018-0216-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 08/01/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022] Open
Abstract
In mammals, urorectal development starts at early embryonic stage, defective urorectal development results in anorectal malformations, which are common congenital developmental defects of the anus and the urethra in newborns. The etiology and embryology of the defects are still largely unknown. Platelet-derived growth factor receptor alpha (Pdgfra) is a cell surface receptor tyrosine kinase, upon binding to its ligands (Pdgfa-d), mediates intracellular signaling and regulates embryonic development. The expression of Pdgfra is tightly regulated in the developing urorectal mesenchyme, and its dysregulation is associated with urorectal defects in animals with urorectal defects. Knockout of Pdgfra induces early embryo lethality which precludes investigation of Pdgfra in urorectal development. To address the temporal requirement of Pdgfra in urorectal development, we conditionally deleted Pdgfra in Pdgfra-expressing tissues using a tamoxifen inducible Cre-loxP approach in mice, examined the urorectal development in Pdgfra conditional knockout (Pdgfra-cKO) embryos. We showed that conditional deletion of Pdgfra in Pdgfra-expressing tissues at E10-E11 caused cloaca septation defect, anteriorly displaced anus, defective urogenital folds development and abnormal urethra tubularization in both male and female mice. Furthermore, we showed that Pdgfra was required for the survival of urorectal mesenchyme, deletion of Pdgfra caused apoptosis in the peri-cloacal, the peri-urethra and the urorectal septum mesenchyme of Pdgfra-cKO mutants, associated with an induction of p53, Ndrg1 and activation of caspase-3 in Pdgfra-cKO embryos. In conclusion, Pdgfra is required for the development and survival of the urorectal mesenchyme in embryo, dysregulated Pdgfra signaling induced urorectal defects in mice resembling human congenital diseases of anorectal malformations and hypospadias. Perturbation of PDGFRA signaling may contribute to anorectal malformations and hypospadias in human.
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Affiliation(s)
- Chen Qian
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Department of Obstetrics and Gynecology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhongluan Wu
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Roy Chun-Laam Ng
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Department of Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Dr Li Dak-Sum Research Centre, The University of Hong Kong-Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, China
| | - Zheng-Wei Yuan
- Key Laboratory of Health Ministry for Congenital Malformation, Shengjing Hospital, China Medical University, Shengyang, China
| | - Kenneth Kak Yuen Wong
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Paul Kwong Hang Tam
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Dr Li Dak-Sum Research Centre, The University of Hong Kong-Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, China
| | - Vincent Chi Hang Lui
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China. .,Dr Li Dak-Sum Research Centre, The University of Hong Kong-Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, China.
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4
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Tang CSM, Gui H, Kapoor A, Kim JH, Luzón-Toro B, Pelet A, Burzynski G, Lantieri F, So MT, Berrios C, Shin HD, Fernández RM, Le TL, Verheij JBGM, Matera I, Cherny SS, Nandakumar P, Cheong HS, Antiñolo G, Amiel J, Seo JM, Kim DY, Oh JT, Lyonnet S, Borrego S, Ceccherini I, Hofstra RMW, Chakravarti A, Kim HY, Sham PC, Tam PKH, Garcia-Barceló MM. Trans-ethnic meta-analysis of genome-wide association studies for Hirschsprung disease. Hum Mol Genet 2017; 25:5265-5275. [PMID: 27702942 DOI: 10.1093/hmg/ddw333] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 09/28/2016] [Indexed: 02/04/2023] Open
Abstract
Hirschsprung disease (HSCR) is the most common cause of neonatal intestinal obstruction. It is characterized by the absence of ganglia in the nerve plexuses of the lower gastrointestinal tract. So far, three common disease-susceptibility variants at the RET, SEMA3 and NRG1 loci have been detected through genome-wide association studies (GWAS) in Europeans and Asians to understand its genetic etiologies. Here we present a trans-ethnic meta-analysis of 507 HSCR cases and 1191 controls, combining all published GWAS results on HSCR to fine-map these loci and narrow down the putatively causal variants to 99% credible sets. We also demonstrate that the effects of RET and NRG1 are universal across European and Asian ancestries. In contrast, we detected a European-specific association of a low-frequency variant, rs80227144, in SEMA3 [odds ratio (OR) = 5.2, P = 4.7 × 10-10]. Conditional analyses on the lead SNPs revealed a secondary association signal, corresponding to an Asian-specific, low-frequency missense variant encoding RET p.Asp489Asn (rs9282834, conditional OR = 20.3, conditional P = 4.1 × 10-14). When in trans with the RET intron 1 enhancer risk allele, rs9282834 increases the risk of HSCR from 1.1 to 26.7. Overall, our study provides further insights into the genetic architecture of HSCR and has profound implications for future study designs.
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Affiliation(s)
- Clara Sze-Man Tang
- Department of Surgery.,Centre for Genomic Sciences.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
| | | | - Ashish Kapoor
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeong-Hyun Kim
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Berta Luzón-Toro
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Anna Pelet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Grzegorz Burzynski
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Courtney Berrios
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyoung Doo Shin
- Research Institute for Basic Science, Sogang University, Seoul 121-742, Republic of Korea.,Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Raquel M Fernández
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Thuy-Linh Le
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Joke B G M Verheij
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ivana Matera
- UOC Genetica Medica, Istituto Giannina Gaslini, 16148 Genova, Italy
| | - Stacey S Cherny
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Priyanka Nandakumar
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Seoul 121-742, Republic of Korea
| | - Guillermo Antiñolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Jeanne Amiel
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Jeong-Meen Seo
- Division of Pediatric Surgery, Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
| | - Dae-Yeon Kim
- Department of Pediatric Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Jung-Tak Oh
- Department of Pediatric Surgery, Severance Children's Hospital, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea
| | - Stanislas Lyonnet
- Laboratory of Embryology and Genetics of Congenital Malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) U1163, Institut Imagine, Paris, France.,Paris Descartes-Sorbonne Paris Cité University, Institut Imagine, Paris, France
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | | | - Robert M W Hofstra
- Department of Clinical Genetic, Erasmus Medical Center, Rotterdam, The Netherlands.,Stem Cells and Regenerative Medicine, Birth Defects Research Centre UCL Institute of Child Health, London, UK
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Hyun-Young Kim
- Department of Pediatric Surgery, Seoul National University Children's Hospital, Seoul 110-744, Republic of Korea
| | - Pak Chung Sham
- Centre for Genomic Sciences.,Department of Psychiatry.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Paul K H Tam
- Department of Surgery.,Dr Li Dak-Sum Research Centre, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong SAR, China
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5
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Cheng G, Chung PHY, Chan EKW, So MT, Sham PC, Cherny SS, Tam PKH, Garcia-Barceló MM. Patient complexity and genotype-phenotype correlations in biliary atresia: a cross-sectional analysis. BMC Med Genomics 2017; 10:22. [PMID: 28416017 PMCID: PMC5392958 DOI: 10.1186/s12920-017-0259-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 04/05/2017] [Indexed: 12/11/2022] Open
Abstract
Background Biliary Atresia (BA) is rare and genetically complex, and the pathogenesis is elusive. The disease course is variable and can represent heterogeneity, which hinders effective disease management. Deciphering the BA phenotypic variance is a priority in clinics and can be achieved by the integrative analysis of genotype and phenotype. We aim to explore the BA phenotypic features and to delineate the source of its variance. Methods The study is a cross-sectional observational study collating with case/control association analysis. One-hundred-and-eighty-one type III non-syndromic BA patients and 431 controls were included for case–control association tests, including 89 patients (47.19% males, born June 15th, 1981 to September 17th, 2007) have detailed clinical records with follow-up of the disease course (median ~17.2 years). BA-association genes from the genome-wide gene-based association test on common genetic variants (CV) and rare copy-number-variants (CNVs) from the genome-wide survey, the later comprise only CNVs > 100 kb and found in the BA patients but not in the local population (N = 1,381) or the database (N = 11,943). Hereby comorbidity is defined as a chronic disease that affects the BA patients but has no known relationship with BA or with the BA treatment. We examined genotype-phenotype correlations of CNVs, connectivity of these novel variants with BA-associated CVs, and their role in the BA candidate gene network. Results Of the 89 patients, 41.57% have comorbidities, including autoimmune-allergic disorders (22.47%). They carried 29 BA-private CNVs, including 3 CNVs underpinning the carriers’ immunity comorbidity and one JAG1 micro-deletion. The BA-CNV-intersected genes (N = 102) and the CV-tagged genes (N = 103) were both enriched with immune-inflammatory pathway genes (FDR q < 0.20), and the two gene sets were interconnected (permutation p = 0.039). The molecular network representing CVs and rare-CNV association genes fit into a core/periphery structure, the immune genes and their related modules are found at the coherence core of all connections, suggesting its dominant role in the BA pathogenesis pathway. Conclusions The study highlights a patient-complexity phenomenon as a novel BA phenotypic feature, which is underpinned by rare-CNVs that biologically converge with CVs into the immune-inflammatory pathway and drives the BA occurrence and the likely BA association with immune diseases in clinics. Electronic supplementary material The online version of this article (doi:10.1186/s12920-017-0259-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guo Cheng
- Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong
| | - Patrick Ho-Yu Chung
- Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong
| | - Edwin Kin-Wai Chan
- Department of Surgery, the Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Man-Ting So
- Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong
| | - Pak-Chung Sham
- Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.,Center for Genomic Sciences, Hong Kong, SAR, China.,Centre for Reproduction, Development, Growth of the Li Ka Shing Faculty of Medicine, Hong Kong, SAR, China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Stacey S Cherny
- Department of Psychiatry, The University of Hong Kong, Hong Kong, SAR, China.,Center for Genomic Sciences, Hong Kong, SAR, China.,State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, SAR, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong.,Centre for Reproduction, Development, Growth of the Li Ka Shing Faculty of Medicine, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, 1/F Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam, Hong Kong. .,Center for Genomic Sciences, Hong Kong, SAR, China. .,Centre for Reproduction, Development, Growth of the Li Ka Shing Faculty of Medicine, Hong Kong, SAR, China.
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6
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Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RWW, Burns AJ, Cherny SS, Dopazo J, Eggen BJL, Griseri P, Jalloh B, Le TL, Lui VCH, Luzón-Toro B, Matera I, Ngan ESW, Pelet A, Ruiz-Ferrer M, Sham PC, Shepherd IT, So MT, Sribudiani Y, Tang CSM, van den Hout MCGN, van der Linde HC, van Ham TJ, van IJcken WFJ, Verheij JBGM, Amiel J, Borrego S, Ceccherini I, Chakravarti A, Lyonnet S, Tam PKH, Garcia-Barceló MM, Hofstra RMW. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biol 2017; 18:48. [PMID: 28274275 PMCID: PMC5343413 DOI: 10.1186/s13059-017-1174-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/17/2017] [Indexed: 12/17/2022] Open
Abstract
Background Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored. We identify and validate novel HSCR genes using whole exome sequencing (WES), burden tests, in silico prediction, unbiased in vivo analyses of the mutated genes in zebrafish, and expression analyses in zebrafish, mouse, and human. Results We performed de novo mutation (DNM) screening on 24 HSCR trios. We identify 28 DNMs in 21 different genes. Eight of the DNMs we identified occur in RET, the main HSCR gene, and the remaining 20 DNMs reside in genes not reported in the ENS. Knockdown of all 12 genes with missense or loss-of-function DNMs showed that the orthologs of four genes (DENND3, NCLN, NUP98, and TBATA) are indispensable for ENS development in zebrafish, and these results were confirmed by CRISPR knockout. These genes are also expressed in human and mouse gut and/or ENS progenitors. Importantly, the encoded proteins are linked to neuronal processes shared by the central nervous system and the ENS. Conclusions Our data open new fields of investigation into HSCR pathology and provide novel insights into the development of the ENS. Moreover, the study demonstrates that functional analyses of genes carrying DNMs are warranted to delineate the full genetic architecture of rare complex diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1174-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongsheng Gui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Duco Schriemer
- Department of Neuroscience, section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - William W Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Rajendra K Chauhan
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Guillermo Antiňolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Courtney Berrios
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Marta Bleda
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Erasmus Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alan J Burns
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands.,Stem Cells and Regenerative Medicine, Birth Defects Research Centre, UCL Institute of Child Health, London, UK
| | - Stacey S Cherny
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Joaquin Dopazo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Bart J L Eggen
- Department of Neuroscience, section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Binta Jalloh
- Department of Biology, Emory University, Atlanta, USA
| | - Thuy-Linh Le
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Vincent C H Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Berta Luzón-Toro
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Ivana Matera
- UOC Genetica Medica, Istituto Gaslini, Genoa, Italy
| | - Elly S W Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Anna Pelet
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Macarena Ruiz-Ferrer
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Pak C Sham
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Yunia Sribudiani
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Herma C van der Linde
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | | | - Joke B G M Verheij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jeanne Amiel
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | | | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Stanislas Lyonnet
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Paul K H Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands. .,Stem Cells and Regenerative Medicine, Birth Defects Research Centre, UCL Institute of Child Health, London, UK.
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7
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Zhang J, Zhang L, Zhang Y, Yang J, Guo M, Sun L, Pan HF, Hirankarn N, Ying D, Zeng S, Lee TL, Lau CS, Chan TM, Leung AMH, Mok CC, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Tong KL, Tse NKC, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Ying SKY, Fung SKS, Lai WM, Garcia-Barceló MM, Cherny SS, Sham PC, Cui Y, Yang S, Ye DQ, Zhang XJ, Lau YL, Yang W. Gene-Based Meta-Analysis of Genome-Wide Association Study Data Identifies Independent Single-Nucleotide Polymorphisms inANXA6as Being Associated With Systemic Lupus Erythematosus in Asian Populations. Arthritis Rheumatol 2015. [PMID: 26202167 DOI: 10.1002/art.39275] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jing Zhang
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and Eye and ENT Hospital of Fudan University; Shanghai China
| | - Lu Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yan Zhang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Jing Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Mengbiao Guo
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | - Dingge Ying
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Shuai Zeng
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tsz Leung Lee
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Chak Sing Lau
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Tak Mao Chan
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Chi Chiu Mok
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Sik Nin Wong
- Tuen Mun Hospital, Tuen Mun, New Territories; Hong Kong China
| | - Ka Wing Lee
- Pamela Youde Nethersole Eastern Hospital; Hong Kong China
| | - Marco Hok Kung Ho
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | - Chun Yin Chong
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | - Mo Yin Mok
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stacey S. Cherny
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Pak Chung Sham
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
| | - Yong Cui
- Anhui Medical University; China Hefei China
| | - Sen Yang
- Anhui Medical University; China Hefei China
| | | | | | - Yu Lung Lau
- Queen Mary Hospital and The University of Hong Kong, Hong Kong, China, and The University of Hong Kong-Shenzhen Hospital; Shenzhen China
| | - Wanling Yang
- Queen Mary Hospital and The University of Hong Kong; Hong Kong China
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8
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Zhu JJ, Kam MK, Garcia-Barceló MM, Tam PKH, Lui VCH. HOXB5 binds to multi-species conserved sequence (MCS+9.7) of RET gene and regulates RET expression. Int J Biochem Cell Biol 2014; 51:142-9. [PMID: 24794774 DOI: 10.1016/j.biocel.2014.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 04/02/2014] [Accepted: 04/14/2014] [Indexed: 12/20/2022]
Abstract
RET gene is crucial for the development of enteric nervous system, and dys-regulation of RET expression causes Hirschsprung disease. HOXB5 regulates RET transcription, and perturbations in transcriptional regulation by HOXB5 caused reduced RET expression and defective enteric nervous system development in mice. The mechanisms by which HOXB5 regulate RET transcription are unclear. Thus, unraveling the regulatory mechanisms of HOXB5 on RET transcription could lead to a better understanding of the etiology of Hirschsprung disease. In this study, we identified and confirmed HOXB5 binding to the multi-species conserved sequence (MCS+9.7) in the first intron of the RET gene. We developed a RET mini-gene reporter system, and showed that MCS+9.7 enhanced HOXB5 trans-activation from RET promoter in human neuroblastoma SK-N-SH cells and in chick embryos. The deletion of HOXB5 binding site interfered with HOXB5 trans-activation. Furthermore, transfection of HOXB5 induced endogenous RET transcription, enhanced the co-precipitation of TATA-box binding protein with the transcription start site of RET, and induced histone H3K4 trimethylation in chromatin regions upstream and downstream of RET transcription start site. In conclusion, (i) HOXB5 physically interacted with MCS+9.7 and enhanced RET transcription, (ii) HOXB5 altered chromatin conformation and histone modification of RET locus, which could facilitate the formation of transcription complex, and enhance RET transcription, (iii) expression of RET was mediated by a complex regulatory network of transcription factors functioning in a synergistic, additive and/or independent manners. Hence, dys-regulation of RET expression by HOXB5 could result in insufficient RET expression and Hirschsprung disease.
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Affiliation(s)
- Joe Jiang Zhu
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region; Faculty of Medicine, Shenzhen University, Shenzhen, Guangdong Province, China
| | - Mandy KaMan Kam
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Paul Kwong Hang Tam
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Vincent Chi Hang Lui
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
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9
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Cheng G, Tang CSM, Wong EHM, Cheng WWC, So MT, Miao X, Zhang R, Cui L, Liu X, Ngan ESW, Lui VCH, Chung PHY, Chan IHY, Liu J, Zhong W, Xia H, Yu J, Qiu X, Wu XZ, Wang B, Dong X, Tou J, Huang L, Yi B, Ren H, Chan EKW, Ye K, O'Reilly PF, Wong KKY, Sham PC, Cherny SS, Tam PKH, Garcia-Barceló MM. Common genetic variants regulating ADD3 gene expression alter biliary atresia risk. J Hepatol 2013; 59:1285-91. [PMID: 23872602 DOI: 10.1016/j.jhep.2013.07.021] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 06/17/2013] [Accepted: 07/10/2013] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS Biliary atresia (BA) is a rare and most severe cholestatic disease in neonates, but the pathogenic mechanisms are unknown. Through a previous genome wide association study (GWAS) on Han Chinese, we discovered association of the 10q24.2 region encompassing ADD3 and XPNPEP1 genes, which was replicated in Chinese and Thai populations. This study aims to fully characterize the genetic architecture at 10q24.2 and to reveal the link between the genetic variants and BA. METHODS We genotyped 107 single nucleotide polymorphisms (SNPs) in 10q24.2 in 339 Han Chinese patients and 401 matched controls using Sequenom. Exhaustive follow-up studies of the association signals were performed. RESULTS The combined BA-association p-value of the GWAS SNP (rs17095355) achieved 6.06×10(-10). Further, we revealed the common risk haplotype encompassing 5 tagging-SNPs, capturing the risk-predisposing alleles in 10q24.2 [p=5.32×10(-11); odds ratio, OR: 2.38; confidence interval, CI: (2.14-2.62)]. Through Sanger sequencing, no deleterious rare variants (RVs) residing in the risk haplotype were found, dismissing the theory of "synthetic" association. Moreover, in bioinformatics and in vivo genotype-expression investigations, the BA-associated potentially regulatory SNPs correlated with ADD3 gene expression (n=36; p=0.0030). Remarkably, the risk haplotype frequency coincides with BA incidences in the population, and, positive selection (favoring the derived alleles that arose from mutations) was evident at the ADD3 locus, suggesting a possible role for the BA-associated common variants in shaping the general population diversity. CONCLUSIONS Common genetic variants in 10q24.2 can alter BA risk by regulating ADD3 expression levels in the liver, and may exert an effect on disease epidemiology and on the general population.
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Affiliation(s)
- Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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10
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Zhang J, Zhang Y, Yang J, Zhang L, Sun L, Pan HF, Hirankarn N, Ying D, Zeng S, Lee TL, Lau CS, Chan TM, Leung AMH, Mok CC, Wong SN, Lee KW, Ho MHK, Lee PPW, Chung BHY, Chong CY, Wong RWS, Mok MY, Wong WHS, Tong KL, Tse NKC, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Ying SKY, Fung SKS, Lai WM, Garcia-Barceló MM, Cherny SS, Tam PKH, Cui Y, Sham PC, Yang S, Ye DQ, Zhang XJ, Lau YL, Yang W. Three SNPs in chromosome 11q23.3 are independently associated with systemic lupus erythematosus in Asians. Hum Mol Genet 2013; 23:524-33. [PMID: 24001599 DOI: 10.1093/hmg/ddt424] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Systemic lupus erythematosus (SLE) has a complex etiology and is affected by both genetic and environmental factors. Although more than 40 loci have shown robust association with SLE, the details of these loci, such as the independent contributors and the genes involved, are still unclear. In this study, we performed meta-analysis of two existing genome-wide association studies (GWASs) on Chinese Han populations from Hong Kong and Anhui, China, and followed the findings by further replication on three additional Chinese and Thailand cohorts with a total of 4254 cases and 6262 controls matched geographically and ethnically. We discovered multiple susceptibility variants for SLE in the 11q23.3 region, including variants in/near PHLDB1 (rs11603023, P(_combined) = 1.25E-08, OR = 1.20), DDX6 (rs638893, P(_combined) = 5.19E-07, OR = 1.22) and CXCR5 (rs10892301, P(_combined) = 2.51E-08, OR = 0.85). Genetic contributions from the newly identified variants were all independent of SNP rs4639966, whose association was reported from the previous GWAS. In addition, the three newly identified variants all showed independent association with the disease through modeling by both stepwise and conditional logistic regression. The presence of multiple independent variants in this region emphasizes its role in SLE susceptibility, and also hints the possibility that distinct biological mechanisms might be involved in the disease involving this genomic region.
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Affiliation(s)
- Jing Zhang
- Department of Paediatrics and Adolescent Medicine
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11
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Cui L, Wong EHM, Cheng G, Firmato de Almeida M, So MT, Sham PC, Cherny SS, Tam PKH, Garcia-Barceló MM. Genetic Analyses of a Three Generation Family Segregating Hirschsprung Disease and Iris Heterochromia. PLoS One 2013; 8:e66631. [PMID: 23840513 PMCID: PMC3694150 DOI: 10.1371/journal.pone.0066631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Accepted: 05/08/2013] [Indexed: 12/15/2022] Open
Abstract
We present the genetic analyses conducted on a three-generation family (14 individuals) with three members affected with isolated-Hirschsprung disease (HSCR) and one with HSCR and heterochromia iridum (syndromic-HSCR), a phenotype reminiscent of Waardenburg-Shah syndrome (WS4). WS4 is characterized by pigmentary abnormalities of the skin, eyes and/or hair, sensorineural deafness and HSCR. None of the members had sensorineural deafness. The family was screened for copy number variations (CNVs) using Illumina-HumanOmni2.5-Beadchip and for coding sequence mutations in WS4 genes (EDN3, EDNRB, or SOX10) and in the main HSCR gene (RET). Confocal microscopy and immunoblotting were used to assess the functional impact of the mutations. A heterozygous A/G transition in EDNRB was identified in 4 affected and 3 unaffected individuals. While in EDNRB isoforms 1 and 2 (cellular receptor) the transition results in the abolishment of translation initiation (M1V), in isoform 3 (only in the cytosol) the replacement occurs at Met91 (M91V) and is predicted benign. Another heterozygous transition (c.-248G/A; -predicted to affect translation efficiency-) in the 5'-untranslated region of EDN3 (EDNRB ligand) was detected in all affected individuals but not in healthy carriers of the EDNRB mutation. Also, a de novo CNVs encompassing DACH1 was identified in the patient with heterochromia iridum and HSCR Since the EDNRB and EDN3 variants only coexist in affected individuals, HSCR could be due to the joint effect of mutations in genes of the same pathway. Iris heterochromia could be due to an independent genetic event and would account for the additional phenotype within the family.
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Affiliation(s)
- Long Cui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Emily Hoi-Man Wong
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | | | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Pak-Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Stacey S. Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong SAR, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Center for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- * E-mail:
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12
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Yang W, Tang H, Zhang Y, Tang X, Zhang J, Sun L, Yang J, Cui Y, Zhang L, Hirankarn N, Cheng H, Pan HF, Gao J, Lee TL, Sheng Y, Lau CS, Li Y, Chan TM, Yin X, Ying D, Lu Q, Leung AMH, Zuo X, Chen X, Tong KL, Zhou F, Diao Q, Tse NKC, Xie H, Mok CC, Hao F, Wong SN, Shi B, Lee KW, Hui Y, Ho MHK, Liang B, Lee PPW, Cui H, Guo Q, Chung BHY, Pu X, Liu Q, Zhang X, Zhang C, Chong CY, Fang H, Wong RWS, Sun Y, Mok MY, Li XP, Avihingsanon Y, Zhai Z, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Gao F, Shotelersuk V, Kang X, Ying SKY, Zhang L, Wong WHS, Zhu D, Fung SKS, Zeng F, Lai WM, Wong CM, Ng IOL, Garcia-Barceló MM, Cherny SS, Shen N, Tam PKH, Sham PC, Ye DQ, Yang S, Zhang X, Lau YL. Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians. Am J Hum Genet 2013; 92:41-51. [PMID: 23273568 DOI: 10.1016/j.ajhg.2012.11.018] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 11/12/2012] [Accepted: 11/28/2012] [Indexed: 11/19/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with a strong genetic involvement and ethnic differences. Susceptibility genes identified so far only explain a small portion of the genetic heritability of SLE, suggesting that many more loci are yet to be uncovered for this disease. In this study, we performed a meta-analysis of genome-wide association studies on SLE in Chinese Han populations and followed up the findings by replication in four additional Asian cohorts with a total of 5,365 cases and 10,054 corresponding controls. We identified genetic variants in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with the disease. These findings point to potential roles of cell-cycle regulation, autophagy, and DNA demethylation in SLE pathogenesis. For the region involving TET3 and that involving CDKN1B, multiple independent SNPs were identified, highlighting a phenomenon that might partially explain the missing heritability of complex diseases.
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Affiliation(s)
- Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Hong Kong
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Tang CSM, Cheng G, So MT, Yip BHK, Miao XP, Wong EHM, Ngan ESW, Lui VCH, Song YQ, Chan D, Cheung K, Yuan ZW, Lei L, Chung PHY, Liu XL, Wong KKY, Marshall CR, Scherer S, Cherny SS, Sham PC, Tam PKH, Garcia-Barceló MM. Genome-wide copy number analysis uncovers a new HSCR gene: NRG3. PLoS Genet 2012; 8:e1002687. [PMID: 22589734 PMCID: PMC3349728 DOI: 10.1371/journal.pgen.1002687] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 03/20/2012] [Indexed: 01/23/2023] Open
Abstract
Hirschsprung disease (HSCR) is a congenital disorder characterized by aganglionosis of the distal intestine. To assess the contribution of copy number variants (CNVs) to HSCR, we analysed the data generated from our previous genome-wide association study on HSCR patients, whereby we identified NRG1 as a new HSCR susceptibility locus. Analysis of 129 Chinese patients and 331 ethnically matched controls showed that HSCR patients have a greater burden of rare CNVs (p = 1.50×10−5), particularly for those encompassing genes (p = 5.00×10−6). Our study identified 246 rare-genic CNVs exclusive to patients. Among those, we detected a NRG3 deletion (p = 1.64×10−3). Subsequent follow-up (96 additional patients and 220 controls) on NRG3 revealed 9 deletions (combined p = 3.36×10−5) and 2 de novo duplications among patients and two deletions among controls. Importantly, NRG3 is a paralog of NRG1. Stratification of patients by presence/absence of HSCR–associated syndromes showed that while syndromic–HSCR patients carried significantly longer CNVs than the non-syndromic or controls (p = 1.50×10−5), non-syndromic patients were enriched in CNV number when compared to controls (p = 4.00×10−6) or the syndromic counterpart. Our results suggest a role for NRG3 in HSCR etiology and provide insights into the relative contribution of structural variants in both syndromic and non-syndromic HSCR. This would be the first genome-wide catalog of copy number variants identified in HSCR. Copy number variations (CNVs) are significant genetic risk factors in disease pathogenesis and represent an important portion of missing heritability for some human diseases, making their discovery essential for the identification of genes and risk factors for a wide range of diseases, including Hirschsprung disease (HSCR, congenital colon aganglionosis). Since the discovery of the major HSCR gene, RET, a number of rare mutations have been reported in RET and other genes involved in the development of the enteric nervous system. However, these mutations contribute to only a small proportion of the disease susceptibility. Taking advantage of the recent technical and methodological advances, we have examined the contribution of CNVs to the disease. We have found that HSCR patients are enriched with CNVs encompassing genes. In particular, we found that deletions of NRG3, a paralog of the previously identified HSCR–susceptibility gene NRG1, were associated with the HSCR phenotype.
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Affiliation(s)
- Clara Sze-Man Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Guo Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Benjamin Hon-Kei Yip
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xiao-Ping Miao
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Department of Epidemiology and Biostatistics, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Emily Hoi-Man Wong
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Elly Sau-Wai Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Vincent Chi-Hang Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - You-Qiang Song
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Danny Chan
- Department of Biochemistry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth Cheung
- Department of Orthopedics and Traumatology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Zhen-Wei Yuan
- Department of Paediatric Surgery, Shengjing Hospital, China Medical University, Shenyang, China
| | - Liu Lei
- Department of Surgery, Shenzhen Children's Hospital, Shenzhen, China
| | - Patrick Ho-Yu Chung
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Xue-Lai Liu
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kenneth Kak-Yuen Wong
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Christian R. Marshall
- Program in Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Steve Scherer
- Program in Genetics and Genome Biology and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- The McLaughlin Centre and the Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Stacey S. Cherny
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Genome Research Centre, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Pak-Chung Sham
- Department of Psychiatry, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Genome Research Centre, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- State Key Laboratory of Brain and Cognitive Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development, and Growth, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- * E-mail:
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Leon TYY, So MT, Lui VCH, Hofstra RMW, Tam PKH, Ngan ESW, Garcia-Barceló MM. Functional analyses of RET mutations in Chinese Hirschsprung disease patients. ACTA ACUST UNITED AC 2011; 94:47-51. [PMID: 22131258 DOI: 10.1002/bdra.22863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Revised: 08/17/2011] [Accepted: 08/25/2011] [Indexed: 01/29/2023]
Abstract
BACKGROUND Hirschsprung disease (HSCR) is a congenital disease characterized by the absence of ganglion cells in various length of distal digestive tract. The rearranged during transfection gene (RET) is considered the major gene in HSCR. Although an increasing number of HSCR-associated RET coding sequence (CDS) mutations have been identified in recent years, not many have been investigated for functional consequence on the RET protein. METHODS AND RESULTS We examined the functional implications of the de novo RET-CDS mutations V145G, Y483X, V636fsX1, and F961L that we first identified in sporadic Chinese patients with HSCR. The V145G disrupted RET glycosylation and F961L RET phosphorylation. Presumably, the truncation mutations would affect the translocation or the anchoring of the RET protein onto the cellular membrane. CONCLUSION The study of RET-CDS mutations that appear de novo is essential not only for understanding the mechanistic of the disease but also for penetrance and recurrence risk estimations, being the ultimate goal for the improvement in disease management and counseling.
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Affiliation(s)
- Thomas Y Y Leon
- Division of Paediatric Surgery, Department of Surgery, The University of Hong Kong, Hong Kong, Special Administrative Region, China
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Ngan ESW, Garcia-Barceló MM, Yip BHK, Poon HC, Lau ST, Kwok CKM, Sat E, Sham MH, Wong KKY, Wainwright BJ, Cherny SS, Hui CC, Sham PC, Lui VCH, Tam PKH. Hedgehog/Notch-induced premature gliogenesis represents a new disease mechanism for Hirschsprung disease in mice and humans. J Clin Invest 2011; 121:3467-78. [PMID: 21841314 DOI: 10.1172/jci43737] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2010] [Accepted: 06/22/2011] [Indexed: 01/17/2023] Open
Abstract
Hirschsprung (HSCR) disease is a complex genetic disorder attributed to a failure of the enteric neural crest cells (ENCCs) to form ganglia in the hindgut. Hedgehog and Notch are implicated in mediating proliferation and differentiation of ENCCs. Nevertheless, how these signaling molecules may interact to mediate gut colonization by ENCCs and contribute to a primary etiology for HSCR are not known. Here, we report our pathway-based epistasis analysis of data generated by a genome-wide association study on HSCR disease, which indicates that specific genotype constellations of Patched (PTCH1) (which encodes a receptor for Hedgehog) and delta-like 3 (DLL3) (which encodes a receptor for Notch) SNPs confer higher risk to HSCR. Importantly, deletion of Ptch1 in mouse ENCCs induced robust Dll1 expression and activation of the Notch pathway, leading to premature gliogenesis and reduction of ENCC progenitors in mutant bowels. Dll1 integrated Hedgehog and Notch pathways to coordinate neuronal and glial cell differentiation during enteric nervous system development. In addition, Hedgehog-mediated gliogenesis was found to be highly conserved, such that Hedgehog was consistently able to promote gliogenesis of human neural crest-related precursors. Collectively, we defined PTCH1 and DLL3 as HSCR susceptibility genes and suggest that Hedgehog/Notch-induced premature gliogenesis may represent a new disease mechanism for HSCR.
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Affiliation(s)
- Elly Sau-Wai Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China.
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16
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Tang CSM, Tang WK, So MT, Miao XP, Leung BMC, Yip BHK, Leon TYY, Ngan ESW, Lui VCH, Chen Y, Chan IHY, Chung PHY, Liu XL, Wu XZ, Wong KKY, Sham PC, Cherny SS, Tam PKH, Garcia-Barceló MM. Fine mapping of the NRG1 Hirschsprung's disease locus. PLoS One 2011; 6:e16181. [PMID: 21283760 PMCID: PMC3024406 DOI: 10.1371/journal.pone.0016181] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Accepted: 12/07/2010] [Indexed: 11/23/2022] Open
Abstract
The primary pathology of Hirschsprung's disease (HSCR, colon aganglionosis) is the absence of ganglia in variable lengths of the hindgut, resulting in functional obstruction. HSCR is attributed to a failure of migration of the enteric ganglion precursors along the developing gut. RET is a key regulator of the development of the enteric nervous system (ENS) and the major HSCR-causing gene. Yet the reduced penetrance of RET DNA HSCR-associated variants together with the phenotypic variability suggest the involvement of additional genes in the disease. Through a genome-wide association study, we uncovered a ∼350 kb HSCR-associated region encompassing part of the neuregulin-1 gene (NRG1). To identify the causal NRG1 variants contributing to HSCR, we genotyped 243 SNPs variants on 343 ethnic Chinese HSCR patients and 359 controls. Genotype analysis coupled with imputation narrowed down the HSCR-associated region to 21 kb, with four of the most associated SNPs (rs10088313, rs10094655, rs4624987, and rs3884552) mapping to the NRG1 promoter. We investigated whether there was correlation between the genotype at the rs10088313 locus and the amount of NRG1 expressed in human gut tissues (40 patients and 21 controls) and found differences in expression as a function of genotype. We also found significant differences in NRG1 expression levels between diseased and control individuals bearing the same rs10088313 risk genotype. This indicates that the effects of NRG1 common variants are likely to depend on other alleles or epigenetic factors present in the patients and would account for the variability in the genetic predisposition to HSCR.
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Affiliation(s)
- Clara Sze-Man Tang
- Department of Psychiatry, University of Hong Kong, Hong Kong, China
- Department of Surgery, University of Hong Kong, Hong Kong, China
| | - Wai-Kiu Tang
- Department of Surgery, University of Hong Kong, Hong Kong, China
| | - Man-Ting So
- Department of Surgery, University of Hong Kong, Hong Kong, China
| | - Xiao-Ping Miao
- Department of Epidemiology and Biostatistics, Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | | | - Benjamin Hon-Kei Yip
- Department of Psychiatry, University of Hong Kong, Hong Kong, China
- Department of Surgery, University of Hong Kong, Hong Kong, China
| | | | - Elly Sau-Wai Ngan
- Department of Surgery, University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development and Growth, University of Hong Kong, Hong Kong, China
| | - Vincent Chi-Hang Lui
- Department of Surgery, University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development and Growth, University of Hong Kong, Hong Kong, China
| | - Yan Chen
- Department of Surgery, University of Hong Kong, Hong Kong, China
| | - Ivy Hau-Yee Chan
- Department of Surgery, University of Hong Kong, Hong Kong, China
| | | | - Xue-Lai Liu
- Department of Surgery, University of Hong Kong, Hong Kong, China
| | - Xuan-Zhao Wu
- Department of Surgery, Guiyang Medical College Affiliated Hospital, Guiyang, China
| | | | - Pak-Chung Sham
- Department of Psychiatry, University of Hong Kong, Hong Kong, China
- Genome Research Centre, University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development and Growth, University of Hong Kong, Hong Kong, China
| | - Stacey S. Cherny
- Department of Psychiatry, University of Hong Kong, Hong Kong, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development and Growth, University of Hong Kong, Hong Kong, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, University of Hong Kong, Hong Kong, China
- Centre for Reproduction, Development and Growth, University of Hong Kong, Hong Kong, China
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Yang J, Yang W, Hirankarn N, Ye DQ, Zhang Y, Pan HF, Mok CC, Chan TM, Wong RWS, Mok MY, Lee KW, Wong SN, Leung AMH, Li XP, Avihingsanon Y, Rianthavorn P, Deekajorndej T, Suphapeetiporn K, Shotelersuk V, Baum L, Kwan P, Lee TL, Ho MHK, Lee PPW, Wong WHS, Zeng S, Zhang J, Wong CM, Ng IOL, Garcia-Barceló MM, Cherny SS, Tam PKH, Sham PC, Lau CS, Lau YL. ELF1 is associated with systemic lupus erythematosus in Asian populations. Hum Mol Genet 2010; 20:601-7. [PMID: 21044949 DOI: 10.1093/hmg/ddq474] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic involvement. The susceptibility genes identified so far can only explain a small proportion of disease heritability. Through a genome-wide association in a Hong Kong Chinese cohort and subsequent replication in two other Asian populations, with a total of 3164 patients and 4482 matched controls, we identified association of ELF1 (E74-like factor 1) with SLE (rs7329174, OR = 1.26, joint P= 1.47 × 10(-8)). ELF1 belongs to the ETS family of transcription factors and is known to be involved in T cell development and function. Database analysis revealed transcripts making use of three alternative exon1s for this gene. Near equivalent expression levels of distinct transcripts initiated from alternative exon1s were detected in peripheral blood mononuclear cells from both SLE patients and healthy controls. Although a direct association of rs7329174 with the three forms of transcripts for this gene was not detected, these findings support an important role of ELF1 in SLE susceptibility and suggest a potentially tight regulation for the expression of this gene.
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Affiliation(s)
- Jing Yang
- Department of Paediatrics and Adolescent Medicine, Queen Mary Hospital, LKS Faculty of Medicine,The University of Hong Kong, 21 Sassoon Road, Hong Kong, China
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Garcia-Barceló MM, Yeung MY, Miao XP, Tang CSM, Cheng G, So MT, Ngan ESW, Lui VCH, Chen Y, Liu XL, Hui KJWS, Li L, Guo WH, Sun XB, Tou JF, Chan KW, Wu XZ, Song YQ, Chan D, Cheung K, Chung PHY, Wong KKY, Sham PC, Cherny SS, Tam PKH. Genome-wide association study identifies a susceptibility locus for biliary atresia on 10q24.2. Hum Mol Genet 2010; 19:2917-25. [PMID: 20460270 DOI: 10.1093/hmg/ddq196] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Biliary atresia (BA) is characterized by the progressive fibrosclerosing obliteration of the extrahepatic biliary system during the first few weeks of life. Despite early diagnosis and prompt surgical intervention, the disease progresses to cirrhosis in many patients. The current theory for the pathogenesis of BA proposes that during the perinatal period, a still unknown exogenous factor meets the innate immune system of a genetically predisposed individual and induces an uncontrollable and potentially self-limiting immune response, which becomes manifest in liver fibrosis and atresia of the extrahepatic bile ducts. Genetic factors that could account for the disease, let alone for its high incidence in Chinese, are to be investigated. To identify BA susceptibility loci, we carried out a genome-wide association study (GWAS) using the Affymetrix 5.0 and 500 K marker sets. We genotyped nearly 500 000 single-nucleotide polymorphisms (SNPs) in 200 Chinese BA patients and 481 ethnically matched control subjects. The 10 most BA-associated SNPs from the GWAS were genotyped in an independent set of 124 BA and 90 control subjects. The strongest overall association was found for rs17095355 on 10q24, downstream XPNPEP1, a gene involved in the metabolism of inflammatory mediators. Allelic chi-square test P-value for the meta-analysis of the GWAS and replication results was 6.94 x 10(-9). The identification of putative BA susceptibility loci not only opens new fields of investigation into the mechanisms underlying BA but may also provide new clues for the development of preventive and curative strategies.
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Tang CS, Sribudiani Y, Miao XP, de Vries AR, Burzynski G, So MT, Leon YY, Yip BH, Osinga J, Hui KJWS, Verheij JBGM, Cherny SS, Tam PKH, Sham PC, Hofstra RMW, Garcia-Barceló MM. Fine mapping of the 9q31 Hirschsprung's disease locus. Hum Genet 2010; 127:675-83. [PMID: 20361209 PMCID: PMC2871095 DOI: 10.1007/s00439-010-0813-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 03/17/2010] [Indexed: 12/18/2022]
Abstract
Hirschsprung’s disease (HSCR) is a congenital disorder characterised by the absence of ganglia along variable lengths of the intestine. The RET gene is the major HSCR gene. Reduced penetrance of RET mutations and phenotypic variability suggest the involvement of additional modifying genes in the disease. A RET-dependent modifier locus was mapped to 9q31 in families bearing no coding sequence (CDS) RET mutations. Yet, the 9q31 causative locus is to be identified. To fine-map the 9q31 region, we genotyped 301 tag-SNPs spanning 7 Mb on 137 HSCR Dutch trios. This revealed two HSCR-associated regions that were further investigated in 173 Chinese HSCR patients and 436 controls using the genotype data obtained from a genome-wide association study recently conducted. Within one of the two identified regions SVEP1 SNPs were found associated with Dutch HSCR patients in the absence of RET mutations. This ratifies the reported linkage to the 9q31 region in HSCR families with no RET CDS mutations. However, this finding could not be replicated. In Chinese, HSCR was found associated with IKBKAP. In contrast, this association was stronger in patients carrying RET CDS mutations with p = 5.10 × 10−6 [OR = 3.32 (1.99, 5.59)] after replication. The HSCR-association found for IKBKAP in Chinese suggests population specificity and implies that RET mutation carriers may have an additional risk. Our finding is supported by the role of IKBKAP in the development of the nervous system.
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Affiliation(s)
- C S Tang
- Department of Psychiatry, The University of Hong Kong, Hong Kong, China
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Miao X, Garcia-Barceló MM, So MT, Tang WK, Dong X, Wang B, Mao J, Ngan ESW, Chen Y, Lui VCH, Wong KKY, Liu L, Tam PKH. Lack of association between nNOS -84G>A polymorphism and risk of infantile hypertrophic pyloric stenosis in a Chinese population. J Pediatr Surg 2010; 45:709-13. [PMID: 20385275 DOI: 10.1016/j.jpedsurg.2009.07.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 07/31/2009] [Accepted: 07/31/2009] [Indexed: 01/03/2023]
Abstract
BACKGROUND Infantile hypertrophic pyloric stenosis (IHPS) is one of the most common gastrointestinal obstructions in the infancy requiring surgery. Reduced expression of neuronal nitric oxide synthase (nNOS), which plays an important role in the regulation of the human pyloric muscle, is thought to underlie IHPS. The role of nNOS in IHPS has been supported by the genetic association of a functional regulatory nNOS polymorphism (-84G>A) with IHPS in whites. We reasoned that the corroboration of this association in a population of different ethnic origin would prompt follow-up studies and further investigation of the IHPS pathology at molecular level. Thus, we attempted to reproduce the original findings in a Chinese population of comparable size in what would be the first genetic study on IHPS conducted in Chinese. METHODS nNOS -84G>A genotypes were analyzed in 56 patients and 86 controls by polymerase chain reaction and DNA sequencing. Logistic regression was used to compute odds ratios. RESULTS Our study could not corroborate the association previously reported. Although the frequency of the IHPS-associated allele (-84A) in controls (0.205) was similar to that reported for white controls, there was a dramatic difference in -84A frequencies between white and Chinese patients (0.198). Similarly, there was no difference in the nNOS -84G>A genotype distribution between patients and controls, even when the GA and AA genotypes were combined to compare GG genotype (odds ratio, 1.01; 95% confidence interval, 0.47-2.19). CONCLUSIONS Failure to replicate the initial finding does not detract from its validity, because genetic effects may differ across populations. Differences across populations in linkage disequilibrium and/or allele frequencies may contribute to this lack of replication. The role nNOS in IHPS awaits further investigation.
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Affiliation(s)
- Xiaoping Miao
- Department of Surgery, Shenzhen Children's Hospital, Shenzhen, China
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Garcia-Barceló MM, Lui VCH, So MT, Miao X, Leon TYY, Yuan ZW, Ngan ESW, Ehsan T, Chung PHY, Khong PL, Wong KKY, Tam PKH. MNX1 (HLXB9) mutations in Currarino patients. J Pediatr Surg 2009; 44:1892-8. [PMID: 19853743 DOI: 10.1016/j.jpedsurg.2009.03.039] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2008] [Revised: 02/07/2009] [Accepted: 03/24/2009] [Indexed: 10/20/2022]
Abstract
PURPOSE The combination of partial absence of the sacrum, anorectal anomalies, and presacral mass constitutes Currarino syndrome (CS), which is associated with mutations in MNX1 motor neuron and pancreas homeobox 1 (previously HLXB9). Here, we report on the MNX1 mutations found in a family segregating CS and in 3 sporadic CS patients, as well as on the clinical characteristics of the affected individuals. METHODS MNX1 mutations were identified by direct sequencing the coding regions, intron/exon boundaries of MNX1 in 5 CS Japanese family members and 3 Chinese sporadic cases and their parents. RESULTS There were 2 novel (P18PfsX37, R243W) and 2 previously described (W288G and IVS2 + 1G > A) mutations. These mutations were not found in 198 control individuals and are predicted to impair the functioning of the MNX1 protein. CONCLUSIONS The variability of the CS phenotype among related or unrelated patients bearing the same mutation advocates for differences in the genetic background of each individual and invokes the implication of additional CS susceptibility genes.
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Affiliation(s)
- Maria-Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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22
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Ngan ESW, Lang BHH, Liu T, Shum CKY, So MT, Lau DKC, Leon TYY, Cherny SS, Tsai SY, Lo CY, Khoo US, Tam PKH, Garcia-Barceló MM. A germline mutation (A339V) in thyroid transcription factor-1 (TITF-1/NKX2.1) in patients with multinodular goiter and papillary thyroid carcinoma. J Natl Cancer Inst 2009; 101:162-75. [PMID: 19176457 DOI: 10.1093/jnci/djn471] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The genetic factors that determine the risk of papillary thyroid carcinoma (PTC) among patients with multinodular goiter (MNG) remain undefined. Because thyroid transcription factor-1 (TTF-1) is important to thyroid development, we evaluated whether the gene that encodes it, TITF-1/NKX2.1, is a genetic determinant of MNG/PTC predisposition. METHODS Twenty unrelated PTC patients with a history of MNG (MNG/PTC), 284 PTC patients without a history of MNG (PTC), and 349 healthy control subjects were screened for germline mutation(s) in TITF-1/NKX2.1 by sequencing of amplified DNA from blood. The effects of the mutation on the growth and differentiation of thyroid cells were demonstrated by ectopic expression of wild-type (WT) and mutant proteins in PCCL3 normal rat thyroid cells, followed by tests of cell proliferation, activation of cell growth pathways, and transcription of TTF-1 target genes. All statistical tests were two-sided. RESULTS A missense mutation (1016C>T) was identified in TITF-1/NKX2.1 that led to a mutant TTF-1 protein (A339V) in four of the 20 MNG/PTC patients (20%). These patients developed substantially more advanced tumors than MNG/PTC or PTC patients without the mutation (P = .022, Fisher exact test). Notably, this germline mutation was dominantly inherited in two families, with some members bearing the mutation affected with MNG, associated with either PTC or colon cancer. The mutation encoding the A339V substitution was not found among the 349 healthy control subjects nor among the 284 PTC patients who had no history of MNG. Overexpression of A339V TTF-1 in PCCL3 cells, as compared with overexpression of WT TTF-1, was associated with increased cell proliferation including thyrotropin-independent growth (average A339V proliferation rate = 134.27%, WT rate = 104.43%, difference = 34.3%, 95% confidence interval = 12.0% to 47.7%, P = .010), enhanced STAT3 activation, and impaired transcription of the thyroid-specific genes Tg, TSH-R, and Pax-8. CONCLUSION This is the first germline mutation identified in MNG/PTC patients. It could contribute to predisposition for MNG and/or PTC and to the pathogenesis of PTC.
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Affiliation(s)
- Elly S W Ngan
- Department of Surgery, University of Hong Kong, Pokfulam, Faculty of Medicine Building, 21 Sassoon Rd, Hong Kong, SAR, China.
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Garcia-Barceló MM, Wong KKY, Lui VCH, Yuan ZW, So MT, Ngan ESW, Miao XP, Chung PHY, Khong PL, Tam PKH. Identification of aHOXD13mutation in a VACTERL patient. Am J Med Genet A 2008; 146A:3181-5. [DOI: 10.1002/ajmg.a.32426] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Garcia-Barceló MM, Chi-Hang Lui V, Miao X, So MT, Yuk-yu Leon T, Yuan ZW, Li L, Liu L, Wang B, Sun XB, Huang LM, Tou JF, Sau-wai Ngan E, Cherny SS, Chan KW, Lee KH, Wang W, Kak-yuen Wong K, Kwong-hang Tam P. Mutational analysis ofSHHandGLI3in anorectal malformations. ACTA ACUST UNITED AC 2008; 82:644-8. [DOI: 10.1002/bdra.20482] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Garcia-Barceló MM, Lau DKC, Ngan ESW, Leon TYY, Liu TT, So MT, Miao XP, Lui VCH, Wong KKY, Ganster RW, Cass DT, Croaker GDH, Tam PKH. Evaluation of the thyroid transcription factor-1 gene (TITF1) as a Hirschsprung's disease locus. Ann Hum Genet 2007; 71:746-54. [PMID: 17640327 DOI: 10.1111/j.1469-1809.2007.00384.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hirschsprung's disease (HSCR, colonic aganglionosis) is an oligogenic entity that usually requires mutations in RET and other interacting loci. Decreased levels of RET expression may lead to the manifestation of HSCR. We previously showed that RET transcription was decreased due to alteration of the TITF1 binding site by two HSCR-associated RET promoter single nucleotide polymorphisms (SNPs). This prompted us to investigate whether DNA alterations in TITF1 could play a role in HSCR by affecting the RET-regulatory properties of the TITF1 protein. Our initial study on 86 Chinese HSCR patients revealed a Gly322Ser amino acid substitution in the TITF1protein. In this study we have examined an additional 102 Chinese and 70 Caucasian patients, and 194 Chinese and 60 Caucasian unselected, unrelated, subjects as controls. The relevance of the DNA changes detected in TITF1 by direct sequencing were evaluated using bioinformatics, reporter and binding-assays, mouse neurosphere culture, immunohistochemistry and immunofluorescence techniques. Met3Leu and Pro48Pro were identified in 2 Caucasian patients and 1 Chinese patient, respectively. In vitro analysis showed that Met3Leu reduced the activity of the RET promoter by 100% in the presence of the wild-type or HSCR-associated RET promoter SNP alleles. The apparent binding affinity of the TITF1 mutated protein was not decreased. The Met3Leu mutation may affect the interaction of TITF1 with its protein partners. The absence of Titf1 expression in mouse gut but not in human gut suggests that the role of TITF1 in gut development differs between the two species. TITF1 mutations could contribute to HSCR by affecting RET expression through defective interactions with other transcription factors.
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Affiliation(s)
- Maria-Mercè Garcia-Barceló
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine of the University of Hong Kong, Hong Kong SAR, China
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Miao X, Garcia-Barceló MM, So MT, Leon TYY, Lau DKC, Liu TT, Chan EKW, Lan LCL, Wong KKY, Lui VCH, Tam PKH. Role of RET and PHOX2B gene polymorphisms in risk of Hirschsprung's disease in Chinese population. Gut 2007; 56:736. [PMID: 17440194 PMCID: PMC1942142 DOI: 10.1136/gut.2006.116145] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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Garcia-Barceló MM, Miao X, Lui VCH, So MT, Ngan ESW, Leon TYY, Lau DKC, Liu TT, Lao X, Guo W, Holden WT, Moore J, Tam PKH. Correlation between genetic variations in Hox clusters and Hirschsprung's disease. Ann Hum Genet 2007; 71:526-36. [PMID: 17274802 DOI: 10.1111/j.1469-1809.2007.00347.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Interactions between migrating neural crest cells and the environment of the gut are crucial for the development of the enteric nervous system (ENS). A key signalling mediator is the RET-receptor-tyrosine-kinase which, when defective, causes Hirschprung's disease (HSCR, colon aganglionosis). RET mutations alone cannot account for the variable HSCR phenotype, invoking interactions with as yet unknown, and probably inter-related, loci involved in ENS development. Homeobox (HOX) genes have a major role in gut development as depicted by the enteric Hox code. We investigated whether DNA alterations in HOX genes, either alone or in combination with RET, are implicated in HSCR. Genotyping effort was minimized by applying the HapMap data on Han Chinese from Beijing (CHB). 194 HSCR patients and 168 controls were genotyped using Sequenom technology for 72 tag, single nucleotide polymorphisms (SNPs) distributed along the HOX clusters. The HapMap frequencies were compared to those in our population and standard statistics were used for frequency comparisons. The multifactor-dimensionality-reduction method was used for multilocus analysis, in which RET promoter SNP genotypes were included. Genetic interactions were found between two HOX loci (5'-HOXA13 and 3'UTR-HOXB7) and the RET loci tested. Minor allele frequencies (MAF) of the SNPs tested in our sample were not significantly different from those reported by HapMap when the sample sizes of the populations compared were considered. This is the first evaluation of the HOX genes in HSCR and the first application of HapMap data in a Chinese population. The interacting HOX loci may affect the penetrance of the RET risk allele. HapMap data for the CHB population correlated well with the general Chinese population.
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Affiliation(s)
- M M Garcia-Barceló
- Division of Paediatric Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine of the University of Hong Kong, Hong Kong SAR, China
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Garcia-Barceló MM, Lam LC, Ungvari GS, Lam VK, Tang WK. Dopamine D3 receptor gene and tardive dyskinesia in Chinese schizophrenic patients. J Neural Transm (Vienna) 2002; 108:671-7. [PMID: 11478419 DOI: 10.1007/s007020170044] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Epidemiological studies have shown a lower prevalence of tardive dyskinesia (TD) among Chinese psychiatric patients compared to Caucasian and Black patient populations. It has been hypothesized that pharmacogenetic factors may underlie this cross-cultural difference. Due to the important implications of the dopamine D3 receptor gene (DRD3) in motor control, we investigated the frequency of polymorphic serine (ser) to glycine (gly) substitution of the gene DRD3 in Chinese schizophrenic patients. The sample size consisted of 65 patients with TD and 66 without TD. Patients were assessed for the severity of TD, the presence of akathisia and parkinsonian symptoms and were subsequently genotyped. We found no evidence that the dopamine D3 receptor gene is likely to confer susceptibility to the development of tardive dyskinesia in Chinese patients with schizophrenia.
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Affiliation(s)
- M M Garcia-Barceló
- Department of Psychiatry, Chinese University of Hong Kong, Hong Kong SAR
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