A complementary study approach unravels novel players in the pathoetiology of Hirschsprung disease

PLoS Genet. 2020 Nov 5;16(11):e1009106. doi: 10.1371/journal.pgen.1009106. eCollection 2020 Nov.

Abstract

Hirschsprung disease (HSCR, OMIM 142623) involves congenital intestinal obstruction caused by dysfunction of neural crest cells and their progeny during enteric nervous system (ENS) development. HSCR is a multifactorial disorder; pathogenetic variants accounting for disease phenotype are identified only in a minority of cases, and the identification of novel disease-relevant genes remains challenging. In order to identify and to validate a potential disease-causing relevance of novel HSCR candidate genes, we established a complementary study approach, combining whole exome sequencing (WES) with transcriptome analysis of murine embryonic ENS-related tissues, literature and database searches, in silico network analyses, and functional readouts using candidate gene-specific genome-edited cell clones. WES datasets of two patients with HSCR and their non-affected parents were analysed, and four novel HSCR candidate genes could be identified: ATP7A, SREBF1, ABCD1 and PIAS2. Further rare variants in these genes were identified in additional HSCR patients, suggesting disease relevance. Transcriptomics revealed that these genes are expressed in embryonic and fetal gastrointestinal tissues. Knockout of these genes in neuronal cells demonstrated impaired cell differentiation, proliferation and/or survival. Our approach identified and validated candidate HSCR genes and provided further insight into the underlying pathomechanisms of HSCR.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • ATP Binding Cassette Transporter, Subfamily D, Member 1 / genetics
  • Animals
  • Cell Differentiation / genetics
  • Cell Line
  • Cell Proliferation / genetics
  • Cell Survival / genetics
  • Computer Simulation
  • Copper-Transporting ATPases / genetics
  • Disease Models, Animal
  • Gene Expression Profiling
  • Gene Knockout Techniques
  • Hirschsprung Disease / genetics*
  • Humans
  • Infant
  • Male
  • Mice
  • Protein Inhibitors of Activated STAT / genetics
  • Sterol Regulatory Element Binding Protein 1 / genetics
  • Whole Exome Sequencing

Substances

  • ABCD1 protein, human
  • ATP Binding Cassette Transporter, Subfamily D, Member 1
  • Abcd1 protein, mouse
  • Atp7a protein, mouse
  • PIAS2 protein, human
  • Protein Inhibitors of Activated STAT
  • SREBF1 protein, human
  • Srebf1 protein, mouse
  • Sterol Regulatory Element Binding Protein 1
  • Pias2 protein, mouse
  • ATP7A protein, human
  • Copper-Transporting ATPases

Grant support

This study was supported by the Heidelberg Stiftung Chirurgie (https://www.stiftung-chirurgie.de) (P. Romero and B. Niesler), the Heinz and Heide Dürr Stiftung (https://www.heinzundheideduerrstiftung.de) (B. Niesler and P. Romero; 2017/2.2.1/04), the Heidelberg University Hospital (https://www.heidelberg-university-hospital.com) (G. Rappold), and the Dres. Majic/Majic Schlez Stiftung (T. Mederer). Tanja Mederer is a PhD fellow of HBIGS (http://www.hbigs.uni-heidelberg.de) and was funded by the Studienstiftung des Deutschen Volkes (https://www.studienstiftung.de). Cristina Martínez is supported by Instituto de Salud Carlos III, Subdirección General de Investigación Sanitaria, Ministerio de Ciencia, Innovación y Universidades (https://www.isciii.es) (CP18/00116). Salud Borrego was supported by Instituto de Salud Carlos III (https://www.isciii.es) through the project "PI16/0142" and "PI19/01550" (Co-funded by European Regional Development Fund/European Social Fund "A way to make Europe"/"Investing in your future"). The WES analysis from 443 HSCR cases and 493 controls of East Asian ethnicity was supported by the Theme-Based Research Scheme (https://www.ugc.edu.hk) (grant no. T12C-714/14-R.) (Paul Tam). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.