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Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development

Hirschsprung disease (HSCR) is a complex genetic disease characterized by absence of ganglia in the intestine. HSCR etiology can be explained by a unique combination of genetic alterations: rare coding variants, predisposing haplotypes and Copy Number Variation (CNV). Approximately 18% of patients h...

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Autores principales: Kuil, Laura E., MacKenzie, Katherine C., Tang, Clara S., Windster, Jonathan D., Le, Thuy Linh, Karim, Anwarul, de Graaf, Bianca M., van der Helm, Robert, van Bever, Yolande, Sloots, Cornelius E. J., Meeussen, Conny, Tibboel, Dick, de Klein, Annelies, Wijnen, René M. H., Amiel, Jeanne, Lyonnet, Stanislas, Garcia-Barcelo, Maria-Mercè, Tam, Paul K. H., Alves, Maria M., Brooks, Alice S., Hofstra, Robert M. W., Brosens, Erwin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8372947/
https://www.ncbi.nlm.nih.gov/pubmed/34358225
http://dx.doi.org/10.1371/journal.pgen.1009698
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author Kuil, Laura E.
MacKenzie, Katherine C.
Tang, Clara S.
Windster, Jonathan D.
Le, Thuy Linh
Karim, Anwarul
de Graaf, Bianca M.
van der Helm, Robert
van Bever, Yolande
Sloots, Cornelius E. J.
Meeussen, Conny
Tibboel, Dick
de Klein, Annelies
Wijnen, René M. H.
Amiel, Jeanne
Lyonnet, Stanislas
Garcia-Barcelo, Maria-Mercè
Tam, Paul K. H.
Alves, Maria M.
Brooks, Alice S.
Hofstra, Robert M. W.
Brosens, Erwin
author_facet Kuil, Laura E.
MacKenzie, Katherine C.
Tang, Clara S.
Windster, Jonathan D.
Le, Thuy Linh
Karim, Anwarul
de Graaf, Bianca M.
van der Helm, Robert
van Bever, Yolande
Sloots, Cornelius E. J.
Meeussen, Conny
Tibboel, Dick
de Klein, Annelies
Wijnen, René M. H.
Amiel, Jeanne
Lyonnet, Stanislas
Garcia-Barcelo, Maria-Mercè
Tam, Paul K. H.
Alves, Maria M.
Brooks, Alice S.
Hofstra, Robert M. W.
Brosens, Erwin
author_sort Kuil, Laura E.
collection PubMed
description Hirschsprung disease (HSCR) is a complex genetic disease characterized by absence of ganglia in the intestine. HSCR etiology can be explained by a unique combination of genetic alterations: rare coding variants, predisposing haplotypes and Copy Number Variation (CNV). Approximately 18% of patients have additional anatomical malformations or neurological symptoms (HSCR-AAM). Pinpointing the responsible culprits within a CNV is challenging as often many genes are affected. Therefore, we selected candidate genes based on gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics. Next, we used a zebrafish model to investigate whether loss of these genes affects enteric neuron development in vivo. This study included three groups of patients, two groups without coding variants in disease associated genes: HSCR-AAM and HSCR patients without associated anomalies (HSCR-isolated). The third group consisted of all HSCR patients in which a confirmed pathogenic rare coding variant was identified. We compared these patient groups to unaffected controls. Predisposing haplotypes were determined, confirming that every HSCR subgroup had increased contributions of predisposing haplotypes, but their contribution was highest in isolated HSCR patients without RET coding variants. CNV profiling proved that specifically HSCR-AAM patients had larger Copy Number (CN) losses. Gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics were used to determine plausible candidate genes located within CN losses. Validation in zebrafish using CRISPR/Cas9 targeting confirmed the contribution of UFD1L, TBX2, SLC8A1, and MAPK8 to ENS development. In addition, we revealed epistasis between reduced Ret and Gnl1 expression and between reduced Ret and Tubb5 expression in vivo. Rare large CN losses—often de novo—contribute to HSCR in HSCR-AAM patients. We proved the involvement of six genes in enteric nervous system development and Hirschsprung disease.
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spelling pubmed-83729472021-08-19 Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development Kuil, Laura E. MacKenzie, Katherine C. Tang, Clara S. Windster, Jonathan D. Le, Thuy Linh Karim, Anwarul de Graaf, Bianca M. van der Helm, Robert van Bever, Yolande Sloots, Cornelius E. J. Meeussen, Conny Tibboel, Dick de Klein, Annelies Wijnen, René M. H. Amiel, Jeanne Lyonnet, Stanislas Garcia-Barcelo, Maria-Mercè Tam, Paul K. H. Alves, Maria M. Brooks, Alice S. Hofstra, Robert M. W. Brosens, Erwin PLoS Genet Research Article Hirschsprung disease (HSCR) is a complex genetic disease characterized by absence of ganglia in the intestine. HSCR etiology can be explained by a unique combination of genetic alterations: rare coding variants, predisposing haplotypes and Copy Number Variation (CNV). Approximately 18% of patients have additional anatomical malformations or neurological symptoms (HSCR-AAM). Pinpointing the responsible culprits within a CNV is challenging as often many genes are affected. Therefore, we selected candidate genes based on gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics. Next, we used a zebrafish model to investigate whether loss of these genes affects enteric neuron development in vivo. This study included three groups of patients, two groups without coding variants in disease associated genes: HSCR-AAM and HSCR patients without associated anomalies (HSCR-isolated). The third group consisted of all HSCR patients in which a confirmed pathogenic rare coding variant was identified. We compared these patient groups to unaffected controls. Predisposing haplotypes were determined, confirming that every HSCR subgroup had increased contributions of predisposing haplotypes, but their contribution was highest in isolated HSCR patients without RET coding variants. CNV profiling proved that specifically HSCR-AAM patients had larger Copy Number (CN) losses. Gene enrichment strategies using mouse enteric nervous system transcriptomes and constraint metrics were used to determine plausible candidate genes located within CN losses. Validation in zebrafish using CRISPR/Cas9 targeting confirmed the contribution of UFD1L, TBX2, SLC8A1, and MAPK8 to ENS development. In addition, we revealed epistasis between reduced Ret and Gnl1 expression and between reduced Ret and Tubb5 expression in vivo. Rare large CN losses—often de novo—contribute to HSCR in HSCR-AAM patients. We proved the involvement of six genes in enteric nervous system development and Hirschsprung disease. Public Library of Science 2021-08-06 /pmc/articles/PMC8372947/ /pubmed/34358225 http://dx.doi.org/10.1371/journal.pgen.1009698 Text en © 2021 Kuil et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Kuil, Laura E.
MacKenzie, Katherine C.
Tang, Clara S.
Windster, Jonathan D.
Le, Thuy Linh
Karim, Anwarul
de Graaf, Bianca M.
van der Helm, Robert
van Bever, Yolande
Sloots, Cornelius E. J.
Meeussen, Conny
Tibboel, Dick
de Klein, Annelies
Wijnen, René M. H.
Amiel, Jeanne
Lyonnet, Stanislas
Garcia-Barcelo, Maria-Mercè
Tam, Paul K. H.
Alves, Maria M.
Brooks, Alice S.
Hofstra, Robert M. W.
Brosens, Erwin
Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development
title Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development
title_full Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development
title_fullStr Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development
title_full_unstemmed Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development
title_short Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development
title_sort size matters: large copy number losses in hirschsprung disease patients reveal genes involved in enteric nervous system development
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8372947/
https://www.ncbi.nlm.nih.gov/pubmed/34358225
http://dx.doi.org/10.1371/journal.pgen.1009698
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