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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oai:doaj.org-article:1c07ad4d76c24f9488439c5f30f264c22021-12-02T20:03:24ZSize matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development.1553-73901553-740410.1371/journal.pgen.1009698https://doaj.org/article/1c07ad4d76c24f9488439c5f30f264c22021-08-01T00:00:00Zhttps://doi.org/10.1371/journal.pgen.1009698https://doaj.org/toc/1553-7390https://doaj.org/toc/1553-7404Hirschsprung 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.Laura E KuilKatherine C MacKenzieClara S TangJonathan D WindsterThuy Linh LeAnwarul KarimBianca M de GraafRobert van der HelmYolande van BeverCornelius E J SlootsConny MeeussenDick TibboelAnnelies de KleinRené M H WijnenJeanne AmielStanislas LyonnetMaria-Mercè Garcia-BarceloPaul K H TamMaria M AlvesAlice S BrooksRobert M W HofstraErwin BrosensPublic Library of Science (PLoS)articleGeneticsQH426-470ENPLoS Genetics, Vol 17, Iss 8, p e1009698 (2021) |
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DOAJ |
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Genetics QH426-470 |
| spellingShingle |
Genetics QH426-470 Laura E Kuil Katherine C MacKenzie Clara S Tang Jonathan D Windster Thuy Linh Le Anwarul Karim Bianca M de Graaf Robert van der Helm Yolande van Bever Cornelius E J Sloots Conny Meeussen Dick Tibboel Annelies de Klein René M H Wijnen Jeanne Amiel Stanislas Lyonnet Maria-Mercè Garcia-Barcelo Paul K H Tam Maria M Alves Alice S Brooks Robert M W Hofstra Erwin Brosens Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development. |
| 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. |
| format |
article |
| author |
Laura E Kuil Katherine C MacKenzie Clara S Tang Jonathan D Windster Thuy Linh Le Anwarul Karim Bianca M de Graaf Robert van der Helm Yolande van Bever Cornelius E J Sloots Conny Meeussen Dick Tibboel Annelies de Klein René M H Wijnen Jeanne Amiel Stanislas Lyonnet Maria-Mercè Garcia-Barcelo Paul K H Tam Maria M Alves Alice S Brooks Robert M W Hofstra Erwin Brosens |
| author_facet |
Laura E Kuil Katherine C MacKenzie Clara S Tang Jonathan D Windster Thuy Linh Le Anwarul Karim Bianca M de Graaf Robert van der Helm Yolande van Bever Cornelius E J Sloots Conny Meeussen Dick Tibboel Annelies de Klein René M H Wijnen Jeanne Amiel Stanislas Lyonnet Maria-Mercè Garcia-Barcelo Paul K H Tam Maria M Alves Alice S Brooks Robert M W Hofstra Erwin Brosens |
| author_sort |
Laura E Kuil |
| title |
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_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_sort |
size matters: large copy number losses in hirschsprung disease patients reveal genes involved in enteric nervous system development. |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2021 |
| url |
https://doaj.org/article/1c07ad4d76c24f9488439c5f30f264c2 |
| work_keys_str_mv |
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