Genetics in Hirschsprung Disease

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Hirschsprung’s disease (HD) is due to a congenital absence of ganglion cells (aganglionosis) in the colon leading to difficult-to-treat constipation as well as the potential for life-threatening enterocolitis from colonic inflammation. A total of 17 genes are associated with HD, with these mutations affecting the RET proto-oncogene encoding the tyrosine kinase receptor and G-protein–coupled receptor EDNRB which are involved in neurogenesis. The authors of this study looked at the phenotypic variation of HD based on these genetic mutations.

Whole exome sequencing was performed in 190 patients with HD and 47 relatives (36 first-degree relatives), and results were compared to a well-described control group from the 1000 Genomes Project and the National Institute of Mental Health Repository to look for differences in sequence variants (via single nucleotide polymorphism or SNP arrays). Three SNPs associated with HD in RET (rs2435357, rs7069590, and rs2506030) and one SNP associated with HD in SEMA3 (rs11766001) involved in the G-protein–coupled receptor EDNRB were used as markers for common noncoding variants (missense and nonsense). Potential HD-associated genes were defined as having more unique pathogenic alleles in the HD cohort compared to the control group. In order to see if a genetic mutation was associated with HD, reverse-transcriptase polymerase chain reaction (RT-PCR) testing was performed to evaluate RNA expression in human embryonic gut samples and in developing mouse gut.

Patients with 5 or more alleles showing mutations in RET and SEMA3 increased the risk of having HD, and the population frequency of HD increased with increasing numbers of risk alleles. The effect of pathogenic allele enrichment then was determined by analysis of 15,963 SNPs in 4027 genes in patients with HD and controls. Interestingly, besides RET and EDNRB mutations associated with neurogenesis, 7 new genetic mutations were found (ACSS2, ADAMTS17, ENO3, FAM213A, SH3PXD2A, SLC27A4, and UBR4). These genes also were expressed in human and mouse embryonic samples during embryogenesis and in zebrafish as markers of cell migratory defects. A larger number of coding copy variants, as opposed to noncoding copy variants, increased the risk of HD. It was noted that 8.9% of the 190 patients with HD had a genetic syndrome, and 16 copy number variants (14 not previously described) were noted in those patients who had both a genetic syndrome and HD. The most common syndrome associated with these variants was Trisomy 21.

In total, 72.1% of HD patients had some type of identified genetic risk factor with a large number of these patients having 5 or more noncoding, rare coding, or copy number variants, and the risk of HD increased in the population as the number pathogenic alleles increased. No genotype-phenotype relationship existed between HD and sex, length of HD segment, family history, or presence of a genetic syndrome. This study provides more much needed information about the genetics and subsequent pathophysiology of HD. In particular, determining the presence and copy number of alleles may be helpful in determining the risk of developing HD in families or during pre-natal screening.

Tilghman J, Ling A, Turner T, Sosa M, Krumm N, Chatterjee S, Kapoor A, Coe B, Nguyen K, Gupta N, Gabriel S, Eichler E, Berrios C, Chakravarti A. Molecular genetic anatomy and risk profile of Hirschsprung’s disease. New England Journal of Medicine 2019; 380: 1421-1432