Molecular Genetic Anatomy and Risk Profile of Hirschsprung’s Disease

Abstract

BACKGROUND Hirschsprung’s disease, or congenital aganglionosis, is a developmental disorder of the enteric nervous system and is the most common cause of intestinal obstruction in neonates and infants. The disease has more than 80% heritability, including significant associations with rare and common sequence variants in genes related to the enteric nervous system, as well as with monogenic and chromosomal syndromes. METHODS We genotyped and exome-sequenced samples from 190 patients with Hirschsprung’s disease to quantify the genetic burden in patients with this condition. DNA sequence variants, large copy-number variants, and karyotype variants in probands were considered to be pathogenic when they were significantly associated with Hirschsprung’s disease or another neurodevelopmental disorder. Novel genes were confirmed by functional studies in the mouse and human embryonic gut and in zebrafish embryos. RESULTS The presence of five or more variants in four noncoding elements defined a widespread risk of Hirschsprung’s disease (48.4% of patients and 17.1% of controls; odds ratio, 4.54; 95% confidence interval [CI], 3.19 to 6.46). Rare coding variants in 24 genes that play roles in enteric neural-crest cell fate, 7 of which were novel, were also common (34.7% of patients and 5.0% of controls) and conferred a much greater risk than noncoding variants (odds ratio, 10.02; 95% CI, 6.45 to 15.58). Large copy-number variants, which were present in fewer patients (11.4%, as compared with 0.2% of controls), conferred the highest risk (odds ratio, 63.07; 95% CI, 36.75 to 108.25). At least one identifiable genetic risk factor was found in 72.1% of the patients, and at least 48.4% of patients had a structural or regulatory deficiency in the gene encoding receptor tyrosine kinase (RET). For individual patients, the estimated risk of Hirschsprung’s disease ranged from 5.33 cases per 100,000 live births (approximately 1 per 18,800) to 8.38 per 1000 live births (approximately 1 per 120). CONCLUSIONS Among the patients in our study, Hirschsprung’s disease arose from common noncoding variants, rare coding variants, and copy-number variants affecting genes involved in enteric neural-crest cell fate that exacerbate the widespread genetic susceptibility associated with RET. For individual patients, the genotype-specific odds ratios varied by a factor of approximately 67, which provides a basis for risk stratification and genetic counseling. (Funded by the National Institutes of Health.)

The gastrointestinal development ‘parts list’: transcript profiling of embryonic gut development in wildtype andRet-deficient mice

“…These findings have three corollaries. First, HSCR patients should routinely be examined by a clinical geneticist who are likely to recognize the many additional phenotypic manifestations in HSCR beyond aganglionosis; indeed, ~32% of HSCR patients have developmental anomalies beyond aganglionosis (12). Second, the HSCR gene universe is considerably larger than currently known or assumed, including genes affecting intestinal smooth muscle and epithelium development.…”

“…RET does not directly bind to its ligand, but requires an additional co-receptor, one of four GDNF family receptor-α (GFRα) members (11). Mutations leading to Hirschsprung disease has been reported in many of these genes, highlighting the importance of this GRN in disease (12). Ret null mice exhibit complete aganglionosis with transcriptional changes in many of these genes (4), making it an ideal model to study how development is compromised in HSCR (10,13) .…”

Whole-genome analysis of noncoding genetic variations identifies multigranular regulatory element perturbations associated with Hirschsprung disease

“…When exploring the functions of the 552 genes, an expanded gene set was created by first adding 26 known HSCR genes, including BACE2, DNMT3B, ECE1, EDN3, EDNRB, FAT3, GDNF, GFRA1, KIAA1279, L1CAM, NRG1, NRG3, NRTN, NTF3, NTRK3, PHOX2B, PROK1, PROKR1, PROKR2, PSPN, SEMA3A/C/D, SOX10, TCF4, and ZFHX1B [8][9][10][11][12][13] . After that, genes involved in ENS function or NC migration that had Reactome functional interactions with at least one gene already in the expanded gene set were further added to it, including CDC42 61 , CUL1 47 , ERBB2/3/4 61 , GNAI1 104 , GRB2 105,106 , NRP1/2 61 , PAX3 71,107 , PLXNB1 108 , ROBO1/2/3 61 , SLIT1/2/3 61 , and TCF12 107 .…”

What is new about the genetic background of Hirschsprung disease?

“…A model for complex disorders has been described, where the individual functional small effects of non‐coding variants were amplified in a gene regulatory network . HSCR seems to compile a combination of common non‐coding/rare coding/copy‐number variants on genes implicated on ENS development, providing a more complete understanding of the genetics of the disease . WES and functional analyses of genes containing de novo mutations, contribute to delineate the genetic background of HSCR .…”

“…172 HSCR seems to compile a combination of common non-coding/rare coding/copy-number variants on genes implicated on ENS development, providing a more complete understanding of the genetics of the disease. 173 WES and functional analyses of genes containing de novo mutations, contribute to delineate the genetic background of HSCR. 157 Recently, it has been established the implication of the in-frameshift variant p.Phe147del in RET in heritable HSCR.…”