Copy number variations in candidate genomic regions confirm genetic heterogeneity and parental bias in Hirschsprung disease

Abstract

BackgroundHirschsprung Disease (HSCR) is a congenital defect of the intestinal innervations characterized by complex inheritance. Many susceptibility genes including RET, the major HSCR gene, and several linked regions and associated loci have been shown to contribute to disease pathogenesis. Nonetheless, a proportion of patients still remains unexplained. Copy Number Variations (CNVs) have already been involved in HSCR, and for this reason we performed Comparative Genomic Hybridization (CGH), using a custom array with high density probes.ResultsA total of 20 HSCR candidate regions/genes was tested in 55 sporadic patients and four patients with already known chromosomal aberrations. Among 83 calls, 12 variants were experimentally validated, three of which involving the HSCR crucial genes SEMA3A/3D, NRG1, and PHOX2B. Conversely RET involvement in HSCR does not seem to rely on the presence of CNVs while, interestingly, several gains and losses did co-occur with another RET defect, thus confirming that more than one predisposing event is necessary for HSCR to develop. New loci were also shown to be involved, such as ALDH1A2, already found to play a major role in the enteric nervous system. Finally, all the inherited CNVs were of maternal origin.ConclusionsOur results confirm a wide genetic heterogeneity in HSCR occurrence and support a role of candidate genes in expression regulation and cell signaling, thus contributing to depict further the molecular complexity of the genomic regions involved in the Enteric Nervous System development. The observed maternal transmission bias for HSCR associated CNVs supports the hypothesis that in females these variants might be more tolerated, requiring additional alterations to develop HSCR disease.

The Emerging Genetic Landscape of Hirschsprung Disease and Its Potential Clinical Applications

“…Importantly, there appears to be a higher burden of rare CNVs in patients with HSCR compared to controls and larger CNVs in syndromic HSCR compared to isolated HSCR ( 116 , 138 , 139 ). Besides those affecting known HSCR genes ( 18 , 19 , 116 , 139 , 140 ), several other genic CNVs have also been detected in patients with HSCR lately, whose contribution to HSCR are yet to be functionally characterized—though many of these are also associated with other neurodevelopmental disorders ( 18 ). Among these, deletions in 16p11.2 appear to be particularly interesting as at least six patients with HSCR have been reported to have deletion in this locus ( 18 , 141 ).…”

“…These groups of CNVs are becoming more and more detectable with the advent of SNP arrays and NGS as well as a plethora of bioinformatic tools and algorithms for accurately detecting CNVs (134)(135)(136)(137). Importantly, there appears to be a higher burden of rare CNVs in patients with HSCR compared to controls and larger CNVs in syndromic HSCR compared to isolated HSCR (116,138,139). Besides those affecting known HSCR genes (18,19,116,139,140), several other genic CNVs have also been detected in patients with HSCR lately, whose contribution to HSCR are yet to be functionally characterized-though many of these are also associated with other neurodevelopmental disorders (18).…”

Expression of the axon guidance factor Slit2 and its receptor Robo1 in patients with Hirschsprung disease

“…It is a typical developmental defect of the enteric nervous system (ENS) [2] . At present, the etiology of HD has not been fully elucidated, but most scholars believe that this disease is caused by an interaction between genetic factors and changes in the microenvironment of the intestinal wall [3] . It has been confirmed that changes in the intestinal microenvironment that are related to the occurrence of HD include changes in the extracellular matrix, cell adhesion molecules, nerve growth factor (NGF), neurotrophic factor-3, and tyrosine kinase C [4] …”

“…[2] At present, the etiology of HD has not been fully elucidated, but most scholars believe that this disease is caused by an interaction between genetic factors and changes in the microenvironment of the intestinal wall. [3] It has been confirmed that changes in the intestinal microenvironment that are related to the occurrence of HD include changes in the extracellular matrix, cell adhesion molecules, nerve growth factor (NGF), neurotrophic factor-3, and tyrosine kinase C. [4] Slit guidance ligand (Slit) is a protein that has been widely studied and is closely related to neurodevelopment. As one of the main members of the NGF family, Slit has a wide range of biological activities and plays vital roles in the migration, proliferation and differentiation of nerve cells, and the growth of axons.…”

Genetic variants in RET, ARHGEF3 and CTNNAL1, and relevant interaction networks, contribute to the risk of Hirschsprung disease

“…Whole exome sequencing study has revealed some novel HSCR genes, including DENND3, NCLN,NUP98 and TBATA, all of which might play a role in neuronal development [10]. More recently, new loci have been uncovered to be associated with Hirschsprung disease, such as ALDH1A2, PLD1, CASQ2 and CCT2 [11][12][13].…”