PUBLICATION
Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes
- Authors
- Gui, H., Schriemer, D., Cheng, W.W., Chauhan, R.K., Antiňolo, G., Berrios, C., Bleda, M., Brooks, A.S., Brouwer, R.W., Burns, A.J., Cherny, S.S., Dopazo, J., Eggen, B.J., Griseri, P., Jalloh, B., Le, T.L., Lui, V.C., Luzón-Toro, B., Matera, I., Ngan, E.S., Pelet, A., Ruiz-Ferrer, M., Sham, P.C., Shepherd, I.T., So, M.T., Sribudiani, Y., Tang, C.S., van den Hout, M.C., van der Linde, H.C., van Ham, T.J., van IJcken, W.F., Verheij, J.B., Amiel, J., Borrego, S., Ceccherini, I., Chakravarti, A., Lyonnet, S., Tam, P.K., Garcia-Barceló, M.M., Hofstra, R.M.
- ID
- ZDB-PUB-170310-9
- Date
- 2017
- Source
- Genome biology 18: 48 (Journal)
- Registered Authors
- Cheng, William Wai-chun, Shepherd, Iain T., van Ham, Tjakko
- Keywords
- De novo mutations, ENS, Hirschsprung disease, Neural crest
- MeSH Terms
-
- Alleles
- Animals
- Case-Control Studies
- Computational Biology/methods
- DNA Mutational Analysis
- Disease Models, Animal
- Exome*
- Gene Knockout Techniques
- Genetic Predisposition to Disease*
- Genome-Wide Association Study*
- Genotype
- High-Throughput Nucleotide Sequencing*
- Hirschsprung Disease/genetics*
- Humans
- Mutation
- Phenotype
- Zebrafish
- PubMed
- 28274275 Full text @ Genome Biol.
Citation
Gui, H., Schriemer, D., Cheng, W.W., Chauhan, R.K., Antiňolo, G., Berrios, C., Bleda, M., Brooks, A.S., Brouwer, R.W., Burns, A.J., Cherny, S.S., Dopazo, J., Eggen, B.J., Griseri, P., Jalloh, B., Le, T.L., Lui, V.C., Luzón-Toro, B., Matera, I., Ngan, E.S., Pelet, A., Ruiz-Ferrer, M., Sham, P.C., Shepherd, I.T., So, M.T., Sribudiani, Y., Tang, C.S., van den Hout, M.C., van der Linde, H.C., van Ham, T.J., van IJcken, W.F., Verheij, J.B., Amiel, J., Borrego, S., Ceccherini, I., Chakravarti, A., Lyonnet, S., Tam, P.K., Garcia-Barceló, M.M., Hofstra, R.M. (2017) Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome biology. 18:48.
Abstract
Background Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored. We identify and validate novel HSCR genes using whole exome sequencing (WES), burden tests, in silico prediction, unbiased in vivo analyses of the mutated genes in zebrafish, and expression analyses in zebrafish, mouse, and human.
Results We performed de novo mutation (DNM) screening on 24 HSCR trios. We identify 28 DNMs in 21 different genes. Eight of the DNMs we identified occur in RET, the main HSCR gene, and the remaining 20 DNMs reside in genes not reported in the ENS. Knockdown of all 12 genes with missense or loss-of-function DNMs showed that the orthologs of four genes (DENND3, NCLN, NUP98, and TBATA) are indispensable for ENS development in zebrafish, and these results were confirmed by CRISPR knockout. These genes are also expressed in human and mouse gut and/or ENS progenitors. Importantly, the encoded proteins are linked to neuronal processes shared by the central nervous system and the ENS.
Conclusions Our data open new fields of investigation into HSCR pathology and provide novel insights into the development of the ENS. Moreover, the study demonstrates that functional analyses of genes carrying DNMs are warranted to delineate the full genetic architecture of rare complex diseases.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping