TY - JOUR
T1 - Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes
AU - Gui, Hongsheng
AU - Schriemer, Duco
AU - Cheng, William W
AU - Chauhan, Rajendra K
AU - Antiňolo, Guillermo
AU - Berrios, Courtney
AU - Bleda, Marta
AU - Brooks, Alice S
AU - Brouwer, Rutger W W
AU - Burns, Alan J
AU - Cherny, Stacey S
AU - Dopazo, Joaquin
AU - Eggen, Bart J L
AU - Griseri, Paola
AU - Jalloh, Binta
AU - Le, Thuy-Linh
AU - Lui, Vincent C H
AU - Luzón-Toro, Berta
AU - Matera, Ivana
AU - Ngan, Elly S W
AU - Pelet, Anna
AU - Ruiz-Ferrer, Macarena
AU - Sham, Pak C
AU - Shepherd, Iain T
AU - So, Man-Ting
AU - Sribudiani, Yunia
AU - Tang, Clara S M
AU - van den Hout, Mirjam C G N
AU - van der Linde, Herma C
AU - van Ham, Tjakko J
AU - van IJcken, Wilfred F J
AU - Verheij, Joke B G M
AU - Amiel, Jeanne
AU - Borrego, Salud
AU - Ceccherini, Isabella
AU - Chakravarti, Aravinda
AU - Lyonnet, Stanislas
AU - Tam, Paul K H
AU - Garcia-Barceló, Maria-Mercè
AU - Hofstra, Robert M W
PY - 2017/3/8
Y1 - 2017/3/8
N2 - 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.
AB - 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.
KW - Alleles
KW - Animals
KW - Case-Control Studies
KW - Computational Biology
KW - DNA Mutational Analysis
KW - Disease Models, Animal
KW - Exome
KW - Gene Knockout Techniques
KW - Genetic Predisposition to Disease
KW - Genome-Wide Association Study
KW - Genotype
KW - High-Throughput Nucleotide Sequencing
KW - Hirschsprung Disease
KW - Humans
KW - Mutation
KW - Phenotype
KW - Zebrafish
KW - Journal Article
U2 - 10.1186/s13059-017-1174-6
DO - 10.1186/s13059-017-1174-6
M3 - Article
C2 - 28274275
VL - 18
SP - 48
JO - Genome Biology
JF - Genome Biology
SN - 1474-7596
IS - 1
ER -