Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes.
Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes.
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DOI：
10.1186/s13059-017-1174-6
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发表时间：
2017-03-08
期刊：
影响因子：
12.3
通讯作者：
Hofstra RM
中科院分区：
文献类型：
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作者：
Gui H;Schriemer D;Cheng WW;Chauhan RK;Antiňolo G;Berrios C;Bleda M;Brooks AS;Brouwer RW;Burns AJ;Cherny SS;Dopazo J;Eggen BJ;Griseri P;Jalloh B;Le TL;Lui VC;Luzón-Toro B;Matera I;Ngan ES;Pelet A;Ruiz-Ferrer M;Sham PC;Shepherd IT;So MT;Sribudiani Y;Tang CS;van den Hout MC;van der Linde HC;van Ham TJ;van IJcken WF;Verheij JB;Amiel J;Borrego S;Ceccherini I;Chakravarti A;Lyonnet S;Tam PK;Garcia-Barceló MM;Hofstra RM
先天性巨结肠(HSCR)是一种先天性肠梗阻，是由于肠神经系统(ENS)前体细胞在远端肠道内迁移、增殖、分化或存活失败所致。以前寻找HSCR相关基因的研究主要集中在ENS相关的途径上，因此不符合当前知识的基因往往被忽视。我们通过全外显子组测序(WES)、负荷测试、电子预测、斑马鱼中突变基因的体内无偏分析以及斑马鱼、小鼠和人类的表达分析来识别和验证新的HSCR基因。我们对24个HSCR三联体进行了从头突变(DNM)筛查。我们在21个不同的基因中识别了28个DNM。我们鉴定的DNM中有8个存在于主要的HSCR基因RET中，其余20个DNM存在于ENS中未报道的基因中。对所有12个错义或功能丧失的DNMS基因的敲除表明，4个基因(DENND3、NCLN、NUP98和TBATA)的同源基因对于斑马鱼ENS的发育是必不可少的，这一结果得到了CRISPR基因敲除的证实。这些基因也在人类和小鼠的肠道和/或ENS祖细胞中表达。重要的是，编码的蛋白质与中枢神经系统和ENS共享的神经元突起相连。我们的数据为HSCR病理学开辟了新的研究领域，并为ENS的发展提供了新的见解。此外，这项研究表明，对携带DNMS的基因进行功能分析是有必要描绘罕见复杂疾病的完整遗传结构的。本文的在线版本(doi：10.1186/s130590171174-6)包含补充材料，授权用户可以使用。
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. 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. 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. The online version of this article (doi:10.1186/s13059-017-1174-6) contains supplementary material, which is available to authorized users.