De novo variants in congenital diaphragmatic hernia identify MYRF as a new syndrome and reveal genetic overlaps with other developmental disorders

Congenital diaphragmatic hernia (CDH) is a severe birth defect that is often accompanied by other congenital anomalies. Previous exome sequencing studies for CDH have supported a role of de novo damaging variants but did not identify any recurrently mutated genes. To investigate further the genetics of CDH, we analyzed de novo coding variants in 362 proband-parent trios including 271 new trios reported in this study. We identified four unrelated individuals with damaging de novo variants in MYRF (P = 5.3x10-8), including one likely gene-disrupting (LGD) and three deleterious missense (D-mis) variants. Eight additional individuals with de novo LGD or missense variants were identified from our other genetic studies or from the literature. Common phenotypes of MYRF de novo variant carriers include CDH, congenital heart disease and genitourinary abnormalities, suggesting that it represents a novel syndrome. MYRF is a membrane associated transcriptional factor highly expressed in developing diaphragm and is depleted of LGD variants in the general population. All de novo missense variants aggregated in two functional protein domains. Analyzing the transcriptome of patient-derived diaphragm fibroblast cells suggest that disease associated variants abolish the transcription factor activity. Furthermore, we showed that the remaining genes with damaging variants in CDH significantly overlap with genes implicated in other developmental disorders. Gene expression patterns and patient phenotypes support pleiotropic effects of damaging variants in these genes on CDH and other developmental disorders. Finally, functional enrichment analysis implicates the disruption of regulation of gene expression, kinase activities, intra-cellular signaling, and cytoskeleton organization as pathogenic mechanisms in CDH.

先天性膈疝（Congenital diaphragmatic hernia, CDH）是一种严重的出生缺陷，常伴随其他先天性异常。既往针对CDH开展的外显子组测序（exome sequencing）研究证实了新发有害变异（de novo damaging variants）的致病作用，但未发现任何复发性突变基因。为进一步阐明CDH的遗传致病机制，本研究对362例先证者-亲代三人组（proband-parent trios）开展了新发编码变异分析，其中包含本研究报道的271例新增三人组。本研究在4例无亲缘关系的患者中检出MYRF基因的新发有害变异（P=5.3×10^-8），其中包括1个可能致基因功能缺失（likely gene-disrupting, LGD）变异与3个有害错义（deleterious missense, D-mis）变异。通过本团队其他遗传学研究及文献检索，本研究额外检出8例携带MYRF基因新发LGD变异或错义变异的个体。携带MYRF新发变异的患者常见表型包括CDH、先天性心脏病及泌尿生殖系统异常，提示该基因变异可构成一种全新的综合征。MYRF基因编码一种膜结合转录因子（membrane associated transcriptional factor），在发育中的膈肌中高表达，且在普通人群中几乎不存在LGD变异。所有新发错义变异均聚集在两个蛋白质功能结构域内。对患者来源的膈肌成纤维细胞（diaphragm fibroblast cells）进行转录组（transcriptome）分析后发现，疾病相关变异可使该转录因子的活性完全丧失。此外，本研究证实，CDH患者中携带有害变异的其余基因，与其他发育障碍相关基因存在显著重叠。基因表达模式与患者表型均支持，这些基因的有害变异对CDH及其他发育障碍均存在多效性影响。最后，功能富集分析（functional enrichment analysis）显示，基因表达调控、激酶活性、细胞内信号转导（intra-cellular signaling）及细胞骨架组织的紊乱，是CDH的潜在致病机制。