598 De Novo Mutations in Histone-Modifying Genes in Congenital Heart Disease Zaidi et al Nature. 2013;498:220–223. C ongenital heart disease (CHD) remains a leading cause of morbidity and mortality in childhood and is the most common human birth defect, affecting nearly 1% of all live births worldwide. The morphogenetic events that are disrupted during cardiogenesis that lead to CHD are now partially understood, as are many of the molec- ular networks that guide normal heart development. 1–4 Studies of rare Mendelian forms of familial CHD, as well as CHD associated with stereotypic syndromes, have re- vealed numerous single-gene mutations that cause CHD. 1–5 However, mutations in these genes are infrequent in the more common sporadic form of CHD. Despite epidemio- logical evidence for an inherited component in sporadic CHD, the contribution of inherited variants or de novo mutations in the setting of CHD has been unclear. A recent landmark article in Nature 6 begins to tackle this question by using modern genetic approaches and suggests that roughly 10% of sporadic CHD cases have de novo muta- tions that contribute significantly to the disease process. The ability to perform DNA sequencing at a reasonable cost now allows the interrogation of rare, as well as common, variants in large populations. Although many complex traits have been studied using whole-genome or exome sequenc- ing, a rate-limiting step in the CHD field has been acquisi- tion of sufficient numbers of cases for meaningful statistical analysis. To address this, a National Heart, Lung, and Blood Institute–funded consortium of centers was established to re- cruit patients and parents into common studies to reveal the genetic underpinnings of CHD (Pediatric Cardiac Genomics Consortium). 7 In the first report from this group, Zaidi et al 6 sequenced the entire protein-coding exome from 362 trios of patients with a variety of sporadic, more complex CHDs and their unaffected parents, as well as a similar number of trios without CHD. Although inherited variants may contribute, the consortium focused on de novo mutations present in an index case but absent in both unaffected parents, with the notion that the new genetic variant may be contributing to the appearance of CHD. Using strict statistical criteria, they identified many de novo mutations that were predicted to be damaging to the open reading frame, in many cases causing premature trunca- tion, frameshifts, or splicing abnormalities. Genes expressed at high levels in the heart (as assessed by RNA sequencing of mouse embryonic hearts) had a higher rate of de novo mutations than those expressed at lower levels, increasing confidence that the affected genes could be involved in heart development. In total, 28 genes harboring de novo mutations in the CHD probands were implicated with high confidence, particularly considering the comparison with sequencing of the control trios. Remarkably, the set of de novo variants that Zaidi et al 6 identified with a high degree of statistical confidence were mainly in genes encoding proteins that are related to histone modifications, which generally function to regulate gene ex- pression. 8 In particular, 5 of the genes identified encode pro- teins that participate in the writing, erasing, or reading of a particular histone modification, trimethylation of lysine 4 of histone H3 (H3K4me3). This modification is largely associ- ated with transcriptionally active genes, and thus its regulation is critical for most cellular processes. The 5 genes included MLL2, which catalyzes the deposition of H3K4me3, WDR5, which is part of the MLL complex, CHD7, which recognizes the histone modification, and KDM5A and KDM5B, both in- volved in removing the methylation mark. Additional genes involved in other histone modifications or other aspects of chromatin remodeling were also identified. Mapping of his- tone modifications in cardiac differentiation has pinpointed the timing and location of H3K4me3 and other histone modi- fications, 9,10 and it is clear that many aspects of cardiac differ- entiation (and by extension development) would be affected by abnormally regulated H3K4me3. Thus, the results from Zaidi et al 6 implicate potential disease-causing de novo muta- tions in the epigenetic machinery involved in controlling gene expression during development. Because epigenetic modifications are used to quantita- tively regulate transcription, the findings of Zaidi et al 6 rein- force a theme involving gene dosage that has emerged from years of more traditional human genetic studies with CHD. The majority of previously identified single-gene causes of CHD involve heterozygous mutations of transcription fac- tors, typically resulting in haploinsufficiency of central de- velopmental regulators. Given that cardiogenesis seems to Congenital Heart Disease Entering a New Era of Human Genetics Benoit G. Bruneau, Deepak Srivastava (Circ Res. 2014;114:598-599.) © 2014 American Heart Association, Inc. Circulation Research is available at http://circres.ahajournals.org DOI: 10.1161/CIRCRESAHA.113.303060 Commentaries on Cutting Edge Science The opinions expressed in this Commentary are not necessarily those of the editors or of the American Heart Association. Commentaries serve as a forum in which experts highlight and discuss articles (published here and elsewhere) that the editors of Circulation Research feel are of particular significance to cardiovascular medicine. Commentaries are edited by Aruni Bhatnagar & Ali J. Marian. From the Gladstone Institute of Cardiovascular Disease, San Francisco, CA (B.G.B., D.S.); and Departments of Pediatrics (B.G.B., D.S.), Biochemistry and Biophysics (D.S.), and Cardiovascular Research Institute (B.G.B.), University of California, San Francisco. Correspondence to Benoit G. Bruneau, PhD, Gladstone Institute of Cardiovascular Disease, 1650 Owens St, San Francisco, CA 94158 (e-mail bbruneau@gladstone.ucsf.edu); or Deepak Srivastava, MD, Gladstone Institute of Cardiovascular Disease, 1650 Owens St, San Francisco, CA 94158 (e-mail dsrivastava@gladstone.ucsf.edu). at University of Cape Town Libraries on September 28, 2015 http://circres.ahajournals.org/ Downloaded from