Genomic and Functional Architecture of Congenital Heart Disease



 DESCRIPTION (provided by applicant): Congenital heart disease (CHD) is the most common cause of non-infectious death in newborns. Although there is evidence to support a genetic etiology, only a small fraction of the disease burden is explained by known inherited mutations and copy number variations. Clinically, however, severe CHD often occurs sporadically and impairs reproductive fitness, suggesting that de novo mutations play a crucial role in its etiology Using next generation exome sequencing, we recently reported a high burden of de novo mutations in severely affected CHD patients in genes expressed at high levels in the developing murine heart (Zaidi et al., Nature, 2013; PMCID# 3706629). We found a marked excess of such mutations in nine chromatin- modifying genes involved in H3K4 or H3K27 methylation or H2BK120 ubiquitination. As defects in the genetic control of cardiac morphogenesis underlie a majority of CHD, it is essential that once new causative genes are discovered we study their effect in an animal model. The Xenopus heart allows the rapid study of effects of gene dosage on specific stages of cardiac morphogenesis. The overall goal of this proposal is to more fully characterize the genomic and functional architecture of severe CHD. Towards this end, we hypothesize that hitherto yet uncharacterized de novo and inherited mutations will be identifiable by next generation sequencing, and that the newly identified genes will act at specific stages of morphogenesis to disrupt normal heart development. In Specific Aim 1, using our self-written, validated Bayesian algorithm, we will identify novel de novo mutations that are present in probands, but are absent in parents. We have obtained samples from a further 445 case (NHLBI's Pediatric Cardiac Genomics Consortium) and 645 control trios (unaffected siblings of autism cases from Simon Simplex Autism Collection). These new trios will be used to expand and independently validate our original cohort. Per our power calculations, an additional 445 trios should identify 44 new (95% CI, 22-66) risk-associated genes. In Specific Aim 2, we will investigate the contribution of rare transmitted variants to CHD by clustering our cohort with CEU HapMap3 (European) individuals, and studying both dominantly and recessively inherited rare variants using population allele frequencies of <0.1% and/or d1%, with or without stratifying for mutation type or heart expression. In Specific Aim 3, we will study the effect of knocking down three of the nine histone-modifying genes, namely Wdr5 (H3K4 methylation), Kdm5b (H3K4 demethylation), and Rnf20 (H2BK120 ubiquitination), on development of the Xenopus heart. We will examine for heart looping, left-right patterning, number, structure, and function of cilia, and heart morphology and function. The Department of Genetics, HHMI, and my mentor, Dr. Richard Lifton, have provided a far- reaching intellectual environment, including enrichment activities, and biostatistical, bioinformatic, and technical support, which together should ensure successful completion. We envisage that the studies should not only improve our understanding of heart development, but may also translate into improved patient care.