Multimodal Characterization of Cardiac-Neurodevelopmental Genes - PROJECT SUMMARY: Congenital heart disease (CHD) is the most common congenital anomaly and affects approximately 1% of people. Neurodevelopmental delay and disability (NDD) are the most common extracardiac complications among people with CHD, but clinical and surgical factors currently only explain approximately one-third of NDD risk. Without knowledge regarding the molecular mechanisms that underly shared risk for altered heart and brain development, people with congenital heart disease cannot benefit from early diagnosis, accurate prognosis, and targeted treatments. Many genetic syndromes affect heart and brain development; we anticipate that these seemingly divergent organs will share dysregulated gene expression during development. Therefore, we propose to identify shared nodal biology disrupted in cardiac and neuronal progenitors with haploinsufficiency of CHD7 or KMT2D, causes of genetic syndromes characterized by CHD/NDD. In support of this goal, we have already generated human induced pluripotent stem cells (iPSCs) that are haploinsufficient for CHD7 or KMT2D. With these reagents in hand, we will combine our expertise in iPSC methods and computational biology to determine sources of shared genetic risk for heart and brain development, as well as advance our approaches for functional assessment of variants. The Overall Aim of this proposal is advance our understanding of the connection between CHD and NDD by (1) identifying mechanisms by which syndromic CHD genes lead to alterations in both heart and brain development, and (2) comparing the yield of transcriptomics, epigenetic and high-throughput high-dimensional cell imaging to assess the functional impact of variants of uncertain significance from people with CHD in iPSC models of heart and brain development. First, we will compare single nucleus and bulk transcriptomics, chromatin accessibility, and cell morphology features of iPSCs that are haploinsufficient for CHD7 and KMT2D as they differentiate to cardiac and neuronal progenitors. This combination of techniques will identify shared and divergent direct targets of CHD7 and KMT2D in each cell lineage. Next, we will compare the ability of transcriptomic and cell morphology approaches to determine whether missense variants of uncertain significance from people with CHD are likely pathogenic, as cell morphology assessment can be higher throughput and significantly lower in cost than transcriptomics. Together this proposal will employ multivariate analysis of biological data in a way that builds upon the ongoing work supported by my K08 award and generates new results that will support a future independent R01 grant application in 2027. These results will contribute towards the long-term objective of understanding the molecular basis of heart development and human disease to improve diagnosis, better define risks, and inspire novel treatments for patients.
