NKX2-5 congenital heart disease mutations show diverse loss and gain of epigenomic, biochemical and chromatin search functions underpinning pathogenicity

Congenital heart defects (CHD) occur in ∼1% of live births, with both inherited and acquired mutations and environmental factors known to contribute to causation. However, network perturbations and epigenetic changes in CHD remain poorly characterised. We report an integrated functional-epigenomics approach to understanding CHD, focusing on the cardiac homeodomain (HD) family transcription factor NKX2-5, mutations in which cause diverse congenital heart structural and conduction defects. We selected twelve NKX2-5 CHD-associated variants affecting different residue classes - DNA base-contacting, backbone-contacting, helix-stabilizing residues of the homeodomain, and those affecting other conserved protein:protein interaction (PPI) domains. In HL-1 cardiomyocytes, we profiled DNA targets of NKX2-5 wild type (WT) and variant proteins genome-wide using DamID, their DNA binding affinity and specificity using comprehensive protein binding microarrays, and PPI with known NKX2-5 cofactors using yeast 2-hybrid assay. We also undertook deep profiling of chromatin search and binding dynamics using single molecule tracking. Variants showed highly diverse but also class-specific behaviours with a range of severities. All variants failed to bind many WT targets but retained binding to a subset of core cardiomyocyte-related WT NKX2-5 targets, as well as hundreds of unique “off-targets”, in part via a regulatory logic that included changes to DNA binding site specificity, homodimerization and lost or enhanced cofactor interactions. All variants tested showed altered chromatin search functions. Our data suggest that complex residue-by-residue scale epigenomic, biochemical and chromatin search perturbations, involving both loss- and gain-of-function, contribute to CHD phenotypes. These findings may inform precision molecular therapeutic approaches in patients with CHD.