Non-coding deletion induces 3D chromatin remodelling and PITX2 expression dysregulation associated with a new syndromic cardiac disorder

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In a first family (family#1), we identified 53 members of whom 17 present a new syndromic cardiac disorder characterized by electrical disorders (sinus node dysfunction, atrial fibrillation..) and developmental defects (atrial septal defect, valvopathy, left ventricle non-compaction..) following an autosomal dominant model. Six are implanted with a pacemaker and one experienced a sudden death at 43yo. Interestingly, 6 additional non-related families presenting the same phenotype have been also identified. Our aims are to identity the causal mutation and the molecular mechanism underlying this complex cardiac syndrome. Genetic study has been performed using whole genome sequencing (WGS). Based on transgenic mouse strains, we assessed the impact of Family#1 mutation on the phenotype and on gene expression. Then, we generated human cardiomyocytes derived iPS cells (CM-iPS) isogenic models to evaluate the epigenome (CUT&RUN and ATAC-seq), transcriptome (RNA-seq) and topological associated domain (TAD) remodelling (Hi-C). By WGS we uncovered a deletion of 15 kb in a gene desert area on 4q25, segregating in all affected relatives of Family#1. The 6 other families present overlapping deletions. Mouse model recapitulates the cardiac phenotype and exhibit an increase of Pitx2 expression in right atria, unchanged in left atria and a decrease in ventricle. Based on human CM-iPS models, epigenetic data highlight among the 15 kb deletion a unique open region containing a CTCF binding site, crucial for delimiting TAD boundaries. Hi-C assay reveals the fusion of 2 TADs and highlights new interactions between PITX2 and atrial specific regulatory elements. We identified a deletion located within a gene desert area associated with a new complex cardiac disorder. The CTCF binding site contained in the deletion seems key for the TAD border. The TAD remodelling leads to new (regulatory) interactions and expression dysregulation of PITX2. We describe a new molecular mechanism implying a yet unidentified non-coding regulatory element of PITX2 and responsible for a complex electrical and developmental cardiac syndrome.