Exploring digenic inheritance in arrhythmogenic cardiomyopathy

Abstract

Background: Arrhythmogenic cardiomyopathy (ACM) is an inherited genetic disorder, characterized by the substitution of heart muscle with fibro-fatty tissue and severe ventricular arrhythmias, often leading to heart failure and sudden cardiac death. ACM is considered a monogenic disorder, but the low penetrance of mutations identified in patients suggests the involvement of additional genetic or environmental factors.

Methods: We used whole exome sequencing to investigate digenic inheritance in two ACM families where previous diagnostic tests have revealed a PKP2 mutation in all affected and some healthy individuals. In family members with PKP2 mutations we determined all genes that harbor variants in affected but not in healthy carriers or vice versa. We computationally prioritized the most likely candidates, focusing on known ACM genes and genes related to PKP2 through protein interactions, functional relationships, or shared biological processes.

Results: We identified four candidate genes in family 1, namely DAG1, DAB2IP, CTBP2 and TCF25, and eleven candidate genes in family 2. The most promising gene in the second family is TTN, a gene previously associated with ACM, in which the affected individual harbors two rare deleterious-predicted missense variants, one of which is located in the protein's only serine kinase domain.

Conclusions: In this study we report genes that might act as digenic players in ACM pathogenesis, on the basis of co-segregation with PKP2 mutations. Validation in larger cohorts is still required to prove the utility of this model.

Keywords: ACM; Arrhythmogenic cardiomyopathy; Digenic inheritance; Exome sequencing; PKP2.

Fig. 1

Pedigrees of the two families analyzed in this study. Only labeled individuals were sequenced. +: Heterozygous variant, filled black symbols: affected individuals; white symbols with +: carrier individuals; white empty symbols: healthy individuals. Left: Family 1 (Fam1); the blue + symbol indicates the presence of the NM_004572.3(PKP2):c.2013delC variant, the orange + symbol indicates the presence of the four Fam1 variants ENSP00000312435.2(DAG1):p.Leu86Phe, ENSP00000263347.7(TCF25):p.Ser390Phe, ENSP00000259371.2(DAB2IP):p.Asp10Gly, ENSP00000357816.5(CTBP2):p.Gly70Arg. Right: Family 2 (Fam2); the pink + symbol indicates the presence of the NG_009000.1(PKP2):c.2569_2577 + 41del variant, the green + symbol indicates the presence of the ENSP00000434586.1(TTN):p.Gln24857His and the ENSP00000434586.1(TTN):p.Arg23483His variants

Fig. 2

Methods summary. Whole exome sequencing and variant calling was performed for each individual in both families. For each family, genes are selected that have at least one variant with a high or moderate variant impact, that differ between healthy and affected PKP2 carriers, that have a coverage of at least 10X, and that are expressed in the heart. These genes are filtered to include only genes related to ACM or PKP2 and are computationally prioritized. Results are presented in Table 2

Fig. 3

Structure of the titin kinase domain (PDB 1tki chain A). Functional residues are represented as ball and stick, D24874 is the catalytic aspartate. The ATP binding site includes residue K24783 as well as the nearby yellow loop. The calcium/calmodulin binding helix is colored blue, the helix in orange blocks the ATP binding site in this autoinhibited conformation. Residue Q24857 is solvent exposed on the side opposite to the functional residues