Identification of a novel variant in N-cadherin associated with dilated cardiomyopathy

Abstract

Background: Dilated cardiomyopathy (DCM), which is a major cause of heart failure, is a primary cardiac muscle disease with high morbidity and mortality rates. DCM is a genetically heritable disease and more than 10 gene ontologies have been implicated in DCM. CDH2 encodes N-cadherin and belongs to a superfamily of transmembrane proteins that mediate cell-cell adhesion in a calcium-dependent manner. Deficiency of CDH2 is associated with arrhythmogenic right ventricular cardiomyopathy (OMIM: 618920) and agenesis of the corpus callosum, cardiac, ocular, and genital syndrome (OMIM: 618929). However, there have been no reports of isolated DCM associated with CDH2 deficiency.

Methods: We performed whole exome sequencing in a 12-year-old girl with non-syndromic DCM and her unaffected parents. Variants in both known DCM-related genes and novel candidate genes were analyzed and pathogenicity confirmation experiments were performed.

Results: No pathogenic/likely pathogenic variant in known DCM-related genes was identified in the patient. We found a de novo variant in a candidate gene CDH2 in the patient, namely, c.474G>C/p.Lys158Asn (NM_001792.5). This variant has not been reported in the ClinVar or Human Gene Mutation Database (HGMD). CDH2 p.Lys158Asn was found in the conserved domain of N-cadherin, which is associated with the hydrolysis of the precursor segment and interference with adhesiveness. Furthermore, we tested the expression and efficiency of cell-cell adhesion while overexpressing the CDH2 Lys158Asn mutant and two previously reported variants in CDH2 as positive controls. The adhesion efficiency was considerably reduced in the presence of the mutated CDH2 protein compared with wild-type CDH2 protein, which suggested that the mutated CDH2 protein's adhesion capacity was impaired. The variant was probably pathogenic after integrating clinical manifestations, genetic analysis, and functional tests.

Conclusion: We identified a CDH2 variant in DCM. We observed a new clinical symptom associated with N-cadherin deficiency and broadened the genetic spectra of DCM.

Keywords: N-cadherin; cell-cell adhesion; de novo variant; dilated cardiomyopathy; whole exome sequencing.

Figure 1

Variant filtration workflow and the phenotype of the patient. (A) Variant filtration workflow employed in this study. AF: allele frequency; Het, heterozygous; Hom, homozygous; CH, compound heterozygous; DCM, dilated cardiomyopathy; ACMG, American College of Medical Genetics and Genomics. (B) The echocardiography showed an apical four-chamber view of the proband's indicating dilation of the right ventricle. RV, right ventricle; RA, right atrium; LV, left ventricle; LA, left atrium. (C) Electrocardiogram (ECG) showed sinus rhythm, P wave changes, and ST-T changes. (D) Sanger sequencing confirmed that the variant CDH2 c.474G>C was heterozygous in the proband and not inherited from her parents. The arrows indicated the mutated nucleotides.

Figure 2

Genetic analysis and functional tests of the de novo variant (c.474G>C/p.Lys158Asn) in CDH2. (A) Sequence alignment of human CDH2 and other species shows the conservation of the affected residue (p.Lys158Asn). (B) Schematic representation of the topological domains of CDH2 protein. Rare heterozygous CDH2 variants linked to ARVC, ACOGs, Peters anomaly, and brain arteriovenous malformation were annotated. (C) The structure of CDH2 and Lys158Asn mutant. The human CDH2 protein structure was modeled from the “AlphaFold Protein Structure Database” (AlphaFoldDB: P19022, https://alphafold.com/). The structure was aligned with the solution structure of neural cadherin prodomain (PDB: 1OP4) and analyzed using UCSF chimera. (D) The cell-cell adhesion efficiency of the wild-type and CDH2 variations. The significance value was set as p < 0.05 (*), p < 0.01 (**), and p < 0.001 (***).