Identification of potential candidate genes and pathways in atrioventricular nodal reentry tachycardia by whole-exome sequencing

Abstract

Background: Atrioventricular nodal reentry tachycardia (AVNRT) is the most common manifestation of paroxysmal supraventricular tachycardia (PSVT). Increasing data have indicated familial clustering and participation of genetic factors in AVNRT, and no pathogenic genes related to AVNRT have been reported.

Methods: Whole-exome sequencing (WES) was performed in 82 patients with AVNRT and 100 controls. Reference genes, genome-wide association analysis, gene-based collapsing, and pathway enrichment analysis were performed. A protein-protein interaction (PPI) network was then established; WES database in the UK Biobank and one only genetic study of AVNRT in Denmark were used for external data validation.

Results: Among 95 reference genes, 126 rare variants in 48 genes were identified in the cases (minor allele frequency < 0.001). Gene-based collapsing analysis and pathway enrichment analysis revealed six functional pathways related to AVNRT as with neuronal system/neurotransmitter release cycles and ion channel/cardiac conduction among the top 30 enriched pathways, and then 36 candidate pathogenic genes were selected. By combining with PPI analysis, 10 candidate genes were identified, including RYR2, NOS1, SCN1A, CFTR, EPHB4, ROBO1, PRKAG2, MMP2, ASPH, and ABCC8. From the UK Biobank database, 18 genes from candidate genes including SCN1A, PRKAG2, NOS1, and CFTR had rare variants in arrhythmias, and the rare variants in PIK3CB, GAD2, and HIP1R were in patients with PSVT. Moreover, one rare variant of RYR2 (c.4652A > G, p.Asn1551Ser) in our study was also detected in the Danish study. Considering the gene functional roles and external data validation, the most likely candidate genes were SCN1A, PRKAG2, RYR2, CFTR, NOS1, PIK3CB, GAD2, and HIP1R.

Conclusion: The preliminary results first revealed potential candidate genes such as SCN1A, PRKAG2, RYR2, CFTR, NOS1, PIK3CB, GAD2, and HIP1R, and the pathways mediated by these genes, including neuronal system/neurotransmitter release cycles or ion channels/cardiac conduction, might be involved in AVNRT.

Keywords: atrioventricular nodal reentry tachycardia, whole-exome sequencing; gene-based collapsing analysis, neurotransmitter release cycles pathway, ion channels-related pathway, ion channel genes.

FIGURE 1

The number of rare variants and cases in referential genes (A, MAF < 0.01; B, MAF < 0.001). The blue box represented the number of the rare variants of the referential gene, and the red box represented the numbers of the patients who carried the rare variants

FIGURE 2

Manhattan plot (A) and pathway enrichment analysis of KEGG (B) and Reactome (C). A, The Manhattan plot showed the significant locus along the genome (P < 10⁻⁶); B, The bubble chart of top30 pathways enriched by KEGG database; C, The bubble chart of top 30 pathways enriched by Reactome database

FIGURE 3

The top 30 pathways in Reactome pathway enrichment. A, The bubble chart of top30 pathways enriched by Reactome database (MAF < 0.001); B, The bubble chart of top30 pathways enriched by Reactome database (MAF < 0.001)

FIGURE 4

Protein‐protein interaction networks. A, The interaction network among the 36 candidate genes in gene‐based collapsing analysis and the 64 reference genes in the present study. B, The interaction network among the 37 candidate genes (including RYR2) in gene‐based collapsing analysis and the genes selected by pathway enrichment analysis in GWAS. C, The interaction network among the genes selected by (A) and (B)

FIGURE 5

The rare variants in the five candidate genes such as SCN1A, PRKAG2, RYR2, CFTR, and NOS1

FIGURE 6

Verification of candidate 37 genes in UK Biobank (A); the three of candidate burden genes, PIK3CB, GAD2, and HIP1R, showed the most significant enrichment in PSVT (P = 0.000174) among 791 phenotypes in UK Biobank (B)

FIGURE 7

Summary of the associated signal pathways and the potential links with AVNRT