Loss-of-function variants in founder population highlight atrial myopathy as susceptibility to atrial fibrillation

Background

Atrial fibrillation (AF) is the most common cardiac arrhythmia, and it's associated with genes responsible for cardiac conduction, cardiogenesis, and cardiac structure. The Finnish population has evolved in relative isolation and undergone several bottlenecks, resulting in enrichment of deleterious variants. This facilitates identification of possible causal genes through protein-truncating variants that likely would not have been identified in other populations.

Purpose

To identify novel genetic associations with large effect on AF risk.

Methods

We accessed publicly available summary statistics on AF (ICD-10 code I48) from the FinnGen project R6, containing 28,670 AF cases and 135,821 controls. Then, we annotated all variants in the summary statistics and extracted variants that were predicted with a high effect impact (n=7,113). To account for multiple testing, a false discovery rate cutoff <10% was applied. The UK Biobank was assessed for comparison of allele frequencies. Afterwards, we investigated protein and single-cell RNA expression of the genes of interest in human atrial tissue. Human atrial tissue was obtained by us from 7 individuals and used for mass spectrometry-based proteomics, while single-nucleus RNA sequencing (snRNAseq) data from human hearts was acquired by Tucker [1].

Results

In a genome-wide association study (GWAS) focusing on loss-of function (LOF) variation, we report two LOF variants in the structural genes SYNPO2L and CTNNA3 with much higher allele frequencies compared to non-Finnish Europeans (85-fold and 80-fold enrichment, respectively). The variants increase the risk of AF considerably, which is emphasized as the two variants show the highest effect sizes of all GWAS variants ever associated with AF (SYNPO2L; odds ratio [OR] = 2.79, P-value = 1.32x10–8 and CTNNA3; OR = 2.43, P-value = 9.40x10–7), exceeding that of most clinical risk factors. We accessed phenome-wide association study (PheWAS) results on both variants. There was no association with other phenotypes for the SYNPO2L variant whereas the CTNNA3 variant showed suggestive association with valvular heart disease (P-value = 2.95x10–5). SYNPO2L and CTNNA3 exhibited high protein and RNA expression levels in atrial tissue and were predominantly expressed in cardiomyocytes (Fig. 1).

Conclusion

We identified novel associations between LOF variation in the structural genes SYNPO2L and CTNNA3 and AF. Our study showed how genetic examination of a European subpopulation facilitates discovery of genetic variants and pathophysiological understanding. The results underline the importance of thoroughly investigating subpopulations as unique variants with large effect sizes can be identified.

Funding Acknowledgement

Type of funding sources: Public hospital(s). Main funding source(s): This work was supported by the Research Foundation at Rigshospitalet and the Hallas-Møller Emerging Investigator Novo Nordisk.

Genome-wide multi-trait analysis on cardioembolic stroke identifies 47 novel loci

Background

Ischemic stroke is one of the leading causes of death and disability-adjusted life-years worldwide. It has several subtypes and cardioembolic stroke (CES) accounts for 15–30% of ischemic strokes. Atrial fibrillation (AF) is the most important risk factor for CES. AF increases the risk of stroke up to 5-fold and there is a substantial overlap in the aetiology of AF and CES. Large genome-wide association studies (GWAS) on AF have identified more than 150 common and rare genetic variants. However, the difficulty in acquiring large sample sizes of CES cohorts has hindered the genetic description of the disease.

Purpose

In this study, we mapped the genetics of CES to increase our understanding of the molecular biology driving the disease. By leveraging the large genetic cohorts of AF through a multi-trait analysis of AF and CES, we aimed to bypass the lack of statistical power for studying the genetics of CES.

Methods

First, we obtained the largest possible sample size of AF GWAS by conducting a meta-analysis on publicly available summary statistics from the FinnGen study (v5) and the largest multi-ethnic meta-analysis on AF to date. Summary statistics for stroke were obtained from the largest multi-ancestry GWAS on stroke to date, MEGASTROKE, which examined different ancestries and stroke subtypes. Multi-trait analysis requires a high genetic correlation. Genetic correlations between the different stroke summary statistics and the AF meta-analysis were assessed with LD Score Regression.

Second, we performed a joint meta-analysis of CES with MTAG using the CES summary statistics from MEGASTROKE and the AF GWAS meta-analysis. MTAG recalculates p-values and effect sizes for each trait separately by leveraging the covariation for correlated traits. The MTAG-computed summary statistics for CES and AF were subjected to genomic loci characterisation, with functional and annotation analysis carried out by FUMA.

Results

We show a high genetic correlation between CES and AF (rg = 0.88). Using MTAG, the GWAS meta-analysis of CES increased the effective sample size by almost 3 folds (n=24,639, Table 1). We discovered 50 CES loci whereof 47 are novel (Fig. 1). We mapped 101 genes to CES MTAG computed summary statistics, obtaining enrichment in gene sets involved in cardiac conduction and contraction, cardiac tissue development and cranial skeleton morphogenesis.

Conclusion

In conclusion, we identified 47 novel CES loci and demonstrated a substantial shared genetic variation with AF. We furthermore mapped 98 genes not previously linked to CES by AF. These results represent findings that potentially could be used for antithrombotic drug discovery and are a major advance in our understanding of the genetic underpinnings of CES

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): John and Birthe Meyer Foundation, the Research Foundation of the Heart Centre, Rigshospitalet, the Research Council at Rigshospitalet.The Hallas-Møller Emerging Investigator Novo Nordisk (NNF17OC0031204), Arvid Nilsson Foundation