Biobank-driven genomic discovery yields new insight into atrial fibrillation biology

Abstract

To identify genetic variation underlying atrial fibrillation, the most common cardiac arrhythmia, we performed a genome-wide association study of >1,000,000 people, including 60,620 atrial fibrillation cases and 970,216 controls. We identified 142 independent risk variants at 111 loci and prioritized 151 functional candidate genes likely to be involved in atrial fibrillation. Many of the identified risk variants fall near genes where more deleterious mutations have been reported to cause serious heart defects in humans (GATA4, MYH6, NKX2-5, PITX2, TBX5)¹, or near genes important for striated muscle function and integrity (for example, CFL2, MYH7, PKP2, RBM20, SGCG, SSPN). Pathway and functional enrichment analyses also suggested that many of the putative atrial fibrillation genes act via cardiac structural remodeling, potentially in the form of an 'atrial cardiomyopathy'², either during fetal heart development or as a response to stress in the adult heart.

Fig. 1 |. Manhattan plot showing known (orange) and novel (red) loci associated with atrial fibrillation.

A total of 34,740,186 genetic variants (each represented by a dot) were tested, comparing 60,620 atrial fibrillation cases and 970,216 controls free of atrial fibrillation. The x axis represents the genome in physical order, and the y axis represents P values (–log₁₀(P value)) of association. The black horizontal dotted line represents a Bonferroni-corrected threshold of statistical significance corresponding to 1,000,000 independent tests (P< 5×10⁻⁸).

Fig. 2 |. Tissues, reconstituted gene sets, and regulatory elements implicated in atrial fibrillation.

a, Based on expression patterns across 37,427 human mRNA microarrays, DEPICT predicted genes within atrial fibrillation-associated loci to be highly expressed across various cardiac tissues. Tissues are grouped by type and significance. Red columns represent statistically significant tissues following Bonferroni correction (P< 0.05/209 = 0.0002). b, Top (P< 1× 10⁻⁶) reconstituted gene sets (out of 826 with FDR < 0.05 and after exclusion of ‘gene subnetworks’) found by DEPICT to be significantly enriched for genes in atrial fibrillation-associated loci. Each node, colored according to the permutation P value, represents a gene set and the gray connecting lines represent pairwise overlap of genes within the gene sets. c, Heatmap indicating the overlap between atrial fibrillation-associated risk variants and regulatory elements across 127 Roadmap Epigenomics tissues (each represented by a row) using GREGOR. Black indicates no data. PSC, pluripotent stem cell; ESC, embryonic stem cell.

Fig. 3 |. Significance of the expression enrichment for the atrial fibrillation candidate genes.

This figure compares the tissue-specific gene expression enrichment for the 151 biological candidate genes (colored dots) to a null distribution derived by randomly selecting the same number of genes from the whole genome or from the associated loci. Tissue-specific gene expression data (n = 25 tissues) were obtained from Genotype-Tissue Expression (GTEx) consortium data. The gray dots represent the P values for each of the permutations for the randomized tests (1,000 for both sampling scenarios for each tissue), and the blue and yellow lines represent the per-tissue P value thresholds comparable to a false positive rate of 0.05.

Fig. 4 |. Atrial fibrillation is associated with heterogeneous changes in left atrial myosin isoform expression.

a, Langendorff-perfused rabbit hearts from control (blue, top) or heart failure rabbits (red, bottom panel) were tested for atrial fibrillation inducibility and duration following burst pacing at 50 ms cycle length. Heart failure was induced by chronic left circumflex artery ligation and was allowed to develop over 6 weeks. During heart failure progression, severe left atrial hypertrophy occurred. b, Heart failure hearts (n = 4) developed long-lasting atrial fibrillation (> 60 s) when intra-atrial pressure was increased to 10 cm H₂O. Control hearts (n = 4) did not develop long-lasting atrial fibrillation until intra-atrial pressure was increased to 30 cm H₂O. The colored bars represent mean atrial fibrillation duration and the black error bars represent the corresponding standard errors of the mean. All individual data points are shown in the more detailed Supplementary Fig. 4. c, Western blotting for MYH7 expression (β -MyHC protein) indicates MYH7 expression exclusively in the remodeled heart failure left atrium. The experiment was repeated for two independent heart failure animals and two control animals with similar results. An uncropped version of the western blot is shown as Supplementary Fig. 5. d, Immunostaining and confocal microscopy revealed heterogeneous MYH7 expression (green) in the heart failure left atrium. Consistent with western blotting data, the heart failure right atrium did not express MYH7. The experiment was repeated for two independent heart failure animals with similar results. Supplementary Figure 6 shows an additional image. LAA, left atrial appendage; RAA, right atrial appendage; V, ventricle; AF, atrial fibrillation; HF, heart failure; SR, sinus rhythm; w, week; LA, left atrium; RA, right atrium.