Cluster Headache Genomewide Association Study and Meta-Analysis Identifies Eight Loci and Implicates Smoking as Causal Risk Factor

Abstract

Objective: The objective of this study was to aggregate data for the first genomewide association study meta-analysis of cluster headache, to identify genetic risk variants, and gain biological insights.

Methods: A total of 4,777 cases (3,348 men and 1,429 women) with clinically diagnosed cluster headache were recruited from 10 European and 1 East Asian cohorts. We first performed an inverse-variance genomewide association meta-analysis of 4,043 cases and 21,729 controls of European ancestry. In a secondary trans-ancestry meta-analysis, we included 734 cases and 9,846 controls of East Asian ancestry. Candidate causal genes were prioritized by 5 complementary methods: expression quantitative trait loci, transcriptome-wide association, fine-mapping of causal gene sets, genetically driven DNA methylation, and effects on protein structure. Gene set and tissue enrichment analyses, genetic correlation, genetic risk score analysis, and Mendelian randomization were part of the downstream analyses.

Results: The estimated single nucleotide polymorphism (SNP)-based heritability of cluster headache was 14.5%. We identified 9 independent signals in 7 genomewide significant loci in the primary meta-analysis, and one additional locus in the trans-ethnic meta-analysis. Five of the loci were previously known. The 20 genes prioritized as potentially causal for cluster headache showed enrichment to artery and brain tissue. Cluster headache was genetically correlated with cigarette smoking, risk-taking behavior, attention deficit hyperactivity disorder (ADHD), depression, and musculoskeletal pain. Mendelian randomization analysis indicated a causal effect of cigarette smoking intensity on cluster headache. Three of the identified loci were shared with migraine.

Interpretation: This first genomewide association study meta-analysis gives clues to the biological basis of cluster headache and indicates that smoking is a causal risk factor. ANN NEUROL 2023;94:713-726.

FIGURE 1

Manhattan plot showing genomewide significant loci associated with cluster headache in meta‐analysis of 10 European cohorts (4,043 cases and 21,729 controls). The horizontal axis shows the chromosomal position and the vertical axis shows the significance (−log10 p value) of tested markers. Each dot represents a genetic variant. The threshold for genomewide significance (p < 5 × 10⁻⁸) is indicated by a red dotted line, and genomewide significance loci are shown in blue. [Color figure can be viewed at www.annalsofneurology.org]

FIGURE 2

Quantile‐quantile (Q‐Q) plot for association with cluster headache in meta‐analysis of 10 European cohorts (4,043 cases and 21,729 controls). The horizontal axis shows −log10 p values expected under the null distribution. The vertical axis shows observed −log10 p values. Genomic inflation factor (λ) = 1.086. Red = common variants (MAF ≥ 5%), blue = low frequency variants (MAF = 0.5–5%), green = rare variants (MAF = 0.1–0.5%), purple = very rare variants (MAF < 0.1%). MAF, minor allele frequency; SNPs, single nucleotide polymorphisms. [Color figure can be viewed at www.annalsofneurology.org]

FIGURE 3

Manhattan plot showing genomewide significant loci associated with cluster headache in trans‐ancestry meta‐analysis (4,777 cases and 31,575 controls). The horizontal axis shows the chromosomal position and the vertical axis shows the significance (−log10 p value) of tested markers. Each dot represents a genetic variant. The threshold for genomewide significance (p < 5 × 10⁻⁸) is indicated by a red dotted line, and genomewide significance loci are shown in blue. Three genomewide significant variants (rs9307511 on chr4 and rs338106 and rs747974 on chr 13) were considered spurious associations as they lacked a supporting LD structure, were driven by the East Asian cohort alone, and were previously interpreted as being spurious associations in this cohort. LD = linkage disequilibrium. [Color figure can be viewed at www.annalsofneurology.org]

FIGURE 4

Miami plot of genetically driven DNA methylation genes in cluster headache. Computational prediction of genetically driven CpG methylation associated with cluster headache, using MetaMeth. Genes annotated to significant CpGs are shown (FDR‐corrected p value < 0.05). Horizontal axis shows the chromosomal position and the vertical axis shows significance (−log10 p value). The top panel shows predicted hypermethylation, whereas the bottom panel shows predicted hypomethylation. CpG = 5′‐C‐phosphate‐G‐3′; FDR = false discovery rate. [Color figure can be viewed at www.annalsofneurology.org]

FIGURE 5

Tissue enrichment for the putative causal genes. Enrichment of the 20 genes with supportive evidence for implication in cluster headache in DEG sets for 54 tissues from GTEX version 8. The analysis was performed using FUMA and based on pre‐calculated DEG sets defined by a two‐sided t test per tissue versus all other tissues. The red line shows the significance threshold after adjustment for multiple testing by Bonferroni correction (p = 0.05/54 tests = 9.26 × 10⁻⁴). DEG = differentially expressed gene; EBV = Epstein–Barr virus. [Color figure can be viewed at www.annalsofneurology.org]