Genome-wide association analysis of pain severity in dysmenorrhea identifies association at chromosome 1p13.2, near the nerve growth factor locus

Abstract

Dysmenorrhea is a common chronic pelvic pain syndrome affecting women of childbearing potential. Family studies suggest that genetic background influences the severity of dysmenorrhea, but genetic predisposition and molecular mechanisms underlying dysmenorrhea are not understood. In this study, we conduct the first genome-wide association study to identify genetic factors associated with dysmenorrhea pain severity. A cohort of females of European descent (n = 11,891) aged 18 to 45 years rated their average dysmenorrhea pain severity. We used a linear regression model adjusting for age and body mass index, identifying one genome-wide significant (P < 5 × 10) association (rs7523086, P = 4.1 × 10, effect size 0.1 [95% confidence interval, 0.074-0.126]). This single nucleotide polymorphism is colocalising with NGF, encoding nerve growth factor. The presence of one risk allele corresponds to a predicted 0.1-point increase in pain intensity on a 4-point ordinal pain scale. The putative effects on NGF function and/or expression remain unknown. However, genetic variation colocalises with active epigenetic marks in fat and ovary tissues, and expression levels in aorta tissue of a noncoding RNA flanking NGF correlate. Participants reporting extreme dysmenorrhea pain were more likely to report being positive for endometriosis, polycystic ovarian syndrome, depression, and other psychiatric disorders. Our results indicate that dysmenorrhea pain severity is partly genetically determined. NGF already has an established role in chronic pain disorders, and our findings suggest that NGF may be an important mediator for gynaecological/pelvic pain in the viscera.

Figure 1.

Manhattan plot of genome-wide significant loci for dysmenorrhea pain severity. The gray line corresponds to P = 5 × 10⁻⁸, and results above this threshold are shown in red. Gene labels are annotated as the nearby genes to the significant SNPs.

Figure 2.

Quantile–quantile plots. (A) Observed P values vs theoretical P values under the null hypothesis of no association, plotted on a log scale. The solid red line is shown with a slope of 1, and dashed red lines represent a 95% confidence envelope under the assumption that the test results are independent. (B) Q-Q plot of residuals from the null model vs a normal distribution.

Figure 3.

Regional plot depicting genome-wide significant association with dysmenorrhea pain severity at chromosome 1p13.2. Colour symbols indicate linkage disequilibrium with the index single nucleotide polymorphism, which is labeled and coloured purple. Open circles indicate imputed variants, filled circles indicate partially genotyped variants, and filled squares indicate fully genotyped variants. Plots were generated using LocusZoom. Results are in NCBI Build 37 coordinates.

Figure 4.

Regional plot depicting epigenetic annotations for genome-wide significant dysmenorrhea pain severity association at chr1p13.2. Chromosome and cytogenetic position (hg19/NCBI Build 37) and gene annotation are depicted (GENCODE v17), alongside dysmenorrhea pain SNPs in high linkage disequilibrium (r² > 0.8) with index association variant (each single nucleotide polymorphism [SNP] represented by one blue line). Further annotation of 1p13.2 with available regulatory information from ENCODE and the Roadmap Epigenomics Project indicate that the dysmenorrhea pain SNPs colocalise with epigenetic marks; marks captured in human ovary (pink peaks) and mesenchymal adipose nuclei (teal peaks), and DNase I hypersensitivity (DHS) mark in myometrium (black peaks); tissues that are relevant to dysmenorrhea pathophysiology. H3K27 acetylation (H3K27Ac), H3K4 monomethylation (H3K4Me1), and H3K4 trimethylation (H3K4Me3) ChIP-seq peaks indicate localised epigenetic activity. For comparison, the level of epigenetic activity inferred from histone modification state (ChromHMM) in peripheral blood mononuclear (PB MNC) cells and various brain tissues is provided (see ChromHMM key panel for further definition, image produced using WashU EpiGenome Browser).

Figure 5.

Expression profiling of noncoding RNA RP4-663N10.1. (A) Variant rs6328 is in high linkage disequilibrium with rs7523086 (the index association identified by dysmenorrhea pain severity GWAS) is an expression quantitative loci (eQTL) in aorta tissue for RP4-663N10.1, a noncoding RNA that flanks NGF at chromosome 1q13.2. (B) Expression profiles across 53 cell and tissue types for RP4-663N10.1 (i) and NGF (ii) (images from GTeX Portal).

Figure 6.

Hypothesised function mechanism for genetic link between dysmenorrhea pain and NGF. (A) Genome-wide association study identified a significant association between genetic variant rs7523086 and severity of pain in dysmenorrhea suggesting by biological evidence the involvement of NGF signalling pathways. Expression of a noncoding RNA (RP4-663N10.1) correlates with variant allelic status, but the link between the noncoding RNA (1), and between the genetic variant and NGF (2) remains to be established. (B) The association of rs7523086 with dysmenorrhea pain severity implicates a contribution to primary dysmenorrhea; however, it is unclear whether rs7523086 is important in pelvic disease pathogenesis (including endometriosis, uterine fibroids, or polycystic ovarian syndrome) or contributes to the severity of secondary dysmenorrhea associated with these conditions.