Genetic associations of neuropathic pain and sensory profile in a deeply phenotyped neuropathy cohort

Abstract

We aimed to investigate the genetic associations of neuropathic pain in a deeply phenotyped cohort. Participants with neuropathic pain were cases and compared with those exposed to injury or disease but without neuropathic pain as control subjects. Diabetic polyneuropathy was the most common aetiology of neuropathic pain. A standardised quantitative sensory testing protocol was used to categorize participants based on sensory profile. We performed genome-wide association study, and in a subset of participants, we undertook whole-exome sequencing targeting analyses of 45 known pain-related genes. In the genome-wide association study of diabetic neuropathy (N = 1541), a top significant association was found at the KCNT2 locus linked with pain intensity (rs114159097, P = 3.55 × 10 -8 ). Gene-based analysis revealed significant associations between LHX8 and TCF7L2 and neuropathic pain. Polygenic risk score for depression was associated with neuropathic pain in all participants. Polygenic risk score for C-reactive protein showed a positive association, while that for fasting insulin showed a negative association with neuropathic pain, in individuals with diabetic polyneuropathy. Gene burden analysis of candidate pain genes supported significant associations between rare variants in SCN9A and OPRM1 and neuropathic pain. Comparison of individuals with the "irritable" nociceptor profile to those with a "nonirritable" nociceptor profile identified a significantly associated variant (rs72669682, P = 4.39 × 10 -8 ) within the ANK2 gene. Our study on a deeply phenotyped cohort with neuropathic pain has confirmed genetic associations with the known pain-related genes KCNT2 , OPRM1 , and SCN9A and identified novel associations with LHX8 and ANK2 , genes not previously linked to pain and sensory profiles, respectively.

Keywords: Diabetes mellitus; GWAS; Neuropathic pain; Neuropathy; Sensory profile.

Figure 1.

Cohorts, recruitment pathways, inclusion, exclusion. (A) Flow diagram for participant recruitment for those included in genome-wide association study. IDNC and GeNeup were included as part of DOLORisk extended cohort as clinical phenotyping was highly aligned from inception with the DOLORisk cohort. Exclusions included those with no blood samples available at the time of genotyping; no or possible neuropathy; incomplete phenotype information; unaffected relatives; failed quality control; and duplicates. Neuropathic Pain NOS is defined as pain with a distinct neuroanatomically plausible distribution; however, no evidence of nerve injury found on clinical examination or specialised investigations. ¶Other diagnosis: neuropathic itch, lumbar radiculopathy, sciatica. (B) Flow diagram for participant recruitment for those included in whole exome sequencing. Participants with a potential Mendelian basis for rare and extreme cases of neuropathic pain were recruited, and unaffected family members were invited to participate (in case they were needed for future studies to understand segregation of variants in pedigrees) but were not included in this study's analysis and unaffected family members were excluded. Exclusions included: n = 338—no blood samples available; n = 76—failed genotyping quality control; n = 71—non-Europeans; n = 4—incomplete phenotype information. *Clinical phenotyping was not performed for the 20 unaffected relatives. ¶Other diagnosis: neuropathic itch and lumbar radiculopathy.

Figure 2.

GWAS of neuropathic pain intensity in diabetic neuropathy cohort showed a significant SNP rs114159097. (A) Manhattan plot at the SNP-level, genome-wide significant level was highlighted by a horizontal red line at a threshold of 5 × 10⁻⁸. (B) Regional plot for the top lead SNP in the GWAS of neuropathic pain intensity in diabetic neuropathy. Each SNP is colour-coded based on the highest r² to the top independent significant SNP. GWAS, genome-wide association study; SNP, single-nucleotide polymorphism.

Figure 3.

Manhattan plot (gene-based test) for binary measures of neuropathic pain vs no pain in diabetic neuropathy cohort revealed 2 significant genes. Input SNPs were mapped to 18,829 protein coding genes. Genome-wide significance (red dashed line in the plot) was defined at P = 0.05/18,829 = 2.655 × 10⁻⁶. SNP, single-nucleotide polymorphism.

Figure 4.

Protein structure pattern of the SCN9A and OPRM1 genes showing localisation of the rare variants within each channel. (A) The schematic representation of the human voltage-gated sodium channel Nav1.7 alpha-subunit (encoded by the SCN9A gene) shows novel SCN9A variants (not previously reported in the literature) in red, and gain of function mutations previously characterised in black (*). The channel consists of 4 domains, each comprising 6 transmembrane segments (1-6). Within each domain, the loops between the transmembrane segments 5 and 6 constitute the ion selectivity filter, whereas the voltage sensor domain is located in transmembrane segment 4. (B) Human OPRM1 (mu opioid receptor) channel, with variants depicted in black. Variants pathogenicity is reported according to ClinVar and functional studies, as shown in Supplementary Tables 11 and 12 (available at http://links.lww.com/PAIN/C169).

Figure 5.

QST irritable nociceptor vs nonirritable nociceptor phenotype GWAS and sensory loss vs hyperalgesia phenotype in the whole cohort. (A) Irritable nociceptor vs nonirritable nociceptor QST phenotype GWAS in the whole cohort Manhattan plot at the SNP-level, genome-wide significant level was highlighted by a horizontal red line at a threshold of 5 × 10⁻⁸. (B) Sensory loss vs hyperalgesia QST phenotype GWAS corrected for TCSS in the whole cohort Manhattan plot. GWAS, genome-wide association study; QST, quantitative sensory testing; SNP, single-nucleotide polymorphism; TCSS, Toronto Clinical Scoring System.