Neanderthal introgression in SCN9A impacts mechanical pain sensitivity

Abstract

The Nav1.7 voltage-gated sodium channel plays a key role in nociception. Three functional variants in the SCN9A gene (encoding M932L, V991L, and D1908G in Nav1.7), have recently been identified as stemming from Neanderthal introgression and to associate with pain symptomatology in UK BioBank data. In 1000 genomes data, these variants are absent in Europeans but common in Latin Americans. Analysing high-density genotype data from 7594 Latin Americans, we characterized Neanderthal introgression in SCN9A. We find that tracts of introgression occur on a Native American genomic background, have an average length of ~123 kb and overlap the M932L, V991L, and D1908G coding positions. Furthermore, we measured experimentally six pain thresholds in 1623 healthy Colombians. We found that Neanderthal ancestry in SCN9A is significantly associated with a lower mechanical pain threshold after sensitization with mustard oil and evidence of additivity of effects across Nav1.7 variants. Our findings support the reported association of Neanderthal Nav1.7 variants with clinical pain, define a specific sensory modality affected by archaic introgression in SCN9A and are consistent with independent effects of the Neanderthal variants on Nav1.7 function.

Fig. 1. Frequency of the D1908G, V991L and M932L Neanderthal variants in SCN9A chromosome segments of Native American, European and African ancestry.

These frequencies were estimated on a total of 12,136 chromosomes (from both the QST and CANDELA cohorts). Additional information on these segments is provided in Table 2. The bottom panel shows the location of the D1908G, V991L and M932L variants in SCN9A (exons are indicated as boxes/vertical lines) using GRCh37 (hg19) genomic coordinates of human chromosome 2 (physical coordinates 2:167,051,695–167,232,511).

Fig. 2. Neanderthal introgression around SCN9A and association with mechanical pain threshold after sensitization by mustard oil (POST_MPT) in the QST cohort.

Only 700 Kb of the 4.18 Mb studied around SCN9A (Table 2) are shown as this region shows the maximum levels of introgression. This region covers the physical coordinates 2:166,500,000-167,200,000 of the GRCh37 (hg19) reference genome. The location of the D1908G, V991L and M932L Neanderthal variants is indicated with vertical dashed lines. The top panel (a) shows (in violet) the frequency of Neanderthal introgression tracts (piling-up tracts across individuals). A similar profile is seen in the CANDELA cohort (Supplementary Fig. 3). The middle panel (b) shows the location of genes in the region with boxes/vertical lines indicating exons (physical coordinates obtained from GENCODE version 34). The bottom panel (c) shows association P values of Neanderthal introgression segments with POST_MPT (on n = 1552 independent samples). The threshold for significance is indicated by a dashed red line (P = 9.75 × 10⁻³, corrected for multiple testing). Significantly associated segments are labelled (further details on these segments are provided in Supplementary Data 8).

Fig. 3. Effect (Beta regression coefficients) of Neanderthal Nav1.7 variants on the pain thresholds evaluated in the QST sample.

a D1908G, b V991L-M932L (considered as a single locus, as indicated in the text). Association P values from the regression analysis (on n = 1623 independent samples) are reported on the right of each panel. Filled red squares indicate Betas exceeding the multiple-testing-corrected significance threshold (P value < 9.75 × 10⁻³). Empty red squares are nominally significant (P value < 5 × 10⁻²). Blue lines indicate 95% confidence intervals of Betas. PPT pressure pain threshold, HPT heat pain threshold, MPT mechanical pain threshold, WUR wind-up ratio, POST pain threshold after sensitization with mustard oil, POST_MPT adjusted POST_MPT adjusted for MPT.

Fig. 4. Five types of association tests of Neanderthal ancestry in the SCN9A region with mechanical pain threshold after sensitization with mustard oil (POST_MPT).

The squares show the Beta regression coefficients for each test of association (estimated on n = 1552 independent samples); their P values are reported on the right of each panel. Filled red squares indicate Betas exceeding the multiple-testing-corrected significance threshold (P value < 9.75 × 10⁻³). Empty red squares are nominally significant (P value < 5 × 10⁻²). Blue lines indicate 95% confidence intervals of Betas. a Effect of D1908G or V991L-M932L in single-locus tests (Fig. 3). b Effects of D1908G and of V991L-M932L in a joint test including these two loci. c Effects of the four possible haplotypes carrying Neanderthal variants at either loci (the haplotype not carrying any Neanderthal variant is shown as its complementary: any haplotype carrying at least one Neanderthal variant). d Effect of the total number of Neanderthal alleles at D1908G and V991L-M932L (Fig. 5). e Effect of Neanderthal introgression segment 33 (from Fig. 2; test results for other introgression segments are shown in Supplementary Data 8).

Fig. 5. Total number of Neanderthal alleles at D1908G and V991L-M932L, and mechanical pain threshold after sensitization with mustard oil (POST_MPT).

Distribution of POST_MPT values for each value of total number of Neanderthal alleles at the two loci (0–4—sample sizes are given between parentheses). Red vertical lines indicate the mean POST_MPT for individuals with 0–4 Neanderthal alleles (horizontal black whiskers indicate standard errors). The trend observed is significant: regression Beta = −0.075, P value < 7.2 × 10⁻⁴ (reported in Fig. 4d).