A human YEATS4 variant confers resistance to TST and IGRA conversion despite Mycobacterium tuberculosis exposure

Abstract

Background: Despite sustained exposure to Mycobacterium tuberculosis (Mtb), some individuals-so-called resisters-have persistently negative results for the tuberculin skin test (TST) and interferon-gamma release assays (IGRAs). "Resistance to immune conversion" is the best-known clinical correlate for absence of Mtb transmission and protection from tuberculosis (TB). We investigated the human genetic basis of this phenotype by hypothesizing that resisters living with HIV, a major risk factor for TB, would be enriched in genotypes conferring resistance.

Methods: We enrolled two cohorts of people living with HIV (PWH), consisting of 55 resisters and 100 controls-either positive for TST and IGRA or with a history of TB-from South Africa, and 66 resisters and 57 controls from Haiti, two regions where TB is hyperendemic. All study participants underwent whole-genome sequencing (WGS). We performed a genome-wide association study (GWAS) of the resister phenotype, focusing on a comprehensive set of 320,629 common protein-altering and regulatory variants.

Results: We identified a cluster of variants on chromosome 12q15, including rs622656, associated with the resister phenotype in both South Africa and Haiti. A meta-analysis revealed that the C allele of rs622656 was associated with the resister phenotype with an odds ratio (OR) of 4.35 (95% CI: 2.44-7.69) (P = 2.47 × 10^-7). The frequency of the C allele in the combined sample was 0.11, and all four CC homozygotes in our sample were resisters. Consistently, we found a significant depletion of homozygous carriers of the rs622656-C resistance-associated allele in three cohorts of HIV-negative TB patients from Haiti, Morocco, and the UK Biobank. In silico analysis suggested that the rs622656-C resistance-associated allele increased the translation of the nearby YEATS4 gene by suppressing an upstream open reading frame. YEATS4 has been shown to play a role in innate lymphoid cell differentiation, a leukocyte subset. We confirmed experimentally that the rs622656-C resistance-associated allele increased the activity of the reporter gene in HEK293T cells.

Conclusions: We report a new cluster of variants on chromosome 12q15, overlapping the YEATS4 gene, strongly associated with the resister phenotype in two populations of PWH. Our results contribute to the understanding of the molecular mechanisms that block transmission of Mtb.

Keywords: Mycobacterium tuberculosis; YEATS4; Genome-wide association study; Human immunodeficiency virus; IGRA; Regulatory variants; Resister; TST; Whole genome sequencing.

Fig. 1

Principal component analysis of the South African and Haitian cohorts using, as a reference, A 2504 individuals from the 1000 Genomes project (KGP) and B 504 individuals of African origin from the KGP. Principal component (PC) scores for the study individuals were predicted from the PC loadings estimated on the reference sample and projected onto the reference sample PC space

Fig. 2

Manhattan plots for the genome-wide association study of candidate common variants and the resister phenotype in the South African sample, assuming A co-dominant, B dominant, and C recessive models of inheritance. The red Line indicates the Bonferroni-corrected threshold of 9.9 × 10⁻⁷. The black dotted line represents the suggestive significance threshold of 10⁻⁴

Fig. 3

Manhattan plot of the GWAS meta-analysis for the South African and Haitian cohorts, assuming a co-dominant inheritance model. The red line indicates the Bonferroni-corrected threshold of 9.9 × 10⁻⁷

Fig. 4

A LocusZoom plot showing the region of the 12q15 signal in the meta-analysis. The LD values displayed correspond to r² calculated for the combined cohort; B proportion of resisters, by genotype, for rs622656 in the combined cohort

Fig. 5

rs622565 affects a uORF in the 5′UTR of the YEATS4 mRNA. A Schematic representation of the 5′UTR of YEATS4 and the effect of rs622656. B Mean normalized RL activity for the C allele (orange) vs. the T allele (blue), nine replicates. The difference in activity between the cells transfected with the T allele vs. the C allele was tested using a one-sided paired samples Wilcoxon test.