Variants of IL6, IL10, FCN2, RNASE3, IL12B and IL17B loci are associated with Schistosoma mansoni worm burden in the Albert Nile region of Uganda

Abstract

Background: Individuals genetically susceptible to high schistosomiasis worm burden may contribute disproportionately to transmission and could be prioritized for control. Identifying genes involved may guide development of therapy.

Methodology/principal findings: A cohort of 606 children aged 10-15 years were recruited in the Albert Nile region of Uganda and assessed for Schistosoma mansoni worm burden using the Up-Converting Particle Lateral Flow (UCP-LF) test detecting circulating anodic antigen (CAA), point-of-care Circulating Cathodic Antigen (POC-CCA) and Kato-Katz tests. Whole genome genotyping was conducted on 326 children comprising the top and bottom 25% of worm burden. Linear models were fitted to identify variants associated with worm burden in preselected candidate genes. Expression quantitative trait locus (eQTL) analysis was conducted for candidate genes with UCP-LF worm burden included as a covariate. Single Nucleotide Polymorphism loci associated with UCP-LF CAA included IL6 rs2066992 (OR = 0.43, p = 0.0006) and rs7793163 (OR = 2.0, p = 0.0007); IL21 SNP kgp513476 (OR 1.79, p = 0.0025) and IL17B SNP kgp708159 (OR = 0.35, p = 0.0028). A haplotype in the IL10 locus was associated with lower worm burden (OR = 0.53, p = 0.015) and overlapped SNPs rs1800896, rs1800871 and rs1800872. Significant haplotypes (p<0.05, overlapping significant SNP) associated with worm burden were observed in IL6 and the Th17 pathway IL12B and IL17B genes. There were significant eQTL in the IL6, IL5, IL21, IL25 and IFNG regions.

Conclusions: Variants associated with S. mansoni worm burden were in IL6, FCN2, RNASE3, IL10, IL12B and IL17B gene loci. However only eQTL associations remained significant after Bonferroni correction. In summary, immune balance, pathogen recognition and Th17 pathways may play a role in modulating Schistosoma worm burden. Individuals carrying risk variants may be targeted first in allocation of control efforts to reduce the burden of schistosomiasis in the community.

Fig 1. Integrated IL6 locus Manhattan plot, conservation score and DNAse signal.

The Manhattan plot was plotted from haplotype p-values in Tables 3, S3 and S4. The strongest Manhattan plot signals are close to regions of high conservation scores and DNAse signals in the IL6 gene locus. Higher conservation scores are associated with conserved regions, where variants are more likely to be functional. High DNAse signal and scores are markers for regulatory and/or transcriptional activity since the chromatin has lost its condensed structure, exposing the DNA and making it accessible for binding of transcription factors.

Fig 2. IL5 and IL6 expression by phenotype and genotype.

Boxplot showing IL5 and IL6 expression by phenotype and genotype in the x-axis; while the y-axis is the normalized read count per gene on a log scale. In both cases there is a significant association with genotype but not with phenotype. (A) IL5 expression by phenotype and (B) IL5 expression by genotype of SNP rs201918473. (C) IL6 expression by phenotype (D) IL6 expression by rs114644824, there were no participants with a GG genotype at this SNP. Case = Those with CAA > = 30 pg/ml and Control = Samples with CAA<30 pg/ml [22,52].