First genome-wide association study of non-severe malaria in two birth cohorts in Benin.

Abstract

Recent research efforts to identify genes involved in the susceptibility to P. falciparum malaria have focused on severe forms of malaria, with several genome-wide association studies (GWAS) and multi-center analyses published this past decade. Here we present the first GWAS performed on mild malaria susceptibility in young children, designed to identify genetic variants involved in innate immunity or innate resistance mechanisms. Two cohorts of infants from southern Benin (525 and 250 individuals respectively), used as discovery and replication cohorts, were closely followed from birth to 18-24 months of age, with an assessment of a space-and time-dependent risk of exposure to vector bites. GWAS was performed on 15.5 million genotyped and imputed variants, with the susceptibility of infants to mild malaria attacks and to malaria infections as a whole (both symptomatic and asymptomatic). Infant susceptibility to malaria was assessed by considering all malaria events occurring during the follow-up using a Cox-model for recurrent events. We found strong statistical support for a role of PTPRT, a tyrosine phosphatase receptors involved in STAT3 pathway, with the protection against both mild malaria attacks and malaria infections (p=9.70x10-8 and p=1.78x10-7 respectively in the discovery cohort, and both p < 0.05 in the replication cohort). Furthermore, our study highlights several other genes, among them, UROC1, ACER3 and the PLAG2 cluster, whose biological functions are relevant in malaria infection. Results show that despite the difficulty of setting up such longitudinal field studies, GWAS on non-severe malaria can successfully identify new candidate genes and inform physiological mechanisms underlying natural protection against malaria.\n\nAUTHOR SUMMARYMalaria remains a major worldwide public health problem with circa 219 million cases and 435,000 deaths per year. As for many infectious diseases, the genetics of the host plays a role in the disease course. So far, most studies on such genetic factors focused on severe malaria forms. Our study aimed to find factors associated with simple forms (asymptomatic forms and uncomplicated clinical forms). We used dense genome-wide data of two cohorts of infants closely followed during two years in Benin, and we incorporated an environmental risk of exposure estimated at individual level from entomological, climatic, and environmental data. This allowed us to unravel several genes that appear to play a role in the susceptibility to malaria infection, thus demonstrating the feasibility of a genome-wide approach on non-severe forms. Functional studies are needed to confirm the role of the genetic factors highlighted here. Some of these genes represent interesting targets for future prevention strategies and drug development.