A novel locus in CSMD1 gene is associated with increased susceptibility to severe malaria in Malian children

Abstract

Background: Plasmodium falciparum malaria is still a leading cause of child mortality in sub-Saharan Africa. The clinical manifestations of malaria range from asymptomatic infection to severe disease. The variation in clinical presentation is partly attributed to host genetic factors with estimated narrow-sense heritability of 23%. Here, we investigate the associations between candidate gene polymorphisms and the likelihood of severe malaria (SM) in a cohort of Malian children.

Methods: Based on our previous genome-wide association studies (GWAS) analysis, candidate genes were selected for in-depth analysis using several criteria including gene-level GWAS scores, functional overlap with malaria pathogenesis, and evidence of association with protection or susceptibility to other infectious or inflammatory diseases. Single Nucleotide Polymorphisms (SNPs) residing within these genes were selected mainly based on p-values from previous severe malaria susceptibility GWAS studies and minor allele frequency (MAF) in West African populations.

Results: Of 182 candidate genes reported in our previous study, 11 genes and 22 SNPs residing in these genes were selected. The selected SNPs were genotyped using KASP technology in 477 DNA samples (87 SM and 390 controls). Logistic regression analysis revealed that a common intron variant, rs13340578 in CUB and Sushi Multi Domain (CSMD1) gene, is associated with increased odds of SM in recessive mode of inheritance (MAF = 0.42, OR = 1.8, 95% CI = [1.78, 1.84], p = 0.029). The SNP is in linkage disequilibrium (LD) with multiple variants with regulatory features.

Conclusion: Taken together, the current study showed that an intron variant rs13340578, residing in CSMD1 gene, is associated with increased susceptibility to malaria. This finding suggests that modified regulation of complement may contribute to malaria disease severity. Further studies are needed to identify the causal variants and the underlying molecular mechanisms.

Keywords: CSMD1; candidate gene; complement control; severe malaria; snps.

FIGURE 1

Workflow for the selection of candidate genes and SNPs.

FIGURE 2

Genomic features and domain structure of CSMD1 gene. The genomic features are plotted using Gvis package in R software based on Ensembl GRCh37 annotations. (A) Location of CSMD1 gene on chromosome 8p13 highlighted in red (position: 2792875-4851494); (B) Location of rs13340578 on CSMD1 gene 63.5 kb upstream to exon 4: ENSE00001541898 (3889621-3889427); (C) CSMD1 transcript and (D) Domain structure of CSMD1 gene. CUB domain is indicated by grey rectangle and Sushi domain is indicted by blue circles. The sushi domain (145-292aa) encoded by Exon 4 (ENSE00001541898) is indicated by arrow.

FIGURE 3

Genomic region containing the rs13340578 (250 kb upstream and downstream of rs13340578) identified by LD-proxy and Haploreg tools that explore proxy and putatively functional variants for a query variant based on a pre-calculated LD structure using the African reference population of 1,000 Genomes v.3. The purple circle indicates rs13340578 and the yellow circles indicate regulatory SNPs in the region.

FIGURE 4

MAF of putative regulatory SNPs in LD (r2 > 6) with rs13340578 that were identified by LDproxy (Purcell et al., 2007) and Haploreg v4.1 (Marees et al., 2018) tools using African populations in 1000 Genome project v.3. The reference locus (rs13340578) is highlighted in red and the SNPs are ordered based on their genetic distance up-stream and downstream of rs13340578.