Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria

Samia Nisar (1, 2) , Magali Torres (1, 2) , Alassane Thiam (3) , Bruno Pouvelle (1, 2) , Florian Rosier (1, 2) , Frederic Gallardo (1, 2) , Oumar Ka (4) , Babacar Mbengue (4) , Rokhaya Ndiaye Diallo (4) , Laura Brosseau (1, 2) , Salvatore Spicuglia (1, 2) , Alioune Dieye (4) , Sandrine Marquet (1, 2) , Pascal Rihet (1, 2)

1 TAGC - Theories and Approaches of Genomic Complexity
2 MarMaRa - Institut Marseille Maladies Rares
3 Institut Pasteur de Dakar
4 UCAD - Université Cheikh Anta Diop [Dakar, Sénégal]

Genome-wide association studies for severe malaria (SM) have identified 30 genetic variants mostly located in non-coding regions. Here, we aimed to identify potential causal genetic variants located in these loci and demonstrate their functional activity. We systematically investigated the regulatory effect of the SNPs in linkage disequilibrium (LD) with the malaria-associated genetic variants. Annotating and prioritizing genetic variants led to the identification of a regulatory region containing five ATP2B4 SNPs in LD with rs10900585. We found significant associations between SM and rs10900585 and our candidate SNPs (rs11240734, rs1541252, rs1541253, rs1541254, and rs1541255) in a Senegalese population. Then, we demonstrated that both individual SNPs and the combination of SNPs had regulatory effects. Moreover, CRISPR/Cas9-mediated deletion of this region decreased ATP2B4 transcript and protein levels and increased Ca2+ intracellular concentration in the K562 cell line. Our data demonstrate that severe malaria-associated genetic variants alter the expression of ATP2B4 encoding a plasma membrane calcium-transporting ATPase 4 (PMCA4) expressed on red blood cells. Altering the activity of this regulatory element affects the risk of SM, likely through calcium concentration effect on parasitaemia.

Keywords: regulatory element; enhancer; promoter; SNP; functional genomics; gene reporter; CRISPR-cas9; ATP2B4; calcium; malaria

Domains: Life Sciences [q-bio]; Human health and pathology; Life Sciences [q-bio]; Biochemistry, Molecular Biology

Samia Nisar, Magali Torres, Alassane Thiam, Bruno Pouvelle, Florian Rosier, et al.. Identification of ATP2B4 Regulatory Element Containing Functional Genetic Variants Associated with Severe Malaria. International Journal of Molecular Sciences, 2022, 23 (9), pp.4849. ⟨10.3390/ijms23094849⟩. ⟨hal-03690258⟩