Human candidate gene polymorphisms and risk of severe malaria in children in Kilifi, Kenya: a case-control association study

Abstract

SummaryBackgroundHuman genetic factors are important determinants of malaria risk. We investigated associations between multiple candidate polymorphisms—many related to the structure or function of red blood cells—and risk for severe Plasmodium falciparum malaria and its specific phenotypes, including cerebral malaria, severe malaria anaemia, and respiratory distress.MethodsWe did a case-control study in Kilifi County, Kenya. We recruited as cases children presenting with severe malaria to the high-dependency ward of Kilifi County Hospital. We included as controls infants born in the local community between Aug 1, 2006, and Sept 30, 2010, who were part of a genetics study. We tested for associations between a range of candidate malaria-protective genes and risk for severe malaria and its specific phenotypes. We used a permutation approach to account for multiple comparisons between polymorphisms and severe malaria. We judged p values less than 0·005 significant for the primary analysis of the association between candidate genes and severe malaria.FindingsBetween June 11, 1995, and June 12, 2008, 2244 children with severe malaria were recruited to the study, and 3949 infants were included as controls. Overall, 263 (12%) of 2244 children with severe malaria died in hospital, including 196 (16%) of 1233 with cerebral malaria. We investigated 121 polymorphisms in 70 candidate severe malaria-associated genes. We found significant associations between risk for severe malaria overall and polymorphisms in 15 genes or locations, of which most were related to red blood cells: ABO, ATP2B4, ARL14, CD40LG, FREM3, INPP4B, G6PD, HBA (both HBA1 and HBA2), HBB, IL10, LPHN2 (also known as ADGRL2), LOC727982, RPS6KL1, CAND1, and GNAS. Combined, these genetic associations accounted for 5·2% of the variance in risk for developing severe malaria among individuals in the general population. We confirmed established associations between severe malaria and sickle-cell trait (odds ratio [OR] 0·15, 95% CI 0·11–0·20; p=2·61 × 10−58), blood group O (0·74, 0·66–0·82; p=6·26 × 10−8), and –α3·7-thalassaemia (0·83, 0·76–0·90; p=2·06 × 10−6). We also found strong associations between overall risk of severe malaria and polymorphisms in both ATP2B4 (OR 0·76, 95% CI 0·63–0·92; p=0·001) and FREM3 (0·64, 0·53–0·79; p=3·18 × 10−14). The association with FREM3 could be accounted for by linkage disequilibrium with a complex structural mutation within the glycophorin gene region (comprising GYPA, GYPB, and GYPE) that encodes for the rare Dantu blood group antigen. Heterozygosity for Dantu was associated with risk for severe malaria (OR 0·57, 95% CI 0·49–0·68; p=3·22 × 10−11), as was homozygosity (0·26, 0·11–0·62; p=0·002).InterpretationBoth ATP2B4 and the Dantu blood group antigen are associated with the structure and function of red blood cells. ATP2B4 codes for plasma membrane calcium-transporting ATPase 4 (the major calcium pump on red blood cells) and the glycophorins are ligands for parasites to invade red blood cells. Future work should aim at uncov...

Human genetics and malaria resistance

“…In a recent GWAS conducted in north-east Tanzania, novel variants were identified in the immune genes IL-23R and IL-12RB2 which were specifically found to be associated with protection against severe malaria anaemia (Ravenhall et al 2018). These genes encode vital pro-inflammatory cytokine receptors which have important immunoregulatory roles in protective immunity against malaria infections (Luty et al 2000;Malaguarnera et al 2002;Ong'echa et al 2008;Zhang et al 2010;Munde et al 2017). In the same cohort, signals of recent positive selection were also found at several loci within the MHC region, immune-related genes that could potentially inform malaria vaccine development.…”

Red blood cell tension controlsPlasmodium falciparuminvasion and protects against severe malaria in the Dantu blood group

“…gDNA was extracted from whole blood using a QIAmp 96 DNA QIcube HT kit on a QIAcube HT System (QIAGEN) following manufacturer's instructions. The restriction fragment length polymorphism (RFLP) assay to detect genotypes at the Dantu marker SNP, rs186873296, has been previously described 4,5 . Briefly, PCR amplification of the region of interest containing rs186873296 was performed using the following primers: Trapping durations were kept short (< 10 seconds) to minimise any possible detrimental effect of local heating because at full laser power, a few degrees Celsius of heating are expected locally around the laser beam focus).…”

“…Recently, we showed that a novel blood group variant, Dantu, provides 74% protection against all forms of severe malaria in homozygous individuals [3][4][5] . This is a similar degree of protection to sickle cell trait and considerably greater than the most advanced malaria vaccine, but until now the mechanism of protection has been unknown.…”

The effects of dyslipidaemia and cholesterol modulation on erythrocyte susceptibility to malaria parasite infection

“…There has been, however, a growing appreciation in the past few years that parasite binding to the erythrocyte, stimulates biophysical changes in the red cell that likely facilitate entry making it energetically more favourable (Koch, et al 2017, Sisquella, et al 2017. Further, several key polymorphisms that protect against malaria infection may do so directly by modulating erythrocyte biophysical properties (Genton, et al 1995, Ndila, et al 2018. These polymorphisms are generally associated with changes in either the erythrocyte cytoskeleton (Genton, et al 1995) or membrane surface proteins, such as components of the glycophorin family, a well-studied group of erythrocyte surface receptors that are known to be under natural selection, likely from malaria (Baum, et al 2002, Malaria Genomic Epidemiology, et al 2015, Ndila, et al 2018.…”

“…Further, several key polymorphisms that protect against malaria infection may do so directly by modulating erythrocyte biophysical properties (Genton, et al 1995, Ndila, et al 2018. These polymorphisms are generally associated with changes in either the erythrocyte cytoskeleton (Genton, et al 1995) or membrane surface proteins, such as components of the glycophorin family, a well-studied group of erythrocyte surface receptors that are known to be under natural selection, likely from malaria (Baum, et al 2002, Malaria Genomic Epidemiology, et al 2015, Ndila, et al 2018. To date, however, there is little study of the effects of lipid changes in mediating susceptibility to invasion and whether changes in erythrocyte membrane lipid composition might be associated with changes in efficiency of malaria parasite entry.…”