Beyond genome-wide scan: Association of a cis-regulatory NCR3 variant with mild malaria in a population living in the Republic of Congo

Abstract

Linkage studies have revealed a linkage of mild malaria to chromosome 6p21 that contains the NCR3 gene encoding a natural killer cell receptor, whereas NCR3-412G>C (rs2736191) located in its promoter region was found to be associated with malaria in Burkina Faso. Here we confirmed the association of rs2736191 with mild malaria in a Congolese cohort and investigated its potential cis-regulatory effect. Luciferase assay results indicated that rs2736191-G allele had a significantly increased promoter activity compared to rs2736191-C allele. Furthermore, EMSAs demonstrated an altered binding of two nuclear protein complexes to the rs2736191-C allele in comparison to rs2736191-G allele. Finally, after in silico identification of transcription factor candidates, pull-down western blot experiments confirmed that both STAT4 and RUNX3 bind the region encompassing rs2736191 with a higher affinity for the G allele. To our knowledge, this is the first report that explored the functional role of rs2736191. These results support the hypothesis that genetic variation within natural killer cell receptors alters malaria resistance in humans.

NCR3 polymorphism, haematological parameters, and severe malaria in Senegalese patients

“…If we assume that there is no association between NCR3-412 and severe malaria, we should keep in mind that there is an association between NCR3-412 and mild malaria ( Baaklini et al, 2017 ; Delahaye et al, 2007 ). This means that there is no allele frequency difference between mild malaria patients and severe malaria patients, on the one hand, and that there is an allele frequency difference between mild malaria patients and individuals with an asymptomatic infection, on the other hand.…”

“…The primer pair to amplify DNA fragments containing NCR3-412 ( rs2736191 ) was designed as described ( Baaklini et al, 2017 ); PCR amplification of DNA fragments was performed with forward (5′-GATGGGTCTGGGTACTGGTG-3′) and reverse (5′-GGGATCTGAGCAGTGAGGTC-3′) primers, respectively. For Hemoglobin S (rs334) and hemoglobin C ( rs33930165 ), the forward primer was 5′-CTGAGGGTTTGAAGTCCAAC- 3′, and the reverse one was 5′-CAGCATCAGGAGTGGACAG-3′.…”

“…NCR3 that is also located within chromosome 6p21.3 has been shown to be associated with mild malaria in Burkina Faso ( Delahaye et al, 2007 ) and in the Republic of Congo ( Baaklini et al, 2017 ). Both population-based and family-based studies showed that NCR3-412C carriers had more frequent mild malaria attacks than NCR3-412GG individuals.…”

“…Both population-based and family-based studies showed that NCR3-412C carriers had more frequent mild malaria attacks than NCR3-412GG individuals. In addition, Baaklini et al (2017) showed that NCR3-412 ( rs2736191 ) alters both the binding of transcription factors to the DNA and the promoter activity. Moreover, Mavoungou et al (2007) reported that NKp30 encoded by NCR3 is involved in the recognition of P. falciparum- infected red blood cells by natural killer (NK) cells.…”

Activatory Receptor NKp30 Predicts NK Cell Activation During Controlled Human Malaria Infection

“…Population based studies conducted in sub-Saharan Africa have identified a single nucleotide polymorphism (SNP) in the promoter for the NCR3 gene that encodes NKp30 that is associated with an increased number of clinical, uncomplicated malaria episodes in individuals over 5 years old (27)(28)(29). The combined data are highly suggestive for a potential functional role of NKp30-mediated NK cells in malaria.…”