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

Sabrina Baaklini; Sarwat Afridi; Thy Ngoc Nguyen; Felix Koukouikila-Koussounda; Mathieu Ndounga; Jean Imbert; Magali Torres; Lydie Pradel; Francine Ntoumi; Pascal Rihet

doi:10.1371/journal.pone.0187818

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

PLoS One. 2017 Nov 9;12(11):e0187818. doi: 10.1371/journal.pone.0187818. eCollection 2017.

Authors

Sabrina Baaklini^{1

2}, Sarwat Afridi^{1

2}, Thy Ngoc Nguyen^{1

2}, Felix Koukouikila-Koussounda^{3

4}, Mathieu Ndounga⁵, Jean Imbert^{1

2}, Magali Torres^{1

2}, Lydie Pradel^{1

2}, Francine Ntoumi^{3

4

6}, Pascal Rihet^{1

2}

Affiliations

¹ INSERM, UMR1090 TAGC, Marseille, France.
² Aix-Marseille Université, Marseille, France.
³ Fondation Congolaise pour la Recherche Médicale (FCRM), Villa D6, Cité OMS AFRO, Brazzaville, République du Congo.
⁴ Faculté des Sciences et Techniques, Université Marien Ngouabi, Brazzaville, République du Congo.
⁵ Unité de Recherche sur le Paludisme, Centre d'Etudes sur les Ressources Végétales (CERVE), Brazzaville, République du Congo.
⁶ Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany.

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.

MeSH terms

Binding Sites
Congo
Core Binding Factor Alpha 3 Subunit / metabolism
Female
Genetic Predisposition to Disease
HEK293 Cells
Humans
K562 Cells
Malaria, Falciparum / genetics*
Male
Natural Cytotoxicity Triggering Receptor 3 / genetics*
Natural Cytotoxicity Triggering Receptor 3 / metabolism*
Polymorphism, Single Nucleotide*
Promoter Regions, Genetic*
STAT4 Transcription Factor / metabolism

Substances

Core Binding Factor Alpha 3 Subunit
NCR3 protein, human
Natural Cytotoxicity Triggering Receptor 3
Runx3 protein, human
STAT4 Transcription Factor
STAT4 protein, human

Grants and funding

This work was supported by Institut National de la Santé et de la Recherche Médicale (Inserm) and Aix-Marseille University. SB, SA and TNN were supported by a PhD fellowship from the French ministry of research and technology, the Higher Education Commission from Pakistan, and the Vietnamese government, respectively. FKK, MD and FN are members of the Central African Network on Tuberculosis, HIV/AIDS and Malaria, CANTAM, supported by EDCTP. The funding body had no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.