Pathogen-Selected Polymorphisms in the PKLR Gene Are Associated with Mycobacterial Susceptibility in Brazilian and African Populations

Background: Pyruvate kinase (PK) gene (PKLR) is a key player in glycolysis controlling the integrity of erythrocytes. Due to Plasmodium selection, mutations for PK deficiency, leading to hemolytic anemia, are associated with resistance to malaria in sub-Saharan Africa and also with susceptibility to intracellular pathogens in experimental models. We investigated whether PKLR malaria-protective single nucleotide polymorphisms (SNPs) are associated with susceptibility to leprosy in Brazil and tuberculosis in Africa. Methods: We fine-mapped the PKLR variants and performed independent case-control studies in different populations across Brazil and Mozambique by Real-Time PCR. We also applied natural selection tests in the PKLR genomic region and evaluated serum iron proteins levels among subjects. Findings: Haplotype T/G/G (rs1052176/rs4971072/rs11264359) is associated with leprosy susceptibility in Rio de Janeiro (OR=1.26, p=0.02) and Salvador (OR=1.35, p=0.07), and with tuberculosis in Mozambique (OR=1.52, p=0.07). TT (rs1052176) was the common risk genotype within populations. Increased frequency of T/G/G was observed in Africa and Brazilian African-descendants compared to Europeans, and Brazilian European-descendants, suggesting the presence of selective footprints in the PKLR. We observed evidences of balancing selection in Africans (Tajima’s D) and positive selection in the HCN3 gene (xpEHH>2 in Europe), of which 6 SNPs are PKLR eQTLs. Ferritin and haptoglobin levels presented a subtle variation in TT (rs1052176) carriers. Interpretation: We provide evidence that PKLR malaria-resistant loci in Africans contribute to mycobacterial susceptibility in African descent population and also highlight, for first, PKLR as a susceptibility gene for leprosy and TB. Funding: Brazilian National Council for Scientific and Technological Development, Coordination for the Improvement of Higher Education Personnel, Foundation for Research Support of the State of Rio de Janeiro, and the Brazilian Ministry of Health. Funding Statement: This study was financed by the Brazilian National Council for Scientific and Technological Development (CNPq; 421852/2017-2018; 307489/2018-3), Brazilian Coordination for the Improvement of Higher Education Personnel (CAPES), Foundation for Research Support of the State of Rio de Janeiro (FAPERJ;E-26/203.053/2016; E-26/203.172/2017), and the National Fund for Health/Brazilian Ministry of Health (MS/SCTIE/DECIT; 404277/2012-8). Declaration of Interests: The authors declare no conflict of interest. Ethics Approval Statement: All collected samples and procedures described in this study were approved by local ethics boards and the Brazilian National Board for Ethics in Research. A written informed consent was obtained from all voluntary participants (Rio de Janeiro – IRB protocol - Fiocruz 151/01; Rondonopolis – ILSL 172/09; Salvador – CEP50/2010 and CONEP 11019; Manaus – 555.620 - 13/03/2013; and Mozambique – No 399/CNBS/11).