Functional single nucleotide polymorphisms in CACNA2D3 and other autophagy-related genes are associated with leprosy among Brazilians

Background Autophagy is a crucial host defense mechanism against intracellular pathogens, including Mycobacterium leprae . Genetic variants in autophagy-related genes have been associated with susceptibility to leprosy, but their functional relevance remains incompletely understood. Methodology/Principal findings We investigate the association of single nucleotide polymorphisms (SNPs) in three genes involved in autophagy, CACNA2D3 , LRRK2 and IRGM . A total of 3,480 individuals from three Brazilian populations were included in a case-control design. We confirmed that the SNP rs1449325 in CACNA2D3 was associated with leprosy per se protection in the overdominant model (ORoverdTC = 0.70; p = 0.00443) in Rio de Janeiro, which was then replicated in samples from Manaus and Rondonópolis. Curiously, CC genotype of rs1449325 was associated with leprosy per se risk in the recessive model in Rio de Janeiro (ORrecCC = 1.51; p = 0.00476), Manaus (ORrecCC = 3.06; p = 1.44E-07) and Rondonópolis (ORrecCC = 1.50; p = 0.0240). Data from public eQTLs databases and gene expression analysis from whole blood samples suggested increasing CACNA2D3 expression levels with TT < CT < CC genotypes. In the literature, CACNA2D3 mRNA levels are positively correlated with calcium influx levels. Taken together, the genetic and expression data support the hypothesis that either low or high levels of calcium leads to M. leprae susceptibility. Associations of SNPs in LRRK2 and IRGM genes were also observed in the Rio de janeiro population, although not confirmed in replication cohorts. However, a protective effect of the LRRK2 haplotype C/G/G/T/G (rs7308720/rs7133914/rs10878434/rs3761863/rs7962370), apparently driven by rs3761863 T allele, was observed in Rio de Janeiro (ORhap = 0.44; p = 0.0121). This allele was associated with lower levels of LRRK2 mRNA expression in skin biopsy samples from leprosy patients, as well as in tibial nerve and fibroblast samples of healthy individuals from public databases. Conclusions/Significance Our results highlight a dual role of calcium signaling and autophagy gene regulation in leprosy susceptibility. Variants in CACNA2D3 and LRRK2 modulate host response to M. leprae infection and represent potential targets for improved therapeutic and preventive approaches.