Genome-Wide Scan for Visceral Leishmaniasis in Mixed-Breed Dogs Identifies Candidate Genes Involved in T Helper Cells and Macrophage Signaling

Abstract

We conducted a genome-wide scan for visceral leishmaniasis in mixed-breed dogs from a highly endemic area in Brazil using 149,648 single nucleotide polymorphism (SNP) markers genotyped in 20 cases and 28 controls. Using a mixed model approach, we found two candidate loci on canine autosomes 1 and 2. The positional association on chromosome 2 mapped to a predicted DNAse sensitive site in CD14+ monocytes that serve as a cis-regulatory element for the expression of interleukin alpha receptors 2 (IL2RA) and 15 (IL15RA). Both interleukins were previously found to lead to protective T helper 1 cell (Th1) response against Leishmania spp. in humans and mice. The associated marker on chromosome 1 was located between two predicted transcription factor binding sites regulating the expression of the transducin-like enhancer of split 1 gene (TLE1), an important player in Notch signaling. This pathway is critical for macrophage activity and CD4+ T cell differentiation into Th1 and T helper 2. Together, these findings suggest that the human and mouse model for protective response against Leishmania spp., which involves Th1 and macrophage modulation by interleukins 2, 15, gamma interferon and Notch signaling, may also hold for the canine model.

Fig 1. Sample screening for Leishmania spp. infection in mixed-breed dogs.

Samples were selected to maximize the likelihood of exposure (by age) and correct infection diagnosis (by concordance of diagnostic tests). Balanced numbers of cases and controls were genotyped and quality-controlled.

Fig 2. A genome-wide scan using a variance components model in mixed-breed dogs identifies two loci associated with infection by Leishmania spp. (p < 1 x 10⁻⁵).

The markers on autosomes 1 (rs22039047, p = 4.6 x 10⁻⁶) and 2 (rs22840096, p = 4.7 x 10⁻⁶) presented estimated B allele (Illumina A/B genotype calls) odds ratios of 16.12 ± 2.09 and 37.34 ± 3.09, respectively.

Fig 3. Regional plot of the chromosome 2 marker (rs22840096) associated with Leishmania spp. infection in mixed-breed dogs.

Of note, the marker is located approximately 200 kb from IL2RA and IL15RA in a predicted CD14+ monocyte DNAse hypersensitive site. At the bottom, the D' measure of linkage disequilibrium shows the extent of SNP tagging nearby the positional association.

Fig 4. Regional plot of the chromosome 1 marker (rs22039047) associated with Leishmania spp. infection in mixed-breed dogs.

The marker is in the vicinity of a predicted transcription factor binding site controlling the expression of TLE1 (Q6JDG1_CANFA). At the bottom, the D' measure of linkage disequilibrium shows the extent of SNP tagging nearby the positional association.