Genetic analysis of IFNG-AS1 implicates opposite effects to Leishmania guyanensis-cutaneous leishmaniasis: rs4913269 confers protection while rs7134599 enhances susceptibility and correlates with high plasma IL-4 and IL-10 levels

Abstract

Background: The long non-coding RNA interferon gamma antisense-1 (IFNGAS-1) is essential for Th1 lineage specific expression of IFNG. IFN-γ is a key component cytokine in host immune response against intracellular pathogens like Leishmania. We investigated the association of two genetic variants of IFNGAS-1, rs4913269 and rs7134599, with susceptibility or protection to Leishmania guyanensis- induced cutaneous leishmaniasis (Lg-CL).

Methods: A case-control study involving 1,714 individuals (855 Lg-CL and 859 healthy controls) was conducted in the state of Amazonas, Brazil. Genotyping of rs4913269 and rs7134599 were performed using direct nucleotide sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), respectively. Plasma cytokines concentrations (IL-10, IL-12p70, IL-4, IL-1β and TNF-α) were quantified using multiplex Luminex platform. Logistic regression, linkage disequilibrium (LD), and haplotype analyses were applied to assess genetic associations and cytokine correlations.

Results: Individuals with the rs4913269 G/G genotype had a 46% reduced risk of developing Lg-CL, (OR adjusted for age and sex [ORadj] = 0.54; 95% CI 0.39-0.75; Pvadj = 0.0001). Carriers of the rs7134599 A/A genotype had a 130% increased risk of progression to Lg- CL (ORadj = 2.3; 95% CI, 1.6-3.4; P = 0.0001). The rs7134599 A/G genotype also showed a 52% increased risk compared to GG genotype (ORadj = 1.52, 95%CI 1.22-1.89; Pvadj = 0.0002). The rs4913269 G/G genotype was associated with lower levels of IL-10 (P = 0.05) and IL-12p70 (P = 0.009) compared to the C/C genotype. Conversely, the rs7134599 AA genotypes were correlated with higher levels of TNF-α, IL-4, IL-10 and IL-1β in comparison to the GG genotype. LD revealed independent segregation of the variants.

Conclusions: The IFNG-AS1 variants rs4913269 and rs7134599 exert opposing effects on Lg-CL risk and modulate key cytokines involved in disease pathogenesis. These findings underscore the regulatory role in immune responses and increase our understanding of the immunogenetic basis of CL and support the potential IFNG-AS1 as a biomarker for susceptibility.

Fig 1. Genomic position of IFNGAS-1 and cluster of cytokines genes IFNG, IL26 and IL22 on human chromosome 12q14-15.

Location of the variants rs4913269 and rs7134599 of IFNGAS-1 on chromosome 12.

Fig 2. Linkage Disequilibrium (LD) among rs4913269 (IFNGAS1), rs7134599 (IFNGAS1), and rs2069705 (IFNG) variants.

The LD plot was performed using Haploview 4.2 and displays R² and D’ measures.

Fig 3. Analysis of plasma cytokines levels of TNF-α, IFN-γ, IL-4, IL-10, IL-6, IL-12p70 and IL-1β by genotypes of variant rs4913269 across all subjects (patients with Lg-CL and HCs).

Statistical analysis was performed using the ANOVA test with P-value adjusted for sex and age (Padj) for distribution among genotypes and post-hoc test for pairwise comparison between genotypes (*P = p-corrected for false discovery rate (FDR)).

Fig 4. Analysis of plasma cytokines levels of TNF-α, IFN-γ, IL-4, IL-10, IL-6, IL-12p70 and IL-1β by genotypes of variant rs7134599 across all subjects (patients with Lg-CL and HCs).

Statistical analysis was performed using the ANOVA test with P-value adjusted for sex and age (Padj) for distribution among genotypes and post-hoc test for pairwise comparison between genotypes (*P = p-corrected for false discovery rate (FDR)).