A fine mapping of single nucleotide variants and haplotype analysis of IL13 gene in patients with Leishmania guyanensis-cutaneous leishmaniasis and plasma cytokines IL-4, IL-5, and IL-13

José do Espírito Santo Junior; Josué Lacerda de Souza; Lener Santos da Silva; Cilana Chagas da Silva; Tuanny Arruda do Nascimento; Mara Lúcia Gomes de Souza; Alyne Farias da Cunha; Jacqueline da Silva Batista; José Pereira de Moura Neto; Marcus Vinitius de Farias Guerra; Rajendranath Ramasawmy

doi:10.3389/fimmu.2023.1232488

A fine mapping of single nucleotide variants and haplotype analysis of IL13 gene in patients with Leishmania guyanensis-cutaneous leishmaniasis and plasma cytokines IL-4, IL-5, and IL-13

Front Immunol. 2023 Oct 16:14:1232488. doi: 10.3389/fimmu.2023.1232488. eCollection 2023.

Authors

José do Espírito Santo Junior^{1

2}, Josué Lacerda de Souza^{2

3}, Lener Santos da Silva^{2

3}, Cilana Chagas da Silva^{4

5}, Tuanny Arruda do Nascimento^{2

4}, Mara Lúcia Gomes de Souza⁴, Alyne Farias da Cunha⁶, Jacqueline da Silva Batista⁶, José Pereira de Moura Neto⁷, Marcus Vinitius de Farias Guerra^{4

5}, Rajendranath Ramasawmy^{1

2

3

4

5

8}

Affiliations

¹ Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, Manaus, Amazonas, Brazil.
² Faculdade de Medicina Nilton Lins, Universidade Nilton Lins, Manaus, Brazil.
³ Programa de Pós-Graduação em Biodiversidade e Biotecnologia da Amazonia Legal (Rede Bionorte), Universidade do Estado do Amazonas, Manaus, Brazil.
⁴ Fundação de Medicina Tropical Doutor Heitor Vieira Dourado, Manaus, Brazil.
⁵ Programa de Pós-Graduação em Medicina Tropical, Universidade do Estado do Amazonas, Manaus, Brazil.
⁶ Instituto Nacional de Pesquisa da Amazônia, Manaus, Brazil.
⁷ Faculdade de Ciência Farmacêuticas, Universidade Federal do Amazonas, Manaus, Brazil.
⁸ Genomic Health Surveillance Network: Optimization of Assistance and Research in The State of Amazonas - REGESAM, Manaus, Amazonas, Brazil.

Abstract

Introduction: Leishmaniasis continues to pose a substantial health burden in 97 countries worldwide. The progression and outcome of Leishmania infection are influenced by various factors, including the cytokine milieu, the skin microbiota at the infection site, the specific Leishmania species involved, the genetic background of the host, and the parasite load. In endemic regions to leishmaniasis, only a fraction of individuals infected actually develops the disease. Overexpression of IL-13 in naturally resistant C57BL/6 mice renders them susceptible to L. major infection. Haplotypes constructed from several single nucleotide variant (SNV) along a chromosome fragment may provide insight into any SNV near the fragment that may be genuinely associated with a phenotype in genetic association studies.

Methods: We investigated nine SNVs (SNV1rs1881457A>C, SNV2rs1295687C>G, SNV3rs2069744C>T, SNV4rs2069747C>T, SNV5rs20541A>G, SNV6rs1295685A>G, SNV7rs848A>C, SNV8rs2069750G >C, and SNV9rs847T>C) spanning the entire IL13 gene in patients with L. guyanensis cutaneous leishmaniasis (Lg-CL).

Results: Our analysis did not reveal any significant association between the SNVs and susceptibility/protection against Lg-CL development. However, haplotype analysis, excluding SNV4rs2069747 and SNV8rs2069750 due to low minor allele frequency, revealed that carriers of the haplotype CCCTAAC had a 93% reduced likelihood developing Lg-CL. Similarly, the haplotypes ACCCGCT (ORadj=0.02 [95% CI 0.00-0.07]; p-value, 6.0×10^-19) and AGCTAAC (ORadj=0.00[95% CI 0.00-0.00]; p-value 2.7×10^-12) appeared to provide protection against the development of Lg-CL. Conversely, carriers of haplotype ACCTGCC have 190% increased likelihood of developing Lg-CL (ORadj=2.9 [95%CI 1.68-5.2]; p-value, 2.5×10^-6). Similarly, haplotype ACCCAAT (ORadj=2.7 [95%CI 1.5-4.7]; p-value, 3.2×10^-5) and haplotype AGCCGCC are associated with susceptibility to the development of Lg-CL (ORadj=1.7[95%CI 1.04-2.8]; p-value, 0.01). In our investigation, we also found a correlation between the genotypes of rs2069744, rs20541, rs1295685, rs847, and rs848 and plasma IL-5 levels among Lg-Cl patients. Furthermore, rs20541 showed a correlation with plasma IL-13 levels among Lg-Cl patients, while rs2069744 and rs848 showed a correlation with plasma IL-4 levels among the same group.

Conclusions: Overall, our study identifies three haplotypes of IL13 associated with resistance to disease development and three haplotypes linked to susceptibility. These findings suggest the possibility of a variant outside the gene region that may contribute, in conjunction with other genes, to differences in susceptibility and partially to the pathology.

Keywords: IL-13; Leishmania guyanensis; cutaneous leishmaniasis; single nucleotide variants; susceptibility.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cytokines / genetics
Genetic Predisposition to Disease
Haplotypes
Humans
Interleukin-13 / genetics
Interleukin-4 / genetics
Interleukin-5 / genetics
Leishmania guyanensis* / genetics
Leishmaniasis, Cutaneous* / parasitology
Mice
Mice, Inbred C57BL
Nucleotides
Polymorphism, Single Nucleotide

Substances

Cytokines
Interleukin-13
Interleukin-4
Interleukin-5
Nucleotides
IL13 protein, human
IL4 protein, human
IL5 protein, human

Grants and funding

This research was funded by the Brazilian Council for Scientific and Technological Development (CNPq), grant number 404181/2012-0 to RR, Fundação de Amparo e Pesquisa do Estado do Amazonas (FAPEAM), grant numbers 06200151/2020 and 01.02.016301.03393/2021-80 to RR, and FAPEAM RESOLUÇÃO N. 002/2008, 007|2018 e 005|2019–PRÓ-ESTADO. Financial supports were also provided in the form of grants from Fundação de Amparo à Pesquisa do Estado do Amazonas (FAPEAM) (POSGRAD Program #008/2021 and #005/2022), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) (PDPG Emergencial de Consolidação Estratégica Program). JJ, JS, LS, and CS have fellowships from FAPEAM and CAPES (Master and PhD students). The funders had no role in the study’s design, data collection and analysis, the decision to publish, or the preparation of the manuscript.