A novel genetic association of IL32 with tuberculosis

IF 3.7 3区医学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Cytokine Pub Date : 2024-10-23 DOI:10.1016/j.cyto.2024.156783

Anuradha Gautam , Chandrika Bhattacharyya , Ahana Dasgupta , Samsiddhi Bhattacharjee , Bhaswati Pandit

{"title":"A novel genetic association of IL32 with tuberculosis","authors":"Anuradha Gautam , Chandrika Bhattacharyya , Ahana Dasgupta , Samsiddhi Bhattacharjee , Bhaswati Pandit","doi":"10.1016/j.cyto.2024.156783","DOIUrl":null,"url":null,"abstract":"<div><h3>Aim</h3><div>IL32 is a pleiotropic intracellular cytokine with an emergent role in tuberculosis. The different isoforms of IL32: α, β, γ and δ have varying pro and anti-inflammatory potentials. We studied the role of genetic variants of <em>IL32</em> and its isoforms in susceptibility to tuberculosis using a case-household contact association study.</div></div><div><h3>Methodology</h3><div>Using a targeted sequencing approach, <em>IL32</em> (+1kb) gene was sequenced in 64 pairs of culture positive TB cases and their culture negative household contacts. Subsequently the identified variants were validated in an independent cohort of cases and household contacts using TaqMan genotyping assay. Regulatory role of the associated variants was assessed using GTExPortal, RegulomeDB score, HaploReg and ENCODE histone ChIP-seq data. Expression of IL32 and its isoforms was evaluated by RT-PCR in PBMC from unexposed healthy controls (N = 25) with different genotype background and stimulated with TB antigens ESAT6 and CFP10. ∼ 200 bp around the associated variant was cloned into pGL3 promoter vector to assess enhancer activity by dual luciferase assay in cell lines.</div></div><div><h3>Results</h3><div>Intronic variant rs9927163(G/T) was found associated with pulmonary TB, T being the risk allele (OR = 2.3(1.40–3.83, p = 0.03)), while G is the protective allele. This finding was validated in independent set of TB cases and household contacts (p = 0.0435). rs9927163 is an eQTL for the genes <em>IL32</em> (p = 4.1e-10) and <em>BICDL2</em> (p = 2.1e-7) in whole blood and interrupts an AP-1 binding site. ENCODE histone ChIP-seq data shows rs9927163 residing within T cell specific H3K4me3 peak. The G allele is associated with greater enhancer activity in a T cell line (2.12 fold, p = 0.0059). The TT genotype showed greater normalized expression of IL32δ, a less proinflammatory isoform compared to the GT and GG genotypes together following ESAT6 (p = 0.02288) and CFP10 (p = 0.04595) treatment. This indicates that greater expression of a potentially less protective IL32 isoform within individuals with the TT genotype might be a risk factor for developing TB.</div></div>","PeriodicalId":297,"journal":{"name":"Cytokine","volume":"184 ","pages":"Article 156783"},"PeriodicalIF":3.7000,"publicationDate":"2024-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cytokine","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1043466624002874","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

Aim

IL32 is a pleiotropic intracellular cytokine with an emergent role in tuberculosis. The different isoforms of IL32: α, β, γ and δ have varying pro and anti-inflammatory potentials. We studied the role of genetic variants of IL32 and its isoforms in susceptibility to tuberculosis using a case-household contact association study.

Methodology

Using a targeted sequencing approach, IL32 (+1kb) gene was sequenced in 64 pairs of culture positive TB cases and their culture negative household contacts. Subsequently the identified variants were validated in an independent cohort of cases and household contacts using TaqMan genotyping assay. Regulatory role of the associated variants was assessed using GTExPortal, RegulomeDB score, HaploReg and ENCODE histone ChIP-seq data. Expression of IL32 and its isoforms was evaluated by RT-PCR in PBMC from unexposed healthy controls (N = 25) with different genotype background and stimulated with TB antigens ESAT6 and CFP10. ∼ 200 bp around the associated variant was cloned into pGL3 promoter vector to assess enhancer activity by dual luciferase assay in cell lines.

Results

Intronic variant rs9927163(G/T) was found associated with pulmonary TB, T being the risk allele (OR = 2.3(1.40–3.83, p = 0.03)), while G is the protective allele. This finding was validated in independent set of TB cases and household contacts (p = 0.0435). rs9927163 is an eQTL for the genes IL32 (p = 4.1e-10) and BICDL2 (p = 2.1e-7) in whole blood and interrupts an AP-1 binding site. ENCODE histone ChIP-seq data shows rs9927163 residing within T cell specific H3K4me3 peak. The G allele is associated with greater enhancer activity in a T cell line (2.12 fold, p = 0.0059). The TT genotype showed greater normalized expression of IL32δ, a less proinflammatory isoform compared to the GT and GG genotypes together following ESAT6 (p = 0.02288) and CFP10 (p = 0.04595) treatment. This indicates that greater expression of a potentially less protective IL32 isoform within individuals with the TT genotype might be a risk factor for developing TB.

查看原文本刊更多论文

IL32 与肺结核的新型遗传关联。

目的：IL32 是一种多效应细胞内细胞因子，在结核病中发挥着重要作用。IL32 的不同异构体：α、β、γ 和 δ 具有不同的促炎和抗炎潜能。我们采用病例-家庭接触关联研究的方法，研究了 IL32 及其同工型的遗传变异在结核病易感性中的作用：方法：采用靶向测序方法，对 64 对培养呈阳性的肺结核病例及其培养呈阴性的家庭接触者的 IL32（+1kb）基因进行测序。随后，使用 TaqMan 基因分型检测法在独立的病例和家庭接触者队列中验证了所发现的变异。利用 GTExPortal、RegulomeDB score、HaploReg 和 ENCODE 组蛋白 ChIP-seq 数据评估了相关变异的调控作用。通过RT-PCR方法评估了未暴露的健康对照组（N = 25）中IL32及其同工酶的表达，这些对照组具有不同的基因型背景，并接受了结核抗原ESAT6和CFP10的刺激：结果：发现基因内变异 rs9927163(G/T) 与肺结核有关，T 是风险等位基因（OR = 2.3(1.40-3.83, p = 0.03)），而 G 是保护性等位基因。rs9927163是全血中IL32（p = 4.1e-10）和BICDL2（p = 2.1e-7）基因的eQTL，它中断了一个AP-1结合位点。ENCODE 组蛋白 ChIP-seq 数据显示，rs9927163 位于 T 细胞特异性 H3K4me3 峰。G 等位基因与 T 细胞系中更强的增强子活性有关（2.12 倍，p = 0.0059）。在 ESAT6（p = 0.02288）和 CFP10（p = 0.04595）处理后，TT 基因型与 GT 和 GG 基因型相比，IL32δ（一种促炎性较低的同工酶）的正常化表达更高。这表明，在 TT 基因型的个体中，保护性较弱的 IL32 同工型的表达量更大，这可能是罹患肺结核的一个风险因素。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Cytokine 医学-免疫学

CiteScore

7.60

自引率

2.60%

发文量

262

审稿时长

48 days

期刊介绍： The journal Cytokine has an open access mirror journal Cytokine: X, sharing the same aims and scope, editorial team, submission system and rigorous peer review. * Devoted exclusively to the study of the molecular biology, genetics, biochemistry, immunology, genome-wide association studies, pathobiology, diagnostic and clinical applications of all known interleukins, hematopoietic factors, growth factors, cytotoxins, interferons, new cytokines, and chemokines, Cytokine provides comprehensive coverage of cytokines and their mechanisms of actions, 12 times a year by publishing original high quality refereed scientific papers from prominent investigators in both the academic and industrial sectors. We will publish 3 major types of manuscripts: 1) Original manuscripts describing research results. 2) Basic and clinical reviews describing cytokine actions and regulation. 3) Short commentaries/perspectives on recently published aspects of cytokines, pathogenesis and clinical results.