Comprehensive Genetic Analysis of Tuberculosis and Identification of Candidate Biomarkers

Zilu Wen; Liwei Wu; Lin Wang; Qinfang Ou; Hui Ma; Qihang Wu; Shulin Zhang; Yanzheng Song; Yanzheng Song

doi:10.3389/fgene.2022.832739

Frontiers in Genetics (Mar 2022)

Comprehensive Genetic Analysis of Tuberculosis and Identification of Candidate Biomarkers

Zilu Wen,
Liwei Wu,
Lin Wang,
Qinfang Ou,
Hui Ma,
Qihang Wu,
Shulin Zhang,
Yanzheng Song,
Yanzheng Song

Affiliations

Zilu Wen: Department of Scientific Research, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Liwei Wu: Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Lin Wang: Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Qinfang Ou: Department of TB, The fifth people’s hospital of Wuxi, Wuxi, China
Hui Ma: Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Qihang Wu: Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Shulin Zhang: Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Yanzheng Song: Department of Thoracic Surgery, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
Yanzheng Song: TB Center, Shanghai Emerging and Re-emerging Infectious Diseases Institute, Shanghai, China

DOI: https://doi.org/10.3389/fgene.2022.832739
Journal volume & issue: Vol. 13

Abstract

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Purpose: The purpose of this study is to use the data in the GEO database to analyze, screen biomarkers that can diagnose tuberculosis, and verification of candidate biomarkers.Materials and methods: GSE158767 dataset were used to process WGCNA analysis, differential gene analysis, Gene ontology and KEGG analysis, protein-protein network analysis and hub genes analysis. Based on our previous study, the intersect between WGCNA and differential gene analysis could be used as candidate biomarkers. Then, the enzyme-linked immunosorbent assay was used to validate candidate biomarkers, and receiver operating characteristic was used to assess diagnose ability of candidate biomarkers.Results: A total of 412 differential genes were screened. And we obtained 105 overlapping genes between DEGs and WGCNA. GO and KEGG analysis showed that most of the differential genes were significantly enriched in innate immunity. A total of 15 hub genes were screened, and four of them were verified by Enzyme-linked immunosorbent assay. CCL5 performed well in distinguishing the healthy group from the TB group (AUC = 0.723). And CCL19 performed well in distinguishing the TB group from the ORD groups (AUC = 0.811).Conclusion: CCL19, C1Qb, CCL5 and HLA-DMB may play important role in tuberculosis, which indicated four genes may become effective biomarkers and could be conveniently used to facilitate the individual tuberculosis diagnosis in Chinese people.

Published in Frontiers in Genetics

ISSN: 1664-8021 (Online)
Publisher: Frontiers Media S.A.
Country of publisher: Switzerland
LCC subjects: Science: Biology (General): Genetics
Website: http://journal.frontiersin.org/journal/genetics

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