Abstract
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.
Highlights
Tuberculosis has been accompanied by human for thousands of years, and it is still a major public health problem that threatens human health
The gene expression data of tuberculosis patients were obtained from GEO database (Barrett et al, 2013)
To find biomarkers associated with focal metabolic activity in TB patients, we constructed a gene co-expression network using the WGCNA package
Summary
Tuberculosis has been accompanied by human for thousands of years, and it is still a major public health problem that threatens human health. According to the World Health Organization tuberculosis report, about a quarter of the world’s population is infected with M. tuberculosis and at risk of developing TB disease (WHO, 2019). In 2018, about 10 million people were infected with TB. There were 1.2 million (range, 1.1–1.3 million) TB deaths among. HIV-negative people in 2018 (a 27% reduction from 1.7 million in 2000), and an additional 251,000 deaths (range, 223,000–281,000) among HIV- positive people (a 60% reduction from 620,000 in 2000). Eight countries accounted for two thirds of the global total: India (27%), China (9%), Indonesia (8%), the Philippines (6%), Pakistan (6%), Nigeria (4%), Bangladesh (4%) and South Africa (3%). Curbing the spread of tuberculosis is an urgent problem to be solved (WHO, 2019)
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