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Leek, J.T., Johnson, W.E., Parker, H.S., Jaffe, A.E. and Storey, J.D. (2012) The SVA Package for Removing Batch Effects and Other Unwanted Variation in High-Throughput Experiments. Bioinformatics, 28, 882-883.
https://doi.org/10.1093/bioinformatics/bts034

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• TITLE: Bioinformatics Analyses Identify Shared Differentially Expressed Genes in Non-Tuberculosis and Tuberculosis Pulmonary Diseases

  AUTHORS: Chaoyue Liang, Hongyun Luo, Ni Zhou, Wenmei Mu, Shouqiang Ma, Zhicheng Yang

  KEYWORDS: Non-Tuberculous Mycobacteria, Tuberculosis, Transcriptomics, Neutrophil Extracellular Traps, ELANE, DEFA4

  JOURNAL NAME: Open Journal of Epidemiology, Vol.15 No.3, June 24, 2025

  ABSTRACT: Background: Nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis (TB) pulmonary infections share clinical features but have divergent outcomes, suggesting distinct host immune adaptations. Methods: We integrated transcriptomic datasets (GSE97298: 32 NTM vs. 9 controls; GSE83456: 45 TB vs. 61 controls) to identify shared and distinct molecular pathways. Differentially expressed genes (DEGs) were analyzed via limma (|log2FC| ≥ 1.5, FDR Results: We identified 48 shared DEGs with bidirectional regulation (e.g., LDHB: NTM ↓ vs. TB ↑; NOD2: NTM ↑ vs. TB ↓). Pathway analysis revealed neutrophil degranulation as a core-shared mechanism (FDR = 2.37 × 10−6). ELANE and DEFA4 showed strong co-expression (Spearman *r* = 0.86, *p* Conclusion: This study defines conserved neutrophil-driven immunopathology in mycobacterial infections and nominates IRAK3/CD28 for host-directed therapies.