AUTHOR=Omrani Maryam , Ghodousi Arash , Cirillo Daniela Maria 

TITLE=An integrative and comprehensive analysis of blood transcriptomes combined with machine learning models reveals key signatures for tuberculosis diagnosis and risk stratification

JOURNAL=Frontiers in Microbiology

VOLUME=Volume 16 - 2025

YEAR=2025

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2025.1546770

DOI=10.3389/fmicb.2025.1546770

ISSN=1664-302X

ABSTRACT=Tuberculosis (TB) remains a major global health challenge, contributing substantially to morbidity and mortality worldwide. The progression from Mycobacterium tuberculosis (Mtb) infection to active disease involves a complex interplay between host immune responses and Mtb’s ability to evade them. However, current diagnostic tools, such as interferon-gamma release assays (IGRAs) and tuberculin skin tests (TSTs), have limited ability to distinguish between different stages of TB or to predict the progression from infection to active disease. In this study, we performed an integrative analysis of 324 previously acquired blood transcriptome samples from TB patients, TB contacts, and controls across diverse geographical regions. Differential gene expression analysis revealed distinct transcriptomic signatures in TB patients, highlighting dysregulated pathways related to immune responses, antimicrobial peptides, and extracellular matrix organization. Using machine learning, we identified a 99-transcript signature that accurately distinguished TB patients from controls, demonstrated strong predictive performance across different cohorts, and identified potential progressors or subclinical cases. Validation in an independent dataset comprising 90 TB patients and 20 healthy controls confirmed the robustness of the 10-gene signature (BATF2, FAM20A, FBLN2, AK5, VAMP5, MMP8, KLHDC8B, LINC00402, DEFA3, and GBP6), achieving high area under the curve (AUC) values in both receiver operating characteristic (ROC) and precision–recall analyses. This 10-gene signature offers promising candidates for further validation and the development of diagnostic and prognostic tools, supporting global efforts to improve TB detection and risk stratification.