Transcriptome analysis for differential gene expression profiles of linezolid-containing anti-tuberculosis regimen in drug-susceptible pulmonary tuberculosis

Blood transcriptomic profiling may reflect host responses to tuberculosis (TB) treatment, yet the transcriptional effects of linezolid-containing regimens in drug-susceptible pulmonary TB remain poorly characterized. We aimed to compare early whole-blood transcriptional responses between standard regimen and linezolid-containing regimens, and to identify candidate biomarkers of early treatment effect. In this prospective sub-study of a randomized phase 2 trial, adults with drug-susceptible pulmonary TB received either standard regimen or regimens in which ethambutol was substituted with linezolid for 2 or 4 weeks. Whole-blood RNA was collected at baseline and week 4 for transcriptome analysis, including RNA sequencing, differential expression, and pathway enrichment. Selected transcripts were validated by quantitative real-time polymerase chain reaction (qRT-PCR), and associations with clinical outcomes were assessed. Paired samples were obtained from 48 participants (12 standard; 18 linezolid 2-week; 18 linezolid 4-week). Transcriptomic analysis identified distinct sets of genes that were up- or down-regulated early in treatment. Linezolid-containing regimens were associated with distinct early transcriptional changes compared with the standard regimen, with exploratory enrichment analyses implicating antigen processing and presentation, T-cell activation, and immune signaling pathways. Differences between 2-week and 4-week linezolid exposure were minimal. In qRT-PCR validation, higher baseline FOXP3 and UBE2D4 levels were independently associated with radiographic improvement at 4 weeks, although no transcript predicted time to negative culture conversion. Transcriptomic analysis demonstrated distinct early, regimen-specific gene expression differences in linezolid-containing regimens compared with the standard regimen, and several candidate genes showed clinically relevant associations, supporting their potential as biomarkers for predicting treatment outcomes in pulmonary TB.