Transcriptomic analysis has allowed researchers to investigate how an individual's gene expression is modulated by Mycobacterium tuberculosis infection and antimycobacterial drugs. However, most studies using short-read RNA sequencing analyse whole gene expression, only one of several gene regulatory layers captured by this technology. Whole gene expression analysis cannot ascertain how alternative transcript usage and 3' UTR lengths potentially impact a gene's post-transcriptional function and localisation. To investigate these new data modalities, we performed paired bulk RNA sequencing on peripheral blood mononuclear cells (PBMCs) collected from 24 Tanzanian patients immediately before and five months after treatment for pulmonary TB. We then bioinformatically compared bulk expression, splicing patterns and 3' UTR shifts across treatment using DESeq2, apatools and rMATs.

Our bulk transcriptomic analysis confirmed previously published gene signatures, notably the downregulation of immunoglobulin-associated genes after treatment. We also identified a number of non-differentially expressed genes with variations in 3' UTR length and splicing patterns across treatment, revealing regulatory signals complementary to expression-based analyses. More specifically, we observed a highly constrained splicing pattern that was relaxed with treatment, as well as a global shortening of 3' UTR lengths post-treatment. This suggests a reduced post-transcriptional regulatory pattern upon recovery. These findings highlight the value of non-expression bulk analyses in expanding our understanding of gene expression shifts. This multipronged approach could deepen our understanding of tuberculosis biology.

Co-authors: Laura Zaragoza-Infante, Lisa Fournier, Zhi Ming Xu, Mariam Ait Oumelloul, Jerry Hella, Raphaëlle Luisier, Klaus Reither, Sebastien Gagneux, Damien Portevin, Jacques Fellay