Uncovering Transcriptional Regulators of Hypoxia-Induced Dormancy in M. Tuberculosis

Overview

Along the pathogenesis of Mycobacterium Tuberculosis (MTB)—the causative agent of human TB—hypoxia-induced dormancy is a process by which bacilli enter a viable but non-replicating state within the oxygen-depleted, nutrient-starved environment of the lung granuloma. Affecting nearly two billion people worldwide, dormant TB can linger inside the host for indefinite periods of time before resuscitating, which significantly challenges the accuracy of existing treatment options and patient prognosis. Transcription factors previously thought to mediate this process have only conferred mild growth defects in experimental settings, highlighting the concerning gaps in our current understanding of MTB gene expression during this latent period. As such, this study aimed to characterize novel regulatory mechanisms underlying the transition of MTB in and out of dormancy. The project methodology first involved constructing an aggregate hypoxia dataset, where genome-wide expression profiling over a defined low-oxygen gradient was (1) integrated across multiple studies and (2) filtered through a rigorous data pre-processing pipeline [PCA analysis, batch effect adjustment, normalization]. Using this data, two gene regulatory network (GRN) inference methods—Inferelator and ARACNE—were applied to map relationships between regulators and gene targets of interest, enabling a holistic look at the regulatory dynamics present across both hypoxia and reaeration timepoints. Finally, several downstream methods, including ranked enrichment analysis, network motif detection, and transcription factor overexpression (TFOE) data, were leveraged to deconstruct the GRNs and identify compelling hypotheses. Results indicated that dormancy is functionally associated with cell redox homeostasis, metal ion cycling, and cell wall metabolism—all of which modulate essential host-pathogen interactions. Additionally, the crosstalk between individual regulons (Rv0821c and Rv0144; Rv1152 and Rv2359) was shown to be critical in facilitating bacterial persistence and allowing MTB to effectively hijack key micronutrients within the cell. These adaptations could serve as anticipatory responses to incoming immune attack and oxidative stress. Defense antioxidants and nutritional immunity were also identified as promising avenues to explore further. In providing some of the first insights into the methods utilized by MTB to endure in a hypoxic environment, this research suggests a range of strategies that could lay the groundwork for improved clinical outcomes of TB treatment.