Targeting non-coding RNAs as host-directed drug therapy for tuberculosis

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PROJECT SUMMARY Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), causes 1.6 million deaths per mated to be infected with Mtb. There is an urgent need to develop new treatment approaches. In this project, we aim to investigate the role of the host non-coding RNA (ncRNA) landscape in driving susceptibility to tuberculosis (TB) across two study sites in Africa (Cape Town, South Africa and Kampala, Uganda). Focusing on human primary macrophages, we plan to integrate, using systems biology approaches, genetic architecture with the coding and non-coding gene expression landscape of response to Mtb infection. We will identify response expression quantitative trait loci (ReQTLs) for coding genes, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs) which will be integrated with coding/non-coding gene expression, co-expression, and deregulation networks to prioritize key variants and regulators orchestrating macrophage response to Mtb infection. The most promising miRNAs and lncRNAs will be validated with orthogonal techniques and considered for functionalization in human macrophages. Here, we will employ loss-of function approaches using antisense oligonucleotides in ex vivo Mtb-infected human monocyte-derived macrophages to evaluate the outcome on intracellular mycobacterial growth and investigation of mechanistic macrophage-specific anti-mycobacterial effector functions. Targeting these identified host miRNAs and lncRNAs could become promising candidates for adjunctive host-directed drug therapy for TB. Our central hypothesis is that a) Mtb hijacks host miRNAs and lncRNAs to establish successful persistence and survival in macrophages, b) that human variation can affect key players and their roles, and c) that an understanding of this can be leveraged to identify, design, implement, and test a novel RNA-based anti-microbial treatment strategy. This hypothesis builds upon our previous unpublished and published data [1] showing that Mtb targets miR-143, miR-365 and lincRNA-MIR99AHG in macrophages to promote mycobacterial growth by fine-tuning expression levels of host genes and is supported by a growing number of other studies [2-16]. Our long-term goal is to develop a host-directed drug system for antisense therapy, specifically inhibiting miRNAs and lncRNAs that are crucially involved in TB pathogenesis. The rationale for this approach would be to create a novel, targeted host-directed RNA-based drug therapy for TB. To achieve this goal, we have assembled a team of experts in ncRNA biology, infectious disease, systems biology, and bioinformatics from multiple sites in Southern Africa, Uganda and the USA.