Epigenetic Reprogramming by Mycobacterium Tuberculosis Infection and Opportunities for Intervention

Abstract

Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), is a deadly infectious lung disease that is among the leading causes of death worldwide. The complex nature of this disease has proven difficult to treat and significant research efforts are now evaluating the feasibility of host-directed, adjunctive therapies (HDT). Given the dysregulation of host epigenetics during Mtb infection, an effective HDT strategy could be to target epigenetic dysregulation to restore optimal immune cell function. However, such a strategy requires a deeper understanding of how Mtb reprograms host epigenetics. Toward this, combinatorial DNA accessibility (ATAC-seq) and transcriptomic (RNA-seq) profiling of human THP-1 macrophages were used to show that Mtb infection induces global chromatin remodeling consistent with changes in gene expression that were enriched for type I interferon (IFN) signaling genes. Genes with the strongest concordant changes in chromatin accessibility and gene expression were validated to be significantly upregulated in Mtb-infected human monocyte-derived macrophages (hMDM). Among upregulated type I IFN response genes were multiple mono-ADP-ribosyltransferases from the poly(ADP-ribose) polymerase (PARP) family of proteins. However, there is limited knowledge of the function of mono-PARPs in the host response to Mtb infection. To address the potential of targeting mono-PARPs for TB HDT, I tested a panel of mono-PARP inhibitors against Mtb in human macrophages. The results show that two inhibitors of PARP14, RBN-012759 and GeA-69, significantly restricted intracellular Mtb survival in a dose-dependent manner. Transcriptome analyses corroborated dose-dependent effects of PARP14 inhibitors, and that changes to gene expression were also inhibitor-specific. Pathway analysis revealed that the transcriptomes of Mtb-infected hMDM treated with PARP14 inhibitors were enriched for DNA repair and pro-inflammatory signaling pathways. This suggests that Mtb exploits upregulation of PARP14 to survive within infected macrophages and inhibition of PARP14 may be a promising strategy to advance HDT for TB. In this thesis, I show the feasibility of using host epigenetics to identify novel targets for TB HDT. That altered type I IFN responses in Mtb-infected macrophages occur due to genome-wide changes in DNA accessibility have implications for TB research because of their role in subverting and reprogramming host immune responses during TB. Genes and pathways identified in my work could be developed as biomarkers or targeted for adjunctive therapies. Furthermore, I contributed knowledge towards the specific role of a type I IFN stimulated gene in Mtb infection. The efficacy of PARP14 inhibitors in restricting intracellular Mtb survival further validates drug-repurposing as a strategy for HDT for TB. Given the persistence of Mtb as a pathogen and the lack of novel antibacterial therapies and preventative strategies, developing potent adjunctive therapy is imperative to combatting TB.