DNA Hypermethylation Correlates With Improving Lung Function During Tuberculosis Therapy

Abstract BACKGROUND: Nearly half of tuberculosis patients are left with persistent lung damage despite microbiologic cure. Twenty percent have persistent lung damage during antibiotic therapy. Previous studies have demonstrated that TB induces prolonged DNA hypermethylation of the IL-12-IFN𝛾;, TNF, and IL-6 pathways that broadly dampens host immunity. METHODS: To understand the role of epigenetics in lung health dynamics, we evaluated the DNA methylation status of host immune cells (peripheral blood mononuclear cells) from a prior clinical trial evaluating standard of care antibiotics (SOC; n = 35) versus SOC plus everolimus (n =34) host directed therapy. Results were validated in comparison to a previously published gene expression signature that correlated with improving lung inflammation as quantified by PET-CT. RESULTS: TB participants receiving SOC + everolimus demonstrated a 6.5% improvement of FEV1 compared to controls, with a corresponding decrease in DNA hypermethylation. Across both arms 27% and 28% of cured participants demonstrated worsening FEV1 and FVC, respectively. TB patients with improving lung function had a global increase in DNA methylation, with pathway level DNA hypermethylation in pathogen induced cytokine storm signaling, chemokine signaling, neutrophil degranulation, phagosome formation, and eicosanoid signaling. Improving FEV1 and FVC correlated with increasing DNA methylation for genes related to the inflammasome (NLRC4), oxidized scavenger receptor signaling (TREM1, TREM2), and neutrophil degranulation (PRG2, ELANE, MPO, NOX1). DNA methylation blocks transcription factor binding, thereby decreasing gene expression. To validate the findings, DNA methylation results associated with improving FEV1 and FVC were compared to gene expression changes that correlated with resolving lung inflammation quantified by PET-CT from a previous study. Improving lung inflammation was associated with decreasing gene expression and increasing DNA methylation for pathogen induced cytokine storm, neutrophil degranulation, IL-8 signaling, and the RHO GTPase cycle. Using the Library of Integrated Network Connections, improving lung inflammation by both PET-CT and spirometry was associated with a gene expression similarity score induced by potential HDT agents sirolimus, tacrolimus, dexamethasone, and the mitochondrial inhibitor fluoropyruvate. CONCLUSIONS: This data demonstrates that TB patients with improving lung function have an increase in epigenetic silencing DNA hypermethylation. While DNA hypermethylation may be beneficial in helping reduce lung-induced pulmonary damage, future studies will need to evaluate if this long-lasting epigenetic landscape dampens host immunity detrimentally, thereby increasing the risk for TB recurrence or secondary infections.