Genome-Wide DNA Methylation Analysis Reveals Immune Genes in Tuberculosis with Potential Relevance for Host-Directed...

Growing evidence suggests that Mycobacterium tuberculosis (M. tb) infection manipulates the host's epigenetic landscape to evade the immune responses and establish a disease phenotype. Among these epigenetic changes, DNA methylation has emerged as a key mechanism that influences the host immune response, playing a crucial role in either controlling the infection or contributing to disease pathogenesis. M. tb and other pathogens can alter the host's epigenetic landscape to weaken immune defenses and facilitate infection.

In this study we aimed to investigate differential DNA methylation patterns in Tuberculosis (TB) phenotypes i.e., Active, Latent, Cured and healthy controls.

In this study, we investigated genome-wide DNA methylation patterns via Infinium Methylation EPIC array in a total of eight M. tb-exposed patients with two biological replicates in each clinical group: active tuberculosis (TB, n=2), latent TB (n=2), therapy-cleared (cured) TB (n=2) and uninfected controls (n=2). Genes linked to hypermethylated promoters were further analyzed through gene ontology (GO) and biological pathways analyses (DAVID). Motif enrichment analysis was performed using differentially methylated regions (DMRs) (>300bp) and promotor CpG site methylation was correlated with corresponding gene expression profile.

Our study identified a repressed immune signature in active TB patients, characterized by hypermethylated genes such as IFNA2, IFNA6, TNFRSF19, IL2, IL21 and TGFβ2 etc. This hypermethylation persists even in cured individuals, despite M. tb clearance and was further reinforced by qPCR analysis showing downregulated expression of hypermethylated genes IFNA2 and IFNA6 in active TB compared to latent and control subjects. Key pathways affected include those associated with tuberculosis, phagosome function, JAK/STAT pathway and cytokine receptors during active M. tb infection, with these effects continuing post-clearance (cured phenotype). Enriched transcription factor motifs within DMRs included ZBTB14, E2F1, and NRF1.

Our findings reveal that M. tb infection is marked by a DNA hypermethylation signature linked to key immune-related genes, driving a repressed immune response and active disease manifestation. This epigenetic signature remains even after M. tb is cleared, suggesting long-term alterations in immune regulation. While preliminary, this methylation signatures once validated in larger cohorts highlight the potential for developing early epigenetic markers to help distinguish active TB from other clinical states or to monitor post-treatment immune recovery.