Correlation of DNA Methylation Status and Immune Function in the Cytotoxic Immune Cells of Tuberculosis Patients

Abstract BACKGROUND Less than 10% of individuals infected with Mtb develop disease. Similarly, in the pre-antibiotic era, ~20% of Tuberculosis (TB) patients overcame the disease. This implies host immunity can control Mtb infection. We evaluated the role of cytotoxic immune cells (CD8, CD56 and CD3+CD56+) among individuals with chronic infections that increase risk of TB progression. METHODS DNA Methyl EPIC was evaluated in patients with helminths, HIV and TB (n = 32) and flow-based immune phenotyping was implemented on 108 individuals. Gene expression of 717 TB patients and 525 healthy controls was downloaded from publicly available databases. RESULTS All evaluated cytotoxic cells displayed DNA methylation perturbations in the IL-2-STAT5, PI3K and IFNγ signaling pathways. TB patients experienced DNA hyper-methylation of perforin in CD56 NK cells and in granzyme A and granzyme B of CD8+ cytotoxic lymphocytes (CTLs). By flow cytometry TB patients up-regulated mycobacterial-specific perforin in CTLs while CD3−CD56+ NK cells expressed decreased perforin. Early evidence suggests that the increased perforin expression from CTLs was heterogenous and only occurs in ~46% of TB patients. Further evidence for heterogenous TB sub-groups was demonstrated by gene expression as 333 TB patients had increased perforin gene expression, while 313 had decreased gene expression (log2 fold change with FDR < 1%). CONCLUSION To evaluate the DNA methylation-immune phenotype associations from this clinical cohort, mechanistic studies manipulating DNA methylation status are undergoing. Identifying how epigenetic modifications alter cytotoxic cells capacity to kill intracellular mycobacteria is critical to future host directed therapeutic options.