CCL5⁺ macrophages promote pulmonary tuberculosis progression by epigenetically remodeling an immunosuppressive microenvironment

Epigenetic remodeling is increasingly recognized as a driver of immune dysregulation in pulmonary tuberculosis, yet the mechanisms by which it shapes the granuloma immune microenvironment remain insufficiently defined. In particular, how chronic inflammation elicits long-term epigenetic reprogramming to establish a suppressive network and promote disease progression warrants investigation. Integrated single-cell RNA sequencing, spatial transcriptomics, bulk transcriptomics, and bisulfite sequencing were used to profile human tuberculosis lesions. Multiplex immunofluorescence validated spatial cellular interactions in both human and mouse tissues. Mycobacterium tuberculosis –infected macrophage–T-cell co-cultures, pharmacological inhibition, gene knockdown/overexpression, and myeloid-specific Dnmt3a knockout mice were employed for mechanistic and functional validation. Multi-omics revealed a DNA methylation–chemokine coupling signature in pulmonary tuberculosis. DNMT3A was predominantly upregulated in lesion macrophages and enriched within CCL5⁺ macrophages, a population concentrated in inflammation-active granulomatous regions and inversely associated with T-cell and NK-cell infiltration. Mechanistically, DNMT3A was linked to PPARGC1B hypermethylation, suppression of PPARγ, activation of NF-κB, and increased CCL5 expression. Functionally, DNMT3A inhibition or knockdown reduced intracellular bacterial burden, while exogenous CCL5 rescued this antibacterial effect. Critically, CCL5⁺ macrophages promoted M2-like polarization and T-cell exhaustion-like phenotype through CCL5–CCR5 autocrine signaling; CCR5 blockade reversed CCL5-driven PD-1⁺TIM-3⁺ T-cell exhaustion-like phenotype and counteracted the increase in CD206⁺CD68⁺ macrophages. CCL5⁺ macrophages further formed an immunosuppressive interaction network involving APOE–TREM2 and HLA-E–CD94/NKG2A signaling. DNMT3A promotes pulmonary tuberculosis progression by driving CCL5⁺ macrophage-mediated immunosuppression through the PPARγ/NF-κB axis and the CCL5–CCR5 autocrine loop. Importantly, long-term inflammation–associated epigenetic reprogramming may be a key determinant of immune homeostasis imbalance and the establishment of a suppressive microenvironment that favors T-cell exhaustion. Targeting this epigenetic pathway and the CCL5–CCR5 axis may represent a promising host-directed therapeutic strategy for pulmonary tuberculosis.