Peripheral T cell methylome reveals accelerated systemic immune aging in early lung cancer

The immune landscape in cancer patients is shaped by dynamic interactions between systemic and local tumor immune responses. While the intratumoral immune microenvironment has been extensively studied, systemic immune alterations, especially in early-stage cancers, remain poorly understood. DNA methylation governs T cell functional and differentiation states, and aberrant patterns have been linked to immune dysfunction. We hypothesized that peripheral blood T cells in early lung cancer exhibit reactive DNA methylation remodeling in response to the presence of cancer. To test this, we profiled circulating CD3+ T cells from 63 patients with early-stage lung cancer (stages I and II) and 70 healthy individuals using Illumina Infinium MethylationEPIC arrays. We identified 824 differentially methylated regions (7373 CpG sites) in T cells from lung cancer patients versus non-cancer controls. Gene ontology analysis revealed promoter hypermethylation in T cell activation and differentiation pathways. Epigenetic clock analysis revealed accelerated biological aging in patient-derived T cells, independent of chronological age. Transcriptomic profiling by RNA-seq further demonstrated enrichment of senescence-associated gene networks. Consistently, deconvolution analysis using MethylCIBERSORT revealed an enrichment of late-differentiated T cell subsets. Similar observations emerged from pseudotime trajectory analysis, which showed peripheral T cells, which shift toward senescent-like states at the in early lung cancer. The extent of senescence correlated with promoter hypermethylation in co-stimulatory gene loci. Furthermore, hypermethylated gene promoters were enriched for binding motifs of the E26 transformation-specific (ETS) transcription factor family, implicating a regulatory role of DNA methylation in T cell state transitions. Finally, using cohort splitting and 10-fold cross-validation, we identified a five-gene immune-derived methylation signature that distinguished early-stage lung cancer from non-cancer subjects with high accuracy (training AUC = 0.953; validation AUC = 0.894). This study reveals previously unrecognized systemic T-cell epigenetic reprogramming in early-stage lung cancer, characterized by senescence features and impaired activation potential, and establishes a framework for developing immune-derived methylation biomarkers for early lung cancer detection.