Abstract 4831: DNA methylation of immune synapse genes drives tumor immune evasion
Authors: Imene Hamaidi, Anders Berglund, Matthew Mills, Ryan M. Putney, James J. Mulé, Sungjune Kim
Journal: Cancer Research (2025)

Abstract Background: While cancer immunotherapies have revolutionized treatment, their efficacy remains limited for most patients, highlighting tumors' capacity to evade immune detection. Epigenetic modifications, particularly DNA methylation, play a pivotal role in silencing immune-related pathways, thereby facilitating immune escape. By modulating gene expression, methylation disrupts immune activation, contributing to reduced tumor immunogenicity. This study examines the methylation landscape of co-stimulatory and immune checkpoint genes across various cancers to elucidate how these changes influence immune responses. Methods: Using The Cancer Genome Atlas (TCGA), we analyzed methylation and gene expression profiles across diverse cancer types. Data from 8,186 solid tumors and 745 adjacent normal tissues were processed via t-distributed stochastic neighbor embedding (t-SNE) with 247 probes targeting 20 immune-related genes. Principal component analysis (PCA) was applied to capture methylation variability across 8,931 tumor and normal samples. To explore the effects of methylation on immune gene expression, we analyzed data from 26 epithelial cancer cell lines treated with 5-azacitidine, a demethylating agent, using the GSE57342 dataset. Post-treatment changes in gene expression were assessed, and survival analyses from prior studies were used to explore clinical correlations. Results: We identified distinct methylation patterns in immune synapse genes, differentiating tumors from adjacent normal tissues. Co-stimulatory genes such as CD40 were hypermethylated in tumors, correlating with decreased expression, whereas immune checkpoint genes like PDL1 and HHLA2 were hypomethylated, correlating with increased expression. This inverse relationship between methylation and gene expression underscores the transcriptional regulatory role of DNA methylation. Treatment with 5-azacitidine reversed hypermethylation in co-stimulatory genes, including CD40, potentially enhancing immune recognition. Methylation levels of these genes were also associated with T cell infiltration into the tumor microenvironment and predicted better outcomes in melanoma patients, underscoring their clinical relevance. Conclusion: This study demonstrates that DNA methylation of immune synapse genes contributes to tumor immune evasion by modulating immune gene expression. Targeting these epigenetic alterations represents a promising strategy to restore tumor immunogenicity and improve immunotherapy outcomes, particularly when combined with immune checkpoint inhibitors. Reversing methylation-driven immune suppression could strengthen the immune response and enhance clinical outcomes for cancer patients. Citation Format: Imene Hamaidi, Anders Berglund, Matthew Mills, Ryan M. Putney, James J. Mulé, Sungjune Kim. DNA methylation of immune synapse genes drives tumor immune evasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4831.