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Methylation of immune synapse genes modulates tumor immunogenicity
Anders Berglund, Matthew Mills, Ryan M. Putney, Imène Hamaidi, James Mulé, Sungjune Kim
Anders Berglund, Matthew Mills, Ryan M. Putney, Imène Hamaidi, James Mulé, Sungjune Kim
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Concise Communication Immunology

Methylation of immune synapse genes modulates tumor immunogenicity

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Abstract

Cancer immune evasion is achieved through multiple layers of immune tolerance mechanisms including immune editing, recruitment of tolerogenic immune cells, and secretion of immunosuppressive cytokines. Recent success with immune checkpoint inhibitors in cancer immunotherapy suggests a dysfunctional immune synapse as a pivotal tolerogenic mechanism. Tumor cells express immune synapse proteins to suppress the immune system, which is often modulated by epigenetic mechanisms. When the methylation status of key immune synapse genes was interrogated, we observed disproportionately hypermethylated costimulatory genes and hypomethylation of immune checkpoint genes, which were negatively associated with functional T cell recruitment to the tumor microenvironment. Therefore, the methylation status of immune synapse genes reflects tumor immunogenicity and correlates with survival.

Authors

Anders Berglund, Matthew Mills, Ryan M. Putney, Imène Hamaidi, James Mulé, Sungjune Kim

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Figure 2

The polarity of methylation patterns for costimulatory and immune checkpoint ligands.

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The polarity of methylation patterns for costimulatory and immune checkp...
(A and B) β Values of methylation probes for TSS1500, TSS200, 5′UTR, body, and 3′UTR of the HHLA2 gene (A), an example of an ICG, or CD40 (B), an example of a CSG, derived from all tumor samples (blue) and normal adjacent tissues (red) are depicted. The methylation level for each probe is represented by a box plot. The left-most column indicates the presence of CpG islands, while the second-column colors indicate where on the gene the probe is located. The average β values for selected probes within TSS1500, TSS200, and 5′UTR are plotted against gene expression for HHLA2 (C) or CD40 (D). Each marker represents an individual tissue sample. (E) A box plot of average β values for selected probes for HHLA2 and CD40 from tumor (blue) and normal adjacent tissue (red) is shown. rP and rS are Pearson’s and Spearman’s correlation coefficients, respectively.

Copyright © 2026 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)

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