UC San Diego

Extrachromosomal DNA (ecDNA) is associated with aggressive tumor biology, but its role in tumor immune escape remains incompletely understood. We combined ecDNA annotations, RNA-seq data, somatic mutations, HLA presentation metrics, tumor purity estimates, and immune deconvolution results from a TCGA pan-cancer cohort. Our goal was to determine if ecDNA-positive tumors are immune-cold and to understand the mechanism behind this phenotype. Once adjusted for cancer type and tumor purity, tumors with ecDNA showed decreased cytolytic activity, a weaker CD8 signal, and reduced inferred cytotoxic immune infiltration, and these effects became more severe with higher ecDNA loads. Conversely, ecDNA-positive tumors did not reveal significant decreases in PHBR-based antigenicity metrics or strong binder fractions, which contradicts the notion of a broad loss of neoantigens. Although HLA-A and B2M showed selective decreases, the broader MHC-I transcriptional program was not coordinately suppressed. The most significant mechanistic finding was the sustained positive link between clonal MHC-II neoantigen load and overall cytolytic activity. However, this association was notably weakened in tumors containing ecDNA. These results indicate that ecDNA tumors are immune-cold due to a reduced ability to translate clonal MHC-II neoantigenicity into effective cytolytic immune activation, rather than a deficiency in antigenicity or widespread MHC loss.