Epigenetic induced increased chromatin accessibility of immune activation loci is associated with response to anti-PD-1 therapy

Immune checkpoint inhibitors (ICIs), including anti-PD-1 antibodies, have transformed the management of genitourinary malignancies, yet a substantial proportion of patients exhibit primary or acquired resistance. Resistance to PD-1 blockade has been associated with an immunosuppressive tumor microenvironment characterized by elevated regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs). Histone deacetylase inhibitors (HDACi) such as vorinostat may overcome these barriers by reprogramming immune and chromatin landscapes to favor antitumor activity. In this study, we integrated transcriptomic, epigenomic, and immunogenetic analyses from a Phase I/IB clinical trial of vorinostat plus the PD-1 inhibitor pembrolizumab and a preclinical mouse model to investigate the mechanisms driving response. ATAC-seq of peripheral blood mononuclear cells (PBMCs) revealed that patients with clinical response maintained global chromatin accessibility from baseline to on-treatment, including at promoter regions of immune activation genes such as IRF1 , IRF4 , and IRF8 . Gene Ontology and motif enrichment analyses demonstrated enrichment of IRF-family transcription factor motifs within regions of increased accessibility. Corresponding RNA-seq analyses showed upregulation of IRF4 and reduced expression of immunosuppressive genes including FOXP3 and TIGIT , consistent with a less suppressive immune phenotype and enhanced effector activation. Interestingly, HLA genotyping identified an overrepresentation of HLA-B44 supertype alleles among responders, suggesting a potential immunogenetic predictive marker. Building on the immune profiling results, we next examined how the combination therapy of vorinostat and anti-PD-1 shaped immune programs in a murine model of kidney cancer (RENCA). We observed significantly reduced tumor burden, decreased metastases, and improved overall survival relative to monotherapies. Single-cell RNA-seq of splenocytes revealed downregulation of myeloid-associated immunosuppressive genes ( Saa1 , Saa3 , S100a8 , S100a9 ) in the combination group, implicating HDAC inhibition in the attenuation of MDSC and neutrophil-mediated resistance pathways. Flow cytometry studies are ongoing to further characterize the immune cell composition and validate these transcriptomic findings at the protein level. In summary, these findings suggest that HDAC inhibition may enhance PD-1 blockade efficacy by maintaining chromatin accessibility at immune activation loci, reducing immunosuppressive signaling, and potentially interacting with host HLA genotype to shape therapeutic outcome. These results support further exploration of HDAC inhibitors as a rational combination strategy to overcome immune resistance in cancer.