Pharmacological inhibition of CDK4/6 augments long-term anti-tumor immunity through the induction of T cell memory [02_patient_samples]

Small molecule inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6) are an approved treatment for hormone receptor-positive breast cancer and are currently under evaluation across hundreds of clinical trials for other cancer types. The clinical success of these inhibitors is largely attributed to well-defined tumor-intrinsic cytostatic mechanisms, while their emerging role as immunomodulatory agents is less understood. Using integrated epigenomic, transcriptomic and proteomic analyses, we demonstrated a novel action of CDK4/6 inhibitors in promoting the phenotypic and functional acquisition of immunological T cell memory. Short-term priming with a CDK4/6 inhibitor promoted long-term endogenous anti-tumor T cell immunity in mice, enhanced the persistence and therapeutic efficacy of chimeric antigen receptor (CAR)-T cells, and induced an RB-dependent T cell phenotype supportive of favorable responses to immune checkpoint blockade in melanoma patients. Taken together, these mechanistic insights significantly broaden the prospective utility of CDK4/6 inhibitors as clinical tools to boost anti-tumor T cell immunity. PBMC were isolated from a melanoma patient during the course of their treatment with combination palbociclib and binimetinib (palbo/bini) for one month, followed by a switch to ipilimumab and nivolumab (ipi/nivo). Samples were collected and cryopreserved prior to and 2 weeks into treatment with palbo/bini, and prior to and 1 month into treatment with ipi/nivo. Following collection of all PBMC samples, T cells were isolated and labelled with oligo-tagged antibodies specific for CD4, CD8, PD-1, TIM3, IL7R, CD7, CXCR3 and CD39 (antibody-derived tags; ADT) and oligo-barcoded hashtagging antibodies (HTO). Labelled cells were then captured for single-cell sequencing of RNA (GEX), TCR (VDJ), ADT and HTO. A total of 4 samples were hashtagged and pooled for a single capture reaction.