Genetic Aberrations in the CDK4 Pathway Are Associated with Innate Resistance to PD-1 Blockade in Chinese Patients with Non-Cutaneous Melanoma.

Abstract

PD-1 checkpoint blockade immunotherapy induces long and durable response in patients with advanced melanoma. However, only a subset of patients with melanoma benefit from this approach. The mechanism triggering the innate resistance of anti-PD-1 therapy remains unclear.<b>Experimental Design:</b> Whole-exome sequencing (WES) and RNA sequencing (RNA-Seq) analyses were performed in a training cohort (<i>n</i> = 31) using baseline tumor biopsies of patients with advanced melanoma treated with the anti-PD-1 antibody. Copy-number variations (CNVs) for the genes <i>CDK4, CCND1</i>, and <i>CDKN2A</i> were assayed using a TaqMan copy-number assay in a validation cohort (<i>n</i> = 85). The effect of CDK4/6 inhibitors combined with anti-PD-1 antibody monotherapy was evaluated in PD-1-humanized mouse (C57BL/6-hPD-1) and humanized immune system (HIS) patient-derived xenograft (PDX) models. WES revealed several significant gene copy-number gains in the patients of no clinical benefit cohort, such as 12q14.1 loci, which harbor <i>CDK4</i>. The association between <i>CDK4</i> gain and innate resistance to anti-PD-1 therapy was validated in 85 patients with melanoma (<i>P</i> < 0.05). RNA-Seq analysis of <i>CDK4</i>-normal cell lines and <i>CDK4</i>-normal tumors showed altered transcriptional output in TNFα signaling via NF-κB, inflammatory response, and IFNγ response gene set. In addition, CDK4/6 inhibitor (palbociclib) treatment increased PD-L1 protein levels and enhanced efficacy (<i>P</i> < 0.05) in the C57BL/6-hPD-1 melanoma cell and the HIS PDX model. In summary, we discovered that genetic aberrations in the CDK4 pathway are associated with innate resistance to anti-PD-1 therapy in patients with advanced melanoma. Moreover, our study provides a strong rationale for combining CDK4/6 inhibitors with anti-PD-1 antibody for the treatment of advanced melanomas.