Biomarker study of pembrolizumab in patients with advanced rare cancers

Rare cancers lack robust, evidence-based treatment options. We conduct a prospective, multi-histology phase 2 clinical trial of pembrolizumab in 154 patients (142 evaluable), observing an objective response rate of 14.8% and clinical benefit (CB) in 26.8%. Multi-modal profiling is performed on baseline, on-treatment, and progression samples. CB associates with high microsatellite instability (MSI-H)/high tumor mutation burden (TMB-H) (odds ratio [OR]: 13.9, p = 0.0013) and programmed cell death ligand 1 (PD-L1) combined positive score (CPS) ≥10 (p = 0.0285), although responses also occur in biomarker-negative tumors and vary by histology. CB tumors exhibit higher pre-treatment immune infiltration and T cell activation, whereas no CB (NCB) tumors show proliferative programs. In moderately infiltrated tumors, CB associates with increased immune content during treatment. Multiplex immunofluorescence confirms higher baseline T cell densities in CB and limited remodeling in NCB tumors. These findings suggest that tumor immune microenvironment features may serve as predictive markers beyond genomic assays and highlight immune cell recruitment during therapy in moderately infiltrated tumors.