Whole Blood Transcriptome Profiling Identifies DNA Replication and Cell Cycle Regulation as Early Marker of Response to Anti-PD-1 in Patients with Urothelial Cancer

Abstract

Simple Summary Unfortunately, not all patients with urothelial cancer benefit from checkpoint inhibitors (ICIs). Currently, the first radiological response evaluation is not performed until after 9 to 12 weeks of ICI therapy. Early response biomarkers might enable an early switch to more effective therapies in patients that do not respond. In this study, we aimed to identify early response biomarkers in the blood of patients treated with ICIs. In whole blood of patients with clinical benefit, genes involved in DNA replication and cell cycle regulation were upregulated after 2 to 6 weeks of treatment. This appeared to be a result of T cell proliferation and was not observed in patients without clinical benefit. Our results suggest that whole blood RNA sequencing can contribute to early response prediction in patients treated with ICIs and warrants further research. Abstract Although immune checkpoint inhibitors improve median overall survival in patients with metastatic urothelial cancer (mUC), only a minority of patients benefit from it. Early blood-based response biomarkers may provide a reliable way to assess response weeks before imaging is available, enabling an early switch to other therapies. We conducted an exploratory study aimed at the identification of early markers of response to anti-PD-1 in patients with mUC. Whole blood RNA sequencing and phenotyping of peripheral blood mononuclear cells were performed on samples of 26 patients obtained before and after 2 to 6 weeks of anti-PD-1. Between baseline and on-treatment samples of patients with clinical benefit, 51 differentially expressed genes (DEGs) were identified, of which 37 were upregulated during treatment. Among the upregulated genes was PDCD1, the gene encoding PD-1. STRING network analysis revealed a cluster of five interconnected DEGs which were all involved in DNA replication or cell cycle regulation. We hypothesized that the upregulation of DNA replication/cell cycle genes is a result of T cell proliferation and we were able to detect an increase in Ki-67+ CD8+ T cells in patients with clinical benefit (median increase: 1.65%, range −0.63 to 7.06%, p = 0.012). In patients without clinical benefit, no DEGs were identified and no increase in Ki-67+ CD8+ T cells was observed. In conclusion, whole blood transcriptome profiling identified early changes in DNA replication and cell cycle regulation genes as markers of clinical benefit to anti-PD-1 in patients with urothelial cancer. Although promising, our findings require further validation before implementation in the clinic.