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.

Sandra Van Wilpe,Jack Schalken,Rutger H T Koornstra,Niven Mehra,Tjitske Duiveman-De Boer,Paolo Angelino,Laura Ciarloni,Victoria Wosika,I Jolanda M De Vries,Rachel Jeitziner,Sahar Hosseinian Ehrensberger,Winald R Gerritsen

doi:10.3390/cancers13184660

Abstract

Simple SummaryUnfortunately, 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.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.

Highlights

Immune checkpoint inhibitors (ICIs) have become an integral part of therapy for patients with metastatic urothelial cancer
By performing a comprehensive, unbiased whole blood transcriptome analysis, we reveal that DNA replication/cell cycle genes and
We show that the upregulation of DNA replication/cell cycle genes is paralleled by an increase in Ki-67+ CD8+ T cells, suggesting that this upregulation is partly due to the proliferation of CD8+ T cells

Summary

Introduction

Immune checkpoint inhibitors (ICIs) have become an integral part of therapy for patients with metastatic urothelial cancer (mUC). ICIs targeting the programmed cell death protein 1 (PD-1)/ programmed cell death ligand 1 (PD-L1) axis are used to treat cisplatin-ineligible patients with a PD-L1 positive tumor as well as patients that have progressed on first-line platinum-based chemotherapy. Maintenance therapy with PD-L1 inhibitor avelumab was recently approved for the treatment of patients who achieved a response or stable disease with first-line chemotherapy [1]. AntiPD-(L) prolongs median overall survival (OS), only a minority of patients benefit from it [1,2]. In a phase III clinical trial, second-line treatment with PD-1 inhibitor pembrolizumab induced responses in 21.1% and disease control in 38.5% of mUC patients [2].

Objectives

Methods

Conclusion