Biomarker analysis and treatment dynamics following preoperative ipilimumab plus nivolumab in locally advanced urothelial cancer from the phase 1B NABUCCO study

Abstract Purpose: In NABUCCO, safety and efficacy of preoperative ipilimumab plus nivolumab were assessed in stage III urothelial cancer. Encouraging responses were achieved and ipilimumab 3 mg/kg (ipilimumab-high) appeared more effective than ipilimumab 1 mg/kg (ipilimumab-low). We explored ipilimumab plus nivolumab response biomarkers and tumor micro environment (TME) treatment dynamics. Experimental Design: Baseline FFPE tumor tissue was analyzed using PD-L1 immunohistochemistry (n=51), whole-exome and transcriptome sequencing (both n=53) and correlated with response. Baseline infiltration of CD8+ T-cells (n=51) and at cystectomy (n=42) was examined. ScRNAseq of CD3+ T-cells was conducted on on-treatment resection tissue of two responders to ipilimumab-high to explore characteristics of CD8+ T-cells within the TME. Results: High tumor mutational burden (TMB) and PD-L1 positivity were associated with response to ipilimumab plus nivolumab. Non-responding patients exhibited increased expression of a TGFβ signature. We observed increased transcription of the g2m checkpoint and e2f target in responders to ipilimumab-high and enhanced transcription of IFN-α and –γ hallmarks in responders to ipilimumab-low. CD8+TCF7+ T-cells accumulated in the TME of responders to ipilimumab-high. ScRNAseq of CD8+TCF7+ T-cells demonstrated enhanced expression of IL7R, CCR7, GPR15, XCL1, SELL and LEF1. Conclusions: Our data indicate that TMB, PD-L1 and TGFβ are potential biomarkers for response to ipilimumab plus nivolumab in stage III urothelial cancer. An inflammatory TME might be relevant for responding to ipilimumab-low. We found that in responders to ipilimumab-high, TCF7+CD8+ T-cells accumulated in the TME. ScRNAseq in two responders suggested that TCF7+CD8+ T-cells express genes associated with immunological memory formation and T-cell homing.