Dissecting innate immune mechanisms of resistance to checkpoint blockade therapy in bladder cancer

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PROJECT SUMMARY Bladder cancer is the fifth most common cancer in the United States, accounting for around 47 deaths per day. Promisingly, five PD-1/PD-L1 immune checkpoint blockade (ICB) therapies were approved for bladder cancer in 2016. Although these ICB treatments have achieved durable clinical responses in a subset of patients (15-25%), the majority of patients have still not benefitted from this therapy. This clinical urgency to extend the benefits of ICB to more patients has led to a need to investigate tumor intrinsic mechanisms underlying resistance. Tumor- promoting inflammation, a hallmark of cancer pathogenesis, is known to contribute to cancer growth in multiple ways including restraining antitumor immunity. We discovered a gene signature from pre-treatment tumor associating with myeloid cells that is enriched in inflammation and innate immune genes and predictive of poor ICB outcomes and survival in two ICB clinical trials. I plan to follow up on this work and dissect the innate immune landscape of bladder cancer and investigate mechanisms of myeloid-cell mediated resistance to ICB therapy. Aim 1 seeks to define the landscape of untreated bladder tumors and provide insight into the immune cell subsets underlying ICB resistance. I will construct a transcriptomic and molecular atlas of bladder cancer at a single-cell resolution, a resource that does not currently exist. I will build atlases of patients’ tumor, blood, and urine using single-cell RNA sequencing, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITEseq), spatial transcriptomics, and O-link proteomics and analyze them using Seurat and other R-based tools. I plan to resolve myeloid cells expressing this resistant gene signature and define their cellular interactions. In Aim 2, I will delve into the transcriptional pathways in myeloid cells that are contributing to ICB resistance. We have identified NLRP3 inflammasome activation and IL-1β signaling in tumor monocyte-macrophages (mono- MΦs) as candidate pathways promoting tumor inflammation and progression. I will model these mono-MΦs by differentiating peripheral blood monocytes into MΦ using GM-CSF and M-CSF under hypoxic conditions with IL- 1β and NLRP3 inflammasome activators., I will test effects on adaptive immunity by co-culturing these mono- MΦs with activated autologous CD8+ T cells. I will also use this model to test drug candidates known to modulate IL-1β and NLRP3 inflammasome activity as potential combinatorial treatments with ICB in bladder cancer. This proposal combines direct ex vivo single cell genomics with in vitro functional experiments for a thorough interrogation of the innate immune contribution to ICB resistance in bladder cancer. Combined, these aims will elucidate innate immune pathway driven resistance to PD-1/PD-L1 ICB therapy in bladder cancer, which can be used to identify critical predictive clinical biomarkers and inform new combinatorial treatment strategies.