Defining the transcriptional landscape of infiltrating immune cells in human and mouse bladder cancer

Summary The tumor immune cell landscape is composed of infiltrating myeloid cells (TIMs) and lymphocytes (TILs) that are important for regulating tumor progression and response to immune therapies. Since at least 70% of bladder cancer patients are poorly responsive to immune checkpoint blockade, there is a need for in depth analysis of the immune landscape both within individual tumor samples and between patients. To facilitate this, we have conducted single cell RNA sequencing (scRNA-seq) to map and transcriptionally define immune cells from 10 human bladder tumors. While all human tumors showed the of presence of major immune cell types, significant differences were observed in the relative numbers of these populations. To determine the translational utility of these findings we also performed scRNA-seq of TIMs-TILs isolated from mouse bladder tumors that were induced by the BBN carcinogen. In human and mouse comparison, we identified significant cross-species conservation in gene expression programs for NK, T, dendritic cells, monocytes and macrophages immune cell populations. Our data identified the conserved expression of key immunotherapy targets between human and mouse tumors including coordinately high gene expression of PD-1 , CTLA and IDO1 while also noting species divergent expression of TIM3 , LAG3 and CD274 (PDL-1). To identify predictive immune cell-tumor interactions we computed conserved ligand-receptor (cell-cell) interaction scores between immune cell subsets and the epithelial tumor compartment. Together, this study defines the transcriptional status of bladder cancer immune cells and provides the rationale for future studies related to treatment response and therapeutic resistance.