Characterization of urine-derived immune cells from bladder cancer patients and comparison to tumor and peripheral blood

Abstract Background Although PD-1/PD-L1 immune checkpoint blockade (ICB) therapy has achieved durable clinical responses in a subset of bladder cancer patients (15–25%), the majority do not respond. This has led to a need to identify clinically predictive biomarkers. Urine is an accessible material that may reflect cellular and/or genetic signatures related to ICB response. It has been shown that bladder cancer patient urine contains immune cells in addition to tumor cells. To study the concordance between urinary immune cells and the tumor immune microenvironment (TIME), we un-biasedly characterized bladder cancer patient urine and compared it to tumor and peripheral blood mononuclear cells (PBMC). Methods Matched tumor, urine, and PBMC from 8 bladder cancer patients were dissociated for single cell RNA sequencing (scRNAseq) and Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) using 10X Genomics. Results scRNAseq of bladder cancer patient urine revealed CD4+ and CD8+ T, T regulatory (Treg), natural killer (NK), and B cells as well as neutrophils, dendritic cells, monocytes, and macrophages. The composition and transcriptional profiles of these cells were more similar to the tumor immune cells than to PBMC. Urine immune cells expressed hypoxia, anergy, and pro-inflammatory gene signatures that were more similar to tumor immune cells than PBMC. Conclusions Our work represents the first scRNAseq and CITE-seq of cancer patient urine. Our study shows several immune cells shed in bladder cancer patient urine and suggests they look phenotypically similar to the TIME. This has implications for future clinical applications as urine can be sampled non-invasively in scenarios when tumor resection may not be feasible. Supported by the NIH grant: R01 CA249175-01.