Circulating transcriptome analysis finds gene signatures and immune cell activation and abundance predict response to immunotherapy in bladder cancer
Background. Immune Checkpoint Blockers (ICB) have revolutionized oncology by achieving durable tumor responses in advanced cancers. Nevertheless, currently approved biomarkers (PD-L1, MSI, TMB) have suboptimal positive and negative predictive values for tumor response and survival. Patients and Methods. We aimed to assess the value of RNA sequencing from circulating blood, a new type of liquid biopsy, to predict responses to ICB. We performed total paired-end RNA sequencing at 20 million reads and analyzed differential gene expression, signaling pathway activation, and immune cell abundances according to cancer outcomes. The analysis was conducted on baseline frozen whole blood samples from 164 patients prospectively enrolled in the IOPREDI study. Results. We found that some immune-related genes and signaling pathways were highly expressed in patients who achieved a durable clinical benefit. Furthermore, analyses of both progression-free survival (PFS) and overall survival (OS) confirmed significantly higher expression levels of immune-related signaling pathways in long-term survivors. Gene expression signatures capable of classifying patients based on clinical response or PFS were also identified. Interestingly, deconvolution analysis revealed a significant higher abundance of resting NK cells in patients with prolonged PFS or OS, in contrast to other cytotoxic cell types. Finally, high expression of the CST7 gene and increased abundance of naïve B lymphocytes were associated with immune-related adverse events (irAEs). Conclusion. Total RNA sequencing from whole blood provides high-quality data to predict clinical response, survival, and occurrence of irAEs. The use of this liquid biopsy prior to immune checkpoint blockage could improve treatment efficacy and irAEs management. Overall design: Whole bloods from 164 patients with urinary tract cancer were collected on EDTA tubes. After RNA extraction, total RNAseq was performed and obtained results were used for statistical analysis with different clinical parameters such as clinical response, progression free and overall survivals, and immune related adverse events.