T Cell-to-Stroma Enrichment (TSE) score: a gene expression metric that predicts response to immune checkpoint inhibitors (ICI) in patients with urothelial cancer
The TSE score is a transcriptomic metric that predicts response to ICIs. The study reported by Rijnders, Nakauma-Gonzalez, et al., entitled Gene-expression-based T-Cell-to-Stroma Enrichment (TSE) score predicts response to immune checkpoint inhibitors in urothelial cancer was published in Nature Communications.
We identified the abundance of T cells as a predictor of response, while the abundance of stromal cells/products is a predictor of non-response to ICI. Both predictors are affected by tumor purity, but when combined into the TSE score, the effect of purity disappears making the TSE score a robust biomarker even for immune cell-riched organs such as lymph nodes (Figure). Additionally, the TSE score can predict responders and non-responders because it combines the positive and negative predictive values of T and stromal cells into one single metric.
Please refer to the R package TSECalculatoR.
The scripts in this repository were used to process the data provided by the Hartwig Medical Foundation (HMF) and to generate figures and results for the manuscript. Access to HMF data is controlled and must be requested under the request number DR-176. WGS data, RNA-seq data and corresponding clinical data are freely available for academic use from the HMF through standardized procedures. Request forms can be found at https://www.hartwigmedicalfoundation.nl.
Rijnders, M., Nakauma-González, J.A., Robbrecht, D.G.J. et al. Gene-expression-based T-Cell-to-Stroma Enrichment (TSE) score predicts response to immune checkpoint inhibitors in urothelial cancer. Nat Commun 15, 1349 (2024). https://doi.org/10.1038/s41467-024-45714-0