Single-cell and bulk RNA-sequence identified fibroblasts signature and CD8+ T-cell - fibroblast subtype predicting prognosis and immune therapeutic response of bladder cancer, based on machine-learning bioinformatics retrospective study

Abstract

Background: Cancer-associated fibroblasts (CAFs) are found in primary and advanced tumours. They are primarily involved in tumour progression through complex mechanisms with other types of cells in the tumour microenvironment. However, essential fibroblasts-related genes (FRG) in bladder cancer still need to be explored, and there is a shortage of an ideal predictive model or molecular subtype for the progression and immune therapeutic assessment for bladder cancer, especially muscular-invasive bladder cancer based on the FRG.

Materials and methods: CAF-related genes of bladder cancer were identified by analyzing single-cell RNA sequence datasets, and bulk transcriptome datasets and gene signatures were used to characterize them. Then, ten types of machine learning algorithms were utilized to determine the hallmark FRG and construct the FRG index (FRGI) and subtypes. Further molecular subtypes combined with CD8+ T-cells were established to predict the prognosis and immune therapy response.

Results: 54 BLCA-related FRG were screened by large-scale scRNA-sequence datasets. The machine learning algorithm established a 3-genes FRG index (FRGI). High FRGI represented a worse outcome. Then, FRGI combined clinical variables to construct a nomogram, which shows high predictive performance for the prognosis of bladder cancer. Furthermore, the BLCA datasets were separated into two subtypes - fibroblast hot and cold types. In five independent BLCA cohorts, the fibroblast hot type showed worse outcomes than the cold type. Multiple cancer-related hallmark pathways are distinctively enriched in these two types. In addition, high FRGI or fibroblast hot type shows a worse immune therapeutic response. Then, four subtypes called CD8-FRG subtypes were established under the combination of FRG signature and activity of CD8+ T-cells, which turned out to be effective in predicting the prognosis and immune therapeutic response of bladder cancer in multiple independent datasets. Pathway enrichment analysis, multiple gene signatures, and epigenetic alteration characterize the CD8-FRG subtypes and provide a potential combination strategy method against bladder cancer.

Conclusions: In summary, we established a novel FRGI and CD8-FRG subtype by large-scale datasets and organized analyses, which could accurately predict clinical outcomes and immune therapeutic response of BLCA after surgery.