Identification and validation of a cancer-associated fibroblasts-related scoring system to predict prognosis and immune landscape in hepatocellular carcinoma through integrated analysis of single-cell and bulk RNA-sequencing

Abstract

Background: Cancer-associated fibroblasts (CAFs) regulate the malignant biological behaviour of hepatocellular carcinoma (HCC) as a significant component of the tumour immune microenvironment (TIME). This study aimed to develop a CAFs-based scoring system to predict the prognosis and TIME of patients with HCC. Methods: Data for the TCGA-LIHC and GSE14520 cohorts were downloaded from The Cancer Genome Atlas and the Gene Expression Omnibus databases. Single-cell RNA-sequencing data for HCC samples were retrieved from the GSE166635 cohort. The Least Absolute Shrinkage and Selection Operator algorithm was employed to develop a CAFs-related scoring system (CAFRss). The predictive value of the CAFRss was determined using Kaplan-Meier, Cox regression and Receiver Operating Characteristic curves. Additionally, the TIMER platform, single sample Gene Set Enrichment Analysis and the Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data algorithms were performed to determine the TIME landscape. Finally, the pRRophic algorithm was utilised for drug sensitivity analysis. Results: The evaluation of the CAFRss system demonstrated its superior ability to predict the clinical outcome of patients with HCC. Additionally, CAFRss effectively distinguished HCC populations with distinct TIME landscapes. Furthermore, CAFRss-based risk stratification identified individuals with immune ‘hot tumours’ and predicted the survival of patients treated with ICBs. Conclusions: The developed CAFRss can serve as a predictive tool for determining the clinical outcome of HCC and differentiating populations with diverse TIME characteristics.

Comprehensive assessment of regulatory T-cells-related scoring system for predicting the prognosis, immune microenvironment and therapeutic response in hepatocellular carcinoma

“…The Human Protein Atlas (HPA) was performed to obtain immunohistochemical staining images [ 20 ] (V.22.0, https://www.proteinatlas.org ) ( Supplementary Table 1 ). Tregs-related genes (TRGs) were downloaded from the Genecards ( https://www.genecards.org/ ) ( Supplementary Table 2 ) [ 21 ].…”