Definition of CAF

We re-analyzed the scRNA-seq data of HCC using the Seurat package (21) to comprehensively characterize the CAF signature. Firstly, we removed the cells with over 6000 or below 250 expressed genes, followed by log normalization of expressed genes. The batch effects for 21 samples were eliminated using the FindIntegrationAnchors function. The non-linear dimensional reduction was conducted using the uniform manifold approximation and projection method, with 15 principal components and a resolution at 0.2. Single cells were clustered into different subgroups by using the functions of FindNeighbors and FindClusters (dim = 40 and resolution = 0.2).Then t-distributed stochastic neighbor embedding (TSNE) dimensional reduction was conducted using the RunTSNE function. Fibroblasts were annotated with 4 marker genes, including ACTA2, FAP, PDGFRB, and NOTCH3. The fibroblasts were re-clustered with the same algorithm of FindNeighbors and FindClusters functions. TSNE dimensionality reduction was further performed on fibroblasts clusters. Marker genes of each CAF cluster were identified using FindAllMarkers function by comparing one cluster with other clusters with logFC = 0.5, minpct = 0.35, and adjusted p-value<0.05. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the marker genes of CAFs clusters using the clusterProfiler package (22), and the CNV characteristics among the CAFs clusters were analyzed using the CopyKAT R package to differentiate between tumor cells and normal cells in each sample (23).