Single-cell sequencing and bulk RNA sequencing reveal a cell differentiation-related multigene panel to predict the prognosis and immunotherapy response of hepatocellular carcinoma

According to log2 fold change [FC] > 0.5 and false discovery rate (FDR) < 0.05, the marker genes in each cluster were identified, and the top 10% of marker genes in each cluster were shown in the heatmap [Supplementary Figure 2H, http://links.lww.com/CM9/B382]. According to the marker genes [Supplementary Table 2, http://links.lww.com/CM9/B191], 12 clusters were annotated as hepatocytes, monocytes, T cells, and natural killer (NK) cells with the “SingleR” package [Supplementary Figure 2I, J, http://links.lww.com/CM9/B382]; and pseudotime and cell trajectory analysis were performed with the “Monocle” package [Supplementary Figure 2K–M, http://links.lww.com/CM9/B382]. Three modules (yellow, blue, and turquoise) were closely related to the grade of HCC [Supplementary Figure 6A–C, http://links.lww.com/CM9/B382]. Because grade is a clinical trait associated with cell differentiation, so we selected them for further performing differential expression analysis between tumor and normal tissues from TCGA, and 136 genes were obtained [Supplementary Figure 6D, http://links.lww.com/CM9/B382]. [...]our research identified and validated a seven-gene signature associated with cell differentiation in HCC patients based on scRNA-seq and bulk RNA-seq.