Of these 29 samples following performance of the WG-DASL array, 16 (55%) samples (HCC-R: 8/10 (80%) and HCC-NR: 8/20 (40%)) met the data analysis QC standard and were selected for further comparative Ixazomib Ki gene expression analysis (Figure 2). Overall, 14 (47%) of the samples were excluded from the final analysis. Figure 2 Experimental strategy for comparative transcriptome analysis of HCV-associated HCC with or without recurrence, using FFPE tissue to determine molecular signatures of HCC recurrence. 3.3. Transcriptome Analysis Defines Differentially Regulated Genes, and Major Canonical Pathways Are Associated with Recurrence of HCC The comparative transcriptome analyses aimed at identifying molecular signatures representative of HCC recurrence were carried out as described in Figure 2.
Hierarchical clustering by gene expression segregated all HCC-R from HCC-NR. A total of 194 genes were identified to be differentially expressed, with 151 genes upregulated and 43 downregulated in HCC-R (Figure 3). Figure 3 Hierarchical clustering for 194 genes differentially expressed in HCC-R (FDR corrected ��0.05). For visual comparison, genes differentially expressed in HCC-R and HCC-NR were clustered by the TreeView program. The red color represents genes upregulated, … The biological significance of the altered gene expression pattern described above was investigated by classifying the associated gene within the context of biologically relevant functions using IPA.
HCC with recurrence exhibited enrichment of upregulated genes mapping to signaling or disease pathways associated with cell cycle regulators (CDKN2B, E2F2, E2F5, GNL3, HDAC2, MDM2, MYC, and PA2G4), including the genes that encode the proteins that control molecular mechanisms of cancer (FANCD2, FZD3, PLCB1, and PMAIP1). (P < 0.0001; Table 2). Gene-encoding proteins implied that nucleo-cytoplasmic transport was also overexpressed (KPNA2, KPNB1, RANBP1, and RCC1). The presence of downregulated pathways reflects the concurrent downregulation of directly related genes categorized in nicotine degradation, complement system, hepatic cholestasis, and catecholamine biosynthesis (P < 0.001; Table 2). FXR/RXR activation, which is associated with hepatoprotection , was downregulated in recurrent HCC tumors. Table 2 Top canonical pathways: significant molecular pathways regulated in HCC-R. 3.4. Network Analysis Defines Top-Scoring Upregulated Genes Associated with HCC Recurrence Interestingly, when network analysis was performed, which allows exploration of the biological relationship Brefeldin_A between any two genes, it was seen that the largest number of genes with higher expression in HCC-R tumor tissue was dominated by major transcriptional regulators.