THE INTEGRATIVE GENOMIC AND FUNCTIONAL IMMUNOLOGICAL ANALYSES OF COLORECTAL CANCER INITIATING CELLS TO MODULATE STEMNESS PROPERTIES AND THE SUSCEPTIBILIY TO IMMUNE RESPONSES [RNA-seq]
We conducted a Total RNAseq profiling of primary CICs-CRC and differentiated tumor cell lines-CRC (FBS), including autologous pairs.  A differential gene expression profile was detected in CICs vs. FBS tumor cells. Overall, N=1187 were detected out of a total of 15,913 genes with measured expression as differentially expressed with p<0.05. Through applying the threshold of p<0.01and LogFC of 1.5, N=132 genes resulted as significantly differentially expressed in CICs as compared to FBS tumor cells. In summary, 33 pathways were found to be signi?cantly impacted highlighting the hub function of differentially expressed genes (DEGs) (N=40) and significant pathways (N=26) (p<0.05). The differentially expressed genes include genes related to cancer development and progression, e.g., the unfolded protein response component CHAC1 as well as the hexokinase domain component 1, HKDC1 which promotes tumor immune evasion in hepatocellular carcinoma by coupling cytoskeleton to STAT1 activation and PD-L1 expression. Moreover, aldolase, fructose-bisphosphate C (ALDOC), that is associated with tumor cell spheroids formation, was 2.5-fold upregulated in CICs compared to FBS tumor cells while LCK kinase, implicated in various oncogenic processes, particularly in colorectal cancer was 5-fold upregulated in CICs. On the other hand, JUNB, a direct target of TGF-ß-Smad signaling, which can act as tumor suppressor or oncogene depending on the cancer entity was found to be downmodulated in CRC-CICs vs. -FBS tumor cell lines. Overall design: Total RNA profiling of 19 CICs primary cell lines or Colorectal cancer initiating cells (CICs) cell lines and 7 FBS (Colorectal cancer differentiated tumor cell lines). We evaluated A differential gene expression profile  detected in CICs vs. FBS tumor cells.