Hepatocellular carcinoma (HCC) is a malignant tumor with a high prevalence and fatality rate. CBX2 has been demonstrated to impact the development and advancement of various cancers, albeit it has received limited attention in relation to HCC. In this study, CBX2 and CEP55 were screened out with the refined triple regulatory networks constructed by total RNA-seq datasets (TCGA-LIHC, GSE140845) and a robust prognostic model. Aberrantly higher expression levels of
CBX2
and
CEP55
in HCC may be caused by CNV alterations, promoter hypo-methylation, open chromatin accessibility, and greater active marks such as H3K4me3, H3K4me1, and H3K27ac. Functionally,
CBX2
, which was highly correlated with CD44, shaped a cancer stem cell-like phenotype by positively regulating cell-cycle progression, proliferation, invasion, metastasis, wound healing, and radiation resistance, revealed by combining bulk RNA-seq and scRNA-seq datasets.
CBX2
knockdown validated its role in affecting the cell cycle. Importantly, we revealed CBX2 could activate gene by cooperating with co-regulators or not rather than a recognizer of the repressive mark H3K27me3. For instance, we uncovered CBX2 bound to promoter of
CTNNB1
and
CEP55
to augment their expressions.
CBX2
showed a highly positive correlation with
CEP55
at pan-cancer level. In addition,
CBX2
and
CEP55
may enhance extracellular matrix reprograming via cancer-associated fibroblast. Surprisingly, patients with high expression of
CBX2
or
CEP55
exhibited a higher response to immunotherapy, indicating that
CBX2
and
CEP55
may be promising therapeutic targets for HCC patients.