The epigenetic regulator SETDB1 as a key component of cancer stem cells and drug resistance in primary liver cancer

Hepatocellular carcinoma (HCC) is a highly heterogeneous malignancy with a poor prognosis and limited response to current therapies. Cancer stem cells (CSCs) contribute to this heterogeneity, driving tumor progression, immune evasion, and therapeutic resistance. Epigenetic regulators have emerged as pivotal modulators of CSC phenotypes. The histone methyltransferase SETDB1, a key stemness factor in both embryonic and adult stem cells, catalyzes H3K9 trimethylation (H3K9me3) and acts as a major oncogenic driver in a wide range of solid and hematological malignancies. Yet, its specific role in maintaining stemness and contributing to therapeutic resistance in HCC remains poorly defined. Integrative analyses of bulk and single-cell transcriptomic datasets from public HCC cohorts were performed. Tumors were stratified by SETDB1 expression, followed by pathway enrichment, immune deconvolution, and stemness scoring. Associations with clinical outcomes, immune phenotypes, drug resistance signatures, and chromatin-binding partners (DNMT3A, TRIM28, HDAC1) were also explored. The role of SETDB1 was then examined in vitro, where a stem-like phenotype was induced in HCC cell lines under hypoxic conditions, and patterns of SETDB1 expression and stemness marker levels were assessed following paclitaxel treatment. SETDB1-low tumors were enriched in well-differentiated, immunologically active subclasses and were associated with increased predicted responsiveness to immune checkpoint blockade (ICB), sorafenib, and transarterial chemoembolization. Conversely, SETDB1-high tumors exhibited transcriptional features of dedifferentiation, elevated stemness scores, and enrichment in aggressive molecular subtypes. These tumors also displayed higher TP53 mutation rates, reduced immune infiltration, immune exclusion signatures, and activation of pathways linked to ferroptosis and ABC transporter dysfunction, consistent with resistance to ICB and conventional therapies. SETDB1 expression was also associated with hypoxia-related pathways, suggesting a role in maintaining CSC niches. In vitro, hypoxia-induced stemness coincided with increased SETDB1 levels, whereas paclitaxel treatment decreased both SETDB1 expression and stemness markers. A chromatin risk score incorporating SETDB1 and its partners predicted poor disease-free survival independently of clinical parameters. SETDB1 defines a stemness-enriched, immune-resistant HCC subtype associated with poor outcomes and therapeutic failure. Correlations between SETDB1 expression and stem-like features in vitro suggest a potential role in maintaining CSC phenotypes, supporting its relevance as a biomarker and candidate for epigenetic- and CSC-directed therapeutic strategies.