The ATF5-GPER1 axis drives female protection in hepatocellular carcinoma through dual tumor-suppressive and immune-modulatory mechanisms.

Hepatocellular carcinoma (HCC) exhibits marked sexual dimorphism, with females demonstrating superior survival, yet the underlying molecular mechanisms remain unclear. We integrated bulk transcriptomics (GSE39791, TCGA-LIHC, GSE14520) and single-cell RNA sequencing (five datasets, n = 58 patients, 238,982 cells) with machine learning (LASSO, SVM, random forest) to identify female-protective genes driving HCC disparities. Activating transcription factor 5 (ATF5) emerged as a female-protective gene with higher expression in females versus males across cohorts. Single-cell analyses revealed ATF5 defines a female-enriched, low-grade malignant subcluster with elevated apoptotic programs and reduced proliferative signaling, and pseudotime analysis showed coordinated ATF5-GPER1 downregulation during malignant progression (Spearman ρ = -0.52 and -0.48; both p < 0.001). In the immune compartment, ATF5 marked a female-enriched IFN-γ⁺ macrophage state with enhanced immunostimulatory programs and preferential CXCL9/10-CXCR3-mediated communication with CD8/NK cells. Mechanistically, ATF5 transcriptionally activates G protein-coupled estrogen receptor 1 (GPER1), forming an estrogen-responsive regulatory module that functionally suppresses proliferation, induces apoptosis (HepG2: 26.45% vs. 11.88%, p < 0.0001), and inhibits migration in a GPER1-dependent manner as demonstrated by rescue experiments. Tissue microarray validation (n = 167) confirmed high ATF5 expression predicts improved recurrence-free survival specifically in female patients (HR = 0.34, p = 0.040) but not males (p = 0.080). The ATF5-GPER1 axis represents a female-protective circuit operating through tumor-intrinsic suppression and immune remodeling, offering mechanistic insight into HCC sexual dimorphism and identifying ATF5 as a sex-specific prognostic biomarker with potential therapeutic implications.