Targeting EP3⁺FAP⁺ stromal reprogramming uncovers a therapeutic vulnerability in early recurrent hepatocellular carcinoma

Early recurrence after curative therapy remains a major obstacle in hepatocellular carcinoma (HCC), yet the stromal determinants of early relapse are poorly defined. Across integrated mouse and human datasets, this stromal program was consistently associated with early relapse. Integrating bulk, single-cell and spatial transcriptomics with functional assays from primary and relapse HCC, we identify a recurrence-enriched cancer-associated fibroblast (CAF) population marked by FAP and EP3. A CAF- and neutrophil-derived high-risk gene signature predicted early relapse and was accompanied by expansion of FAP⁺EP3⁺ CAFs, immunosuppressive neutrophils and stem-like tumor epithelial cells in relapsed lesions. Lineage and perturbation studies indicate that CD36⁺ lipid-associated CAFs are reprogrammed by tumor-derived PGE₂ into FAP⁺EP3⁺ matrix CAFs, linking stromal plasticity to recurrence. Mechanistically, FAP physically associates with EP3 on CAFs to potentiate PGE₂-induced EP3 signaling, thereby amplifying downstream cAMP-PKA activation. This FAP-EP3 complex drives a proline-metabolic, senescent and inflammatory CAF phenotype characterized by PYCR1-dependent proline production and SASP factors including IL-6 and TIMP1. PGE₂-FAP-EP3-cAMP/PKA signaling engages the chromatin reader BRD9 and pioneer factor FOXA1 to establish super-enhancer landscapes at IL6, FAP, PYCR1 and TIMP1, locking EP3⁺FAP⁺CAFs into a relapse-permissive state and sustaining SASP output. Imaging mass cytometry and spatial analyses revealed that EP3⁺FAP⁺ CAFs organize relapse-associated niches enriched for neutrophils, CD44⁺/CD133⁺ stem-like tumor cells, FOXP3⁺ Tregs and CD163⁺ macrophages, in close apposition to invasive tumor fronts. In autochthonous HCC models, genetic deletion of EP3 in fibroblasts or pharmacologic blockade of EP3 or BRD9 reduced tumor burden, decreased pro-tumoral neutrophils and exhausted CD8⁺ T cells, and enhanced effector CD8⁺ differentiation. Combined EP3 inhibition and anti-PD-1 therapy produced superior tumor control, indicating that stromal targeting can sensitize HCC to immune checkpoint blockade. In human HCC cohorts, EP3⁺FAP⁺ CAF signatures correlated with T cell exhaustion, high PTGES expression and poor survival, validating the clinical relevance of this stromal program. Together, our data uncover a PGE₂-FAP-EP3-cAMP/PKA-BRD9-FOXA1 axis that epigenetically locks CAFs into a relapse-permissive, metabolically active SASP state and remodels the immune microenvironment. Targeting EP3⁺FAP⁺ CAFs or their epigenetic circuitry represents a promising strategy to limit HCC recurrence and improve responsiveness to immunotherapy.