Epigenetic divergence of the AKAP12-LMOD1 axis drives opposing epithelial and stromal functions in colorectal cancer

Colorectal cancer (CRC) progression is shaped in part by stromal-epithelial crosstalk. Using integrated multi-omics analyses, including single-cell RNA sequencing, spatial transcriptomics, and genomic profiling, we identified compartment-specific regulation of the A-kinase anchoring protein 12 (AKAP12)-Leiomodin-1 (LMOD1) signaling axis. Promoter methylation of AKAP12 was a major factor: hypermethylation in epithelial cells was associated with low AKAP12 expression, whereas fibroblasts maintained a hypomethylated state that supported higher AKAP12 expression. This difference was linked to distinct cytoskeletal and junctional programs. In epithelial cells, AKAP12-LMOD1 signaling was linked to preserved tight junctions and barrier integrity, whereas in cancer-associated fibroblasts (CAFs) it was associated with actin remodeling, gap junction communication, and a more activated state. Fibroblast AKAP12-LMOD1 activity was also associated with stronger IGF signaling and enhanced M2-like macrophage features. Single-cell and spatial analyses showed a marked split in mucinous adenocarcinoma (MA), with enhanced stromal AKAP12-LMOD1 activity and marked epithelial suppression. Through structure-based virtual screening and experimental validation, we identified the natural compound hederagenin as an LMOD1-engaging compound that attenuated LMOD1-dependent CAF activation. Treatment of the CAF compartment with hederagenin (HG) attenuated CAF-induced epithelial dysfunction and malignant phenotypes in CRC cells and mucinous organoids, supporting stromal LMOD1 as a potential intervention point. Together, these data suggest that epigenetic control of AKAP12 positions the AKAP12-LMOD1 axis as a context-dependent regulator of tumor-stroma crosstalk, and support further evaluation of stromal LMOD1-directed intervention, particularly in stroma-rich CRC. AKAP12 promoter methylation shapes AKAP12 expression in CRC epithelium and stroma. AKAP12 scaffolds PKA to phosphorylate CREB1 and drive LMOD1 transcription. LMOD1 remodels actin to tune tight junctions in CRC cells and gap junctions in CAFs. The AKAP12-LMOD1 axis reshapes epithelial–stromal crosstalk and links to M2-like features. Stromal AKAP12-LMOD1 is elevated in MA; hederagenin targets LMOD1 in CAFs.