Deciphering colorectal cancer progression through integrative epigenomic analysis for precision therapeutics.

Abstract

e15561 Background: Colorectal cancer (CRC), the third most prevalent cancer globally, remains a major cause of cancer-related mortality. Genomic and epigenomic plasticity during CRC progression, particularly metastasis, poses significant challenges to effective treatment. Patient-derived organoids (PDOs) reflect the heterogeneous genetic and morphological composition of cancer cells, enabling ex vivo disease modeling. This study investigates the epigenomic makeup of human primary and metastatic CRC to advance precision epigenetic therapies. Methods: We analyzed 45 organoid models, including 40 CRC organoids (from primary tumors and liver/lung metastases) and 5 generated from healthy colonic tissue. Using integrative epigenomic profiling, including chromatin accessibility, chromatin state mapping (via six histone modifications), and 3D genome conformation, we constructed a comprehensive CRC epigenomic landscape. Results: Our analysis of CRC patient-derived organoids revealed a core set of accessible genomic regions shared across all organoids, irrespective of tumor location or metastatic status. This conserved chromatin signature highlights common regulatory pathways in CRC during disease progression. Unsupervised clustering based on epigenomic features revealed four distinct CRC subtypes, encompassing both primary and metastatic models. Notably, organoids derived from liver and lung metastases did not cluster by metastatic site, underscoring epigenomic convergence. Subtype D comprised 57.1% (8/14) of primary tumors, while subtypes B and C contained 47.3% (9/19) of liver metastases and 42.8% (3/7) of lung metastases, respectively. KRAS mutation status further stratified subtypes, with wild-type KRAS observed exclusively in subtypes A and B, while KRAS-mutant variants were enriched in subtypes C (6/7) and D (4/10). Histone modification patterns, defined by six marks (H3K4me1, H3K4me3, H3K27me3, H3K27ac, H3K36me3, and H3K9me3) revealed subtype-specific regulatory chromatin landscapes. Three-dimensional chromatin interactions were mapped, and genome-wide interaction contacts are used to identify various chromatin structures that may influence metastatic capacity. Conclusions: This study highlights distinct and shared epigenomic signatures in CRC PDOs, offering novel insights into tumor progression and metastasis. Integrative chromatin analysis provides a framework for identifying epigenetic biomarkers and epigenome targeting strategies.