Combining AI to reveal CCDC3-mediated pathways of colorectal cancer liver metastasis.

In colorectal cancer liver metastases, chromosomal instability (CIN) serves as a critical hallmark linked to tumor aggressiveness and poor prognosis. This study integrated single-cell RNA sequencing, weighted gene co-expression network analysis, and non-negative matrix factorization to construct a comprehensive CIN index, revealing that CIN-high tumor cells exhibit more aggressive phenotypes and reside in an immune-excluded tumor microenvironment. Cancer-associated fibroblasts (CAFs) showed enhanced communication with CIN-high tumor cells, and a key CAF-derived gene, CCDC3, was experimentally validated to promote metastasis, proliferation, and CIN in vitro and in vivo. The bio-knowledge graph analysis based on artificial intelligence further revealed the core regulation of CCDC3 in chromosomal instability and liver metastasis of colorectal cancer. Mechanistically, CCDC3 physically interacts with CXCR3 on CRC cells, activating STAT3 phosphorylation and subsequent CDT1 transcription, forming a CCDC3/CXCR3/STAT3/CDT1 signaling axis. Disruption of this axis-either by genetic knockdown or pharmacological inhibition-significantly suppressed metastatic traits, tumor growth, and liver colonization in mouse models. Clinically, high CCDC3 expression correlated with elevated CIN signatures and worse patient survival. These findings uncover a novel CAF-driven signaling pathway that promotes CIN and metastatic progression in CRC, highlighting its potential as a therapeutic target for aggressive, CIN-high colorectal cancer.