CODEX2: A novel scoring system for CDX2 loss in colon cancer—Unraveling prognostic insights and therapeutic opportunities.

e15661 Background: CDX2 protein loss in colorectal cancer (CRC) correlates with poor prognosis, yet the mechanisms driving its loss and associated molecular alterations remain unclear. There is a pressing need for standardized methodologies to evaluate CDX2 expression to enhance patient stratification and therapeutic decision-making. Methods: A 48-patient CRC cohort was analyzed for CDX2 expression using immunohistochemistry, as per Dalerba et al. To address limitations, we developed the CODEX2 scoring system, integrating staining intensity and positive tumor cell percentages into a 0-300 Histo score. Patients were categorized into CODEX2-high ( > 65) and CODEX2-low ( < 65) groups, validated in a 164-patient cohort. Molecular profiling employed RNA sequencing, whole exome sequencing, and EPIC methylation panels. Results: CODEX2 improves cohort inclusivity and identifies low CDX2 expression as a marker for worse survival in discovery (p = 0.013) and validation cohorts (p = 9.3x10⁻⁴). Multivariate analysis confirmed CODEX2 as an independent prognostic indicator. CDX2-low tumors exhibited co-methylation with 1,561 genes, notably WNT5 and HOX genes, linked to morphogenesis and signaling. They also displayed hypermethylation of HRR DNA repair genes and increased M2 macrophages, γδ T cells, and epithelial-to-mesenchymal transition (EMT). Genomic distinctions included KRAS , APC , and PIK3CA mutations in CODEX2-high tumors, and ERBB2 , RB1 , and NSD1 mutations in CODEX2-low. Copy Number Alterations revealed chromosome 22 loss in CODEX2-low and chromosome 20 gains amplifying ERBB pathway genes in CODEX2-high. Conclusions: CODEX2 offers a robust system for CRC classification by CDX2 expression, highlighting distinct prognostic and molecular profiles. CODEX2-low tumors exhibit worse outcomes, EMT features, and immune evasion, suggesting therapeutic targets to improve high-risk patient management.