Molecular Advances in Gastrointestinal Pathology

Gastrointestinal adenocarcinomas, including colorectal cancer (CRC) and gastroesophageal junction (GEJ) carcinoma, represent a significant global health burden. Recent advances in large-scale multi-omics profiling, particularly through The Cancer Genome Atlas (TCGA), have revealed the genetic heterogeneity and underlying biology of these tumors. Integrating molecular biomarkers with histopathology into routine practice guides classification, prognosis, and targeted interventions. In CRC, hypermutated subtypes-defined by microsatellite instability (MSI) or polymerase epsilon (POLE) mutations-demonstrate high tumor mutational burden (TMB) and robust response to immune checkpoint blockade. Alternatively, non-hypermutated tumors, driven by chromosomal instability, harbor recurrent alterations in RAS, BRAF, HER2, and NTRK, enabling biomarker-based stratification for targeted therapies. Exploratory markers such as PIK3CA mutations and TMB are being investigated, although their predictive value in microsatellite-stable CRC remains limited. Similarly, GEJ carcinomas can be classified into four molecular subgroups: Epstein-Barr virus (EBV)-associated, MSI, chromosomal instability, and genomically stable. Each subtype is defined by characteristic biology and carries distinct therapeutic implications, with actionable targets including HER2 amplification, PD-L1 expression, and claudin 18.2 (CLDN18.2). Established clinical biomarkers such as MSI, PD-L1, and HER2 are standard in precision oncology, while emerging markers like CLDN18.2, TMB, and KRAS G12C, extend the therapeutic landscape. Combining biomarker-driven immunotherapy and targeted approaches such as PD-1 blockade in MSI-H or EBV-positive tumors, HER2-directed therapy, and CLDN18.2 inhibition, has demonstrated a paradigm shift in the clinical management. This review highlights a pathologist-centered perspective on molecularly defined subgroups, actionable biomarkers, and evolving therapeutic paradigms in CRC and GEJ carcinoma, advancing precision oncology.