Genomic and Transcriptomic Determinants of Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer: Insights into Sex-Associated Differences

Background Locally advanced rectal cancer (LARC, stage II–III) is treated with neoadjuvant chemoradiotherapy (nCRT) followed by total mesorectal excision (TME). Although this approach improves local control and survival, response to nCRT varies widely. Up to 30% of patients achieve a pathological complete response (pCR), while about 20% show minimal benefit. Reliable biomarkers to predict response are lacking, and current clinical and radiologic parameters fail to capture tumor biological complexity. Molecular profiling, including RAS/RAF mutations, may refine patient stratification and support personalized therapy. Aims This doctoral thesis aims to identify and characterize predictive genomic and transcriptomic markers that, when integrated with established clinicopathological parameters, can support personalized nCRT in LARC and improve clinical outcomes. Materials and Methods A retrospective cohort of 139 patients with histologically confirmed LARC treated between 2011 and 2020 at the National Cancer Institute of Aviano was analyzed. Comprehensive clinical and treatment data were collected, and pre-treatment formalin-fixed paraffin-embedded (FFPE) tumor biopsies were used for molecular analyses. Targeted next-generation sequencing (71-gene colorectal panel) and RNA sequencing were performed to characterize genomic and transcriptomic profiles. Associations between clinical or molecular variables and nCRT response were assessed through Fisher’s exact test, logistic regression, and survival analyses (Kaplan–Meier and Cox models). Results Several clinical parameters—including clinical T stage (p = 0.003), tumor length (p = 0.030), and baseline CEA levels (p = 0.002)—were significantly associated with treatment response. Sex also emerged as an independent determinant, with male patients achieving higher complete response rates (42.1% vs. 20.0%, p = 0.029), while females experienced greater toxicity despite comparable treatment intensity. At the molecular level, RTK–RAS pathway alterations were more frequent in females (67% vs. 44%, p = 0.025) and showed a suggestive trend toward lower rates of CR (25.0% in mutated vs. 42.2% in wild-type; Fisher’s p = 0.086). Moreover, RTK–RAS pathway alterations were associated with shorter 5-year disease-free survival (p = 0.0454). A combined clinical-molecular score integrating tumor length, CEA levels, and RTK–RAS status improved predictive accuracy (pseudo-R² = 0.166 vs. 0.105) and effectively stratified patients by DFS risk (p = 0.0308). Transcriptomic profiling revealed 62 differentially expressed genes distinguishing responders from non-responders, offering insight into mechanisms of sensitivity and resistance to nCRT. Conclusions This study provides novel evidence that integrating clinical and molecular data significantly enhances prediction of nCRT response and long-term outcomes in LARC. The results support the development of precision oncology models for patient-tailored therapy and emphasize the relevance of sex-specific biological mechanisms in rectal cancer treatment and prognosis.