Splicing-based Predictive Learning for Individual Chemotherapy Evaluation in Colorectal Cancer

Colorectal cancer (CRC) remains a major global health burden, with adjuvant chemotherapy representing the standard of care after curative resection. However, patient responses to therapy vary widely, and no validated molecular model currently guides adjuvant treatment selection.

Recent studies suggest that aberrant alternative splicing-rather than gene-level expression alone-plays a crucial role in shaping chemotherapy sensitivity and tumor recurrence. Yet, these complex transcriptomic variations are often missed by standard differential expression analyses.

The ASPAIRE framework (Alternative Splicing and Predictive mAchIne learnIng for Response Evaluation) applies advanced computational modeling to capture multidimensional splicing features from RNA-seq data and transform them into clinically actionable predictions.

In this research effort, the investigators will leverage machine learning to predict adjuvant chemotherapy response for CRC. The research plan will employ three phases:

• Identification of alternative splicing patterns associated with adjuvant chemotherapy response through RNA sequencing and computational feature extraction.
• The investigators will then develop an assay based on reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and train a machine-learning model to predict chemotherapy response.
• The investigators will independently validate the assay. This assay is provisionally termed " SPLICE " (Splicing-based Predictive Learning for Individual Chemotherapy Evaluation in Colorectal Cancer) and will be tested for disease free survival up to five years after treatment.

At the end of this study, this assay will have been developed and validated to help clinical decision-making by predicting both disease free survival.

Inclusion criteria

• Histologically confirmed stage II-III colorectal cancer (TNM classification, 8th edition)
• Received standard adjuvant chemotherapy after curative resection
• Availability of tumor tissue (FFPE or frozen) before chemotherapy
• Sufficient clinical data for outcome analysis (recurrence, survival)
• Age 18-80 years Stage

Exclusion criteria

• Inflammatory bowel disease
• Inadequate RNA quality or lack of consent