Pre- and On-treatment Multi-omics Profiling of Locally Advanced Rectal Cancer

This prospective observational study characterises the tumour immune microenvironment and microbial ecology of locally advanced rectal cancer before and during neoadjuvant therapy. Tumour tissue and peripheral blood are profiled by whole-genome sequencing, single-cell RNA sequencing with paired T-cell and B-cell receptor repertoire sequencing, spatial transcriptomics of formalin-fixed paraffin-embedded sections, multiplex immunofluorescence, and blood-based proteomic, cytokine and bulk T-cell receptor analyses. The study examines how immune and stromal states change during treatment and how they relate to major pathological response.

Inclusion Criteria: * Age 18 to 75 years * Eastern Cooperative Oncology Group performance status 0-1 * Histologically confirmed rectal adenocarcinoma * Locally advanced disease staged as cT3-T4N0 or cT2-T4N+ without distant metastasis (AJCC 8th edition) * Lower border of the tumour within 10 cm of the anal verge * Scheduled to receive neoadjuvant therapy followed by surgery, with tumour tissue and peripheral blood available before and during neoadjuvant therapy * Written informed consent for fresh biopsy or surgical tissue, or a waiver granted by the institutional ethics committee for archival specimens Exclusion Criteria: * Insufficient tissue or nucleic acid quality for the planned profiling assays * Incomplete clinical records precluding assessment of pathological or clinical response * A history of other malignancy within 5 years other than adequately treated carcinoma in situ or basal cell carcinoma