Abstract PR004: Multi-omic spatial analysis reveals reshaping of tumour-immune dynamics at the transition to invasive colorectal cancer

Abstract The introduction of bowel cancer screening has led to an increase in the detection and removal of pre-malignant adenomas, however many of these would never progress to colorectal cancer (CRC) within a patient’s lifetime. This implies a key evolutionary bottleneck at the transition from adenoma to carcinoma, with immune surveillance likely playing a central role in suppressing the outgrowth of invasive cells. Here we analysed a cohort of “ca-in-ads” (adenomas with a small focus of cancer) to provide a unique snapshot of the invasive transition. We combined genomics, spatial transcriptomics, digital pathology and multiplex imaging, concurrently deriving the distribution of tumour clones, their gene expression and their interplay with the immune microenvironment. We performed multi-region low-coverage whole genome sequencing (lcWGS) and T-cell receptor sequencing (using FUME-TCRseq, a novel method developed in our lab) on archival ca-in-ads from 40 patients. For a subset of cases we performed spatial transcriptomics using the 10x Genomics Visium platform, including custom probes to detect T-cell clonotypes of interest. We applied a deep learning cell classifier to haematoxylin and eosin (H&E) stained sections to determine the abundance and spatial distribution of eight cell types, with detailed immunophenotyping on selected cases (using a 50-marker panel on Akoya’s PhenoCycler-Fusion platform). We found a significant increase in copy number alterations in carcinoma regions relative to adenomas, and this was accompanied by a large shift in the composition of the local T-cell repertoire. TCR sequencing revealed expanded T-cell clonotypes that were adenoma-specific or carcinoma-specific, and we validated the spatial exclusivity of these using a custom Visium assay. Although overall lymphocyte density remained unchanged, digital pathology and cyclic immunofluorescence revealed significantly increased infiltration of macrophage and neutrophil populations in regions of invasive cancer. Taken together our analysis suggests a striking reshaping of tumour-immune dynamics at the transition to an invasive phenotype in CRC. Understanding what governs this invasive shift could highlight new avenues for cancer prevention or identify individuals at risk of CRC. Citation Format: Ann-Marie Baker, Eleanor Smith, Chirine Sakr, Konstantin Bräutigam, Nick Trahearn, Holly Eggington, Miangela M. Lacle, Manuel Rodriguez-Justo, Simon J. Leedham, Trevor A. Graham. Multi-omic spatial analysis reveals reshaping of tumour-immune dynamics at the transition to invasive colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Cancer Evolution: The Dynamics of Progression and Persistence; 2025 Dec 4-6; Albuquerque, NM. Philadelphia (PA): AACR; Cancer Res 2025;85(23_Suppl):Abstract nr PR004.