Abstract 65: Integrating spatial transcriptomics and digital pathology with whole-genome data from Genomics England to characterise the tumour and it's microenvironment in colorectal cancer.

Key Points

• This research aims to combine spatial transcriptomics with genomic data to characterize the tumour and microenvironment in colorectal cancer.
• Utilized Bruker Spatial Biology's CosMx™ platform for spatial transcriptomics on TMA cores.
• Performed AI-based detection of lymphocytes and stroma from H&E-stained tissue sections.
• Conducted cell segmentation and gene expression quantification on detected cells.
• Integrated genomic variant data with spatial and histological information for analysis.
• Successfully detected 935,262 high-quality cells for downstream analyses.
• Identified distinct spatial and transcriptional signatures between MMR-proficient and MMR-deficient tumours.
• Revealed transcriptional programmes associated with phenotypic divergence based on integrated genomic data.
• Demonstrated the ability to contextualize genomic alterations within the tumour microenvironment.