ESTRO 2023 - Abstract Book

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ESTRO 2023

was high loss of tumour cells following cryopreservation due to epithelial cell type. Transcripts from approximately 4000 viable cells per sample were captured using the Chromium Gene Expression Assay (10x Genomics) and sequencing, read mapping and cell quality metrics passed acceptable thresholds as defined in Cell Ranger. We separately analysed each cell type by splitting into main subsets as determined by scPRED(1). Granulocytes and plasma cells were removed. The top 10 markers for each cell type were plotted in a heatmap. Our early analysis reveals distinct patterns of cell heterogeneity in patients with LARC. The rectal cell markers appeared to be driven by a subset of cells in one patient. There are clear differences between the gene expression signatures in the heat map for most cell types between pre- and post-treatment. 1 Alquicira-Hernandez J, Sathe A, Ji HP, Nguyen Q, Powell JE. scPred: accurate supervised method for cell-type classification from single-cell RNA-seq data. Genome Biology 2019;20:264.

Conclusion Our study demonstrates feasibility of single cell RNA sequencing in tissue of patients with LARC.