High Dimensional Analysis of Myeloid Cells in Colorectal Cancer

Abstract

Development of immune therapy requires an in-depth knowledge of immune cells, how they act in a tumour, and how they can be manipulated. Colorectal cancer (CRC) patients have shown less favourable outcomes with immune therapy compared to those with other cancers, but the reason for this is unknown. Myeloid cells are heterogeneous and plastic; this makes their associations with tumour progression, regression, or treatment failure difficult to determine. High dimensional analysis is an exploratory approach that can help visualise and characterise datasets from complex populations. Flow cytometry was used to obtain single cell data from CRC patient tumour, normal bowel, and blood samples. After trialing a conventional biaxial gating analysis strategy, I developed a novel high dimensional analysis strategy specific for the myeloid cell infiltrate in CRC. To develop this analysis pathway, I used multiple tools and determined flowSOM and tSNE are the most useful in my specific cancer immunology research. Using this analysis strategy I determined that the myeloid cell content of CRC patient blood is not representative of the myeloid cell infiltrate of the tumour. Inclusion of more parameters and further quantification of analysed data may in the future produce significant findings that are of clinical relevance.