Chapter 3 Outputs

This item contains a transcriptomic signature that a derived for Chapter 3 of my thesis using single-cell RNA-seq data from liquid biopsies of malignant pleural effusions (MPEs) from 7 patients with advanced breast cancer. The single-cell data is publicly available via GEO (GSE208532) and the R scripts I used to analyse the data can be found on my github (github.com/hwhitfield/MPE_analysis_scripts). 

The signature represent phenotypic differences between resident mesothelial populations and invading malignant cells in the pleural microenvironment. I used a pseudobulk differential expression approach to derive the signature and only used patients with sufficient populations of both cell types. This transcriptomic signature captures a CAF-like phenotype in pleural mesothelial populations that is observed without evidence of a fibroblast conversion. In my thesis I show that mesothelial cells may be providing a CAF-like role to support the survival of breast cancer cells.

The excel file contains the differential expression output and the gmt file contains the signatures as a GeneSetCollection object. The signatures can be loaded into R using GSEABase::getGmt() for further analyses.