Chapter 3 Outputs

<p>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 (<a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE208532" target="_blank">GSE208532</a>) and the R scripts I used to analyse the data can be found on my github (<a href="https://github.com/hwhitfield/MPE_analysis_scripts" target="_blank">github.com/hwhitfield/MPE_analysis_scripts</a>). </p> <p>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.</p> <p>The excel file contains the differential expression output and the gmt file contains the signatures as a <a href="https://rdrr.io/bioc/GSEABase/man/GeneSetCollection-class.html" target="_blank">GeneSetCollection </a>object. The signatures can be loaded into R using GSEABase::getGmt() for further analyses. </p>