Decoupling epithelial-mesenchymal transitions from stromal profiles by integrative expression analysis
Open Access
- 10 May 2021
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Communications
- Vol. 12 (1), 1-13
- https://doi.org/10.1038/s41467-021-22800-1
Abstract
Epithelial-to-mesenchymal transition (EMT) is the most commonly cited mechanism for cancer metastasis, but it is difficult to distinguish from profiles of normal stromal cells in the tumour microenvironment. In this study we use published single cell RNA-seq data to directly compare mesenchymal signatures from cancer and stromal cells. Informed by these comparisons, we developed a computational framework to decouple these two sources of mesenchymal expression profiles using bulk RNA-seq datasets. This deconvolution offers the opportunity to characterise EMT across hundreds of tumours and examine its association with metastasis and other clinical features. With this approach, we find three distinct patterns of EMT, associated with squamous, gynaecological and gastrointestinal cancer types. Surprisingly, in most cancer types, EMT patterns are not associated with increased chance of metastasis, suggesting that other steps in the metastatic cascade may represent the main bottleneck. This work provides a comprehensive evaluation of EMT profiles and their functional significance across hundreds of tumours while circumventing the confounding effect of stromal cells.Keywords
This publication has 58 references indexed in Scilit:
- Gene Expression Classification of Colon Cancer into Molecular Subtypes: Characterization, Validation, and Prognostic ValuePLoS Medicine, 2013
- A colorectal cancer classification system that associates cellular phenotype and responses to therapyNature Medicine, 2013
- Comprehensive molecular portraits of human breast tumoursNature, 2012
- Comprehensive genomic characterization of squamous cell lung cancersNature, 2012
- ECM microenvironment regulates collective migration and local dissemination in normal and malignant mammary epitheliumProceedings of the National Academy of Sciences of the United States of America, 2012
- clusterProfiler: an R Package for Comparing Biological Themes Among Gene ClustersOMICS: A Journal of Integrative Biology, 2012
- The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivityNature, 2012
- Integrated genomic analyses of ovarian carcinomaNature, 2011
- The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem CellsCell, 2008
- Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profilesProceedings of the National Academy of Sciences of the United States of America, 2005