Extracellular matrix gene expression signatures as cell type and cell state identifiers

Sacher, Fabio and Feregrino, Christian and Tschopp, Patrick and Ewald, Collin. (2021) Extracellular matrix gene expression signatures as cell type and cell state identifiers. Matrix Biol Plus, 10. pp. 1-14.

Full text not available from this repository.

Official URL: https://edoc.unibas.ch/87385/

Downloads: Statistics Overview


Transcriptomic signatures based on cellular mRNA expression profiles can be used to categorize cell types and states. Yet whether different functional groups of genes perform better or worse in this process remains largely unexplored. Here we test the core matrisome – that is, all genes coding for structural proteins of the extracellular matrix – for its ability to delineate distinct cell types in embryonic single-cell RNA-sequencing (scRNA-seq) data. We show that even though expressed core matrisome genes correspond to less than 2% of an entire cellular transcriptome, their RNA expression levels suffice to recapitulate essential aspects of cell type-specific clustering. Notably, using scRNA-seq data from the embryonic limb, we demonstrate that core matrisome gene expression outperforms random gene subsets of similar sizes and can match and exceed the predictive power of transcription factors. While transcription factor signatures generally perform better in predicting cell types at early stages of chicken and mouse limb development, i.e., when cells are less differentiated, the information content of the core matrisome signature increases in more differentiated cells. Moreover, using cross-species analyses, we show that these cell type-specific signatures are evolutionarily conserved. Our findings suggest that each cell type produces its own unique extracellular matrix, or matreotype, which becomes progressively more refined and cell type-specific as embryonic tissues mature.
Faculties and Departments:05 Faculty of Science > Departement Umweltwissenschaften > Integrative Biologie > Regulatory Evolution (Tschopp)
UniBasel Contributors:Tschopp, Patrick
Item Type:Article, refereed
Article Subtype:Research Article
Note:Publication type according to Uni Basel Research Database: Journal article
Identification Number:
Last Modified:17 Feb 2022 10:08
Deposited On:17 Feb 2022 10:08

Repository Staff Only: item control page