Extracellular matrix gene expression signatures as cell type and cell state identifiers
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Date
2021-06
Publication Type
Journal Article
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yes
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Abstract
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.
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Publication status
published
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Book title
Journal / series
Volume
10
Pages / Article No.
100069
Publisher
Elsevier
Event
Edition / version
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Software
Geographic location
Date collected
Date created
Subject
Matrisome; Matreotype; Cell type; scRNA-seq; Limb development
Organisational unit
09598 - Ewald, Collin Y. (ehemalig) / Ewald, Collin Y. (former)
Notes
Funding
163898 - The role of extracellular matrix enhancement in promoting healthy aging (SNF)
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