Systematic Analysis of Actively Transcribed Core Matrisome Genes Across Tissues and Cell Phenotypes.

Autor: Tellman TV; Department of Diagnostic & Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, 1941 East Road, BBS-4220, Houston, TX 77054, USA., Dede M; Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, P.O. Box 301402 Houston, TX 77230, USA., Aggarwal VA; Departments of BioSciences and Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA., Salmon D; Department of Diagnostic & Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, 1941 East Road, BBS-4220, Houston, TX 77054, USA., Naba A; Department of Physiology and Biophysics, University of Illinois at Chicago, 835 S. Wolcott, Rm E202 (MC901), Chicago, IL 60612, USA., Farach-Carson MC; Department of Diagnostic & Biomedical Sciences, University of Texas Health Science Center at Houston School of Dentistry, 1941 East Road, BBS-4220, Houston, TX 77054, USA.; Departments of BioSciences and Bioengineering, Rice University, 6100 Main St., Houston, TX 77005, USA.; Center for Theoretical Biological Physics, Rice University, 6100 Main St., Houston, TX 77005, USA.. Electronic address: Mary.C.FarachCarson@uth.tmc.edu.
Jazyk: angličtina
Zdroj: Matrix biology : journal of the International Society for Matrix Biology [Matrix Biol] 2022 Aug; Vol. 111, pp. 95-107. Date of Electronic Publication: 2022 Jun 14.
DOI: 10.1016/j.matbio.2022.06.003
Abstrakt: The extracellular matrix (ECM) is a highly dynamic, well-organized acellular network of tissue-specific biomolecules, that can be divided into structural or core ECM proteins and ECM-associated proteins. The ECM serves as a blueprint for organ development and function and, when structurally altered through mutation, altered expression, or degradation, can lead to debilitating syndromes that often affect one tissue more than another. Cross-referencing the FANTOM5 SSTAR (Semantic catalog of Samples, Transcription initiation And Regulators) and the defined catalog of core matrisome ECM (glyco)proteins, we conducted a comprehensive analysis of 511 different human samples to annotate the context-specific transcription of the individual components of the defined matrisome. Relative log expression normalized SSTAR cap analysis gene expression peak data files were downloaded from the FANTOM5 online database and filtered to exclude all cell lines and diseased tissues. Promoter-level expression values were categorized further into eight core tissue systems and three major ECM categories: proteoglycans, glycoproteins, and collagens. Hierarchical clustering and correlation analyses were conducted to identify complex relationships in promoter-driven gene expression activity. Integration of the core matrisome and curated FANTOM5 SSTAR data creates a unique tool that provides insight into the promoter-level expression of ECM-encoding genes in a tissue- and cell-specific manner. Unbiased clustering of cap analysis gene expression peak data reveals unique ECM signatures within defined tissue systems. Correlation analysis among tissue systems exposes both positive and negative correlation of ECM promoters with varying levels of significance. This tool can be used to provide new insight into the relationships between ECM components and tissues and can inform future research on the ECM in human disease and development. We invite the matrix biology community to continue to explore and discuss this dataset as part of a larger and continuing conversation about the human ECM. An interactive web tool can be found at matrixpromoterome.github.io along with additional resources that can be found at dx.doi.org/10.6084/m9.figshare.19794481 (figures) and https://figshare.com/s/e18ecbc3ae5aaf919b78 (python notebook).
Competing Interests: Conflict of Interest The authors, T.V.T., M.D., V.A.A., D.S., A.N. and M.C.F-C., declare no conflicts of interest.
(Copyright © 2022 Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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