Deciphering the Kidney Matrisome: Identification and Quantification of Renal Extracellular Matrix Proteins in Healthy Mice

Author:

Rende Umut12ORCID,Ahn Seong Beom2,Adhikari Subash234,Moh Edward S. X.5,Pollock Carol A.6,Saad Sonia6,Guller Anna12ORCID

Affiliation:

1. ARC Centre of Excellence in Nanoscale Biophotonics, The Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW 2052, Australia

2. Macquarie Medical School, Macquarie University, Macquarie Park, NSW 2109, Australia

3. Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia

4. Department of Medical Biology, University of Melbourne, Melbourne, VIC 3052, Australia

5. ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW 2109, Australia

6. Department of Medicine, Kolling Institute of Medical Research, University of Sydney, St. Leonards, NSW 2065, Australia

Abstract

Precise characterization of a tissue’s extracellular matrix (ECM) protein composition (matrisome) is essential for biomedicine. However, ECM protein extraction that requires organ-specific optimization is still a major limiting factor in matrisome studies. In particular, the matrisome of mouse kidneys is still understudied, despite mouse models being crucial for renal research. Here, we comprehensively characterized the matrisome of kidneys in healthy C57BL/6 mice using two ECM extraction methods in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS), protein identification, and label-free quantification (LFQ) using MaxQuant. We identified 113 matrisome proteins, including 22 proteins that have not been previously listed in the Matrisome Database. Depending on the extraction approach, the core matrisome (structural proteins) comprised 45% or 73% of kidney ECM proteins, and was dominated by glycoproteins, followed by collagens and proteoglycans. Among matrisome-associated proteins, ECM regulators had the highest LFQ intensities, followed by ECM-affiliated proteins and secreted factors. The identified kidney ECM proteins were primarily involved in cellular, developmental and metabolic processes, as well as in molecular binding and regulation of catalytic and structural molecules’ activity. We also performed in silico comparative analysis of the kidney matrisome composition in humans and mice based on publicly available data. These results contribute to the first reference database for the mouse renal matrisome.

Funder

NSW HEALTH DEPARTMENT, UNSW AND PHARMAXIS LTD.

Publisher

MDPI AG

Subject

Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis

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