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Benefits and limits of decellularization on mass-spectrometry-based extracellular matrix proteome analysis of mouse kidney
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  • Teresa Frattini,
  • Hanne Devos,
  • Manousos Makridakis,
  • Maria Roubelakis,
  • Antonia Vlahou,
  • Agnieszka Latosinska,
  • Harald Mischak,
  • Joost P. Schanstra,
  • Jean Sébastien Saulnier-Blache
Teresa Frattini
INSERM
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Hanne Devos
Academy of Athens
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Manousos Makridakis
Academy of Athens
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Maria Roubelakis
Academy of Athens
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Antonia Vlahou
Academy of Athens
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Agnieszka Latosinska
Mosaiques diagnostics GmbH
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Harald Mischak
Mosaiques diagnostics GmbH
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Joost P. Schanstra
INSERM
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Jean Sébastien Saulnier-Blache
INSERM

Corresponding Author:jean-sebastien.saulnier-blache@inserm.fr

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Abstract

Extracellular matrix (ECM) proteins, including collagens, ECM glycoproteins, and proteoglycans, are critical components of tissue structure and function. In addition to the core matrisome, there are matrisome-associated proteins that balance ECM production and degradation. The identification and quantification of ECM proteins using mass spectrometry is often hindered by their low abundance and their tendency to aggregate, forming insoluble macromolecules in aqueous solutions. In this study, we aimed to investigate the effectiveness of a decellularization strategy that combined freeze-thaw cycles and sodium dodecyl sulphate treatment, in identifying and quantifying ECM proteins in mouse kidney using mass spectrometry. This decellularization strategy preserved 95% of the Core matrisome proteins detected in non-decellularized kidney and revealed additional once. Decellularization also led to an increase in the abundance of 96% of the core matrisome ECM proteins by an average of 59 times due to the successful removal of cellular and matrisome-associated proteins. However, the enrichment varied greatly among ECM proteins, resulting in a misrepresentation of the native ECM protein composition of the kidney. This should be brought to the attention of the matrisome research community, as it highlights the need for caution when interpreting proteomic data obtained following a decellularization procedure.
08 Feb 2024Submitted to PROTEOMICS
09 Feb 2024Submission Checks Completed
09 Feb 2024Assigned to Editor
09 Feb 2024Reviewer(s) Assigned
09 Apr 2024Review(s) Completed, Editorial Evaluation Pending
11 Apr 2024Editorial Decision: Revise Minor
24 Apr 2024Review(s) Completed, Editorial Evaluation Pending
07 Jun 20242nd Revision Received