Benefits and limits of decellularization on mass-spectrometry-based
extracellular matrix proteome analysis of mouse kidney
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.