A mass spectrometry-based atlas of extracellular matrix proteins across 25 mouse organs

Abstract

The extracellular matrix is a critical non-cellular component of multi-cellular organisms containing a variety of proteins, glycoproteins, and proteoglycans which has been implicated in a wide variety of essential biological processes, including development, wound healing, and aging. Due to low solubility, many ECM proteins have been underrepresented in previous proteomics datasets. Using an optimized 3-step decellularization and ECM extraction method involving chaotrope extraction and digestion via hydroxylamine hydrochloride, we have generated coverage of the matrisome across 25 organs. We observe that the top 100 most abundant proteins from the ECM fractions of all tissues are generally present in all tissues, indicating that tissue matrices are principally composed of a shared set of ECM proteins. However, these proteins vary up to 4,000-fold between tissues, resulting in highly unique matrix profiles even with the same primary set of proteins. A data reduction approach was used to reveal related networks of expressed ECM proteins across varying tissues, including basement membrane and collagen subtypes.

Data‐independent acquisition and quantification of extracellular matrix from human lung in chronic inflammation‐associated carcinomas

“…The core matrisome includes collagens, ECM glycoproteins and proteoglycans, whereas the matrisomeassociated proteins are composed of ECM-affiliated proteins, ECM regulators and secreted factors. Very recently, McCabe et al reported an extensive mouse ECM atlas 6 based upon the characterization of the ECM profiles of 25 organs by liquid chromatography-tandem mass spectrometry (LC-MS/MS) [13].…”

Cardiac fibroblasts regulate cardiomyocyte hypertrophy through dynamic regulation of type I collagen

“…Preparation of tissue samples was performed as previously described. 19 Briefly, 5 mg of lyophilized tissue samples were processed by a stepwise extraction with CHAPS and high salt, guanidine hydrochloride and chemical digestion with hydroxylamine hydrochloride (HA) in Gnd-HCl generating cellular, soluble ECM (sECM), and insoluble ECM (iECM) fractions for each sample, respectively. Protein concentration of each fraction for each sample was measured using A660 Protein Assay (Pierce™).…”

“…Liquid chromatography mass spectrometry (LC-MS/MS) was performed using an Easy nLC 1200 instrument coupled to a Orbitrap Fusion Lumos Tribrid mass spectrometer (all from ThermoFisher Scientific) as previously described. 19 Fragmentation spectra were searched against the UniProt Mus musculus proteome database (Proteome ID # UP000000589 downloaded 1 December 2021) using the MSFragger-based FragPipe computational platform. 21 Contaminants and reverse decoys and were added to the database automatically.…”

The kidney matrisome in health, aging, and disease

“…A recently published mass-spectrometry atlas of the matrix in 25 different organs confirmed very similar composition of matrix proteins across different organs with tissue-specific differences in protein abundances. 66 The glomerular matrisome contains comparatively higher abundance of basement membrane components; type IV collagen α4, laminin β2, agrin and nidogen-1; whereas the TI matrix showed enrichment for other structural proteins such as von Willebrand factor and EMILIN-2. Whilst the main function of the TI is forming a scaffold around tubules, the glomerular matrix organizes into the mesangial matrix and the glomerular basement membrane, which forms an integral part of the glomerular filtration barrier.…”