Compartment-resolved Proteomic Analysis of Mouse Aorta during Atherosclerotic Plaque Formation Reveals Osteoclast-specific Protein Expression

Abstract

Atherosclerosis leads to vascular lesions that involve major rearrangements of the vascular proteome, especially of the extracellular matrix (ECM). Using single aortas from ApoE knock out mice, we quantified formation of plaques by single-run, high-resolution mass spectrometry (MS)-based proteomics. To probe localization on a proteome-wide scale we employed quantitative detergent solubility profiling. This compartment- and time-resolved resource of atherogenesis comprised 5117 proteins, 182 of which changed their expression status in response to vessel maturation and atherosclerotic plaque development. In the insoluble ECM proteome, 65 proteins significantly changed, including relevant collagens, matrix metalloproteinases and macrophage derived proteins. Among novel factors in atherosclerosis, we identified matrilin-2, the collagen IV crosslinking enzyme peroxidasin as well as the poorly characterized MAM-domain containing 2 (Mamdc2) protein as being up-regulated in the ECM during atherogenesis. Intriguingly, three subunits of the osteoclast specific V-ATPase complex were strongly increased in mature plaques with an enrichment in macrophages thus implying an active de-mineralization function.

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

“…We previously developed the quantitative detergent solubility profiling (QDSP) method to add an additional dimension of protein solubility to tissue proteomes 31–33 . In QDSP, proteins are extracted from tissue homogenates with increasing stringency of detergents, which typically leaves ECM proteins enriched in the insoluble last fraction.…”

Filling the Gaps – A Call for Comprehensive Analysis of Extracellular Matrix of the Glial Scar in Region- and Injury-Specific Contexts

“…In our investigation of the adult neurogenic niche (Kjell et al, 2020), also using the QDSP protocol, we found that ECM proteins, such as Tn-C, are more soluble compared to the brain parenchyma. Tn-C is also highly soluble in the scar region analyzed by QDSP at 28 dpi here, which is opposite to its insoluble nature in lung injury and atherosclerotic plaques (Schiller et al, 2015;Wierer et al, 2018). These are examples of how any quantification and information regarding ECM architecture would be lost without adopting a protocol that allows composition-dependent sample analysis.…”

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

“…Alterations in ECM composition and possibly architecture in the aging lung have been suggested 25 , however experimental evidence using unbiased mass spectrometry is scarce. We previously developed the quantitative detergent solubility profiling (QDSP) method to add an additional dimension of protein solubility to tissue proteomes [26][27][28] . In QDSP, proteins are extracted from tissue homogenates with increasing stringency of detergents, which typically leaves ECM proteins enriched in the insoluble last fraction.…”