Molecular analysis of the extracellular microenvironment: from form to function

Abstract

The extracellular matrix (ECM) proteome represents an important component of the tissue microenvironment that controls chemical flux and induces cell signaling through encoded structure. The analysis of the ECM represents an analytical challenge through high levels of post‐translational modifications, protease‐resistant structures, and crosslinked, insoluble proteins. This review provides a comprehensive overview of the analytical challenges involved in addressing the complexities of spatially profiling the extracellular matrix proteome. A synopsis of the process of synthesizing the ECM structure, detailing inherent chemical complexity, is included to present the scope of the analytical challenge. Current chromatographic and spatial techniques addressing these challenges are detailed. Capabilities for multimodal multiplexing with cellular populations are discussed with a perspective on developing a holistic view of disease processes that includes both the cellular and extracellular microenvironment.

The Spatial Extracellular Proteomic Tumor Microenvironment Distinguishes Molecular Subtypes of Hepatocellular Carcinoma

“…Following epitope retrieval, the tris-buffer was sequentially exchanged with HPLC-grade H 2 O by diluting three times prior to drying via a desiccator. Collagenase type III was used for localized digestion of the extracellular matrix as done previously. − In addition to the manufacturer’s characterization, collagenase type III was characterized by collagen activity assays (Abcam ab196999) prior to use. The absence of tryptic activity was validated by using a colorimetric trypsin activity assay kit (Abcam ab102531).…”