Degradomics and proteomics

Intro

Fibrogenesis and fibrosis resolution are governed by a wide range of proteases that generate specific protein fragments, known as matrikines. This session will address how we can identify, discover, and target these fragments

A unified proteomic framework for discovering extracellular matrix damage mechanisms

Alexander Eckersley, lecturer in Skin Health, Division of Musculoskeletal & Dermatological Sciences, at University of Manchester

Abstract: Extracellular matrix (ECM) degradation underlies many degenerative and fibrotic disorders associated with ageing and disease. Owing to their longevity (e.g. fibrillar collagens and elastic fibres with half‑lives spanning decades), ECM components are highly susceptible to cumulative structural damage. This damage arises from multiple mechanisms, including proteolytic cleavage, oxidation, and denaturation caused by chronic exposure to matrix metalloproteinases (MMPs), reactive oxygen species (ROS), and environmental stressors such as ultraviolet radiation (UVR). Identifying which ECM proteins are most vulnerable, and determining the mechanisms responsible, remains challenging but is essential for understanding tissue degeneration and developing new diagnostics and targeted therapies

Proteomics by tandem mass spectrometry (LC‑MS/MS) has advanced significantly in detecting specific protein damage, including ROS‑mediated oxidation and endogenous proteolysis (using degradomic strategies such as N‑TAILS). However, these techniques typically focus on single mechanisms and require distinct workflows, even though multiple mechanisms often act concurrently on the same ECM component.

To address these limitations, our lab has developed several complementary proteomic and bioinformatic approaches. Peptide location fingerprinting (PLF) enables unbiased identification of structural damage patterns across protein sequences, while the proteome susceptibility calculator (PSC) predicts MMP, ROS and UVR susceptibility. Integrating these tools with degradomics and redox proteomics has allowed us to identify damaged ECM proteins and infer their underlying mechanisms across tissues, species and disease states. We have demonstrated heightened, MMP‑mediated collagen II degradation and reduced synthesis in aged tissues: a conserved signature across human intervertebral disc, mouse articular cartilage and rat bone. In studies of basement membrane ageing, we identified consistent alterations within the NC1 domain of collagen IV α2 in human kidney and mouse lung, with degradomics indicating MMP3‑mediated release of the matrikine canstatin.

Most recently, we showed that basement membranes remain structurally compromised 21 days after symptomatic recovery from influenza infection. Elevated MMP2 and MMP19 levels and increased collagen IV oxidation highlight proteolysis and oxidative damage as key mechanisms underlying persistent dysfunction. Similar ECM damage signatures were also identified in Alport syndrome, COPD, and even detected non‑invasively in nasal swab from lung cancer patients.

Together, these next‑generation proteomic and computational tools enable integrative mapping of ECM damage, facilitating the discovery of biomarkers, disease pathways, and therapeutically targetable mechanisms.