Acute exposure to ultraviolet radiation targets proteins involved in collagen fibrillogenesis

Introduction: Exposure to chronic, low-dose UV irradiation (UVR) can lead to premature ageing of the skin. Understanding which proteins are affected by acute UVR and photo-dynamically produced reactive oxygen species (ROS) could help to inform strategies to delay photoageing. Conventional biochemical analyses can be used to characterize UVR/ROS-induced damage on a protein-by-protein basis and we have previously shown using SDS-PAGE that collagen I and plasma fibronectin are respectively resistant and susceptible to physiological doses of UVR. The aim of this study was to screen a complex proteome for UVR-affected proteins.Methods: This study employed a sensitive mass spectrometry technique (peptide location fingerprinting: PLF) which can identify structure associated differences following trypsin digestion to characterize the impact of UVR exposure on purified collagen I and tissue fibronectin and to identify UVR-susceptible proteins in an ECM-enriched proteome.Results: Using LC/MS-MS and PLF we show that purified mature type-I collagen is resistant to UVR, whereas purified tissue fibronectin is susceptible. UV irradiation of a human dermal fibroblast-deposited ECM-enriched proteome in vitro, followed by LC/MS-MS and PLF analysis revealed two protein cluster groups of UV susceptible proteins involved in i) matrix collagen fibril assembly and ii) protein translation and motor activity. Furthermore, PLF highlighted UV susceptible domains within targeted matrix proteins, suggesting that UV damage of matrix proteins is localized.Discussion: Here we show that PLF can be used to identify protein targets of UVR and that collagen accessory proteins may be key targets in UVR exposed tissues

Peptide Location Fingerprinting Reveals Tissue Region-Specific Differences in Protein Structures in an Ageing Human Organ

From MDPI via Jisc Publications RouterHistory: accepted 2021-09-14, pub-electronic 2021-09-27Publication status: PublishedFunder: Manchester Institute for Collaborative Research on Ageing; Grant(s): n/aFunder: Walgreens Boots Alliance; Grant(s): n/aIn ageing tissues, long-lived extracellular matrix (ECM) proteins are susceptible to the accumulation of structural damage due to diverse mechanisms including glycation, oxidation and protease cleavage. Peptide location fingerprinting (PLF) is a new mass spectrometry (MS) analysis technique capable of identifying proteins exhibiting structural differences in complex proteomes. PLF applied to published young and aged intervertebral disc (IVD) MS datasets (posterior, lateral and anterior regions of the annulus fibrosus) identified 268 proteins with age-associated structural differences. For several ECM assemblies (collagens I, II and V and aggrecan), these differences were markedly conserved between degeneration-prone (posterior and lateral) and -resistant (anterior) regions. Significant differences in peptide yields, observed within collagen I α2, collagen II α1 and collagen V α1, were located within their triple-helical regions and/or cleaved C-terminal propeptides, indicating potential accumulation of damage and impaired maintenance. Several proteins (collagen V α1, collagen II α1 and aggrecan) also exhibited tissue region (lateral)-specific differences in structure between aged and young samples, suggesting that some ageing mechanisms may act locally within tissues. This study not only reveals possible age-associated differences in ECM protein structures which are tissue-region specific, but also highlights the ability of PLF as a proteomic tool to aid in biomarker discovery

Peptide location fingerprinting reveals modification‐associated biomarker candidates of ageing in human tissue proteomes

From Wiley via Jisc Publications RouterHistory: received 2020-10-08, rev-recd 2021-02-18, accepted 2021-03-15, pub-electronic 2021-04-08, pub-print 2021-05Article version: VoRPublication status: PublishedFunder: Walgreens Boots AllianceAbstract: Although dysfunctional protein homeostasis (proteostasis) is a key factor in many age‐related diseases, the untargeted identification of structurally modified proteins remains challenging. Peptide location fingerprinting is a proteomic analysis technique capable of identifying structural modification‐associated differences in mass spectrometry (MS) data sets of complex biological samples. A new webtool (Manchester Peptide Location Fingerprinter), applied to photoaged and intrinsically aged skin proteomes, can relatively quantify peptides and map statistically significant differences to regions within protein structures. New photoageing biomarker candidates were identified in multiple pathways including extracellular matrix organisation (collagens and proteoglycans), protein synthesis and folding (ribosomal proteins and TRiC complex subunits), cornification (keratins) and hemidesmosome assembly (plectin and integrin α6β4). Crucially, peptide location fingerprinting uniquely identified 120 protein biomarker candidates in the dermis and 71 in the epidermis which were modified as a consequence of photoageing but did not differ significantly in relative abundance (measured by MS1 ion intensity). By applying peptide location fingerprinting to published MS data sets, (identifying biomarker candidates including collagen V and versican in ageing tendon) we demonstrate the potential of the MPLF webtool for biomarker discovery

Matrikines in kidney ageing and age-related disease

Purpose of review Matrikines are cell-signalling extracellular matrix fragments and they have attracted recent attention from basic and translational scientists, due to their diverse roles in age-related disease and their potential as therapeutic agents. In kidney, the matrix undergoes remodelling by proteolytic fragmentation, so matrikines are likely to play a substantial, yet understudied, role in ageing and pathogenesis of age-related diseases.Recent findings This review presents an up-to-date description of known matrikines with either a confirmed or highly anticipated role in kidney ageing and disease, including their point of origin, mechanism of cleavage, a summary of known biological actions and the current knowledge which links them to kidney health. We also highlight areas of interest, such as the prospect of matrikine cross-tissue communication, and gaps in knowledge, such as the unexplored signalling potential of many kidney disease-specific matrix fragments.Summary We anticipate that knowledge of specific matrikines, and their roles in controlling processes of kidney pathology, could be leveraged for the development of exciting new future therapies through inhibition or even with their supplementation

Predicting and characterising protein damage in the extracellular matrix

Chronic UVR exposure of human skin can result in photo-ageing which manifests both externally and internally (as remodelling of skin layers including the extracellular matrix-rich dermis). However, the intermittent nature of UVR exposure over a timescale of decades combined with the longevity of many structural dermal proteins makes the identification of dermal photo-ageing targets and mechanisms challenging. Over the past ten years work in our group has demonstrated that: (i) proteins which are rich in amino acid chromophores are susceptible to physiologically relevant doses of solar simulated radiation, (ii) this protein degradation is mediated primarily by the photodynamic production of reaction oxygen species and (iii) UVR-chromophore rich proteins are located in tissue regions where they may act as endogenous sunscreens. We have also shown that ECM proteases selectively degrade UVR-damaged assemblies in vitro and have developed new machine learning-based models to predict protease cleavage sites and hence relative protease susceptibilities in the human skin proteome. The recent development of peptide location fingerprinting applied to conventional mass spectrometry datasets has allowed the identification of novel candidate biomarkers of UVR-induced damage as a consequence of photo-ageing. For example, this approach is able to identify structure-associated modifications in collagen VI alpha chains, although collagen VI remodeling is not evident by conventional histological analysis. These methods and resources (skin proteome database, protein susceptibility prediction and peptide location fingerprinting analysis) are available for use at www.manchesterproteome.manchester.ac.uk. Key areas for future research include using peptide location fingerprinting to: (i) characterise the structural hallmarks of ageing and photo-ageing mechanisms across different phototypes and (ii) evaluate the efficacy of rejuvenating treatments against novel protein biomarkers

Mass spectrometry detection of photodamage in human extracellular matrix assemblies

Photoageing in skin is commonly recognised by architectural remodelling of dermal extracellular matrix components. Mass spectrometry was previously used to identify tissue-specific patterns of fibrillin-1 and collagen VI peptide spectrum matches (PXD008450). This study aimed to determine if the same mass spectrometry-based approach could detect peptide spectrum match patterns and significantly differences in relative abundance of peptide sequences characteristic of damage following exposure to UVR of co-purified suspensions of fibrillin and collagen VI microfibrils. Human dermal fibroblast-derived suspensions of microfibrils were irradiated with either broadband UVB or solar simulated radiation (SSR). UVR-induced molecular damage was characterised by proteolytic peptide generation with elastase followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). This allowed the molecular scale identification of UV-induced structural changes within two skin matrix assemblies. The proteomic approaches used have the potential to facilitate the rapid, protein-specific identification of differential molecular fingerprints of damage in key extracellular matrix protein