James A. Broadbent

Proteomic profiling of distinct clonal populations of bone marrow mesenchymal stem cells.

Mesenchymal stem cells (MSCs) have attracted immense research interest in the field of regenerative medicine due to their ability to be cultured for successive passages and multi‐lineage differentiation. The molecular mechanisms governing MSC self‐renewal and differentiation remain largely unknown. The development of sophisticated techniques, in particular clinical proteomics, has enabled researchers in various fields to identify and characterize cell specific biomarkers for therapeutic purposes. This study seeks to understand the cellular and sub‐cellular processes responsible for the existence of stem cell populations in bone marrow samples by revealing the whole cell proteome of the clonal cultures of bone marrow‐derived MSCs (BMSCs). Protein profiling of the MSC clonal populations was conducted by Two‐Dimensional Liquid Chromatography/Matrix‐Assisted Laser Desorption/Ionisation (MALDI) Mass Spectrometry (MS). A total of 83 proteins were identified with high confidence of which 11 showed differential expression between subpopulations, which included cytoskeletal and structural proteins, calcium binding proteins, cytokinetic proteins, and members of the intermediate filament family. This study generated a proteome reference map of BMSCs from the clonal populations, which will be valuable to better understand the underlying mechanism of BMSC self‐renewal and differentiation. J. Cell. Biochem. 106: 776–786, 2009.

Development of an enhanced proteomic method to detect prognostic and diagnostic markers of healing in chronic wound fluid.

Background  Chronic venous leg ulcers are a significant cause of pain, immobility and decreased quality of life for patients with these wounds. In view of this, research efforts are focused on multiple factors in the wound environment to obtain information regarding the healing of ulcers.

Proteomics in chronic wound research: Potentials in healing and health

Chronic wounds, such as venous and diabetic leg ulcers, represent a significant health and financial burden to individuals and healthcare systems. In worst‐case scenarios this condition may require the amputation of an affected limb, with significant impact on patient quality of life and health. Presently, there are no clinical biochemical analyses used in the diagnosis and management of this condition; moreover few biochemical therapies are accessible to patients. This presents a significant challenge in the efficient and efficacious treatment of chronic wounds by medical practitioners. A number of protein‐centric investigations have analyzed the wound environment and implicated a suite of molecular species predicted to be involved in the initiation or perpetuation of the condition. However, comprehensive proteomic investigation is yet to be engaged in the analysis of chronic wounds for the identification of molecular diagnostic/prognostic markers of healing or therapeutic targets. This review examines clinical chronic wound research and recommends a path toward proteomic investigation for the discovery of medically significant targets. Additionally, the Supporting Information documents associated with this review provide the first comprehensive summary of protein‐centric, small molecule and elemental analyses in clinical chronic wound research.

Urinary biomarkers of physical activity: candidates and clinical utility

Chronic physical inactivity is a major risk factor for a number of important lifestyle diseases, while inappropriate exposure to high physical demands is a risk factor for musculoskeletal injury and fatigue. Proteomic and metabolomic investigations of the physical activity continuum – extreme sedentariness to extremes in physical performance – offer increasing insight into the biological impacts of physical activity. Moreover, biomarkers, revealed in such studies, may have utility in the monitoring of metabolic and musculoskeletal health or recovery following injury. As a diagnostic matrix, urine is non-invasive to collect and it contains many biomolecules, which reflect both positive and negative adaptations to physical activity exposure. This review examines the utility and landscape of biomarkers of physical activity with particular reference to those found in urine.

A pre-clinical functional assessment of an acellular scaffold intended for the treatment of hard-to-heal wounds.

The majority of the population experience successful wound‐healing outcomes; however, 1–3% of those aged over 65 years experience delayed wound healing and wound perpetuation. These hard‐to‐heal wounds contain degraded and dysfunctional extracellular matrix (ECM); yet, the integrity of this structure is critical in the processes of normal wound healing. Here, we evaluated a novel synthetic matrix protein for its ability to act as an acellular scaffold that could replace dysfunctional ECM. In this regard, the synthetic protein was subjected to adsorption and diffusion assays using collagen and human dermal tissues; evaluated for its ability to influence keratinocyte and fibroblast attachment, migration and proliferation and assessed for its ability to influence in vivo wound healing in a porcine model. Critically, these experiments demonstrate that the matrix protein adsorbed to collagen and human dermal tissue but did not diffuse through human dermal tissue within a 24‐hour observation period, and facilitated cell attachment, migration and proliferation. In a porcine wound‐healing model, significantly smaller wound areas were observed in the test group compared with the control group following the third treatment. These data provide evidence that the synthetic matrix protein has the ability to function as an acellular scaffold for wound‐healing purposes.

Evaluation of haemoglobin in blister fluid as an indicator of paediatric burn wound depth

The early and accurate assessment of burns is essential to inform patient treatment regimens; however, this first critical step in clinical practice remains a challenge for specialist burns clinicians worldwide. In this regard, protein biomarkers are a potential adjunct diagnostic tool to assist experienced clinical judgement. Free circulating haemoglobin has previously shown some promise as an indicator of burn depth in a murine animal model. Using blister fluid collected from paediatric burn patients, haemoglobin abundance was measured using semi-quantitative Western blot and immunoassays. Although a trend was observed in which haemoglobin abundance increased with burn wound severity, several patient samples deviated significantly from this trend. Further, it was found that haemoglobin concentration decreased significantly when whole cells, cell debris and fibrinous matrix was removed from the blister fluid by centrifugation; although the relationship to depth was still present. Statistical analyses showed that haemoglobin abundance in the fluid was more strongly related to the time between injury and sample collection and the time taken for spontaneous re-epithelialisation. We hypothesise that prolonged exposure to the blister fluid microenvironment may result in an increased haemoglobin abundance due to erythrocyte lysis, and delayed wound healing.

Mass spectrometry based data of the blister fluid proteome of paediatric burn patients

The data presented here are associated with the article “The blister fluid proteome of paediatric burns” (Zang et al., 2016) [1]. Burn injury is a highly traumatic event for children. The degree of burn severity (superficial-, deep-, or full-thickness injury) often dictates the extent of later scar formation which may require long term surgical operation or skin grafting. The data were obtained by fractionating paediatric burn blister fluid samples, which were pooled according to burn depth and then analysed using data dependent acquisition LC–MS/MS. The data includes a table of all proteins identified, in which burn depth category they were found, the percentage sequence coverage for each protein and the number of high confidence peptide identifications for each protein. Further Gene Ontology enrichment analysis shows the significantly over-represented biological processes, molecular functions, and cellular components of the burn blister fluid proteome. In addition, tables include the proteins associated with the biological processes of “wound healing” and “response to stress” as examples of highly relevant processes that occur in burn wounds.

The blister fluid proteome of paediatric burns

UNLABELLED Burn injury is highly traumatic for paediatric patients, with the severity of the burn often dictating the extent of scar formation. The diagnosis of burn wound severity is largely determined by the attending clinicians experience. Thus, a greater understanding of the biochemistry at burn wound site environment and the biology of burns of different severities at an earlier stage may reduce the reliance on subjective diagnoses. In this study, blister fluid was collected from superficial thickness, deep-partial thickness, and full-thickness paediatric burn wounds. Samples were combined together based on burn depth classification and then subjected to four different fractionation methods followed by trypsin digestion. Peptides were analysed by liquid chromatography tandem mass spectrometry in order to measure the proteome of each fraction. In total, 811 individual proteins were identified, including 107, 84, and 146 proteins unique to superficial, deep-partial thickness and full-thickness burn wounds, respectively. The differences in the protein inventory and the associated gene ontologies represented within each burn depth category demonstrated that there are subtle, yet significant, variations in the biochemistry of burn wounds according to severity. Importantly, this study has produced the most comprehensive catalogue of proteins from the paediatric burn wound microenvironment to date. SIGNIFICANCE To our knowledge, this study has been the first to comprehensively measure the paediatric burn blister fluid proteome and has provided insight into the proteomic response to burn injury. The study contributes to the knowledge of blister fluid biochemistry of burn injury and provides clinically relevant knowledge through the qualitative evaluation of biochemical differences between burns of different depths. A better understanding of the burn wound environment will ultimately assist with more accurate clinical decision making and improved wound healing and scar reduction procedures.

Choose wisely: Network, ontology and annotation resources for the analysis of Staphylococcus aureus omics data.

Staphylococcus aureus (S. aureus) is a prominent human and livestock pathogen investigated widely using omic technologies. Critically, due to availability, low visibility or scattered resources, robust network and statistical contextualisation of the resulting data is generally under-represented. Here, we present novel meta-analyses of freely-accessible molecular network and gene ontology annotation information resources for S. aureus omics data interpretation. Furthermore, through the application of the gene ontology annotation resources we demonstrate their value and ability (or lack-there-of) to summarise and statistically interpret the emergent properties of gene expression and protein abundance changes using publically available data. This analysis provides simple metrics for network selection and demonstrates the availability and impact that gene ontology annotation selection can have on the contextualisation of bacterial omics data.

Differential Expression of Keratinocyte-Derived Extracellular Vesicle Mirnas Discriminate Exosomes From Apoptotic Bodies and Microvesicles

Extracellular vesicles (EVs) are mammalian cell-derived nano-scale structures enclosed by a lipid bilayer that were previously considered to be cell debris with little biological value. However, EVs are now recognized to possess biological function, acting as a packaging, transport and delivery mechanisms by which functional molecules (i.e., miRNAs) can be transferred to target cells over some distance. To examine the miRNA from keratinocyte-derived EVs, we isolated three distinct populations of EVs from both HaCaT and primary human keratinocytes (PKCs) and characterized their biophysical, biochemical and functional features by using microscopy, immunoblotting, nanoparticle tracking, and next generation sequencing. We identified 1,048; 906; and 704 miRNAs, respectively, in apoptotic bodies (APs), microvesicles (MVs) and exosomes (EXs) released from HaCaT, and 608; 506; and 622 miRNAs in APs, MVs and EXs released from PKCs. In which, there were 623 and 437 identified miRNAs common to three HaCaT-derived EVs and PKC-derived EVs, respectively. In addition, we found hundreds of exosomal miRNAs that were previously un-reported. Differences in the abundance levels of the identified EV miRNAs could discriminate between the three EV populations. These data contribute substantially to knowledge within the EV-identified miRNA database, especially with regard to keratinocyte-derived EV miRNA content.