In Vivo Assessment of Protease Dynamics in Cutaneous Wound Healing by Degradomics Analysis of Porcine Wound Exudates

Proteases control complex tissue responses by modulating inflammation, cell proliferation and migration, and matrix remodeling. All these processes are orchestrated in cutaneous wound healing to restore the skin''s barrier function upon injury. Altered protease activity has been implicated in the pathogenesis of healing impairments, and proteases are important targets in diagnosis and therapy of this pathology. Global assessment of proteolysis at critical turning points after injury will define crucial events in acute healing that might be disturbed in healing disorders. As optimal biospecimens, wound exudates contain an ideal proteome to detect extracellular proteolytic events, are noninvasively accessible, and can be collected at multiple time points along the healing process from the same wound in the clinics. In this study, we applied multiplexed Terminal Amine Isotopic Labeling of Substrates (TAILS) to globally assess proteolysis in early phases of cutaneous wound healing. By quantitative analysis of proteins and protein N termini in wound fluids from a clinically relevant pig wound model, we identified more than 650 proteins and discerned major healing phases through distinctive abundance clustering of markers of inflammation, granulation tissue formation, and re-epithelialization. TAILS revealed a high degree of proteolysis at all time points after injury by detecting almost 1300 N-terminal peptides in ∼450 proteins. Quantitative positional proteomics mapped pivotal interdependent processing events in the blood coagulation and complement cascades, temporally discerned clotting and fibrinolysis during the healing process, and detected processing of complement C3 at distinct time points after wounding and by different proteases. Exploiting data on primary cleavage specificities, we related candidate proteases to cleavage events and revealed processing of the integrin adapter protein kindlin-3 by caspase-3, generating new hypotheses for protease-substrate relations in the healing skin wound in vivo. The data have been deposited to the ProteomeXchange Consortium with identifier PXD001198.Proteases play pivotal roles in complicated tissue processes by influencing immune responses, epithelial and mesenchymal cell integrity, proliferation and migration, as well as extracellular matrix maturation and remodeling. As a prime example, they control all phases of cutaneous wound healing by participating in coagulation, complement activation, recruitment of immune cells, migration of keratinocytes and fibroblasts, angiogenesis, and formation of the scar tissue (1, 2). Immediately after injury a blood clot is formed through a series of interconnected proteolytic processing events of coagulation factors to initially seal the site of damage and to provide a provisional fibrin matrix (3, 4). Soon after and interfacing with coagulation, the complement system is activated to fight invading bacteria. During the inflammatory phase (day 1 to 3) the kallikrein–kinin axis controls vasodilation and vascular permeability, and leukocytes enter the wounded tissue in response to pro-inflammatory chemo-attractants whose activity is regulated by limited proteolysis (5). Upon activation of the plasmin system, the fibrin clot is proteolytically degraded to facilitate migration of keratinocytes from the epidermis and the hair follicles as well as of macrophages and fibroblasts in the granulation tissue. These migratory events that occur during the phase of new tissue formation (days 3–10) are further promoted by matrix metalloproteinases (MMPs)¹ that are activated by plasmin and concomitantly modulate tissue influx of immune cells and resolution of inflammation (6, 7). MMPs are also heavily involved in matrix remodeling and scar formation as the final step of skin repair that starts 1 to 2 weeks after injury, but may continue for up to 1 year or more (8).As a consequence of their crucial roles in the healing skin, wound proteases have been implicated in the pathogenesis of healing disorders (9). Impaired wound healing has detrimental consequences and often leads to the development of chronic, nonhealing ulcers. In particular, patients suffering from vascular disease, diabetes, or autoimmune disorders frequently develop chronic skin ulcers. Chronic wounds have become a major problem in industrialized western countries with their rising rates of obesity and the increasing life expectancy, putting also an enormous burden on health systems (10). Because MMPs received much attention in chronic wound repair (11, 12), current diagnostic tests rely on assessment of general MMP activity in wound swabs (13), but suffer from lack of specificity and fail in many cases in predicting the actual wound status. Hence, novel multiparameter point-of-care tests are needed that integrate multiple proteolytic events to deliver robust results on aberrant proteolysis as an indicator for chronic wound progression (14).Proteolytic cleavages in major cascades, such as blood coagulation and complement activation, have been mapped in great detail through seminal biochemical studies (15, 16). In vitro studies used purified or recombinant proteins or monitored processing of radioactively labeled components spiked into activated blood plasma (17, 18). Later, the invention of monoclonal antibodies and/or active site labels also enabled the analysis of endogenous proteolytically activated coagulation factors and complement components in in vivo samples (19). However, none of these techniques allowed directly recording the actual interconnected cleavage events of these complex proteolytic activation cascades in vivo and in response to a natural incidence like tissue injury, a prerequisite to better understand their disturbances in pathology. Addressing this limitation, mass spectrometry-based degradomics technologies have been developed that identify and relatively quantify protein N termini in complex biological samples (20–22). One of these methods, Terminal Amine Isotopic Labeling of Substrates (TAILS), was successfully applied in vitro to identify novel substrates of individual proteases (23–28) and more recently also in vivo to systematically assess protease activity in complex tissue samples (29, 30). TAILS has unique multiplexing capabilities and thus is particularly suited for analyzing the N-terminome at multiple time points after the stimulus (31) as required for the time-resolved analysis of proteolytic events at critical turning points after skin injury (32).An optimal sample for the system-wide analysis of protease activity in cutaneous wound healing should be easily and preferentially noninvasively accessible, cover most cleavage events, and be ideally obtained from the same wound at multiple time points after wounding. This is the case for wound exudates, which can be either directly collected from the wound site (33, 34) or extracted from wound dressings (35). Several proteomic analyses of wound fluids have been performed that mostly focused on the quantitative comparison of proteins in fluids from normal and impaired healing (33, 35). The most recent studies covered a significant proportion of the wound proteome and recorded differential protein abundances at single states of chronic manifestation or normal healing (35). However, these analyses did not integrate data on healing progression and/or functional modifications to the wound proteome along the healing process. Importantly, several studies suggest a higher predictive power of post-translational modifications than relative protein abundances for disease progression (36, 37). Hence, recording proteolytic signatures at critical time points after wounding is a promising approach to define pivotal events in acute healing that might be disturbed in healing impairments.Here, we exploited the power of multiplexed iTRAQ-TAILS to globally analyze the wound fluid proteome and N-terminome at multiple time points after injury. We identified more than 650 proteins and almost 1300 protein N termini from exudates collected in a clinically relevant pig wound healing model. By combining quantitative proteome and N-terminome analyses, we temporally discerned major phases of acute wound healing and mapped key cleavages in blood coagulation and complement activation. Further, we revealed protease dynamics through identification, quantification, and relative weighting of multiple cleavages in complement C3. Finally, by integrating data on known cleavage site specificities we related groups of proteases to identified cleavage sites and established direct cleavage of the integrin adapter protein kindlin-3 by caspase-3, which might play an important role in immune cell apoptosis during cutaneous wound healing.     

Leukocyte- and platelet-derived microvesicle interactions following in vitro and in vivo activation of toll-like receptor 4 by lipopolysaccharide

Background

Pro-coagulant membrane microvesicles (MV) derived from platelets and leukocytes are shed into the circulation following receptor-mediated activation, cell-cell interaction, and apoptosis. Platelets are sentinel markers of toll-like receptor 4 (TLR4) activation. Experiments were designed to evaluate the time course and mechanism of direct interactions between platelets and leukocytes following acute activation of TLR4 by bacterial lipopolysaccharide (LPS).

Methodology/Principal Findings

Blood from age-matched male and female wild type (WT) and TLR4 gene deleted (dTLR4) mice was incubated with ultra-pure E. coli LPS (500 ng/ml) for up to one hour. At designated periods, leukocyte antigen positive platelets, platelet antigen positive leukocytes and cell-derived MV were quantified by flow cytometry. Numbers of platelet- or leukocyte-derived MV did not increase within one hour following in vitro exposure of blood to LPS. However, with LPS stimulation numbers of platelets staining positive for both platelet- and leukocyte-specific antigens increased in blood derived from WT but not dTLR4 mice. This effect was blocked by inhibition of TLR4 signaling mediated by My88 and TRIF. Seven days after a single intravenous injection of LPS (500 ng/mouse or 20 ng/gm body wt) to WT mice, none of the platelets stained for leukocyte antigen. However, granulocytes, monocytes and apoptotic bodies stained positive for platelet antigens.

Conclusions/Significance

Within one hour of exposure to LPS, leukocytes exchange surface antigens with platelets through TLR4 activation. In vivo, leukocyte expression of platelet antigen is retained after a single exposure to LPS following turn over of the platelet pool. Acute expression of leukocyte antigen on platelets within one hour of exposure to LPS and the sustained expression of platelet antigen on leukocytes following a single acute exposure to LPS in vivo explains, in part, associations of platelets and leukocytes in response to bacterial infection and changes in thrombotic propensity of the blood.     

Preparation and characterization of chitosan-carbon nanotube scaffolds for bone tissue engineering

In recent years, significant development has been given to chitosan for orthopedic application. In this study, we have prepared scaffolds with the use of low and high molecular weight chitosan with 0.0025%, 0.005% and 0.01% weight of f-multiwalled carbon nanotube (f-MWCNT) by freezing and lyophilization method and physiochemically characterized as bone graft substitutes. Fourier Transform Infrared Spectroscopy, X-Ray Diffraction Analysis, Thermal Gravimetric Analysis, Scanning Electron Microscopy and Optical Microscopy results indicated that the f-MWCNT was uniformly dispersed in chitosan matrix and there was a chemical interaction between chitosan and f-MWCNT. The water uptake ability and porosity of scaffolds increased with an increase the amount of f-MWCNT. The cell proliferation, protein content, alkaline phosphatase and mineralization of the composite scaffolds were higher than chitosan scaffold due to the addition of f-MWCNT. Herewith, we are suggesting that chitosan/f-MWCNT scaffolds are promising biomaterials for bone tissue engineering.     

Assessment of Microbial Richness in Pelagic Sediment of Andaman Sea by Bacterial Tag Encoded FLX Titanium Amplicon Pyrosequencing (bTEFAP)

Microbial diversity of 1,000 m deep pelagic sediment from off Coast of Andaman Sea was analyzed by a culture independent technique, bacterial tag encoded FLX titanium amplicon pyrosequencing. The hypervariable region of small subunit ribosomal rRNA gene covering V6–V9, was amplified from the metagenomic DNA and sequenced. We obtained 19,271 reads, of which 18,206 high quality sequences were subjected to diversity analysis. A total of 305 operational taxonomic units (OTUs) were obtained corresponding to the members of firmicutes, proteobacteria, plantomycetes, actinobacteria, chloroflexi, bacteroidetes, and verucomicrobium. Firmicutes was the predominant phylum, which was largely represented with the family bacillaceae. More than 44 % of sequence reads could not be classified up to the species level and more than 14 % of the reads could not be assigned to any genus. Thus, the data indicates the possibility for the presence of uncultivable or unidentified novel bacterial species. In addition, the community structure identified in this study significantly differs with other reports from marine sediments.     

Design, synthesis, stereochemistry and antioxidant properties of various 7-alkylated 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-ones

We used the modified Mannich condensation to synthesize three closely-related series of 7-alkylated 3-ABNs 1-5 viz., 7-methylated 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-ones (7-Me ABNs 1-5), 7-ethylated 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-ones (7-Et ABNs 1-5) and 7-tert-pentylated 2,4-diaryl-3-azabicyclo[3.3.1]nonan-9-ones (7-tert-pentyl ABNs 1-5). All compounds yielded good as single isomers by the use of PPA·SiO(2) as a heterogeneous Bronsted acidic catalyst. The 1D, 2D NMR, and single-crystal XRD interpretations unambiguously characterized the stereochemistry of the synthesized compounds. In solution as well as solid-state, all compounds exist in the twin-chair conformation with equatorial orientations of all substitutions, despite their nature and positions. The chemical methods viz., DPPH, reducing power, and phospho-molybdenum methods identified some of the target curcumin analogs as active compounds. Among them, 7-Me ABN 4 (7-methyl-2,4-bis(3-methoxy-4-hydroxyphenyl)-3-azabicyclo[3.3.1]nonan-9)-one exerted the best antioxidant profile that comparable to standard l-ascorbic acid, α-tocopherol and curcumin. Hence, we evaluated further for its intracellular ROS inhibition potency on RAW 264.7 macrophage cells, and found to be effective as well as non-toxic at 100μM.     

Induction of apoptosis and cell cycle arrest by Bis (2-ethylhexyl) phthalate produced by marine Bacillus pumilus MB 40

Marine microorganisms represent a potential source for the production of biomedically useful compounds active against inflammation, cancer, diabetes, etc. Marine Bacillus pumilus MB 40 (GenBank accession no. HQ705771) isolated from deep sea water column (1000m depth) near Andaman and Nicobar islands produced a bioactive lead, Bis (2-ethylhexyl) phthalate (BEHP) with a molecular formula of C(6)H(4)(CO(2)C(8)H(17))(2) and a molecular ion at m/z 391 (M(+)). Anti proliferative effect of the isolated compound was examined by MTT assay in human erythroleukemic K562 cells and the IC(50) of BEHP was found to be 21μM. BEHP was able to induce apoptosis involving caspases pathway, besides regulating mitochondrial enzymes. Further, western blot analysis revealed the activation of caspases family proteins viz., caspase 8, caspase-9 and caspase-3. An increase in the expression of Bax mRNA concomitant with a decrease in mRNA of Bcl-2 in BEHP treated K562 cells was also observed. AO/EB staining of BEHP treated K562 cells further confirmed the progression of apoptosis as evidenced by morphological changes including nuclear condensation, cell shrinkage, and formation of apoptotic bodies. Treatment of K562 cells with BEHP induced the progressive accumulation of fragmented DNA in a time dependent manner. This pattern appeared as a typical laddering distribution of DNA fragmentation due to intranucleosomal cleavage associated with apoptosis. Based on flow cytometric analysis it has become evident that the compound was also effective in arresting the cell cycle at a sub G0/G1 phase.     

Studies on hydrogenase activity and chlorobenzene respiration in <Emphasis Type="Italic">Dehalococcoides</Emphasis> sp. strain CBDB1

Hydrogen oxidation and electron transport were studied in the chlorobenzene-utilizing anaerobe Dehalococcoides sp. strain CBDB1. While Cu²⁺ and Hg²⁺ ions irreversibly inhibited hydrogenase activity in intact cells, Ni²⁺ ions inhibited reversibly. About 80% of the initial hydrogenase activity was inactivated within 30 s when the cells were exposed to air. In contrast, hydrogenase was active at a redox potential of +10 mV when this redox potential was established anoxically with a redox indicator. Viologen dyes served both as electron acceptor for hydrogenase and electron donor for the dehalogenase. A menaquinone analogue, 2,3-dimethyl 1,4-naphthoquinone, served neither as electron acceptor for the hydrogenase nor as electron donor for the dehalogenase. In addition, the menaquinone antagonist 2-n-heptyl-4-hydroxyquinoline-N-oxide had no effect on dechlorination catalyzed by cell suspensions or isolated membranes with hydrogen as electron donor, lending further support to the notion that menaquinone is not involved in electron transport. The ionophores tetrachlorosalicylanilide and carbonylcyanide m-chlorophenylhydrazone did not inhibit dechlorination by cell suspensions, indicating that strain CBDB1 does not require reverse electron transport. The ATP-synthase inhibitor N,N-dicyclohexylcarbodiimide inhibited the dechlorination reaction with cell suspensions; however, the latter effect was partially relieved by the addition of tetrachlorosalicylanilide. 1,2,3,4-Tetrachlorobenzene strongly inhibited dechlorination of other chlorobenzenes by cell suspensions with hydrogen as electron donor, but it did not interfere with either hydrogenase or dehalogenase activity.     

Differential effects of 17beta-estradiol and raloxifene on VSMC phenotype and expression of osteoblast-associated proteins

Several studies demonstrate an association between osteoporosis and arterial calcific disease, both of which being common in elderly women. Estradiol and raloxifene, a selective estrogen receptor modulator, prevent bone loss in postmenopausal women. Little is known regarding how these agents affect arterial calcification. The aim of this study was to determine whether or not 17beta-estradiol and raloxifene reduced vascular smooth muscle cell (VSMC) differentiation and expression of bone-associated proteins during phosphate-induced calcification in vitro. Aortic VSMC were cultured from adult, gonadally intact, and ovariectomized (OVX) female pigs. Calcifying medium was added, and cells were treated with solvent (control), 17beta-estradiol (E(2)), or raloxifene. Extent of calcification and phenotypic expression of bone-associated proteins [matrix gla protein (MGP), osteoprotegerin (OPG), and bone sialoprotein (BSP)] were examined at 3-day intervals over 2 wk. Calcium content increased in all groups but was greater in VSMC derived from intact compared with OVX animals. E(2) reduced calcification and preserved a contractile phenotype. Expression of OPG significantly decreased with time; this decrease was significantly greater in VSMC derived from OVX compared with gonadally intact pigs. E(2) and raloxifene preserved expression of OPG only in VSMC from intact pigs. Expression of MGP increased significantly with time and was not affected by E(2) or raloxifene treatments. E(2) treatment significantly inhibited synthesis of BSP in cells from both groups. In conclusion, E(2) slows differentiation of VSMC induced by excess phosphate. Effectiveness of raloxifene to preserve expression of bone cell-associated proteins depends on the hormonal status of the tissue donor.