Comparative proteomic analysis of extracellular matrix proteins secreted by two types of skin fibroblasts

Recent omics advances in hair aging biology and hair biomarkers analysis

Aging is a complex natural process that leads to a decline in physiological functions, which is visible in signs such as hair graying, thinning, and loss. Although hair graying is characterized by a loss of pigment in the hair shaft, the underlying mechanism of age-associated hair graying is not fully understood. Hair graying and loss can have a significant impact on an individual's self-esteem and self-confidence, potentially leading to mental health problems such as depression and anxiety. Omics technologies, which have applications beyond clinical medicine, have led to the discovery of candidate hair biomarkers and may provide insight into the complex biology of hair aging and identify targets for effective therapies. This review provides an up-to-date overview of recent omics discoveries, including age-associated alterations of proteins and metabolites in the hair shaft and follicle, and highlights the significance of hair aging and graying biomarker discoveries. The decline in hair follicle stem cell activity with aging decreased the regeneration capacity of hair follicles. Cellular senescence, oxidative damage and altered extracellular matrix of hair follicle constituents characterized hair follicle and hair shaft aging and graying. The review attempts to correlate the impact of endogenous and exogenous factors on hair aging. We close by discussing the main challenges and limitations of the field, defining major open questions and offering an outlook for future research.

Macromolecular crowding in the development of a three-dimensional organotypic human breast cancer model

Although cell-derived matrices are at the forefront of scientific research and technological innovation for the development of in vitro tumour models, their two-dimensional structure and low extracellular matrix composition restrict their capacity to accurately predict toxicity of candidate molecules. Herein, we assessed the potential of macromolecular crowding (a biophysical phenomenon that significantly enhances and accelerates extracellular matrix deposition, resulting in three-dimensional tissue surrogates) in improving cell-derived matrices in vitro tumour models. Among the various decellularisation protocols assessed (NH4OH, DOC, SDS/EDTA, NP40), the NP40 appeared to be the most effective in removing cellular matter and the least destructive to the deposited matrix. Among the various cell types (mammary, skin, lung fibroblasts) used to produce the cell-derived matrices, the mammary fibroblast derived matrices produced under macromolecular crowding conditions and decellularised with NP40 resulted in significant increase in focal adhesion molecules, matrix metalloproteinases and proinflammatory cytokines, when seeded with MDA-MB-231 cells. Further, macromolecular crowding derived matrices significantly increased doxorubicin resistance and reduced the impact of intracellular reactive oxygen species mediated cell death. Collectively our data clearly illustrate the potential of macromolecular crowding in the development of cell-derived matrices-based in vitro tumour models that more accurately resemble the tumour microenvironment.

Inhibitory Effect of Seawater Pearl Hydrolysate on UVA-Induced Photoaging of Human Skin Fibroblasts

This study is an investigation into the inhibitory effect of seawater pearl hydrolysate (SPH) on the UVA-induced photoaging of human skin fibroblast (HSF) cells, and the mechanism thereof. HSF cells were cultured and irradiated with a UVA 0–50 J·cm⁻² dose gradient. The cell inhibition rate was detected using the CCK8 method, and the half-inhibitory dose was determined. Based on this, the dose of UVA irradiation for the follow-up experiment was selected to establish a photoaging model of the HSF cells. The cells were divided into a normal (N) group, UVA-irradiated (UVA) group, SPH low dose (SPHL) group, SPH medium dose (SPHM) group, and SPH high dose (SPHH) group. The photoaging model of HSF cells was established by UVA irradiation in the UVA, SPHL, SPHM, and SPHH groups; the SPHL, SPHM, and SPHH groups were treated with SPH at concentrations of 50, 100, and 200 mg·L⁻¹, respectively, at the same time. After 24 and 48 h of culture, the reactive oxygen species (ROS) level of the HSF cells was detected by flow cytometry, and the required culture time of the HSF cells for the follow-up experiment was selected. The malondialdehyde and glutathione contents, as well as the activities of the superoxide dismutase, catalase, and glutathione peroxidase in the HSF cells, were detected by biochemical methods. The levels of expression of MMP-1 and collagen I protein in HSF cells were detected by the western blot test, the extent of aging of HSF cells was detected by β-galactosidase staining, and the apoptosis level of HSF cells was detected by flow cytometry. The results show that SPH inhibits the UVA-induced photoaging of HSF cells in a dose-dependent manner within a certain concentration range, and the effect of a concentration of 200 mg·L^–1 was the most significant. The mechanism is related to improving the antioxidant activity of photoaging HSF cells to eliminate excessive ROS. It can inhibit apoptosis, reduce the protein expression of MMP-1, and effectively control the degradation of collagen I protein in photoaging HSF cells. Therefore, SPH offers potential for use in sunscreen cosmetics.

Shotgun proteomics of extracellular matrix in late senescent human dermal fibroblasts reveals a down-regulated fibronectin-centered network

Extracellular matrix (ECM) proteins play a pivotal role in cell growth and differentiation. To characterize aged ECM proteins, we compared the proteomes by shotgun method of young (passage #15) and late senescent (passage #40) human dermal fibroblasts (HDFs) using SDS-PAGE coupled with LC–MS/MS. The relative abundance of identified proteins was determined using mol% of individual proteins as a semi-quantitative index. Fifteen ECM proteins including apolipoprotein B (APOB) and high-temperature requirement factor 1 (HTRA1) were up-regulated, whereas 50 proteins including fibronectin 1 (FN1) and vitronectin (VTN) were down-regulated in late senescent HDFs. The identified ECM proteins combined with plasma membrane were queried to construct the protein–protein interaction network using Ingenuity Pathways Analysis, resulting in a distinct FN1-centered network. Of differentially abundant ECM proteins in shotgun proteomics, the protein levels of FN1, VTN, APOB, and HTRA1 were verified by immunoblot analysis. The results suggest that the aging process in HDFs might be finally involved in the impaired FN1 regulatory ECM network combined with altered interaction of neighboring proteins. Shotgun proteomics of highly aged HDFs provides insight for further studies of late senescence-related alterations in ECM proteins.

Collagen analysis with mass spectrometry

Mass spectrometry-based techniques can be applied to investigate collagen with respect to identification, quantification, supramolecular organization, and various post-translational modifications. The continuous interest in collagen research has led to a shift from techniques to analyze the physical characteristics of collagen to methods to study collagen abundance and modifications. In this review, we illustrate the potential of mass spectrometry for in-depth analyses of collagen.

Quantitative proteomic profiling of extracellular matrix and site-specific collagen post-translational modifications in an in vitro model of lung fibrosis

Lung fibrosis is characterized by excessive deposition of extracellular matrix (ECM), in particular collagens, by fibroblasts in the interstitium. Transforming growth factor-β1 (TGF-β1) alters the expression of many extracellular matrix (ECM) components produced by fibroblasts, but such changes in ECM composition as well as modulation of collagen post-translational modification (PTM) levels have not been comprehensively investigated. Here, we performed mass spectrometry (MS)-based proteomics analyses to assess changes in the ECM deposited by cultured lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients upon stimulation with transforming growth factor β1 (TGF-β1). In addition to the ECM changes commonly associated with lung fibrosis, MS-based label-free quantification revealed profound effects on enzymes involved in ECM crosslinking and turnover as well as multiple positive and negative feedback mechanisms of TGF-β1 signaling. Notably, the ECM changes observed in this in vitro model correlated significantly with ECM changes observed in patient samples. Because collagens are subject to multiple PTMs with major implications in disease, we implemented a new bioinformatic platform to analyze MS data that allows for the comprehensive mapping and site-specific quantitation of collagen PTMs in crude ECM preparations. These analyses yielded a comprehensive map of prolyl and lysyl hydroxylations as well as lysyl glycosylations for 15 collagen chains. In addition, site-specific PTM analysis revealed novel sites of prolyl-3-hydroxylation and lysyl glycosylation in type I collagen. Interestingly, the results show, for the first time, that TGF-β1 can modulate prolyl-3-hydroxylation and glycosylation in a site-specific manner. Taken together, this proof of concept study not only reveals unanticipated TGF-β1 mediated regulation of collagen PTMs and other ECM components but also lays the foundation for dissecting their key roles in health and disease.

The proteomic data has been deposited to the ProteomeXchange Consortium via the MassIVE partner repository with the data set identifier MSV000082958.

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Quantitative proteomics of TGF-β-induced changes in ECM composition and collagen PTM in pulmonary fibroblasts

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TGF-β promotes crosslinking and turnover as well as complex feedback mechanisms that alter fibroblast ECM homeostasis.

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A novel bioinformatic workflow for MS data analysis enabled global mapping and quantitation of known and novel collagen PTMs

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Quantitative assessment of prolyl-3-hydroxylation site occupancy and lysine-O-glycosylation microheterogeneity

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TGF-β1 modulates collagen PTMs in a site-specific manner that may favor collagen accumulation in lung fibrosis

Quantitative proteomic analysis of dermal papilla from male androgenetic alopecia comparing before and after treatment with low-level laser therapy

BACKGROUND

Currently, low-level laser therapy (LLLT) has been approved as a new treatment for androgenetic alopecia (AGA). However, it has not been elucidated how LLLT promotes hair growth in vivo.

OBJECTIVES

To investigate the change in protein expression from dermal papilla (DP) tissues in male AGA patients after LLLT treatment using liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis.

METHODS

This is an open-label, prospective, single-arm study obtained punch scalp biopsy specimens from patients with AGA before and after LLLT treatment. Each subject was self-treated with helmet type of LLLT (655 nm, 5 mW) device at home for 25 minutes per treatment every other day for 24 weeks. LC-MS/MS analysis based on the dimethyl labeling strategy for protein quantification was used to identify proteins expressed in DP tissues from AGA patients.

RESULTS

Proteomic analysis revealed 11 statistically significant up-regulated and 2 down-regulated proteins in LLLT treated DP compared with baseline (P < 0.05). A bioinformatic analysis signifies that these proteins are involved in several biological processes such as regulation of cellular transcription, protein biosynthesis, cell energy, lipid homeostasis, extracellular matrix (ECM), ECM structural constituent, cell-cell/cell-matrix adhesion as well as angiogenesis. ATP-binding cassette sub-family G member, a transporter involved in cellular lipid homeostasis, was the most up-regulated protein. Additionally, LLLT increased the main ECM proteins in DP which results in a bigger volume of DP and a clinical improvement of hair diameter in AGA patients.

CONCLUSION

We identified the proteome set of DP proteins of male patients with AGA treated with LLLT which implicates the role of LLLT in promoting hair growth and reversing of miniaturization process of AGA by enhancing DP cell function. Our results strongly support the benefit of LLLT in the treatment of AGA. Lasers Surg. Med. © 2019 Wiley Periodicals, Inc.

The effects of the metformin on inhibition of UVA-induced expression of MMPs and COL-I in human skin fibroblasts

This study was to investigate the effects of metformin (MF) on ultraviolet A (UVA)-induced expression of matrix metalloproteinases (MMPs) and type I collagen (COL-I) in human skin fibroblasts (HSFs). HSFs were cultured in vitro and divided into control group, UVA group, and UVA + MF group. Cell proliferation was detected by CCK-8 method, and intracellular reactive oxygen species (ROS) level was detected by flow cytometry with fluorescent probe 2′,7′-dichlorofluorescein diacetate (DCF-DA) staining. Meanwhile, real-time polymerase chain reaction (PCR) was used to examine the relative messenger RNA (mRNA) expression of aging-related genes, including MMP1, MMP3, and COL-I. Moreover, the expression of MMP1, MMP3, and COL-I proteins was further detected by western blot. Compared with the control group, the ROS content in the UVA group was increased significantly ( P < 0.05), while the ROS content in the UVA + MF group was evidently lower than that in the UVA group ( P < 0.05). In addition, the MMP1 and MMP3 mRNA levels were significantly elevated, while the COL-I mRNA was significantly decreased in UVA-induced HSF cells compared with the control cells. However, MF could significantly inhibit the improved MMP1 and MMP3 mRNA level and increase the COL-I mRNA level. Moreover, MF could significantly reverse the increasing MMP1 and MMP3 protein level and decreasing COL-I protein level induced by UVA. In conclusion, MF can increase the antioxidant capacity of cells and increase the synthesis of COL-I by inhibiting the level of intracellular ROS and the expression of related MMPs, thereby inhibiting the UVA-induced photoaging effect of HSF.

Hair follicle dermal condensation forms via Fgf20 primed cell cycle exit, cell motility, and aggregation

Mesenchymal condensation is a critical step in organogenesis, yet the underlying molecular and cellular mechanisms remain poorly understood. The hair follicle dermal condensate is the precursor to the permanent mesenchymal unit of the hair follicle, the dermal papilla, which regulates hair cycling throughout life and bears hair inductive potential. Dermal condensate morphogenesis depends on epithelial Fibroblast Growth Factor 20 (Fgf20). Here, we combine mouse models with 3D and 4D microscopy to demonstrate that dermal condensates form de novo and via directional migration. We identify cell cycle exit and cell shape changes as early hallmarks of dermal condensate morphogenesis and find that Fgf20 primes these cellular behaviors and enhances cell motility and condensation. RNAseq profiling of immediate Fgf20 targets revealed induction of a subset of dermal condensate marker genes. Collectively, these data indicate that dermal condensation occurs via directed cell movement and that Fgf20 orchestrates the early cellular and molecular events.

All mammal hair springs from hair follicles under the skin. These follicles sit in the dermis, beneath the outermost skin layer, the epidermis. In the embryo, hair follicles develop from unspecialized cells in two tissues, the epithelium and the mesenchyme, which will later develop into the dermis and epidermis, respectively. As development progresses, the cells of these tissues begin to cluster, and signals passing back and forth between the epithelium and mesenchyme instruct the cells what to do. In the mesenchyme, cells called fibroblasts squeeze up against their neighbors, forming patches called dermal condensates. These mature into so-called dermal papillae, which supply specific molecules called growth factors that regulate hair formation throughout lifetime.

Fibroblasts in the developing skin respond to a signal from the epithelium called fibroblast growth factor 20 (Fgf20), but we do not yet understand its effects. It is possible that Fgf20 tells the cells to divide, forming clusters of daughter cells around their current location. Or, it could be that Fgf20 tells the cells to move, encouraging them to travel towards one another to form groups.

To address this question, Biggs, Mäkelä et al. examined developing mouse skin grown in the laboratory. They traced cells marked with fluorescent tags to analyze their behavior as the condensates formed. This revealed that the Fgf20 signal acts as a rallying call, triggering fibroblast movement. The cells changed shape and moved towards one another, rather than dividing to create their own clusters. In fact, they switched off their own cell cycle as the condensates formed, halting their ability to divide. A technique called RNA sequencing revealed that Fgf20 also promotes the use of genes known to be active in dermal condensates.

Dermal papillae control hair growth, and transplanting them under the skin can form new hair follicles. However, these cells lose this ability when grown in the laboratory. Understanding how they develop could be beneficial for future hair growth therapy. Further work could also address fundamental questions in embryology. Condensates of cells from the mesenchyme also precede the formation of limbs, bones, muscles and organs. Extending this work could help us to understand this critical developmental step.

Subpopulations of dermal skin fibroblasts secrete distinct extracellular matrix: implications for using skin substitutes in the clinic

Background

While several commercial dermoepidermal scaffolds can promote wound healing of the skin, the achievement of complete skin regeneration still represents a major challenge.

Objectives

To perform biological characterization of self‐assembled extracellular matrices (ECMs) from three different subpopulations of fibroblasts found in human skin: papillary fibroblasts (Pfi), reticular fibroblasts (Rfi) and dermal papilla fibroblasts (DPfi).

Methods

Fibroblast subpopulations were cultured with ascorbic acid to promote cell‐assembled matrix production for 10 days. Subsequently, cells were removed and the remaining matrices characterized. Additionally, in another experiment, keratinocytes were seeded on the top of cell‐depleted ECMs to generate epidermal‐only skin constructs.

Results

We found that the ECM self‐assembled by Pfi exhibited randomly oriented fibres associated with the highest interfibrillar space, reflecting ECM characteristics that are physiologically present within the papillary dermis. Mass spectrometry followed by validation with immunofluorescence analysis showed that thrombospondin 1 is preferentially expressed within the DPfi‐derived matrix. Moreover, we observed that epidermal constructs grown on DPfi or Pfi matrices exhibited normal basement membrane formation, whereas Rfi matrices were unable to support membrane formation.

Conclusions

We argue that inspiration can be taken from these different ECMs, to improve the design of therapeutic biomaterials in skin engineering applications.

What's already known about this topic?

There are several types of skin fibroblasts within the dermis that can be defined by their spatial location: papillary fibroblasts (Pfi), reticular fibroblasts (Rfi) and dermal papilla fibroblasts (DPfi).

Extracellular matrix (ECM) composition is distinct with regard to composition and architecture within the papillary, reticular and hair follicle dermis in vivo.

When skin is injured, dermal replacement substitutes used for tissue repair do not reflect the heterogeneity observed within the skin dermis.

What does this study add?

Self‐assembled ECMs from different subpopulations of skin fibroblasts can be generated in vitro.

Cell‐assembled ECMs made in vitro from Pfi, Rfi and DPfi reflect dermal heterogeneity seen in vivo and are morphologically, functionally and compositionally distinct from one another.

Inspiration should be taken from cell‐assembled ECMs from distinct fibroblast subpopulations, to improve the design of therapeutic biomaterials in skin engineering applications.

What is the translational message?

Cell‐assembled ECMs from DPfi and Pfi, but not Rfi, can support formation of a basement membrane in adjacent keratinocytes in vitro.

Inspiration should be taken from cell‐assembled ECMs from distinct fibroblast subpopulations, to improve the design of therapeutic biomaterials in skin engineering applications.

Linked Comment: https://doi.org/10.1111/bjd.16773.

https://doi.org/10.1111/bjd.16946 available online

https://goo.gl/Uqv3dl

Serum Gp96 is a chaperone of complement-C3 during graft-versus-host disease

Better identification of severe acute graft-versus-host disease (GvHD) may improve the outcome of this life-threatening complication of allogeneic hematopoietic stem cell transplantation. GvHD induces tissue damage and the release of damage-associated molecular pattern (DAMP) molecules. Here, we analyzed GvHD patients (n = 39) to show that serum heat shock protein glycoprotein 96 (Gp96) could be such a DAMP molecule. We demonstrate that serum Gp96 increases in gastrointestinal GvHD patients and its level correlates with disease severity. An increase in Gp96 serum level was also observed in a mouse model of acute GvHD. This model was used to identify complement C3 as a main partner of Gp96 in the serum. Our biolayer interferometry, yeast two-hybrid and in silico modeling data allowed us to determine that Gp96 binds to a complement C3 fragment encompassing amino acids 749-954, a functional complement C3 hot spot important for binding of different regulators. Accordingly, in vitro experiments with purified proteins demonstrate that Gp96 downregulates several complement C3 functions. Finally, experimental induction of GvHD in complement C3-deficient mice confirms the link between Gp96 and complement C3 in the serum and with the severity of the disease.

Mass spectrometry comparison of nerve allograft decellularization processes

Peripheral nerve repair using nerve grafts has been investigated for several decades using traditional techniques such as histology, immunohistochemistry, and electron microscopy. Recent advances in mass spectrometry techniques have made it possible to study the proteomes of complex tissues, including extracellular matrix rich tissues similar to peripheral nerves. The present study comparatively assessed three previously described processing methods for generating acellular nerve grafts by mass spectrometry. Acellular nerve grafts were additionally examined by F-actin staining and nuclear staining for debris clearance. Application of newer techniques allowed us to detect and highlight differences among the 3 treatments. Isolated proteins were separated by mass on polyacrylamide gels serving 2 purposes. This further illustrated that these treatments differ from one another and it allowed for selective protein extractions within specific bands/molecular weights. This approach resulted in small pools of proteins that could then be analyzed by mass spectrometry for content. In total, 543 proteins were identified, many of which corroborate previous findings for these processing methods. The remaining proteins are novel discoveries that expand the field. With this pilot study, we have proven that mass spectrometry techniques complement and add value to peripheral nerve repair studies.

RhoA determines lineage fate of mesenchymal stem cells by modulating CTGF-VEGF complex in extracellular matrix

Mesenchymal stem cells (MSCs) participate in the repair/remodelling of many tissues, where MSCs commit to different lineages dependent on the cues in the local microenvironment. Here we show that TGFβ-activated RhoA/ROCK signalling functions as a molecular switch regarding the fate of MSCs in arterial repair/remodelling after injury. MSCs differentiate into myofibroblasts when RhoA/ROCK is turned on, endothelial cells when turned off. The former is pathophysiologic resulting in intimal hyperplasia, whereas the latter is physiological leading to endothelial repair. Further analysis revealed that MSC RhoA activation promotes formation of an extracellular matrix (ECM) complex consisting of connective tissue growth factor (CTGF) and vascular endothelial growth factor (VEGF). Inactivation of RhoA/ROCK in MSCs induces matrix metalloproteinase-3-mediated CTGF cleavage, resulting in VEGF release and MSC endothelial differentiation. Our findings uncover a novel mechanism by which cell–ECM interactions determine stem cell lineage specificity and offer additional molecular targets to manipulate MSC-involved tissue repair/regeneration.

It is unclear what regulates the fate of mesenchymal stem cells (MSCs) in arterial repair following injury. Here, the authors show that MSC differentiation following injury is triggered by RhoA which in turn stimulates the release of connective tissue growth factor and vascular endothelial growth factor.

Proteomic analysis of naturally-sourced biological scaffolds

A key challenge to the clinical implementation of decellularized scaffold-based tissue engineering lies in understanding the process of removing cells and immunogenic material from a donor tissue/organ while maintaining the biochemical and biophysical properties of the scaffold that will promote growth of newly seeded cells. Current criteria for evaluating whole organ decellularization are primarily based on nucleic acids, as they are easy to quantify and have been directly correlated to adverse host responses. However, numerous proteins cause immunogenic responses and thus should be measured directly to further understand and quantify the efficacy of decellularization. In addition, there has been increasing appreciation for the role of the various protein components of the extracellular matrix (ECM) in directing cell growth and regulating organ function. We performed in-depth proteomic analysis on four types of biological scaffolds and identified a large number of both remnant cellular and ECM proteins. Measurements of individual protein abundances during the decellularization process revealed significant removal of numerous cellular proteins, but preservation of most structural matrix proteins. The observation that decellularized scaffolds still contain many cellular proteins, although at decreased abundance, indicates that elimination of DNA does not assure adequate removal of all cellular material. Thus, proteomic analysis provides crucial characterization of the decellularization process to create biological scaffolds for future tissue/organ replacement therapies.

Comparative proteomic analysis of extracellular matrix proteins secreted by hypertrophic scar with normal skin fibroblasts

The formation of hypertrophic scars (HSs) is a fibroproliferative disorder of abnormal wound healing. HSs usually characterize excessive proliferation of fibroblasts, abnormal deposition of extracellular matrix (ECM) during wound healing, associated with cosmetic, functional, and psychological problems. Owing to the role of ECM proteins in scar formation, we comparatively analyzed matrix proteins secreted by normal skin fibroblasts (NSFs) and HS fibroblasts (HSFs). The acetone-extracted secreted proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and identified by mass spectrometry (MS). Based on Go annotation of MS data, the profiling of ECM proteins was established and scar-related proteins have been screened out. The functions of several ECM proteins identified by MS have been discussed, such as collagens I, VI, XII, fibronectin, decorin, lumican, and protein procollagen C endopeptidase enhancer 1 (PCPE-1). Among them, the MS result of PCPE-1 was supported by Western blotting that PCPE-1 from HSFs were significantly upregulated than that from NSFs. It is suggested that PCPE-1 could be a potential target for scar treatment. The exploration of scar related proteins may provide new perspectives on understanding the mechanism of scar formation and open a new way to scar treatment and prevention.

Identification of novel PAMP-triggered phosphorylation and dephosphorylation events in Arabidopsis thaliana by quantitative phosphoproteomic analysis

Signaling cascades rely strongly on protein kinase-mediated substrate phosphorylation. Currently a major challenge in signal transduction research is to obtain high confidence substrate phosphorylation sites and assign them to specific kinases. In response to bacterial flagellin, a pathogen-associated molecular pattern (PAMP), we searched for rapidly phosphorylated proteins in Arabidopsis thaliana by combining multistage activation (MSA) and electron transfer dissociation (ETD) fragmentation modes, which generate complementary spectra and identify phosphopeptide sites with increased reliability. Of a total of 825 phosphopeptides, we identified 58 to be differentially phosphorylated. These peptides harbor kinase motifs of mitogen-activated protein kinases (MAPKs) and calcium-dependent protein kinases (CDPKs), as well as yet unknown protein kinases. Importantly, 12 of the phosphopeptides show reduced phosphorylation upon flagellin treatment. Since protein abundance levels did not change, these results indicate that flagellin induces not only various protein kinases but also protein phosphatases, even though a scenario of inhibited kinase activity may also be possible.

Cardiac fibroblast-derived 3D extracellular matrix seeded with mesenchymal stem cells as a novel device to transfer cells to the ischemic myocardium

PURPOSE

Demonstrate a novel manufacturing method to generate extracellular matrix scaffolds from cardiac fibroblasts (CF-ECM) as a therapeutic mesenchymal stem cell-transfer device.

MATERIALS AND METHODS

Rat CF were cultured at high-density (~1.6×10⁵/cm²) for 10-14 days. Cell sheets were removed from the culture dish by incubation with EDTA and decellularized with water and peracetic acid. CF-ECM was characterized by mass spectrometry, immunofluorescence and scanning electron microscopy. CF-ECM seeded with human embryonic stem cell derived mesenchymal stromal cells (hEMSCs) were transferred into a mouse myocardial infarction model. 48 hours later, mouse hearts were excised and examined for CF-ECM scaffold retention and cell transfer.

RESULTS

CF-ECM scaffolds are composed of fibronectin (82%), collagens type I (13%), type III (3.4%), type V (0.2%), type II (0.1%) elastin (1.3%) and 18 non-structural bioactive molecules. Scaffolds remained intact on the mouse heart for 48 hours without the use of sutures or glue. Identified hEMSCs were distributed from the epicardium to the endocardium.

CONCLUSIONS

High density cardiac fibroblast culture can be used to generate CF-ECM scaffolds. CF-ECM scaffolds seeded with hEMSCs can be maintained on the heart without suture or glue. hEMSC are successfully delivered throughout the myocardium.

Texas 3-step decellularization protocol: looking at the cardiac extracellular matrix

The extracellular matrix (ECM) is a critical tissue component, providing structural support as well as important regulatory signaling cues to govern cellular growth, metabolism, and differentiation. The study of ECM proteins, however, is hampered by the low solubility of ECM components in common solubilizing reagents. ECM proteins are often not detected during proteomics analyses using unbiased approaches due to solubility issues and relatively low abundance compared to highly abundant cytoplasmic and mitochondrial proteins. Decellularization has become a common technique for ECM protein-enrichment and is frequently used in engineering studies. Solubilizing the ECM after decellularization for further proteomic examination has not been previously explored in depth. In this study, we describe testing of a series of protocols that enabled us to develop a novel optimized strategy for the enrichment and solubilization of ECM components. Following tissue decellularization, we use acid extraction and enzymatic deglycosylation to facilitate re-solubilization. The end result is the generation of three fractions for each sample: soluble components, cellular components, and an insoluble ECM fraction. These fractions, developed in mass spectrometry-compatible buffers, are amenable to proteomics analysis. The developed protocol allows identification (by mass spectrometry) and quantification (by mass spectrometry or immunoblotting) of ECM components in tissue samples.

BIOLOGICAL SIGNIFICANCE

The study of extracellular matrix (ECM) proteins in pathological and non-pathological conditions is often hampered by the low solubility of ECM components in common solubilizing reagents. Additionally, ECM proteins are often not detected during global proteomic analyses due to their relatively low abundance compared to highly abundant cytoplasmic and mitochondrial proteins. In this manuscript we describe testing of a series of protocols that enabled us to develop a final novel optimized strategy for the enrichment and solubilization of ECM components. The end result is the generation of three fractions for each sample: soluble components, cellular components, and an insoluble ECM fraction. By analysis of each independent fraction, differences in protein levels can be detected that in normal conditions would be masked. These fractions are amenable to mass spectrometry analysis to identify and quantify ECM components in tissue samples. The manuscript places a strong emphasis on the immediate practical relevance of the method, particularly when using mass spectrometry approaches; additionally, the optimized method was validated and compared to other methodologies described in the literature.

Fibroblast morphogenesis on 3D collagen matrices: the balance between cell clustering and cell migration

Fibroblast clusters have been observed in tissues under a variety of circumstances: in fibrosis and scar, in the formation of hair follicle dermal papilla, and as part of the general process of mesenchymal condensation that takes place during development. Cell clustering has been shown to depend on features of the extracellular matrix, growth factor environment, and mechanisms to stabilize cell-cell interactions. In vitro studies have shown that increasing the potential for cell-cell adhesion relative to cell-substrate adhesion promotes cell clustering. Experimental models to study fibroblast clustering have utilized centrifugation, hanging drops, and substrata with poorly adhesive, soft and mechanically unstable properties. In this review, we summarize work on a new, highly tractable, cell clustering research model in which human fibroblasts are incubated on the surfaces of collagen matrices. Fibroblast clustering occurs under procontractile growth factor conditions (e.g., serum or the serum lipid agonist lysophosphatidic acid) but not under promigratory growth factor conditions (e.g., platelet-derived growth factor) and can be reversed by switching growth factor environments. Cell contraction plays a dual role in clustering to bring cells closer together and to stimulate cells to organize fibronectin into a fibrillar matrix. Binding of fibroblasts to a shared fibronectin fibrillar matrix stabilizes clusters, and fragmentation of the fibrillar matrix occurs when growth factor conditions are switched to promote cell dispersal.

Global remodelling of cellular microenvironment due to loss of collagen VII

Loss of collagen VII causes recessive dystrophic epidermolysis bullosa. Quantitative proteomics analysis of the extracellular matrix and secretome of human fibroblasts derived from pathologically altered skin reveals a global remodelling of the cellular microenvironment.

A global analysis of the microenvironment of human skin fibroblasts was carried out to reveal disease-related alterations in the extracellular proteome.

The loss of collagen VII causes a deregulation of the basement membrane and dermal matrix proteome.

Post-translational modifications of secreted proteins were altered in fibroblasts from recessive dystrophic epidermolysis bullosa samples.

Metalloproteases displayed reduced activity and turnover in collagen VII-deficient cells.

The mammalian cellular microenvironment is shaped by soluble factors and structural components, the extracellular matrix, providing physical support, regulating adhesion and signalling. A global, quantitative mass spectrometry strategy, combined with bioinformatics data processing, was developed to assess proteome differences in the microenvironment of primary human fibroblasts. We studied secreted proteins of fibroblasts from normal and pathologically altered skin and their post-translational modifications. The influence of collagen VII, an important structural component, which is lost in genetic skin fragility, was used as model. Loss of collagen VII had a global impact on the cellular microenvironment and was associated with proteome alterations highly relevant for disease pathogenesis including decrease in basement membrane components, increase in dermal matrix proteins, TGF-β and metalloproteases, but not higher protease activity. The definition of the proteome of fibroblast microenvironment and its plasticity in health and disease identified novel disease mechanisms and potential targets of intervention.

Strategies to enhance epithelial-mesenchymal interactions for human hair follicle bioengineering

Hair follicle morphogenesis and regeneration depend on intensive but well-orchestrated interactions between epithelial and mesenchymal components. Accordingly, the enhancement of this crosstalk represents a promising approach to achieve successful bioengineering of human hair follicles. The present article summarizes the techniques, both currently available and potentially feasible, to promote epithelial-mesenchymal interactions (EMIs) necessary for human hair follicle regeneration. The strategies include the preparation of epithelial components with high receptivity to trichogenic dermal signals and/or mesenchymal cell populations with potent hair inductive capacity. In this regard, bulge epithelial stem cells, keratinocytes predisposed to hair follicle fate or keratinocyte precursor cells with plasticity may provide favorable epithelial cell populations. Dermal papilla cells sustaining intrinsic hair inductive capacity, putative dermal papilla precursor cells in the dermal sheath/neonatal dermis or trichogenic dermal cells derived from undifferentiated stem/progenitor cells are promising candidates as hair inductive dermal cells. The most established protocol for in vivo hair follicle reconstitution is co-grafting of epithelial and mesenchymal components into immunodeficient mice. In theory, combination of individually optimized cellular components of respective lineages should elicit most intensive EMIs to form hair follicles. Still, EMIs can be further ameliorated by the modulation of non-cell autonomous conditions, including cell compartmentalization to replicate the positional relationship in vivo and humanization of host environment by preparing human stromal bed. These approaches may not always synergistically intensify EMIs, however, step-by-step investigation probing optimal combinations should maximally enhance EMIs to achieve successful human hair follicle bioengineering.

Defining the extracellular matrix using proteomics

The cell microenvironment has a profound influence on the behaviour, growth and survival of cells. The extracellular matrix (ECM) provides not only mechanical and structural support to cells and tissues but also binds soluble ligands and transmembrane receptors to provide spatial coordination of signalling processes. The ability of cells to sense the chemical, mechanical and topographical features of the ECM enables them to integrate complex, multiparametric information into a coherent response to the surrounding microenvironment. Consequently, dysregulation or mutation of ECM components results in a broad range of pathological conditions. Characterization of the composition of ECM derived from various cells has begun to reveal insights into ECM structure and function, and mechanisms of disease. Proteomic methodologies permit the global analysis of subcellular systems, but extracellular and transmembrane proteins present analytical difficulties to proteomic strategies owing to the particular biochemical properties of these molecules. Here, we review advances in proteomic approaches that have been applied to furthering our understanding of the ECM microenvironment. We survey recent studies that have addressed challenges in the analysis of ECM and discuss major outcomes in the context of health and disease. In addition, we summarize efforts to progress towards a systems-level understanding of ECM biology.

Comparative secretome analysis of human follicular dermal papilla cells and fibroblasts using shotgun proteomics

The dermal papilla cells (DPCs) of hair follicles are known to secrete paracrine factors for follicular cells. Shotgun proteomic analysis was performed to compare the expression profiles of the secretomes of human DPCs and dermal fibroblasts (DFs). In this study, the proteins secreted by DPCs and matched DFs were analyzed by 1DE/LTQ FTICR MS/MS, semi-quantitatively determined using emPAI mole percent values and then characterized using protein interaction network analysis. Among the 1,271 and 1,188 proteins identified in DFs and DPCs, respectively, 1,529 were further analyzed using the Ingenuity Pathway Analysis tool. We identified 28 DPC-specific extracellular matrix proteins including transporters (ECM1, A2M), enzymes (LOX, PON2), and peptidases (C3, C1R). The biochemically- validated DPC-specific proteins included thrombospondin 1 (THBS1), an insulin-like growth factor binding protein3 (IGFBP3), and, of particular interest, an integrin beta1 subunit (ITGB1) as a key network core protein. Using the shotgun proteomic technique and network analysis, we selected ITGB1, IGFBP3, and THBS1 as being possible hair-growth modulating protein biomarkers.

Restoration of the intrinsic properties of human dermal papilla in vitro

The dermal papilla (DP) plays pivotal roles in hair follicle morphogenesis and cycling. However, characterization and/or propagation of human DPs have been unsatisfactory because of the lack of efficient isolation methods and the loss of innate characteristics in vitro. We hypothesized that culture conditions sustaining the intrinsic molecular signature of the human DP could facilitate expansion of functional DP cells. To test this, we first characterized the global gene expression profile of microdissected, non-cultured human DPs. We performed a 'two-step' microarray analysis to exclude the influence of unwanted contaminants in isolated DPs and successfully identified 118 human DP signature genes, including 38 genes listed in the mouse DP signature. The bioinformatics analysis of the DP gene list revealed that WNT, BMP and FGF signaling pathways were upregulated in intact DPs and addition of 6-bromoindirubin-3'-oxime, recombinant BMP2 and basic FGF to stimulate these respective signaling pathways resulted in maintained expression of in situ DP signature genes in primarily cultured human DP cells. More importantly, the exposure to these stimulants restored normally reduced DP biomarker expression in conventionally cultured DP cells. Cell growth was moderate in the newly developed culture medium. However, rapid DP cell expansion by conventional culture followed by the restoration by defined activators provided a sufficient number of DP cells that demonstrated characteristic DP activities in functional assays. The study reported here revealed previously unreported molecular mechanisms contributing to human DP properties and describes a useful technique for the investigation of human DP biology and hair follicle bioengineering.

Proteomic characterization of the greening process in rice seedlings using the MS spectral intensity-based label free method

Illumination-induced greening in dark-grown plants is one of the most dramatic developmental processes known in plants. In our current study, we characterized the greening process of rice seedlings using comparative proteome analysis. We identified 886 different proteins in both whole cell lysates of illuminated and nonilluminated rice shoots and performed comparative proteome analysis based on the MS spectral intensities obtained for unique peptides from respective proteins. Furthermore, the changes in the levels of individual proteins were then compared with those of the corresponding mRNAs. The results revealed well-coordinated increases in the enzymes involved in the Calvin cycle at both the protein and mRNA levels during greening, and that the changes at the mRNA level precede those at the protein level. Although a much lower effect of illumination was found on the enzymes associated with glycolysis and the TCA cycle, coordinated increases during greening were evident for the enzymes involved in photorespiration and nitrogen assimilation as well as the components of the chloroplastic translational machinery. These results thus define the differential regulation of distinct biological systems during greening in rice and demonstrate the usefulness of comprehensive and comparative proteome analysis for the characterization of biological processes in plant cells.

Platelet type III collagen binding protein (TIIICBP) presents high biochemical and functional similarities with kindlin-3

Type III collagen binding protein (TIIICBP) was previously described as a platelet membrane protein that recognizes the KOGEOGPK peptide sequence within type III collagen. In order to better characterize this protein, we performed different approaches including mass spectrometry sequencing and functional experiments. This study leads to identify high biochemical and functional similarities between TIIICBP and kindlin-3, a member of a family of focal adhesion proteins. Indeed, mass spectrometry surveys indicated that TIIICBP contains several peptides identical to kindlin-3, covering 41% of the amino acid sequence. Polyclonal antibodies raised against a kindlin-3 specific N-terminal sequence, recognized and immunoprecipitated TIIICBP from platelet lysates. Electron microscopy and flow cytometry experiments showed that kindlin-3, as well as TIIICBP, were present associated to platelet membrane and a translocation of cytosolic kindlin-3 to the platelet membrane was observed after platelet activation. Similarly to anti-TIIICBP antibodies and the KOGEOGPK peptide, anti-kindlin-3 antibodies inhibited platelet interactions with type III collagen under flow conditions and slowed down platelet aggregation induced by glycoprotein VI agonists; e.g. collagen-related peptides and convulxin. In addition, the anti-kindlin-3 antibody inhibited platelet aggregation induced by low - but not high - doses of ADP or thrombin which depends on α(IIb)β(3) integrin function. In conclusion, our results show that the peptides identified by mass spectrometry from purified TIIICBP correspond to the kindlin-3 protein and demonstrate biochemical and functional similarities between TIIICBP and kindlin-3, strengthening a key role for TIIICBP/kindlin-3 in platelet interactions with collagen by cooperating with glycoprotein VI activation and integrin clustering in focal adhesion complexes.

Differential expression of extracellular matrix proteins in senescent and young human fibroblasts: a comparative proteomics and microarray study

The extracellular matrix (ECM) provides an essential structural framework for cell attachment, proliferation, and differentiation, and undergoes progressive changes during senescence. To investigate changes in protein expression in the extracellular matrix between young and senescent fibroblasts, we compared proteomic data (LTQ-FT) with cDNA microarray results. The peptide counts from the proteomics analysis were used to evaluate the level of ECM protein expression by young cells and senescent cells, and ECM protein expression data were compared with the microarray data. After completing the comparative analysis, we grouped the genes into four categories. Class I included genes with increased expression levels in both analyses, while class IV contained genes with reduced expression in both analyses. Class II and Class III contained genes with an inconsistent expression pattern. Finally, we validated the comparative analysis results by examining the expression level of the specific gene from each category using Western blot analysis and semiquantitative RT-PCR. Our results demonstrate that comparative analysis can be used to identify differentially expressed genes.

Spatial mapping by imaging mass spectrometry offers advancements for rapid definition of human skin proteomic signatures

Investigations into the human skin proteome by classical analytical procedures have not addressed spatial molecular distributions in whole-skin biopsies. The aim of this study was to develop methods for the detection of protein signatures and their spatial disposition in human skin using advanced molecular imaging technology based on mass spectrometry technologies. This technology allows for the generation of protein images at specific molecular weight values without the use of antibody while maintaining tissue architecture. Two experimental approaches were employed: MALDI-MS profiling, where mass spectra were taken from discrete locations based on histology, and MALDI-IMS imaging, where complete molecular images were obtained at various MW values. In addition, proteins were identified by in situ tryptic digestion, sequence analysis of the fragment peptides and protein database searching. We have detected patterns of protein differences that exist between epidermis and dermis as well as subtle regional differences between the papillary and reticular dermis. Furthermore, we were able to detect proteins that are constitutive features of human skin as well as those associated with unique markers of individual variability.

Cross-sample validation provides enhanced proteome coverage in rat vocal fold mucosa

The vocal fold mucosa is a biomechanically unique tissue comprised of a densely cellular epithelium, superficial to an extracellular matrix (ECM)-rich lamina propria. Such ECM-rich tissues are challenging to analyze using proteomic assays, primarily due to extensive crosslinking and glycosylation of the majority of high M_r ECM proteins. In this study, we implemented an LC-MS/MS-based strategy to characterize the rat vocal fold mucosa proteome. Our sample preparation protocol successfully solubilized both proteins and certain high M_r glycoconjugates and resulted in the identification of hundreds of mucosal proteins. A straightforward approach to the treatment of protein identifications attributed to single peptide hits allowed the retention of potentially important low abundance identifications (validated by a cross-sample match and de novo interpretation of relevant spectra) while still eliminating potentially spurious identifications (global single peptide hits with no cross-sample match). The resulting vocal fold mucosa proteome was characterized by a wide range of cellular and extracellular proteins spanning 12 functional categories.

Mapping surface accessibility of the C1r/C1s tetramer by chemical modification and mass spectrometry provides new insights into assembly of the human C1 complex

C1, the complex that triggers the classic pathway of complement, is a 790-kDa assembly resulting from association of a recognition protein C1q with a Ca(2+)-dependent tetramer comprising two copies of the proteases C1r and C1s. Early structural investigations have shown that the extended C1s-C1r-C1r-C1s tetramer folds into a compact conformation in C1. Recent site-directed mutagenesis studies have identified the C1q-binding sites in C1r and C1s and led to a three-dimensional model of the C1 complex (Bally, I., Rossi, V., Lunardi, T., Thielens, N. M., Gaboriaud, C., and Arlaud, G. J. (2009) J. Biol. Chem. 284, 19340-19348). In this study, we have used a mass spectrometry-based strategy involving a label-free semi-quantitative analysis of protein samples to gain new structural insights into C1 assembly. Using a stable chemical modification, we have compared the accessibility of the lysine residues in the isolated tetramer and in C1. The labeling data account for 51 of the 73 lysine residues of C1r and C1s. They strongly support the hypothesis that both C1s CUB(1)-EGF-CUB(2) interaction domains, which are distant in the free tetramer, associate with each other in the C1 complex. This analysis also provides the first experimental evidence that, in the proenzyme form of C1, the C1s serine protease domain is partly positioned inside the C1q cone and yields precise information about its orientation in the complex. These results provide further structural insights into the architecture of the C1 complex, allowing significant improvement of our current C1 model.

Culture of human cells and synthesis of extracellular matrix on materials compatible with direct analysis by mass spectrometry

The extracellular matrix (ECM) is a complex three-dimensional network of macromolecules synthesized by cells and is essential for the structure and the function of a tissue. The aim of our approach was to propose a surface allowing cell culture and subsequent analysis of ECM produced by cells directly on materials compatible with Surface Enhanced Laser Desorption Ionization-Time Of Flight (SELDI-TOF) mass spectrometry on a 96-well format. Surfaces were made of aluminium and spots of 2 mm in diameter were covered with specific chemical groups (silica, C(6) and C(12) alkyl groups, carboxyl, quaternary amine, or nitrilotriacetic acid groups). We found that among the chemically modified aluminium spots, only silica groups allowed the culture of human vascular cells. The wettability was an essential parameter for cell culture on the surfaces. Indeed, cells could only be cultured on surfaces presenting a moderate wettability with water contact angles of ca. 60 degrees. Then, by treatment of confluent cells with detergents (Triton X100 and deoxycholate), we were able to obtain ECM on the surfaces that were subsequently analyzed using a mass spectrometer, which is currently impossible with any type of cell culture system. As an example, the analysis of ECM from human vascular smooth muscle cells (hVSMCs) and human umbilical vein endothelial cells (HUVECs) appeared to be reproducible and evidenced different ECM patterns from the two cell types. Applications based on these materials can be proposed for biomarker discovery or characterization of cells for biomedical/diagnostic purposes.

The mesenchymal component of hair follicle neogenesis: background, methods and molecular characterization

Hair follicle morphogenesis and regeneration occur by an extensive and collaborative crosstalk between epithelial and mesenchymal skin components. A series of pioneering studies, which revealed an indispensable role of follicular dermal papilla and dermal sheath cells in this crosstalk, has led workers in the field to study in detail the anatomical distribution, functional properties, and molecular signature of the trichogenic dermal cells. The purpose of this paper was to provide a practical summary of the development and recent advances in the study of trichogenic dermal cells. Following a short review of the relevant literature, the methods for isolating and culturing these cells are summarized. Next, the bioassays, both in vivo and in vitro, that enable the evaluation of trichogenic properties of tested dermal cells are described in detail. A list of trichogenic molecular markers identified by those assays is also provided. Finally, this methods review is completed by defining some of the major questions needing resolution.

An in-solution ultrasonication-assisted digestion method for improved extracellular matrix proteome coverage

Epithelial cell behavior is coordinated by the composition of the surrounding extracellular matrix (ECM); thus ECM protein identification is critical for understanding normal biology and disease states. Proteomic analyses of ECM proteins have been hindered by the insoluble and digestion-resistant nature of ECM. Here we explore the utility of combining rapid ultrasonication- and surfactant-assisted digestion for the detailed proteomics analysis of ECM samples. When compared with traditional overnight digestion, this optimized method dramatically improved the sequence coverage for collagen I, revealed the presence of hundreds of previously unidentified proteins in Matrigel, and identified a protein profile for ECM isolated from rat mammary glands that was substantially different from that found in Matrigel. In a three-dimensional culture assay to investigate epithelial cell-ECM interactions, mammary epithelial cells were found to undergo extensive branching morphogenesis when plated with mammary gland-derived matrix in comparison with Matrigel. Cumulatively these data highlight the tissue-specific nature of ECM composition and function and underscore the need for optimized techniques, such as those described here, for the proteomics characterization of ECM samples.

Interaction of heat-shock protein 90β isoform (HSP90β) with cellular inhibitor of apoptosis 1 (c-IAP1) is required for cell differentiation

Members of the inhibitor of apoptosis protein (IAP) family have demonstrated functions in cell death, cell signalling, cell migration and mitosis. Several of them are E3 enzymes in the ubiquitination of proteins that leads to their degradation by the proteosomal machinery. We previously reported that one of them, cellular inhibitor of apoptosis protein-1 (c-IAP1), migrated from the nucleus to the surface of the Golgi apparatus in cells undergoing differentiation. Here, we show that c-IAP1 is a client protein of the stress protein HSP90β. In three distinct cellular models, the two proteins interact and migrate from the nucleus to the cytoplasm along the differentiation process through a leptomycin B-sensitive pathway. Inhibition of HSP90 proteins by small chemical molecules and specific depletion of HSP90β isoform by siRNA both lead to auto-ubiquitination of c-IAP1 and its degradation by the proteasome machinery. This chaperone function of HSP90 towards c-IAP1 is specific of its β isoform as specific depletion of HSP90α does not affect c-IAP1 content. Chemical inhibition of HSP90 or siRNA-mediated depletion of HSP90β both inhibit cell differentiation, which can be reproduced by siRNA-mediated depletion of c-IAP1. Altogether, these results suggest that HSP90β prevents auto-ubiquitination and degradation of its client protein c-IAP1, whose depletion would be sufficient to inhibit cell differentiation.Cell Death and Differentiation advance online publication, 1 February 2008; doi:10.1038/sj.cdd.4402320.