Proteomic analysis of protein components in periodontal ligament fibroblasts

Obesity affects the proteome profile of periodontal ligament submitted to mechanical forces induced by orthodontic tooth movement in rats

The prevalence of obesity has increased significantly worldwide. Therefore, this study aimed to evaluate the influence of obesity on the proteomic profile of periodontal ligament (PDL) tissues of rat first maxillary molars (1 M) submitted to orthodontic tooth movement (OTM). Ten Holtzman rats were distributed into two groups (n = 5): the M group (OTM), and the OM group (obesity induction plus OTM). Obesity was induced by a high-fat diet for the entire experimental periods After that period, the animals were euthanized and the hemimaxillae removed and processed for laser capture microdissection of the PDL tissues of the 1 M. Peptide extracts were obtained and analyzed by LC-MS/MS. Data are available via ProteomeXchange with identifier PXD033647. Out of the 109 proteins with differential abundance, 49 were identified in the OM group, including Vinculin, Cathepsin D, and Osteopontin, which were selected for in situ localization by immunohistochemistry analysis (IHC). Overall, Gene Ontology (GO) analysis indicated that enriched proteins were related to the GO component cellular category. IHC validated the trends for selected proteins. Our study highlights the differences in the PDL proteome profiling of healthy and obese subjects undergoing OTM. These findings may provide valuable information needed to better understand the mechanisms involved in tissue remodeling in obese patients submitted to orthodontic treatment. SIGNIFICANCE: The prevalence of obesity is increasing worldwide. Emerging findings in the field of dentistry suggest that obesity influences the tissues around the teeth, especially those in the periodontal ligament. Therefore, evaluation of the effect of obesity on periodontal tissues remodeling during orthodontic tooth movement is a relevant research topic. To our knowledge, this is the first study to evaluate proteomic changes in periodontal ligament tissue in response to the association between orthodontic tooth movement and obesity. Our study identified a novel protein profile associated with obesity by using laser microdissection and proteomic analysis, providing new information to increase understanding of the mechanisms involved in obese patients undergoing orthodontic treatment which can lead to a more personalized orthodontic treatment approach.

Proteomic Analysis in Nifedipine Induced Gingival Overgrowth: A Pilot Study

Objective: The aims of the present study were to investigate the proteomic profile of nifedipine induced overgrown gingiva and compare with non-overgrown gingival tissues obtained from the same patients. Methods: Seven subjects under nifedipine medication for at least 6 months and diagnosed as nifedipine induced gingival overgrowth (NIGO) participated in the study. Periodontal clinical parameters were recorded. Gingival tissue samples were harvested from overgrown (GO+ Group, n=7) and non-overgrown regions (GO- Group, n=7) of the same patients. Proteomics was performed using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) technique. The identified proteins were further classified according to their molecular functions, biological processes and cellular component distribution for functional gene ontology analysis using a web-based bioinformatics tool. Mann Whitney-U and ANOVA tests were performed to compare clinical parameters and identified proteins with proteomics, respectively. Results: Bleeding on probing and gingival overgrowth index of the GO+ group were statistically significantly higher than the GO- group (p

Proteomic profiling of various human dental stem cells - a systematic review

BACKGROUND

The proteomic signature or profile best describes the functional component of a cell during its routine metabolic and survival activities. Additional complexity in differentiation and maturation is observed in stem/progenitor cells. The role of functional proteins at the cellular level has long been attributed to anatomical niches, and stem cells do not deflect from this attribution. Human dental stem cells (hDSCs), on the whole, are a combination of mesenchymal and epithelial coordinates observed throughout craniofacial bones to pulp.

AIM

To specify the proteomic profile and compare each type of hDSC with other mesenchymal stem cells (MSCs) of various niches. Furthermore, we analyzed the characteristics of the microenvironment and preconditioning changes associated with the proteomic profile of hDSCs and their influence on committed lineage differentiation.

METHODS

Literature searches were performed in PubMed, EMBASE, Scopus, and Web of Science databases, from January 1990 to December 2018. An extra inquiry of the grey literature was completed on Google Scholar, ProQuest, and OpenGrey. Relevant MeSH terms (PubMed) and keywords related to dental stem cells were used independently and in combination.

RESULTS

The initial search resulted in 134 articles. Of the 134 full-texts assessed, 96 articles were excluded and 38 articles that met the eligibility criteria were reviewed. The overall assessment of hDSCs and other MSCs suggests that differences in the proteomic profile can be due to stem cellular complexity acquired from varied tissue sources during embryonic development. However, our comparison of the proteomic profile suffered inconsistencies due to the heterogeneity of various hDSCs. We believe that the existence of a heterogeneous population of stem cells at a given niche determines the modalities of regeneration or tissue repair. Added prominences to the differences present between various hDSCs have been reasoned out.

CONCLUSION

Systematic review on proteomic studies of various hDSCs are promising as an eye-opener for revisiting the proteomic profile and in-depth analysis to elucidate more refined mechanisms of hDSC functionalities.

Abundant proteins in platelet-rich fibrin and their potential contribution to wound healing: An explorative proteomics study and review of the literature

Background/purpose

It is well-known that diverse types of blood proteins contribute to healing process via different mechanisms. Presence and potential involvements of blood-derived abundant proteins in the platelet-rich fibrin (PRF) to its regenerative capacity have not been sufficiently emphasized in the literature. The aim of this paper was to analyze the abundant proteome content of PRF and summarize previously reported effects of identified proteins on wound healing via a literature review.

Materials and methods

The PRF samples obtained from non-smoking, systemically healthy volunteers were subjected to 2D gel electrophoresis after extracting the proteins from fibrin matrices. All matching spots were excised from the gels and identified by MALDI TOF/TOF MS/MS analysis. A literature review was conducted to reveal possible contributions of identified proteins to wound healing.

Results

Totally, thirty-five blood proteins were commonly identified among all studied samples. These proteins included serine protease inhibitors, such as alpha-1-antitrypsin, alpha-1-antichymotrypsin, alpha-1-acid glycoprotein, inter-alpha-trypsin-inhibitor, protease C1 inhibitor, and complement proteins. In addition, abundant presence of immunoglobulin G was observed. The abundance of albumin, haptoglobin, ceruloplasmin vitronectin, fetuin-A, ficolin-3 and transthyretin was also detected.

Conclusion

The results of this study indicated that PRF abundantly contains blood-origin actors which were previously reported for their direct contribution to wound healing. Further studies exploring the protein content of PRF are needed to reveal its undisclosed potential roles in the healing process.

Anticancer activity of biogenerated silver nanoparticles: an integrated proteomic investigation

Silver nanoparticles (AgNPs), embedded into a specific polysaccharide (EPS), were biogenerated by Klebsiella oxytoca DSM 29614 under aerobic (AgNPs-EPS^aer) and anaerobic conditions (AgNPs-EPS^anaer). Both AgNPs-EPS matrices were tested by MTT assay for cytotoxic activity against human breast (SKBR3 and 8701-BC) and colon (HT-29, HCT 116 and Caco-2) cancer cell lines, revealing AgNPs-EPS^aer as the most active, in terms of IC50, with a more pronounced efficacy against breast cancer cell lines. Therefore, colony forming capability, morphological changes, generation of reactive oxygen species (ROS), induction of apoptosis and autophagy, inhibition of migratory and invasive capabilities and proteomic changes were investigated using SKBR3 breast cancer cells with the aim to elucidate AgNPs-EPS^aer mode of action. In particular, AgNPs-EPS^aer induced a significant decrease of cell motility and MMP-2 and MMP-9 activity and a significant increase of ROS generation, which, in turn, supported cell death mainly through autophagy and in a minor extend through apoptosis. Consistently, TEM micrographs and the determination of total silver in subcellular fractions indicated that the Ag⁺ accumulated preferentially in mitochondria and in smaller concentrations in nucleus, where interact with DNA. Interestingly, these evidences were confirmed by a differential proteomic analysis that highlighted important pathways involved in AgNPs-EPS^aer toxicity, including endoplasmic reticulum stress, oxidative stress and mitochondrial impairment triggering cell death trough apoptosis and/or autophagy activation.

Proteomic differences between native and tissue-engineered tendon and ligament

Tendons and ligaments (T/Ls) play key roles in the musculoskeletal system, but they are susceptible to traumatic or age‐related rupture, leading to severe morbidity as well as increased susceptibility to degenerative joint diseases such as osteoarthritis. Tissue engineering represents an attractive therapeutic approach to treating T/L injury but it is hampered by our poor understanding of the defining characteristics of the two tissues. The present study aimed to determine differences in the proteomic profile between native T/Ls and tissue engineered (TE) T/L constructs. The canine long digital extensor tendon and anterior cruciate ligament were analyzed along with 3D TE fibrin‐based constructs created from their cells. Native tendon and ligament differed in their content of key structural proteins, with the ligament being more abundant in fibrocartilaginous proteins. 3D T/L TE constructs contained less extracellular matrix (ECM) proteins and had a greater proportion of cellular‐associated proteins than native tissue, corresponding to their low collagen and high DNA content. Constructs were able to recapitulate native T/L tissue characteristics particularly with regard to ECM proteins. However, 3D T/L TE constructs had similar ECM and cellular protein compositions indicating that cell source may not be an important factor for T/L tissue engineering.

Investigation of the Cell Surface Proteome of Human Periodontal Ligament Stem Cells

The present study examined the cell surface proteome of human periodontal ligament stem cells (PDLSC) compared to human fibroblasts. Cell surface proteins were prelabelled with CyDye before processing to extract the membrane lysates, which were separated using 2D electrophoresis. Selected differentially expressed protein “spots” were identified using Mass spectrometry. Four proteins were selected for validation: CD73, CD90, Annexin A2, and sphingosine kinase 1 previously associated with mesenchymal stem cells. Flow cytometric analysis found that CD73 and CD90 were highly expressed by human PDLSC and gingival fibroblasts but not by keratinocytes, indicating that these antigens could be used as potential markers for distinguishing between mesenchymal cells and epithelial cell populations. Annexin A2 was also found to be expressed at low copy number on the cell surface of human PDLSC and gingival fibroblasts, while human keratinocytes lacked any cell surface expression of Annexin A2. In contrast, sphingosine kinase 1 expression was detected in all the cell types examined using immunocytochemical analysis. These proteomic studies form the foundation to further define the cell surface protein expression profile of PDLSC in order to better characterise this cell population and help develop novel strategies for the purification of this stem cell population.

Advances of Proteomic Sciences in Dentistry

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

Proteomics - The research frontier in periodontics

Periodontitis is an inflammatory condition resulting from the interplay between the infectious agents and host factors. Various protein molecules play a vital role in the initiation, progression and severity of periodontal diseases. The study of proteins as biomarkers in periodontal diseases has been highlighted during the last few years. In periodontitis multiple bacteria derived (e.g. collagen degrading enzymes, elastase like enzymes etc) and host derived mediators (eg. PGE2, TNF, IL1, IL6, MMP's etc) expressed in the saliva and gingival crevicular fluid, can be utilized as diagnostic markers for the disease. Another significant development regarding human genes and proteins has been the discovery of potential new drugs for the treatment of periodontal diseases. Therefore the information of the proteins involved in the pathogenesis of periodontal diseases can be utilized for its diagnosis, prevention and treatment.

Periodontal proteomics: wonders never cease!

Proteins are vital parts of living organisms, as they are integral components of the physiological metabolic pathways of cells. Periodontal tissues comprise multicompartmental groups of interacting cells and matrices that provide continuous support, attachment, proprioception, and physical protection for the teeth. The proteome map, that is, complete catalogue of the matrix and cellular proteins expressed in alveolar bone, cementum, periodontal ligament, and gingiva, is to be explored for more in-depth understanding of periodontium. The ongoing research to understand the signalling pathways that allow cells to divide, differentiate, and die in controlled manner has brought us to the era of proteomics. Proteomics is defined as the study of all proteins including their relative abundance, distribution, posttranslational modifications, functions, and interactions with other macromolecules, in a given cell or organism within a given environment and at a specific stage in the cell cycle. Its application to periodontal science can be used to monitor health status, disease onset, treatment response, and outcome. Proteomics can offer answers to critical, unresolved questions such as the biological basis for the heterogeneity in gingival, alveolar bone, and cemental cell populations.

Histological evaluation of the periodontal ligament from aged wistar rats supplemented with ascorbic acid

Ascorbic acid (AA) is able to neutralize reactive oxygen species and is essential for collagen synthesis. In aging process oxidative stress is elevated. This study aims to investigate the effects of AA supplementation on the periodontal ligament (PL) of rats during aging. Twenty five rats were used and divided into groups: J90 (90-day-old control), E345 (345-day-old control), E428 (428-day-old control), EA345 (345-day-old supplemented with AA from 90-day-old on) and EA428 (428-day-old supplemented with AA from 90-day-old on). We analyzed the thickness, density of fibroblasts and blood vessels and collagen fibers types in the PL. In group J90 there was predominantly type III collagen fibers (87.64%). In animals supplemented with AA, the area filled by type I fibers (group EA345: 65.67%, group EA428: 52.23%) was higher than type III fibers. PL in group EA428 was thicker than the one observed in group E428 (P < 0.05). During natural aging process, AA promoted the maturation of collagen fibers and enhanced angiogenesis in periodontal ligament. One can conclude that the supplementation with AA represented a beneficial factor for the development of PL in aged rats.

Transcriptomes and Proteomes of Dental Follicle Cells

Ectomesenchymal dental stem cells could be feasible tools for dental tissue engineering. Dental follicle cells are a promising example, since they are capable of differentiation into various dental tissue cells, such as osteoblasts or cementoblasts. However, cellular mechanisms of cell proliferation and differentiation are not understood in detail. Basic knowledge of these molecular processes may shorten the time before ectomesenchymal dental stem cells can be exploited for bone augmentation in regenerative medicine. Recent developments in proteomics and transcriptomics have made information about genome-wide expression profiles accessible, which can aid in clarifying molecular mechanisms of cells. This review describes the transcriptomes and proteomes of dental follicle cells before and after differentiation, and compares them with differentially expressed populations from dental tissue or bone marrow.

Early osteogenic differential protein profile detected by proteomic analysis in human periodontal ligament cells

BACKGROUND AND OBJECTIVE

Human periodontal ligament cells play a pivotal role in maintaining periodontal ligament space, contain progenitors that are able to differentiate into cementoblasts/osteoblasts and have a tremendous potential to regenerate periodontal tissue. However, the exact molecular mechanisms governing the differentiation mechanisms of progenitors in periodontal ligament cells remain largely unknown. This study was carried out to investigate the differentially expressed proteins involved in the osteogenic differentiation of progenitors presented in periodontal ligament cells.

MATERIAL AND METHODS

Using two-dimensional gel electrophoresis, mass spectrometry and peptide mass fingerprinting, we analyzed the differential protein profiles of periodontal ligament cells undergoing mineralization.

RESULTS

Compared with undifferentiated periodontal ligament cells, 61 proteins in periodontal ligament cells undergoing differentiation showed at least a 1.5-fold change in intensity, of which 29 differentially expressed proteins were successfully identified by matrix-assisted laser-desorption ionization time-of-flight mass spectrometry. The expression of some of the identified proteins was further confirmed by western blotting and reverse transcription-polymerase chain reaction analysis. The identified proteins were cytoskeleton proteins and cytoskeleton-associated proteins, nuclear proteins and cell membrane-bound molecules.

CONCLUSION

Our results suggest that the proteins identified in this study may be associated with the unique function of periodontal ligament cells in maintaining periodontal tissue homeostasis, thus providing a comprehensive reference for understanding and investigating in greater detail the molecular mechanisms of periodontal ligament cells involved in periodontal regeneration.

Different proteomic protein patterns in saliva of Sjögren's syndrome patients

OBJECTIVE

To investigate the salivary protein profile in patients with Sjögren's syndrome (SS), and healthy control subjects.

MATERIALS AND METHODS

Unstimulated whole saliva samples were collected from 16 age-matched females; eight healthy subjects and eight patients diagnosed with SS (six primary SS, one incomplete SS and one primary SS associated with B cell lymphoma). Proteins were extracted and separated individually by 2D sodium dodecyl sulphate-polyacrylamide gel electrophoresis. Selected protein spots of interest were analysed by electrospray ionization--tandem mass spectrometry. Obtained data were searched against the Swiss-Prot and NCBI non-redundant protein databases using Mascot software.

RESULTS

Two groups of patterns of protein expression were observed in the eight SS patients: a major group (six patients) with significant expression differences from the healthy subjects and the second group (two patients) with a pattern similar to the eight healthy subjects.

CONCLUSION

In this preliminary study, protein expression differences were found between SS patients and healthy subjects. Individual analysis of SS patients exhibited two patterns of protein expression with no direct relation to the clinical, serological or histological severity of disease. This study emphasizes the difficulty of the present proteomic knowledge to diagnose and monitor the sequel of SS development.

Vimentin Is the Specific Target in Skin Glycation

Until now, the glycation reaction was considered to be a nonspecific reaction between reducing sugars and amino groups of random proteins. We were able to identify the intermediate filament vimentin as the major target for the AGE modification N(epsilon)-(carboxymethyl)lysine (CML) in primary human fibroblasts. This glycation of vimentin is neither based on a slow turnover of this protein nor on an extremely high intracellular expression level, but remarkably it is based on structural properties of this protein. Glycation of vimentin was predominantly detected at lysine residues located at the linker regions using nanoLC-ESI-MS/MS. This modification results in a rigorous redistribution of vimentin into a perinuclear aggregate, which is accompanied by the loss of contractile capacity of human skin fibroblasts. CML-induced rearrangement of vimentin was identified as an aggresome. This is the first evidence that CML-vimentin represents a damaged protein inside the aggresome, linking the glycation reaction directly to aggresome formation. Strikingly, we were able to prove that the accumulation of modified vimentin can be found in skin fibroblasts of elderly donors in vivo, bringing AGE modifications in human tissues such as skin into strong relationship with loss of organ contractile functions.

Advances in defining regulators of cementum development and periodontal regeneration

Substantial advancements have been made in defining the cells and molecular signals that guide tooth crown morphogenesis and development. As a result, very encouraging progress has been made in regenerating crown tissues by using dental stem cells and recombining epithelial and mesenchymal tissues of specific developmental ages. To date, attempts to regenerate a complete tooth, including the critical periodontal tissues of the tooth root, have not been successful. This may be in part due to a lesser degree of understanding of the events leading to the initiation and development of root and periodontal tissues. Controversies still exist regarding the formation of periodontal tissues, including the origins and contributions of cells, the cues that direct root development, and the potential of these factors to direct regeneration of periodontal tissues when they are lost to disease. In recent years, great strides have been made in beginning to identify and characterize factors contributing to formation of the root and surrounding tissues, that is, cementum, periodontal ligament, and alveolar bone. This review focuses on the most exciting and important developments over the last 5 years toward defining the regulators of tooth root and periodontal tissue development, with special focus on cementogenesis and the potential for applying this knowledge toward developing regenerative therapies. Cells, genes, and proteins regulating root development are reviewed in a question-answer format in order to highlight areas of progress as well as areas of remaining uncertainty that warrant further study.

Expanding the protein catalogue in the proteome reference map of human breast cancer cells

In this report we present a catalogue of 162 proteins (including isoforms and variants) identified in a prototype of proteomic map of breast cancer cells. This work represents the prosecution of previous studies describing the protein complement of breast cancer cells of the line 8701-BC, which has been well characterized for several parameters, providing to be a useful model for the study of breast cancer-associated candidate biomarkers. In particular, 110 spots were identified ex novo by PMF, or validated following previous gel matching identification method; 30 were identified by N-terminal microsequencing and the remaining by gel matching with maps available from our former work. As a consequence of the expanded number of proteins, we have updated our previous classification extending the number of protein groups from 4 to 13. In order to facilitate comparative proteome studies of different kinds of breast cancers, in this report we provide the whole complement of proteins so far identified and grouped into the new classification. A consistent number of them were not described before in other proteomic maps of breast cancer cells or tissues, and therefore they represent a valuable contribution for breast cancer protein databases and for future application in basic and clinical researches.