Proteome data set of human gingival crevicular fluid from healthy periodontium sites by multidimensional protein separation and mass spectrometry

Proteomic profile of human gingival crevicular fluid reveals specific biological and molecular processes during clinical progression of periodontitis

BACKGROUND AND OBJECTIVE

There is no clear understanding of molecular events occurring in the periodontal microenvironment during clinical disease progression. Our aim was to explore qualitative and quantitative differences in gingival crevicular fluid (GCF) protein profiles from patients diagnosed with periodontitis between non-progressive and progressive periodontal sites.

METHODS

Five systemically healthy patients diagnosed with periodontitis were monitored weekly in their progression of the disease and GCF samples from 10 candidate sites were obtained. Two groups of five sites, matched from an equal number of teeth, were selected from the five patients: Progression (PG) and Non-Progression (NP). Global protein identification was performed with high-throughput proteomic approaches and label-free analysis determined their relative abundances. Proteins were identified by Proteome Discoverer v2.4 and searched against human SwissProt protein databases. Enrichment bioinformatic analyses were performed in STRING-DB and ShinyGO environment.

RESULTS

1504 and 1500 proteins were identified in NP and PG respectively. Forty-eight proteins were exclusively identified in PG, while 52 were identified in NP. Moreover, 35 proteins were more abundant in PG and 29 proteins in NP (twofold change, p < .05). The NP group was mainly represented by proteins from "response to biotic stimuli and other organisms," "processes of cell death regulation," "peptidase regulation," "protein ubiquitination," and "ribosomal activity" GO categories. The most represented GO categories of the PG group were "assembly of multiprotein complexes," "catabolic processes," "lipid metabolism," and "binding to hemoglobin and haptoglobin."

CONCLUSIONS

There are quantitative and qualitative differences in the proteome of GCF from periodontal sites according to the status of clinical progression of periodontitis. Progressive periodontitis sites are characterized by a protein profile associated with catabolic processes, immune response, and response to cellular stress, while stable periodontitis sites show a protein profile mainly related to wound repair and healing processes, cell death regulation, and chaperone-mediated autophagy. Understanding the etiopathogenic role of these profiles in progressive periodontitis may help to develop new diagnostic and therapeutic approaches.

Detection of orthodontically induced inflammatory root resorption-associated biomarkers from the gingival crevicular fluid by proteomics analysis: a randomized-controlled clinical trial

Orthodontically induced inflammatory root resorption (OIIRR) is an undesirable complication of orthodontic treatment (OT) with an ambiguous aetiologic mechanism. This study aimed to identify OIIRR-associated biomarkers in the gingival crevicular fluid (GCF) using proteomic analysis. In this randomized clinical trial, the upper first premolars (UFP) were exposed either to light or heavy force. The GCF was collected at 1 h, 1 day, 7 days, 14 days, 21 days, and 28 days following force application. After extraction of UFP, roots were imaged and resorption premolar, was used to deliver either light forcecraters were measured. Proteomic analysis of GCF was performed using 2D gel electrophoresis with MALDI-TOF/TOF MS/MS. Results were further analyzed by bioinformatics analyses showing the biological functions and predicted pathways. The predicted canonical pathways showed that the expression of immunoglobulin kappa (IGKC), neutrophil gelatinase-associated lipocalin (NGAL), neurolysin mitochondrial (NEUL), keratin, type II cytoskeletal 1 (K2C1), S100-A9, and the extracellular calcium-sensing receptor (CASR) were significantly associated with a range of biological and inflammatory processes. In conclusion, up-regulation of S100A9, CASR, and K2C1 suggested a response to force-related inflammation, chemotactic activities, osteoclastogenesis, and epithelial cell breakdown. Meanwhile, the up-regulation of IGKC, NGAL, and K2C1 indicated a response to the inflammatory process, innate immunity activation, and epithelial cell breakdown.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03572-5.

Systems Biology in Periodontitis

Systems biology is a promising scientific discipline that allows an integrated investigation of host factors, microbial composition, biomarkers, immune response and inflammatory mediators in many conditions such as chronic diseases, cancer, neurological disorders, and periodontitis. This concept utilizes genetic decoding, bioinformatic, flux-balance analysis in a comprehensive approach. The aim of this review is to better understand the current literature on systems biology and identify a clear applicability of it to periodontitis. We will mostly focus on the association between this condition and topics such as genomics, transcriptomics, proteomics, metabolomics, as well as contextualize delivery systems for periodontitis treatment, biomarker detection in oral fluids and associated systemic conditions.

Potential Treponema denticola-based periodontal vaccine to resolve a global public health challenge: a narrative literature review

INTRODUCTION

Periodontitis is a diseased condition of the gum which imposes considerable costs on healthcare systems. It progresses further beyond the inflammation of supportive tissues of the teeth, and the collateral damages are closely associated with Alzheimer's disease, cardiovascular disease, and diabetes mellitus.

AREAS COVERED

A comprehensive literature review was performed to summarize published studies in English during the period of 1990-2021 to discuss the rationales for developing periodontal vaccine, cost-effectiveness analyses on the prevention of periodontitis, Treponema denticola-based vaccine candidates, as well as immunological mechanisms in animal models.

EXPERT OPINION

Preventive strategies against periodontitis may halt the onset of gum inflammation itself and the consequent chronic diseases. Considering the multi-microbial condition of periodontitis, an ideal periodontal vaccine should target multiple pathological pathways. Preventive approaches compared to surgical treatments evidently have significant impact on the healthcare budget and long-term health of the individuals in different communities. Despite many advances in periodontal vaccine research, there are still significant hurdles to overcome in developing a vaccine. Investment in research and development activities on key periodontal pathogens including Treponema denticola and Porphyromonas gingivalis in the foreseeable future is a worthy and cost-effective approach for the policymakers to prevent deleterious impacts of periodontitis.

A qualitative and quantitative analysis of the human gingival crevicular fluid proteome and metaproteome

Gingival crevicular fluid (GCF) is an integral part of oral fluid that plays a special role in maintaining the structure of junctional epithelium and defending against bacterial infection. In this study, we comprehensively analysed the composition of the human GCF proteome and metaproteome simultaneously to obtain multidimensional information about GCF. A total of 3680 human proteins (2540 with at least two unique peptides) were identified in the normal GCF sample, and their functions were mainly associated with immune function and inflammation. Among these proteins, 1874 proteins could be quantified by the iBAQ algorithm, and their abundances spanned a dynamic range of six orders of magnitude. For the GCF metaproteome, a total of 3082 proteins and 69 genera were found. In addition, 16 genera were not identified by GCF metagenomic analysis. Compared to the saliva metaproteome, 32 genera were found to be in common. The protein quantitative analysis showed that the abundance of GCF metaproteome contributed to approximately 4.17% of the total GCF proteome. The top three most abundant genera were Fusobacterium, Corynebacterium, and Leptotrichia. The above data will be useful for future research on GCF-related diseases.

Metaproteome and metabolome of oral microbial communities

The emergence of high-throughput technologies for the comprehensive measurement of biomolecules, also referred to as "omics" technologies, has helped us gather "big data" and characterize microbial communities. In this article, we focus on metaproteomic and metabolomic approaches that support hypothesis-driven investigations on various oral biologic samples. Proteomics reveals the working units of the oral milieu and metabolomics unveils the reactions taking place; and so these complementary techniques can unravel the functionality and underlying regulatory processes within various oral microbial communities. Current knowledge of the proteomic interplay and metabolic interactions of microorganisms within oral biofilm and salivary microbiome communities is presented and discussed, from both clinical and basic research perspectives. Communities indicative of, or from, health, caries, periodontal diseases, and endodontic lesions are represented. Challenges, future prospects, and examples of best practice are given.

Label-free quantitative proteomic analysis of gingival crevicular fluid to identify potential early markers for root resorption

Background

Orthodontically-induced root resorption is an iatrogenic effect and it cannot be examined regularly due to the harmful effects of sequential doses of radiation with more frequent radiography. This study aims to compare protein abundance (PA) of pre-treatment and during orthodontic treatment for root resorption and to determine potential early markers for root resorption.

Methods

Ten subjects (n = 10) who had upper and lower fixed appliances (MBT, 3 M Unitek, 0.022″ × 0.028″) were recruited for this study. Human gingival crevicular fluid (GCF) was obtained using periopaper strips at pre-treatment (T0), 1 month (T1), 3 months (T3), and 6 months (T6) of orthodontic treatment. Periapical radiographs of the upper permanent central incisors were taken at T0 and T6 to measure the amount of root resorption. Identification of changes in PA was performed using liquid chromatography-tandem mass spectrometry. Student’s t-test was then performed to determine the significance of the differences in protein abundance before and after orthodontic treatment.

Results

Our findings showed that all ten subjects had mild root resorption, with an average resorption length of 0.56 ± 0.30 mm. A total of 186 proteins were found to be commonly present at T0, T1, T3, and T6. There were significant changes in the abundance of 16 proteins (student’s t-test, p ≤ 0.05). The increased PA of S100A9, immunoglobulin J chain, heat shock protein 1A, immunoglobulin heavy variable 4–34 and vitronectin at T1 suggested a response to stress that involved inflammation during the early phase of orthodontic treatment. On the other hand, the increased PA of thymidine phosphorylase at T3 suggested growth promotion and, angiogenic and chemotactic activities.

Conclusions

The identified proteins can be potential early markers for root resorption based on the increase in their respective PA and predicted roles during the early phase of orthodontic treatment. Non-invasive detection of root resorption using protein markers as early as possible is extremely important as it can aid orthodontists in successful orthodontic treatment.

Gingival Crevicular Fluid Peptidome Profiling in Healthy and in Periodontal Diseases

Given its intrinsic nature, gingival crevicular fluid (GCF) is an attractive source for the discovery of novel biomarkers of periodontal diseases. GCF contains antimicrobial peptides and small proteins which could play a role in specific immune-inflammatory responses to guarantee healthy gingival status and to prevent periodontal diseases. Presently, several proteomics studies have been performed leading to increased coverage of the GCF proteome, however fewer efforts have been done to explore its natural peptides. To fill such gap, this review provides an overview of the mass spectrometric platforms and experimental designs aimed at GCF peptidome profiling, including our own data and experiences gathered from over several years of matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS) based approach in this field. These tools might be useful for capturing snapshots containing diagnostic clinical information on an individual and population scale, which may be used as a specific code not only for the diagnosis of the nature or the stage of the inflammatory process in periodontal disease, but more importantly, for its prognosis, which is still an unmet medical need. As a matter of fact, current peptidomics investigations suffer from a lack of standardized procedures, posing a serious problem for data interpretation. Descriptions of the efforts to address such concerns will be highlighted.

Salivary proteome of a Neotropical primate: potential roles in host defense and oral food perception

BACKGROUND

Saliva contains a very complex mixture of proteins for defense against microbiological pathogens and for oral food perception. Howler monkeys are Neotropical primates that can consume a mostly leaf diet. They are well known to thrive in highly disturbed habitats where they may cope with a diversity of dietary challenges and infection risks. We aimed to describe the salivary proteome of howlers to contribute to better understanding of their physiology.

METHODS

We analyzed the salivary proteins of wild black howler monkeys (Alouatta pigra), by SDS-PAGE-1-D and Nano LC-MS/MS and categorized them by their function involved in host defense and oral food perception.

RESULTS

Our proteomic analysis identified 156 proteins in howler saliva including a number of host defense peptides that are the first line of defense in mammals, such as defensin, cathelicidin, dermcidin, and lactotransferrin, and proteins with anti-bacterial, anti-fungal, and anti-viral capacity, such as IgA, IgG, IgM, BPI, salivary heat shock 70 kDa protein, beta-2-microbulin, and protein S-100. We also identified key proteins necessary for taste perception, including salivary carbonic anhydrase VI, cystatin D, IgA, and fatty acid-binding protein. Proteins to detect astringent foods were identifying, including four members of cystatins (A, B, C and D), lactoperoxidase, and histidine-rich proteins. No chitinase and amylase were identified as would be expected because howlers do not eat insects and little starch. These findings provide basic information to future studies in oral biology, ingestive physiology, and physiological ecology of mammals and non-human primates.

Host-microbe interactions: Profiles in the transcriptome, the proteome, and the metabolome

Periodontal studies using transcriptomics, proteomics, and metabolomics encompass the collection of mRNA transcripts, proteins, and small-molecule chemicals in the context of periodontal health and disease. The number of studies using these approaches has significantly increased in the last decade and they have provided new insight into the pathogenesis and host-microbe interactions that define periodontal diseases. This review provides an overview of current molecular findings using -omic approaches that underlie periodontal disease, including modulation of the host immune response, tissue homeostasis, and complex metabolic processes of the host and the oral microbiome. Integration of these -omic approaches will broaden our perspective of the molecular mechanisms involved in periodontal disease, advancing and improving the diagnosis and treatment of various stages and forms of periodontal disease.

Plaque-induced gingivitis: Case definition and diagnostic considerations

OBJECTIVE

Clinical gingival inflammation is a well-defined site-specific condition for which several measurement systems have been proposed and validated, and epidemiological studies consistently indicate its high prevalence globally. However, it is clear that defining and grading a gingival inflammatory condition at a site level (i.e. a "gingivitis site") is completely different from defining and grading a "gingivitis case" (GC) (i.e. a patient affected by gingivitis), and that a "gingivitis site" does not necessarily mean a "GC". The purpose of the present review is to summarize the evidence on clinical, biochemical, microbiologic, genetic markers as well as symptoms associated with plaque-induced gingivitis and to propose a set of criteria to define GC.

IMPORTANCE

A universally accepted case definition for gingivitis would provide the necessary information to enable oral health professionals to assess the effectiveness of their prevention strategies and treatment regimens; help set priorities for therapeutic actions/programs by health care providers; and undertake surveillance.

FINDINGS

Based on available methods to assess gingival inflammation, GC could be simply, objectively and accurately identified and graded using bleeding on probing score (BOP%) CONCLUSIONS: A patient with intact periodontium would be diagnosed as a GC according to a BOP score ≥ 10%, further classified as localized (BOP score ≥ 10% and ≤30%) or generalized (BOP score > 30%). The proposed classification may also apply to patients with a reduced periodontium, where a GC would characterize a patient with attachment loss and BOP score ≥ 10%, but without BOP in any site probing ≥4 mm in depth.

Differential proteomic analysis of serum exosomes reveals alterations in progression of Parkinson disease

Exosomes are nanometer-sized vesicles with intercellular communication functions, and their encapsulated proteins may participate in the pathological process of neurodegenerative disorders. The aim of this study was to identify the protein changes of serum exosomes in Parkinson disease (PD) patients with different disease progress types, and to identify potential biomarkers. The exosomes of PD patients with different severity and healthy control group were isolated from serum. The exosome proteins were analyzed by mass spectrometry with label-free quantitative proteomics. A total of 429 proteins were identified, of which 14 were significantly different in mild and severe PD patients. The expression levels of 7 proteins, including pigmented epithelium-derived factor, afamin, apolipoprotein D and J, were significantly increased in PD patients. The expression levels of 7 proteins, including complement C1q and protein Immunoglobulin Lambda Variable 1-33 (IGLV1-33)Cluster -33, were decreased in PD patients. These differentially expressed proteins were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, which confirmed that the interaction between prion diseases and ECM receptors was the most significant pathways of enrichment. The changes of proteins and pathways may be related to the pathophysiological mechanism of PD. Therefore, some of these proteins could be considered as potential biomarkers for early PD diagnosis.

Treponema denticola transcriptional profiles in serum-restricted conditions

Treponema denticola is a major pathogen in periodontal disease and is frequently isolated from the lesions of patients with chronic periodontitis. Treponema denticola utilizes serum components as nutrient sources so as to colonize and proliferate in the gingival crevice. However, the mechanisms of serum utilization remain unclear. Therefore, the aim of the present study was to identify T. denticola serum utilization genes. Precultured T. denticola cells were suspended in a tryptone-yeast extract-gelatin-volatile fatty acids medium containing 0, 1% and 10% serum, respectively, and incubated anaerobically for 17 h. Total RNA was isolated, and T. denticola gene expression was compared by microarray and reverse transcription-polymerase chain reaction. In serum-depleted conditions, the expression levels of a potential hydroxylamine reductase, several ABC transporters, and phosphoenolpyruvate synthase were increased, while those of genes encoding methyl-accepting chemotaxis proteins and a transcriptional regulator were decreased. These results suggest that T. denticola may uptake serum components mainly through the action of ABC transporters. In particular, the decrease in the dmcA expression level with decreasing serum concentration suggests its involvement in chemotaxis toward serum-rich environments.

Quantitative gingival crevicular fluid proteome in type 2 diabetes mellitus and chronic periodontitis

OBJECTIVE

The aim of this study was to investigate the proteome of the gingival crevicular fluid comparing the relative abundance of proteins from type 2 diabetes mellitus (2DM) individuals and chronic periodontitis (CP) affected sites, subjects affected by both conditions and healthy individuals.

MATERIAL AND METHODS

Twenty individuals were equally allocated in four groups, 2DM with CP, 2DM periodontally healthy, CP without 2DM, and periodontally healthy without 2DM. The relative quantification of proteins was accessed with iTRAQ labeling and mass spectrometry.

RESULTS AND CONCLUSION

A total of 104 proteins showed significant differences in abundance in pairwise comparisons. Some presented different levels in all diseased groups as compared to control, either increasing (rap guanine nucleotide exchange factor, S100A8, S100A9, and immunoglobulins) or decreasing (actins, myristoylated alanine-rich C-kinase substrate, and glutathione S-transferase). Other differences were specific for a given condition: Titin, neutrophil elastase, and myeloperoxidase levels were higher in the DP group, cathelicidin antimicrobial peptide decreased in CP, and annexin decreased in DH. These differences in the proteome can provide clues for further studies that will validate the variation in their levels and their role in both diseases.

Novel Two-Component System of Streptococcus sanguinis Affecting Functions Associated with Viability in Saliva and Biofilm Formation

Streptococcus sanguinis is a pioneer species of teeth and a common opportunistic pathogen of infective endocarditis. In this study, we identified a two-component system, S. sanguinis SptRS (SptRS _Ss ), affecting S. sanguinis survival in saliva and biofilm formation. Isogenic mutants of sptR_Ss (SKsptR) and sptS_Ss (SKsptS) showed reduced cell counts in ex vivo assays of viability in saliva compared to those of parent strain SK36 and complemented mutants. Reduced counts of the mutants in saliva were associated with reduced growth rates in nutrient-poor medium (RPMI) and increased susceptibility to the deposition of C3b and the membrane attach complex (MAC) of the complement system, a defense component of saliva and serum. Conversely, sptR_Ss and sptS_Ss mutants showed increased biofilm formation associated with higher levels of production of H₂O₂ and extracellular DNA. Reverse transcription-quantitative PCR (RT-qPCR) comparisons of strains indicated a global role of SptRS _Ss in repressing genes for H₂O₂ production (2.5- to 15-fold upregulation of spxB, spxR, vicR, tpk, and ackA in sptR_Ss and sptS_Ss mutants), biofilm formation, and/or evasion of host immunity (2.1- to 11.4-fold upregulation of srtA, pcsB, cwdP, iga, and nt5e). Compatible with the homology of SptR _Ss with AraC-type regulators, duplicate to multiple conserved repeats were identified in 1,000-bp regulatory regions of downstream genes, suggesting that SptR _Ss regulates transcription by DNA looping. Significant transcriptional changes in the regulatory genes vicR, spxR, comE, comX, and mecA in the sptR_Ss and sptS_Ss mutants further indicated that SptRS _Ss is part of a regulatory network that coordinates cell wall homeostasis, H₂O₂ production, and competence. This study reveals that SptRS _Ss is involved in the regulation of crucial functions for S. sanguinis persistence in the oral cavity.

Microproteome of dentoalveolar tissues

Proteomic analysis of extracellular matrices (ECM) of dentoalveolar tissues can provide insights into developmental, pathological, and reparative processes. However, targeted dissection of mineralized tissues, dental cementum (DC), alveolar bone (AB), and dentin (DE), presents technical difficulties. We demonstrate an approach combining EDTA decalcification and laser capture microdissection (LCM), followed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), to analyze proteome profiles of these tissues. Using the LCM-LC-MS/MS approach, a total of 243 proteins was identified from all tissues, 193 proteins in DC, 147 in AB, and 135 proteins DE. Ninety proteins (37% of total) were common to all tissues, whereas 52 proteins (21%) were overlapping in only two. Also, 101 (42%) proteins were exclusively detected in DC (60), AB (15), or DE (26). Identification in all tissues of expected ECM proteins including collagen alpha-1(I) chain (COL1A1), collagen alpha-1(XII) chain (COL12A1), biglycan (BGN), asporin (ASPN), lumican (LUM), and fibromodulin (FMOD), served to validate the approach. Principal component analysis (PCA) and hierarchical clustering identified a high degree of similarity in DC and AB proteomes, whereas DE presented a distinct dataset. Exclusively and differentially identified proteins were detected from all three tissues. The protein-protein interaction network (interactome) of DC was notable for its inclusion of several indicators of metabolic function (e.g. mitochondrial proteins, protein synthesis, and calcium transport), possibly reflecting cementocyte activity. The DE proteome included known and novel mineralization regulators, including matrix metalloproteinase 20 (MMP-20), 5' nucleotidase (NT5E), and secreted phosphoprotein 24 (SPP-24 or SPP-2). Application of the LCM-LC-MS/MS approach to dentoalveolar tissues would be of value in many experimental designs, including developmental studies of transgenic animals, investigation of treatment effects, and identification of novel regenerative factors.

Human Gingival Crevicular Fluids (GCF) Proteomics: An Overview

Like other fluids of the human body, a gingival crevicular fluid (GCF) contains proteins, a diverse population of cells, desquamated epithelial cells, and bacteria from adjacent plaque. Proteomic tools have revolutionized the characterization of proteins and peptides and the detection of early disease changes in the human body. Gingival crevicular fluids (GCFs) are a very specific oral cavity fluid that represents periodontal health. Due to their non-invasive sampling, they have attracted proteome research and are used as diagnostic fluids for periodontal diseases and drug analysis. The aim of this review is to explore the proteomic science of gingival crevicular fluids (GCFs), their physiology, and their role in disease detection.

Qualitative and Quantitative Proteome Analysis of Oral Fluids in Health and Periodontal Disease by Mass Spectrometry

The significance of protein identification and characterization by classical protein chemistry approaches is clearly highlighted by our detailed understanding of the biological systems assembled over a time period of almost a century. The advent of state-of-the-art mass spectrometry (MS) with sensitivity, speed, and global protein analysis capacity without individual protein purification has transformed the classical protein chemistry with premise to accelerate discovery. These combined with the ability of the oral fluids such as whole saliva (WS) and gingival crevicular fluid (GCF) to reflect both systemic and locally derived proteins have generated significant interest to characterize these fluids more extensively by MS technology. This chapter deals with the experimental details of preanalytical steps using multidimensional protein separation combined with MS analysis of WS and GCF to achieve detailed protein composition at qualitative and quantitative levels. These approaches are interfaced with gold standard "stable-isotope" labeling technologies for large-scale quantitative MS analysis which is a prerequisite to determine accurate alterations in protein levels as a function of disease progression. The latter incorporates two stable-isotope chemistries one specific for cysteine containing proteins and the other universal amine-specific reagent in conjunction with oral fluids in health and periodontal disease to perform quantitative MS analysis. In addition, specific preanalytical steps demanded by the oral fluids such as GCF and WS for sample preparations to overcome limitations and uncertainties are elaborated for reliable large-scale quantitative MS analysis.

Dysbiosis by neutralizing commensal mediated inhibition of pathobionts

Dysbiosis in the periodontal microbiota is associated with the development of periodontal diseases. Little is known about the initiation of dysbiosis. It was hypothesized that some commensal bacteria suppress the outgrowth of pathobionts by H₂O₂ production. However, serum and blood components released due to inflammation can neutralize this suppressive effect, leading to the initiation of dysbiosis. Agar plate, dual-species and multi-species ecology experiments showed that H₂O₂ production by commensal bacteria decreases pathobiont growth and colonization. Peroxidase and blood components neutralize this inhibitory effect primarily by an exogenous peroxidase activity without stimulating growth and biofilm formation of pathobionts directly. In multi-species environments, neutralization of H₂O₂ resulted in 2 to 3 log increases in pathobionts, a hallmark for dysbiosis. Our data show that in oral biofilms, commensal species suppress the amounts of pathobionts by H₂O₂ production. Inflammation can neutralize this effect and thereby initiates dysbiosis by allowing the outgrowth of pathobionts.

The Treponema denticola FhbB Protein Is a Dominant Early Antigen That Elicits FhbB Variant-Specific Antibodies That Block Factor H Binding and Cleavage by Dentilisin

The Treponema denticola FhbB protein contributes to immune evasion by binding factor H (FH). Cleavage of FH by the T. denticola protease, dentilisin, may contribute to the local immune dysregulation that is characteristic of periodontal disease (PD). Although three FhbB phyletic types have been defined (FhbB1, FhbB2, and FhbB3), the in vivo expression patterns and antigenic heterogeneity of FhbB have not been assessed. Here, we demonstrate that FhbB is a dominant early antigen that elicits FhbB type-specific antibody (Ab) responses. Using the murine skin abscess model, we demonstrate that the presence or absence of FhbB or dentilisin significantly influences Ab responses to infection and skin abscess formation. Competitive binding analyses revealed that α-FhbB Ab can compete with FH for binding to T. denticola and block dentilisin-mediated FH cleavage. Lastly, we demonstrate that dentilisin cleavage sites reside within critical functional domains of FH, including the complement regulatory domain formed by CCPs 1 to 4. Analysis of the FH cleavage products revealed that they lack cofactor activity. The data presented here provide insight into the in vivo significance of dentilisin, FhbB and its antigenic diversity, and the potential impact of FH cleavage on the regulation of complement activation.

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.

Trends in Laboratory Diagnostic Methods in Periodontology

This work presents a summary of current knowledge on the laboratory diagnosis of periodontitis. It focuses on the theoretical foundations and is supplemented with new knowledge. It subsequently describes specifically the laboratory diagnosis methods of periodontitis: the protein expression of inflammation, oral microbiology and molecular diagnostics. Periodontitis is a serious disease worldwide and its confirmed association with systemic diseases means its severity is increasing. Its laboratory diagnosis has the potential to rise to the level of clinical and diagnostic imaging. The transfer of diagnostic methods from laboratory to clinical use is increasingly used in the prevention and monitoring of the exacerbation and treatment of periodontal disease, as well as of its impact on systemic disease.

N-acetylcysteine and the human serum components that inhibit bacterial invasion of gingival epithelial cells prevent experimental periodontitis in mice

PURPOSE

We previously reported that human serum significantly reduces the invasion of various oral bacterial species into gingival epithelial cells in vitro. The aims of the present study were to characterize the serum component(s) responsible for the inhibition of bacterial invasion of epithelial cells and to examine their effect on periodontitis induced in mice.

METHODS

Immortalized human gingival epithelial (HOK-16B) cells were infected with various 5- (and 6-) carboxy-fluorescein diacetate succinimidyl ester-labeled oral bacteria, including Fusobacterium nucleatum, Provetella intermedia, Porphyromonas gingivalis, and Treponiema denticola, in the absence or presence of three major serum components (human serum albumin [HSA], pooled human IgG [phIgG] and α1-antitrypsin). Bacterial adhesion and invasion were determined by flow cytometry. The levels of intracellular reactive oxygen species (ROS) and activation of small GTPases were examined. Experimental periodontitis was induced by oral inoculation of P. gingivalis and T. denticola in Balb/c mice.

RESULTS

HSA and phIgG, but not α1-antitrypsin, efficiently inhibited the invasion of various oral bacterial species into HOK-16B cells. HSA but not phIgG decreased the adhesion of F. nucleatum onto host cells and the levels of intracellular ROS in HOK-16B cells. N-acetylcysteine (NAC), a ROS scavenger, decreased both the levels of intracellular ROS and invasion of F. nucleatum into HOK-16B cells, confirming the role of ROS in bacterial invasion. Infection with F. nucleatum activated Rac1, a regulator of actin cytoskeleton dynamics. Not only HSA and NAC but also phIgG decreased the F. nucleatum-induced activation of Rac1. Furthermore, both HSA plus phIgG and NAC significantly reduced the alveolar bone loss in the experimental periodontitis induced by P. gingivalis and T. denticola in mice.

CONCLUSIONS

NAC and the serum components HSA and phIgG, which inhibit bacterial invasion of oral epithelial cells in vitro, can successfully prevent experimental periodontitis.

Gingival crevicular fluid proteomes in health, gingivitis and chronic periodontitis

OBJECTIVE

The aim of this study was to compare the proteome composition of gingival crevicular fluid obtained from healthy periodontium, gingivitis and chronic periodontitis affected sites.

BACKGROUND

Owing to its site-specific nature, gingival crevicular fluid is ideal for studying biological processes that occur during periodontal health and disease progression. However, few studies have been conducted into the gingival crevicular fluid proteome due to the small volumes obtained.

METHODS

Fifteen males were chosen for each of three different groups, healthy periodontium, gingivitis and chronic periodontitis. They were categorized based on clinical measurements including probing depth, bleeding on probing, plaque index, radiographic bone level, modified gingival index and smoking status. Gingival crevicular fluid was collected from each patient, pooled into healthy, gingivitis and chronic periodontitis groups and their proteome analyzed by gel electrophoresis and liquid chromatography electrospray ionization ion trap tandem mass spectrometry.

RESULTS

One hundred and twenty-one proteins in total were identified, and two-thirds of these were identified in all three conditions. Forty-two proteins were considered to have changed in abundance. Of note, cystatin B and cystatin S decreased in abundance from health to gingivitis and further in chronic periodontitis. Complement proteins demonstrated an increase from health to gingivitis followed by a decrease in chronic periodontitis. Immunoglobulins, keratin proteins, fibronectin, lactotransferrin precursor, 14-3-3 protein zeta/delta, neutrophil defensin 3 and alpha-actinin exhibited fluctuations in levels.

CONCLUSION

The gingival crevicular fluid proteome in each clinical condition was different and its analysis may assist us in understanding periodontal pathogenesis.

Physiological adaptations of key oral bacteria

Oral colonising bacteria are highly adapted to the various environmental niches harboured within the mouth, whether that means while contributing to one of the major oral diseases of caries, pulp infections, or gingival/periodontal disease or as part of a commensal lifestyle. Key to these infections is the ability to adhere to surfaces via a range of specialised adhesins targeted at both salivary and epithelial proteins, their glycans and to form biofilm. They must also resist the various physical stressors they are subjected to, including pH and oxidative stress. Possibly most strikingly, they have developed the ability to harvest both nutrient sources provided by the diet and those derived from the host, such as protein and surface glycans. We have attempted to review recent developments that have revealed much about the molecular mechanisms at work in shaping the physiology of oral bacteria and how we might use this information to design and implement new treatment strategies.

Uncovering the molecular networks in periodontitis

Periodontitis is a complex immune-inflammatory disease that results from a preestablished infection in gingiva, mainly due to Gram-negative bacteria that colonize deeper in gingival sulcus and latter periodontal pocket. Host inflammatory and immune responses have both protective and destructive roles. Although cytokines, prostaglandins, and proteases struggle against microbial burden, these molecules promote connective tissue loss and alveolar bone resorption, leading to several histopathological changes, namely destruction of periodontal ligament, deepening of periodontal pocket, and bone loss, which can converge to attain tooth loss. Despite the efforts of genomics, transcriptomics, proteomics/peptidomics, and metabolomics, there is no available biomarker for periodontitis diagnosis, prognosis, and treatment evaluation, which could assist on the established clinical evaluation. Nevertheless, some genes, transcripts, proteins and metabolites have already shown a different expression in healthy subjects and in patients. Though, so far, 'omics approaches only disclosed the host inflammatory response as a consequence of microbial invasion in periodontitis and the diagnosis in periodontitis still relies on clinical parameters, thus a molecular tool for assessing periodontitis lacks in current dental medicine paradigm. Saliva and gingival crevicular fluid have been attracting researchers due to their diagnostic potential, ease, and noninvasive nature of collection. Each one of these fluids has some advantages and disadvantages that are discussed in this review.

Quantitative gingival crevicular fluid proteome in health and periodontal disease using stable isotope chemistries and mass spectrometry

AIM

Application of quantitative stable isotope-labelling chemistries and mass spectrometry (MS) to determine alterations in gingival crevicular fluid (GCF) proteome in periodontal disease.

MATERIAL AND METHODS

Quantitative proteome of GCF from 40 healthy individuals versus 40 patients with periodontal disease was established using 320 GCF samples and stable isotope-labelling reagents, ICAT and mTRAQ, with MS technology and validated by enzyme-linked immunosorbent methods.

RESULTS

We have identified 238 distinct proteins of which 180 were quantified in GCF of both healthy and periodontal patients with additional 26 and 32 distinct proteins that were found only in GCF of healthy or periodontal patients. In addition, 42 pathogenic bacterial proteins and 11 yeast proteins were quantified. The data highlighted a series of proteins not quantified previously by large-scale MS approaches in GCF with relevance to periodontal disease, such as host-derived Ig alpha-2 chain C, Kallikrein-4, S100-A9, transmembrane proteinase 13, peptidase S1 domain, several collagen types and pathogenic bacterial proteins, e.g. formamidase, leucine aminopeptidase and virulence factor OMP85.

CONCLUSIONS

The innovative analytical approaches provided detailed novel changes in both host and microbial derived GCF proteomes of periodontal patients. The study defined 50 host and 16 pathogenic bacterial proteins significantly elevated in periodontal disease most of which were novel with significant potential for application in the clinical arena of periodontal disease.

The link between chronic periodontitis and COPD: a common role for the neutrophil?

BACKGROUND

The possible relationship between chronic inflammatory diseases and their co-morbidities has become an increasing focus of research. Both chronic periodontitis and chronic obstructive pulmonary disease are neutrophilic, inflammatory conditions characterized by the loss of local connective tissue. Evidence suggests an association and perhaps a causal link between the two diseases. However, the nature of any relationship between them is unclear, but if pathophysiologically established may have wide-reaching implications for targeted treatments to improve outcomes and prognosis.

DISCUSSION

There have been a number of epidemiological studies undertaken demonstrating an independent association between chronic periodontitis and chronic obstructive pulmonary disease. However, many of them have significant limitations, and drawing firm conclusions regarding causality may be premature. Although the pathology of both these diseases is complex and involves many cell types, such as CD8 positive cells and macrophages, both conditions are predominantly characterized by neutrophilic inflammation. Increasingly, there is evidence that the two conditions are underpinned by similar pathophysiological processes, especially centered on the functions of the neutrophil. These include a disturbance in protease/anti-protease and redox state balance. The association demonstrated by epidemiological studies, as well as emerging similarities in pathogenesis at the level of the neutrophil, suggest a basis for testing the effects of treatment for one condition upon the severity of the other.

SUMMARY

Although the evidence of an independent association between chronic periodontitis and chronic obstructive pulmonary disease grows stronger, there remains a lack of definitive studies designed to establish causality and treatment effects. There is a need for future research to be focused on answering these questions.

Quantitative proteomic analysis of gingival crevicular fluid in different periodontal conditions

AIM

To quantify the proteome composition of the GCF in periodontal health (HH) and in sites with different clinical conditions in chronic periodontitis (CP) subjects.

MATERIAL AND METHODS

5 subjects with HH and 5 with CP were submitted to full-mouth periodontal examination, and GCF sampling. Sites in the CP group were classified and sampled as periodontitis (P, probing depth, PD>4 mm), gingivitis (G, PD≤3 mm with bleeding on probing, BOP), and healthy sites (H, PD≤3 mm without BOP). GCF proteins were subjected to liquid chromatography electrospray ionization mass spectrometry for identification, characterization and quantification.

RESULTS

230 proteins were identified; 145 proteins were detected in HH, 214 in P, 154 in G, and 133 in H. Four proteins were exclusively detected at HH, 43 proteins at P, 7 proteins at G, and 1 protein at H. Compared to HH group, 35 and 6 proteins were more abundant in P and G (p<0.001), respectively; and 4, 15 and 37 proteins were less abundant in P, G and H (p≤0.01), respectively.

CONCLUSIONS

There are marked differences in the GCF proteome according to disease profile. Comprehension of the role of the identified proteins in the etiopathogenesis of periodontal disease may lead to biomarkers definition.

Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization

AIM

To identify optimal combination(s) of proteomic based biomarkers in gingival crevicular fluid (GCF) samples from chronic periodontitis (CP) and periodontally healthy individuals and validate the predictions through known and blind test sets.

MATERIALS AND METHODS

GCF samples were collected from 96 CP and periodontally healthy subjects and analysed using high-performance liquid chromatography, tandem mass spectrometry and the PILOT_PROTEIN algorithm. A mixed-integer linear optimization (MILP) model was then developed to identify the optimal combination of biomarkers which could clearly distinguish a blind subject sample as healthy or diseased.

RESULTS

A thorough cross-validation of the MILP model capability was performed on a training set of 55 samples and greater than 99% accuracy was consistently achieved when annotating the testing set samples as healthy or diseased. The model was then trained on all 55 samples and tested on two different blind test sets, and using an optimal combination of 7 human proteins and 3 bacterial proteins, the model was able to correctly predict 40 out of 41 healthy and diseased samples.

CONCLUSIONS

The proposed large-scale proteomic analysis and MILP model led to the identification of novel combinations of biomarkers for consistent diagnosis of periodontal status with greater than 95% predictive accuracy.

One decade of salivary proteomics: current approaches and outstanding challenges

Efforts have been made in the last decade towards the complete characterization of saliva proteome using gel-based and gel-free approaches. The combination of these strategies resulted in the increment of the dynamic range of saliva proteome, which yield in the identification of more than 3,000 different protein species. Comparative protein profiling using isotope labeling and label free approaches has been used for the identification of novel biomarkers for oral and related diseases. Although progresses have been made in saliva proteome characterization, the comparative profiling in different pathophysiological conditions is still at the beginning if compared to other bodily fluids. The potential biomarkers identified so far lack specificity once common differentially expressed proteins were detected in the saliva of patients with distinct diseases. In addition, recent research works focused on saliva peptidome profiling already allowed a better understanding of peptides' physiological role in oral cavity. This review provides an overview of the major achievements in saliva proteomics giving emphasis to methodological concerns related with saliva collection, treatment and analysis, as well as the main advantages and pitfalls underlying salivary proteomic strategies and potential clinical outcomes.

Protease profiling of different biofluids in type 1 diabetes mellitus

OBJECTIVES

We aimed to disclose the proteolytic events underlying type 1 diabetes and related complication through protease profiling in the bodily fluids serum, urine and saliva.

DESIGN AND METHODS

Zymography followed by LC-MS/MS was performed for protease identification and quantitative comparison of proteolytic activity between healthy, type 1 diabetic patients with no complications and with retinopathy and nephropathy. Western blotting was also accomplished for MMP-9 and MMP-2 identification and expression analysis.

RESULTS

Only MMP-2 and MMP-9 were observed in serum with significantly increased levels and activity observed in diabetic patients. In urine and saliva other proteases besides MMPs were identified by MS and presented disease-dependent activity variations. Among these are complex MMP-9/Neutrophil gelatinase-associated lipocalin, aminopeptidase N, azurocidin and kallikrein 1 with more activity noticed in type 1 diabetes patients with nephropathy and/or retinopathy.

CONCLUSION

Our data highlight the usefulness of urine and saliva for the monitoring of type-1 diabetes-related proteolytic events, where aminopeptidase N, azurocidin and kallikrein 1 appear as promising screening targets for type 1 diabetes-related complications.