Proteomics - The research frontier in periodontics

Diagnostic Accuracy of Novel Protein Biomarkers in Saliva to Detect Periodontitis Using Untargeted 'SWATH' Mass Spectrometry

AIM

To discover new salivary biomarkers to diagnose periodontitis and evaluate the impact of age and smoking on predictive capacity.

MATERIAL AND METHODS

Saliva samples were collected from 44 healthy periodontal individuals and 41 with periodontitis. Samples were analysed by sequential window acquisition of all theoretical mass spectra (SWATH-MS), and proteins were identified by employing the UniProt database. The diagnostic capacity of the molecules was determined with generalized additive models. The models obtained were single-protein unadjusted and adjusted for age and smoking status, besides two-protein combinations.

RESULTS

Eight single salivary proteins had a bias-corrected accuracy (bc-ACC) of 78.8%-86.8% (bc-sensitivity/bc-specificity of 62.5%-86.9%/60.9%-98.1%) to diagnose periodontitis. Predictive capacity increased more by adjusting for age (bc-ACC: 94.1%-98.2%; bc-sensitivity/bc-specificity: 90.2%-98.6%/93.6%-97.2%) than smoking (bc-ACC: 83.9%-90.4%; bc-sensitivity/bc-specificity: 73.6%-89.9%/76.2%-96.4%). These proteins were keratin, type II cytoskeletal 1, protein S100-A8, β-2-microglobulin, neutrophil defensin 1, lysozyme C, ubiquitin-60S ribosomal protein L40, isoform 2 of tropomyosin α-3 chain and resistin. Two dual combinations showed bc-sensitivity/bc-specificity of > 90%: β-2-microglobulin with profilin-1, and lysozyme C with zymogen granule protein 16 homologue B.

CONCLUSIONS

New salivary biomarkers show good or excellent ability to diagnose periodontitis. Age has a more significant influence on the accuracy of the single biomarkers than smoking, with results comparable to two-protein combinations.

The New Era of Salivaomics in Dentistry: Frontiers and Facts in the Early Diagnosis and Prevention of Oral Diseases and Cancer

Nowadays, with the development of new and highly sensitive, blood is not the only medium of choice for the diagnosis of several diseases and pathological conditions. Saliva is now considered a safe and non-invasive sample to study oral and systemic diseases, showing great diagnostic potential. According to several recent studies, saliva has emerged as an emerging biofluid for the early diagnosis of several diseases, indicated as a mirror of oral and systemic health and a valuable source of clinically relevant information. Indeed, several studies have observed that saliva is useful for detecting and diagnosing malignant tumours, human immunodeficiency virus, heart disease, and autoimmune diseases. The growing realisation that saliva is an inexhaustible source of information has led to the coining of the term ‘Salivaomics’, which includes five “omics” in connection with the main constituents of saliva: genome and epigenome, transcriptomics, metabolomics, lipidomics, proteomics and microbiota. All those may be changed by disease state, so they offer significant advantages in the early diagnosis and prognosis of oral diseases. The aim of the present review isto update and highlight the new frontiers of salivaomics in diagnosing and managing oral disorders, such as periodontitis, premalignant disorders, and oral squamous cell carcinoma (OSCC).

Neutrophil elastase aggravates periodontitis by disrupting gingival epithelial barrier via cleaving cell adhesion molecules

Neutrophil elastase (NE) functions as a host defense factor; however, excessive NE activity can potentially destroy human tissues. Although NE activity is positively correlated to gingival crevicular fluid and clinical attachment loss in periodontitis, the underlying mechanisms by which NE aggravates periodontitis remain elusive. In this study, we investigated how NE induces periodontitis severity and whether NE inhibitors were efficacious in periodontitis treatment. In a ligature-induced murine model of periodontitis, neutrophil recruitment, NE activity, and periodontal bone loss were increased in the periodontal tissue. Local administration of an NE inhibitor significantly decreased NE activity in periodontal tissue and attenuated periodontal bone loss. Furthermore, the transcription of proinflammatory cytokines in the gingiva, which was significantly upregulated in the model of periodontitis, was significantly downregulated by NE inhibitor injection. An in vitro study demonstrated that NE cleaved cell adhesion molecules, such as desmoglein 1, occludin, and E-cadherin, and induced exfoliation of the epithelial keratinous layer in three-dimensional human oral epithelial tissue models. The permeability of fluorescein-5-isothiocyanate-dextran or periodontal pathogen was significantly increased by NE treatment in the human gingival epithelial monolayer. These findings suggest that NE induces the disruption of the gingival epithelial barrier and bacterial invasion in periodontal tissues, aggravating periodontitis.

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.

Association between periodontitis and bipolar disorder: A nationwide cohort study

Whether periodontitis is a risk factor for developing bipolar disorders (BD) has not been investigated. We aimed to determine whether periodontitis is associated with the subsequent development of BD and examine the risk factors for BD among patients with periodontitis.Using ambulatory and inpatient claims data from the National Health Insurance Research Database (NHIRD), we identified 12,337 patients who were aged at least 20 years and newly diagnosed with periodontitis between 2000 and 2004. The date of the first claim with a periodontitis diagnosis was set as the index date. For each patient with periodontitis, 4 subjects without a history of periodontitis were randomly selected from the NHIRD and frequency-matched with the patients with periodontitis according to sex, age (in 5-year bands), and index year.The periodontitis group had a mean age of 44.0 ± 13.7 years and slight predominance of men (51.3%). Compared with the subjects without periodontitis, the patients with periodontitis had higher prevalence of diabetes mellitus, hyperlipidemia, hypertension, ischemic heart disease, stroke, head injury, major depressive disorder, chronic obstructive pulmonary disease (COPD), and asthma (P < .001). The incidence rate of BD was higher in the periodontitis group than in the non-periodontitis group (2.74 vs 1.46 per 1000 person-year), with an adjusted hazard ratio of 1.82 (95% confidence interval = 1.59-2.08) after adjustment for sex, age, and comorbidities.The patients with periodontitis exhibited a significantly higher risk of developing BD. Keep the better oral hygiene to reduce periodontitis might be a preventive strategy for BD.

Proteomics approach for biomarkers and diagnosis of periodontitis: systematic review

Quantitative proteomic workflow based on mass spectrometry (MS) is recently developed by the researchers to screen for biomarkers in periodontal diseases comprising periodontitis. Periodontitis is known for chronic inflammatory disease characterized by progressive destruction of the tooth-supporting apparatus, yet has a lack of clear pathobiology based on a discrepancy between specified categories and diagnostic vagueness. The objective of this review was to outlined the accessible information related to proteomics studies on periodontitis. The Preferred Reporting Items for Systematical Reviews and Meta-Analysis (PRISMA) statement guides to acquaint proteomic analysis on periodontal diseases was applied. Three databases were used in this study, such as Pubmed, ScienceDirect and Biomed Central from 2009 up to November 2019. Proteomics analysis platforms that used in the studies were outlined. Upregulated and downregulated proteins findings data were found, in which could be suitable as candidate biomarkers for this disease.

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.

Saliva proteomics updates in biomedicine

In the years of personalized (or precision) medicine the 'omics' methodologies in biomedical sciences-genomics, transcriptomics, proteomics and metabolomics-are helping researchers to detect quantifiable biological characteristics, or biomarkers, that will best define the human physiology and pathologies. Proteomics use high throughput and high efficiency approaches with the support of bioinformatic tools in order to identify and quantify the total protein content of cells, tissues or biological fluids. Saliva receives a lot of attention as a rich biological specimen that offers a number of practical and physiological advantages over blood and other biological fluids in monitoring human health. The aim of this review is to present the latest advances in saliva proteomics for biomedicine.

Clinical, microbiological and oxidative stress evaluation of periodontitis patients treated with two regimens of systemic antibiotics, adjunctive to non-surgical therapy: A placebo-controlled randomized clinical trial

Aim of research was to evaluate and compare the clinical and microbiological effects of two different regimens of amoxicillin (AMX) and metronidazole (MTZ) combined with non-surgical periodontal therapy in patients with chronic periodontitis (CP), and identify antibiotic-resistant bacteria and changes in oxidative stress (OS). Forty-six patients with generalized CP were randomly assigned to group A [scaling and root planing within 24 h (SRP) + placebo for 7 days), group B [SRP + AMX + MTZ, both 500 mg three times daily (TID), 3 days), and group C [SRP + AMX + MTZ, both 500 mg TID, 7 days). Periodontal pocket depth (PPD-primary outcome), clinical attachment level (CAL), full-mouth bleeding scores (FMBS), plaque scores (FMPS), blood and subgingival plaque were assessed at baseline and after three months. OS was evaluated via derivatives of reactive oxygen metabolites (d-ROMs) and assessments of biological antioxidant potential (BAP). Bacterial profiling was performed by PCR. Antibiotic resistance was evaluated in cultures. PPD, CAL, number of sites with PPD ≥6 mm, their PPD, CAL and FMBS decreased (P<0.05) in all groups, as well as FMPS in groups A and B, and d-ROMs in group C. There were significant differences among groups regarding decreases in the frequency of detection for Aa and Tf. For Aa, there were differences between groups A and C (P=0.048) and between groups B and C (P=0.048), but not between groups A and B; whereas for Tf, groups A and B were different from group C (P<0.001), but not from each other (P=0.920). No resistance to AMX was identified prior to treatment; two strains were resistant after treatment. Before treatment, 13 strains were resistant to MTZ, and 2 were resistant after. One strain in the same patient was sensitive prior to treatment, and later became resistant to both antibiotics. SRP with a 7-day course of antibiotic therapy was more effective for improving clinical parameters, in decrease of detection of several periopathogens, and in improvement of OS when compared to a 3-day regimen. Resistance was found in fewer strains after treatment than before.

Systems Biology Approaches and Precision Oral Health: A Circadian Clock Perspective

A vast majority of the pathophysiological and metabolic processes in humans are temporally controlled by a master circadian clock located centrally in the hypothalamic suprachiasmatic nucleus of the brain, as well as by specialized peripheral oscillators located in other body tissues. This circadian clock system generates a rhythmical diurnal transcriptional-translational cycle in clock genes and protein expression and activities regulating numerous downstream target genes. Clock genes as key regulators of physiological function and dysfunction of the circadian clock have been linked to various diseases and multiple morbidities. Emerging omics technologies permits largescale multi-dimensional investigations of the molecular landscape of a given disease and the comprehensive characterization of its underlying cellular components (e.g., proteins, genes, lipids, metabolites), their mechanism of actions, functional networks and regulatory systems. Ultimately, they can be used to better understand disease and interpatient heterogeneity, individual profile, identify personalized targetable key molecules and pathways, discover novel biomarkers and genetic alterations, which collectively can allow for a better patient stratification into clinically relevant subgroups to improve disease prediction and prevention, early diagnostic, clinical outcomes, therapeutic benefits, patient's quality of life and survival. The use of “omics” technologies has allowed for recent breakthroughs in several scientific domains, including in the field of circadian clock biology. Although studies have explored the role of clock genes using circadiOmics (which integrates circadian omics, such as genomics, transcriptomics, proteomics and metabolomics) in human disease, no such studies have investigated the implications of circadian disruption in oral, head and neck pathologies using multi-omics approaches and linking the omics data to patient-specific circadian profiles. There is a burgeoning body of evidence that circadian clock controls the development and homeostasis of oral and maxillofacial structures, such as salivary glands, teeth and oral epithelium. Hence, in the current era of precision medicine and dentistry and patient-centered health care, it is becoming evident that a multi-omics approach is needed to improve our understanding of the role of circadian clock-controlled key players in the regulation of head and neck pathologies. This review discusses current knowledge on the role of the circadian clock and the contribution of omics-based approaches toward a novel precision health era for diagnosing and treating head and neck pathologies, with an emphasis on oral, head and neck cancer and Sjögren's syndrome.

Current Status and Future Opportunities of Omics Tools in Mycotoxin Research

Mycotoxins are toxic secondary metabolites of low molecular weight produced by filamentous fungi, such as Aspergillus, Fusarium, and Penicillium spp. Mycotoxins are natural contaminants of agricultural commodities and their prevalence may increase due to global warming. Dangerous mycotoxins cause a variety of health problems not only for humans, but also for animals. For instance, they possess carcinogenic, immunosuppressive, hepatotoxic, nephrotoxic, and neurotoxic effects. Hence, various approaches have been used to assess and control mycotoxin contamination. Significant challenges still exist because of the complex heterogeneous nature of food composition. The potential of combined omics approaches such as metabolomics, genomics, transcriptomics, and proteomics would contribute to our understanding about pathogen fungal crosstalk as well as strengthen our ability to identify, isolate, and characterise mycotoxins pre and post-harvest. Multi-omics approaches along with advanced analytical tools and chemometrics provide a complete annotation of such metabolites produced before/during the contamination of crops. We have assessed the merits of these individual and combined omics approaches and their promising applications to mitigate the issue of mycotoxin contamination. The data included in this review focus on aflatoxin, ochratoxin, and patulin and would be useful as benchmark information for future research.

Oral microbiome and peri-implant diseases: where are we now?

Peri-implant infective diseases (PIIDs) in oral implantology are commonly known as peri-implant mucositis (PIM) and periimplantitis (PI). While PIM is restricted to the peri-implant mucosa and is reversible, PI also affects implant-supporting bone and, therefore, is very difficult to eradicate. PIIDs in clinical outcome may resemble gingivitis and periodontitis, as they share similar risk factors. However, recent study in the field of proteomics and other molecular studies indicate that PIIDs exhibit significant differences when compared to periodontal diseases. This review aims to elucidate the current knowledge of PIIDs, their etiopathology and diversified microbiology as well as the role of molecular studies, which may be a key to personalized diagnostic and treatment protocols of peri-implant infections in the near future.

Identification of a discriminative metabolomic fingerprint of potential clinical relevance in saliva of patients with periodontitis using 1H nuclear magnetic resonance (NMR) spectroscopy

Periodontitis is characterized by the loss of the supporting tissues of the teeth in an inflammatory-infectious context. The diagnosis relies on clinical and X-ray examination. Unfortunately, clinical signs of tissue destruction occur late in the disease progression. Therefore, it is mandatory to identify reliable biomarkers to facilitate a better and earlier management of this disease. To this end, saliva represents a promising fluid for identification of biomarkers as metabolomic fingerprints. The present study used high-resolution ¹H-nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical analysis to identify the metabolic signature of active periodontitis. The metabolome of stimulated saliva of 26 patients with generalized periodontitis (18 chronic and 8 aggressive) was compared to that of 25 healthy controls. Principal Components Analysis (PCA), performed with clinical variables, indicated that the patient population was homogeneous, demonstrating a strong correlation between the clinical and the radiological variables used to assess the loss of periodontal tissues and criteria of active disease. Orthogonal Projection to Latent Structure (OPLS) analysis showed that patients with periodontitis can be discriminated from controls on the basis of metabolite concentrations in saliva with satisfactory explained variance (R2X = 0.81 and R2Y = 0.61) and predictability (Q2Y = 0.49, CV-AUROC = 0.94). Interestingly, this discrimination was irrespective of the type of generalized periodontitis, i.e. chronic or aggressive. Among the main discriminating metabolites were short chain fatty acids as butyrate, observed in higher concentrations, and lactate, γ-amino-butyrate, methanol, and threonine observed in lower concentrations in periodontitis. The association of lactate, GABA, and butyrate to generate an aggregated variable reached the best positive predictive value for diagnosis of periodontitis. In conclusion, this pilot study showed that 1H-NMR spectroscopy analysis of saliva could differentiate patients with periodontitis from controls. Therefore, this simple, robust, non-invasive method, may offer a significant help for early diagnosis and follow-up of periodontitis.

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.

Analysis of protein expression in periodontal pocket tissue: a preliminary study

Background

The periodontal disease is caused by a set of inflammatory disorders characterized by periodontal pocket formation that lead to tooth loss if untreated. The proteomic profile and related molecular conditions of pocket tissue in periodontally-affected patients are not reported in literature. To characterize the proteomic profile of periodontally-affected patients, their interproximal periodontal pocket tissue was compared with that of periodontally-healthy patients. Pocket-associated and healthy tissue samples, harvested during surgical therapy, were treated to extract the protein content. Tissues were always collected at sites where no periodontal-pathogenic bacteria were detectable. Proteins were separated using two-dimensional gel electrophoresis and identified by liquid chromatography/mass spectrometry. After identification, four proteins were selected for subsequent Western Blot quantitation both in pathological and healty tissues.

Results

A significant unbalance in protein expression between healthy and pathological sites was recorded. Thirty-two protein spots were overall identified, and four proteins (S100A9, HSPB1, LEG7 and 14-3-3) were selected for Western blot analysis of both periodontally-affected and healthy patients. The four selected proteins resulted over-expressed in periodontal pocket tissue when compared with the corresponding tissue of periodontally-healthy patients. The results of Western blot analysis are congruent with the defensive and the regenerative reaction of injured periodontal tissues.

Conclusions

The proteomic analysis was performed for the first time directly on periodontal pocket tissue. The proteomic network highlighted in this study enhances the understanding of periodontal disease pathogenesis necessary for specific therapeutic strategies setting.