Proteomic profile of root canal contents in teeth with post-treatment endodontic disease

Technological development of multidimensional liquid chromatography-mass spectrometry in proteome research

Liquid chromatography-mass spectrometry (LC-MS) is the method of choice for high-throughput proteomic research. Limited by the peak capacity, the separation performance of conventional single-dimensional LC hampers the development of proteomics. Combining different separation modes orthogonally, multidimensional liquid chromatography (MDLC) with high peak capacity was developed to address this challenge. MDLC has evolved rapidly since its establishment, and the progress of proteomics has been greatly facilitated by the advent of novel MDLC-MS-based methods. In this paper, we will review the advances of MDLC-MS-based methodologies and technologies in proteomics studies, from different perspectives including novel application scenarios and proteomic targets, automation, miniaturization, and the improvement of the classic methods in recent years. In addition, attempts regarding new MDLC-MS models are also mentioned together with the outlook of MDLC-MS-based proteomics methods.

Microbiological profile of root canals indicated for endodontic retreatment due to secondary endodontic infections or for prosthetic reasons

OBJECTIVE

The objective of this study was to evaluate the microbiological profile of root canals indicated for endodontic retreatment due to secondary endodontic infections evidenced by the presence of chronic apical periodontitis (G1) or for prosthetic reasons, without clinical and radiographic signs of endodontic reinfection (G2).

METHODS

Microbiological samples were collected from thirty teeth (N=30) out of which 15 were indicated for retreatment due to the presence of chronic apical periodontitis (G1) and 15 were indicated exclusively for prosthetic reasons (G2). Samples were collected from root canals before (S1), after chemomechanical preparation (S2), and after 30 days of intracanal medication composed of calcium hydroxide and 2% chlorhexidine gel (S3). The molecular analysis was performed using Nested-PCR for the detection of 17 bacterial species. The efficacy of each stage of the retreatment in reducing the microbial load was verified by counting colony-forming units (CFU). The statistical analysis considered a significance level of 5%.

RESULTS

The results showed that bacteria were detected in 100% of the cases in S1, in both groups, by Nested PCR. The most frequently found species in S1 in both groups were Enterococcus faecalis, Fusobacterium nucleatum, Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Parvimonas micra. The microbial load of G1 was higher than G2 in the initial samples (S1). Endodontic retreatment was effective in reducing the microbial load in G1 and G2. Statistically significant associations were found between specific bacteria and clinical signs and symptoms.

CONCLUSION

It was concluded that the microbial community present in the root canal of teeth indicated for endodontic retreatment is mixed and heterogeneous. G1 and G2 differ in the number of species per case and microbial load.

CLINICAL RELEVANCE

Endodontic retreatment was effective in reducing the microbial load. Statistically significant associations were found between specific bacteria and clinical signs and symptoms.

Teeth with acute apical abscess vs. teeth with chronic apical periodontitis: a quantitative and qualitative proteomic analysis

OBJECTIVE

To quantitatively and qualitatively analyze the proteomic profile of teeth with acute apical abscesses (AAA) compared with teeth with chronic apical periodontitis (CAP) and to correlate the expression of detected human proteins with their main biological functions.

MATERIALS AND METHODS

Samples were obtained from root canals of 9 patients diagnosed with AAA and 9 with CAP. Samples were analyzed by reversed-phase liquid chromatography coupled to mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in protein expression were calculated using the t-test (p < 0.05).

RESULTS

In total, 246 human proteins were identified from all samples. Proteins exclusively found in the AAA group were mainly associated with the immunoinflammatory response and oxidative stress response. In the quantitative analysis, 17 proteins were upregulated (p < 0.05) in the AAA group, including alpha-1-acid glycoprotein, hemopexin, fibrinogen gamma chain, and immunoglobulin. Additionally, 61 proteins were downregulated (p < 0.05), comprising cathepsin G, moesin, gelsolin, and transketolase. Most of the proteins were from the extracellular matrix, cytoplasm, and nucleus.

CONCLUSIONS

The common proteins between the groups were mainly associated with the immune response at both expression levels. Upregulated proteins mostly belonged to the acute-phase proteins, while the downregulated proteins were associated with DNA/RNA regulation and repair, and structural function.

CLINICAL RELEVANCE

The host response is directly related to the development of apical abscesses. Thus, understanding the behavior of human proteins against the endodontic pathogens involved in this condition might contribute to the study of new approaches related to the treatment of this disease.

Proteomic analysis of infected root canals with apical periodontitis in patients with type 2 diabetes mellitus: A cross-sectional study

AIM

This study aimed to quantitatively and qualitatively determine the proteomic profile of apical periodontitis (AP) in type 2 diabetes mellitus (T2DM) patients in comparison with systemically noncompromised patients and to correlate the protein expression of both groups with their biological functions.

METHODOLOGY

The sample consisted of 18 patients with asymptomatic AP divided into two groups according to the presence of T2DM: diabetic group-patients with T2DM (n = 9) and control group-systemically healthy patients (n = 9). After sample collection, the root canal samples were prepared for proteomic analysis using reverse-phase liquid chromatography-mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in protein expression between groups were calculated using t-test (p < .05). Biological functions were analysed using the Homo sapiens UniProt database.

RESULTS

A total of 727 human proteins were identified in all samples. Among them, 124 proteins common to both groups were quantified, out of which 65 proteins from the diabetic group showed significant differences compared with the control: 43 upregulated (p < .05) and 22 downregulated (p < .05) proteins. No significant differences in protein expression were seen for the remaining 59 proteins (p > .05). Most proteins with differences in expression were related to immune/inflammatory response. Neutrophil gelatinase-associated lipocalin, Plastin-2, Lactotransferrin and 13 isoforms of immunoglobulins were upregulated. In contrast, Protein S100-A8, Protein S100-A9, Histone H2B, Neutrophil defensin 1, Neutrophil defensin 3 and Prolactin-inducible protein were downregulated.

CONCLUSIONS

Quantitative differences were demonstrated in the expression of proteins common to diabetic and control groups, mainly related to immune response, oxidative stress, apoptosis and proteolysis. These findings revealed biological pathways that provide the basis to support clinical findings on the relationship between AP and T2DM.

Application of Proteomics in Apical Periodontitis

Apical periodontitis is an inflammatory reaction of the periradicular tissues as a consequence of multispecies microbial communities organized as biofilms within the root canal system. Periradicular tissue changes at the molecular level initiate and orchestrate the inflammatory process and precede the presentation of clinical symptoms. Inflammatory mediators have been studied at either the proteomic, metabolomic, or transcriptomic levels. Analysis at the protein level is the most common approach used to identify and quantify analytes from diseased periradicular tissues during root canal treatment, since it is more representative of definitive and active periradicular inflammatory mediator than its transcript expression level. In disease, proteins expressed in an altered manner could be utilized as biomarkers. Biomarker proteins in periradicular tissues have been qualitatively and quantitatively assessed using antibodies (immunoassays and immunostaining) or mass spectrometry-based approaches. Herein, we aim to provide a comprehensive understanding of biomarker proteins identified in clinical studies investigating periradicular lesions and pulp tissue associated with apical periodontitis using proteomics. The high throughput mass spectrometry-based proteomics has the potential to improve the current methods of monitoring inflammation while distinguishing between progressive, stable, and healing lesions for the identification of new diagnostic and therapeutic targets. This method would provide more objective tools to (a) discover biomarkers related to biological processes for better clinical case selection, and (b) determine tissue response to novel therapeutic interventions for more predictable outcomes in endodontic treatment.

Microbiological Aspects of Root Canal Infections and Disinfection Strategies: An Update Review on the Current Knowledge and Challenges

The oral cavity is the habitat of several hundreds of microbial taxa that have evolved to coexist in multispecies communities in this unique ecosystem. By contrast, the internal tissue of the tooth, i.e., the dental pulp, is a physiologically sterile connective tissue in which any microbial invasion is a pathological sign. It results in inflammation of the pulp tissue and eventually to pulp death and spread of inflammation/infection to the periradicular tissues. Over the past few decades, substantial emphasis has been placed on understanding the pathobiology of root canal infections, including the microbial composition, biofilm biology and host responses to infections. To develop clinically effective treatment regimens as well as preventive therapies, such extensive understanding is necessary. Rather surprisingly, despite the definitive realization that root canal infections are biofilm mediated, clinical strategies have been focused more on preparing canals to radiographically impeccable levels, while much is left desired on the debridement of these complex root canal systems. Hence, solely focusing on "canal shaping" largely misses the point of endodontic treatment as the current understanding of the microbial aetiopathogenesis of apical periodontitis calls for the emphasis to be placed on "canal cleaning" and chemo-mechanical disinfection. In this review, we dissect in great detail, the current knowledge on the root canal microbiome, both in terms of its composition and functional characteristics. We also describe the challenges in root canal disinfection and the novel strategies that attempt to address this challenge. Finally, we provide some critical pointers for areas of future research, which will serve as an important area for consideration in Frontiers in Oral Health.

Present status and future directions - microbiology of endodontic infections

Apical periodontitis has a microbial aetiology and is one of the most common inflammatory diseases that affect humans. Fungi, archaea and viruses have been found in association with apical periodontitis, but bacteria are by far the most prevalent and dominant microorganisms in endodontic infections. Bacterial infection of the root canal system only occurs when the pulp is necrotic or was removed for previous treatment. In some specific cases, including acute and chronic abscesses, the bacterial infection may reach the periradicular tissues. Intracanal bacteria are usually observed as sessile multispecies communities (biofilms) attached to the dentinal root canal walls. Infection in the main root canal lumen can spread to other areas of the root canal system. Although more than 500 bacterial species have been detected in endodontic infections, a selected group of 20 to 30 species are most frequently detected and may be considered as the core microbiome. There is a high interindividual variability in the endodontic microbiome in terms of species composition and relative abundance. Obligate anaerobic species are more abundant in the intraradicular bacterial communities of teeth with primary apical periodontitis, while both anaerobes and facultatives dominate the communities in post-treatment apical periodontitis. Bacterial interactions play an essential role in determining the overall virulence of the community, which has been regarded as the unit of pathogenicity of apical periodontitis. This article reviews the microbiologic aspects of endodontic infections and provides perspectives for future research and directions in the field.

A critical analysis of research methods and experimental models to study the root canal microbiome

Endodontic microbiology deals with the study of the microbial aetiology and pathogenesis of pulpal and periradicular inflammatory diseases. Research in endodontic microbiology started almost 130 years ago and since then has mostly focussed on establishing and confirming the infectious aetiology of apical periodontitis, identifying the microbial species associated with the different types of endodontic infections and determining the efficacy of treatment procedures in eradicating or controlling infection. Diverse analytical methods have been used over the years, each one with their own advantages and limitations. In this review, the main features and applications of the most used technologies are discussed, and advice is provided to improve study designs in order to properly address the scientific questions and avoid setbacks that can compromise the results. Finally, areas of future research are described.

Quantitative proteomic analysis in symptomatic and asymptomatic apical periodontitis

AIM

To quantitatively and qualitatively compare the host proteomic profile in samples of symptomatic and asymptomatic apical periodontitis (AP) using nano-liquid chromatography-electron spray tandem mass spectrometry.

METHODOLOGY

Samples were obtained from 18 patients with radiographically evident AP, divided into symptomatic and asymptomatic groups (nine per group) according to clinical characteristics. After sample collection, protein extraction, purification and quantification of the samples were performed, which were analysed by reverse-phase liquid chromatography coupled to mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in expression of proteins between the groups were calculated using the Monte Carlo algorithm, considering P < 0.05 for down-regulated proteins and 1 - P > 0.95 for up-regulated proteins. Proteins were identified with the embedded ion accounting algorithm in the software and a search of the Homo sapiens UniProt database.

RESULTS

A total of 853 individual human proteins were identified. In the quantitative analysis, common proteins to both groups accounted for 143 proteins. Differences in expression between groups resulted in 51 up-regulated proteins (1 - P > 0.95) in the symptomatic group, including alpha-1-antitrypsin, protein S100-A8, myeloperoxidase, peroxiredoxin and lactotransferrin. This group also had 43 down-regulated proteins (P < 0.05), comprising immunoglobulin, neutrophil defensin, pyruvate kinase and alpha-enolase. The qualitative analysis considered only the exclusive proteins of each group. For the symptomatic group, 318 complete proteins and 29 fragments were identified, such as dedicator of cytokinesis protein, intersectin, prostaglandin, phospholipase DDHD2 and superoxide dismutase. For the asymptomatic group, 326 complete proteins and 37 fragments were identified, including azurocidin, C-reactive protein, collagen alpha, cathepsin, heat shock and laminin.

CONCLUSIONS

Quantitative differences in the expression of common proteins in cases of symptomatic and asymptomatic AP were found, which were mostly related to host immune response in both groups. Exclusive proteins in the symptomatic group were mainly related to the host response to the presence of viruses in endodontic infections, oxidative stress and proteolytic enzymes. The results provide a basis for a better understanding of cellular and molecular pathways involved in AP, establishing specific proteomic profiles for symptomatic and asymptomatic conditions.

Pathogenic potential of Enterococcus faecalis strains isolated from root canals after unsuccessful endodontic treatment

OBJECTIVES

To evaluate strains of Enterococcus faecalis isolated from endodontic failures cases for (a) presence of virulence genes, namely, gelatinase production (gelE), surface protein (esp), collagen-binding adhesin (ace), cytolysin activator (cylA), E. faecalis antigen A (efaA) and aggregation substance (asa), all by using PCR; (b) biofilm formation capacity; and (c) activity of gelatinase and β-lactamase.

MATERIALS AND METHODS

Twenty-five strains of E. faecalis were tested. The DNA extracted from these strains was used for identification of virulence genes by PCR and 1% agarose gel. Biofilm formation was performed on polystyrene microplates by using the violet crystal staining method. For assessment of the gelatinase activity, inoculum of pure cultures was deposited in tubes containing gelatin and a nutrient broth, whereas nitrocefin disks were used to assess the β-lactamase action.

RESULTS

The virulence genes efaA and cylA were detected in 100% of the strains, whereas gelE was present in 84%, ace in 68%, esp in 56% and asa in 48%. Four strains had no biofilm formation, 17 had poor formation and four had moderate formation. Gelatinase production was observed in three strains and β-lactamase resistance in five strains of E. faecalis.

TOPIC

Diverse patterns of virulence gene detection were observed among the E. faecalis strains, with predominance of those capable of forming biofilm. A few strains have been found to hydrolyze gelatin proteins, whereas β-lactamase resistance was detected in different isolates.

CLINICAL RELEVANCE

To understand the influence of virulence factors in E. faecalis on the host heath status.

Phenotypic and Genotypic Characterization of Streptococcus mutans Strains Isolated from Endodontic Infections

Streptococcus mutans plays an important role in caries etiology and eventually in systemic infections. However, it is often found in infected root canals, but the pathophysiological characteristics of strains residing in this site are largely unknown. Here, we characterized strains of S. mutans isolated from root canals of primary (PI) and secondary/persistent (SI) endodontic infections in relation to serotype and genotype; presence of genes coding for collagen binding proteins (CBPs); collagen binding activity and biofilm formation capacity; ability to withstand environmental stresses; systemic virulence in Galleria mellonella; and invasion of human coronary artery endothelial cells and human dental pupal fibroblasts. Samples from 10 patients with PI and 10 patients with SI were collected, and a total of 14 S. mutans isolates, belonging to 3 genotypes, were obtained. Of these, 13 were serotype c, and 1 was serotype k. When compared with the reference strains, the clinical isolates were hypersensitive to hydrogen peroxide. Remarkably, all 14 strains harbored and expressed the CBP-encoding gene cbm, showing increased binding to collagen, enhanced systemic virulence in G. mellonella, and ability to invade human coronary artery endothelial cells and human dental pupal fibroblasts when compared with CBP-negative strains. Whole genome sequence analysis of PI and SI isolates revealed that these strains are phylogenetically related but genetically distinct from each other. Our findings highlight the importance of CBPs in facilitating colonization and persistence of S. mutans in collagenous substrates such as root canals and their potential role in the pathogenesis of endodontic infections.

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.

Comparative Analysis of the Proteomic Profile of the Dental Pulp in Different Conditions. A Pilot Study

Abstract This study aimed to quantitatively compare the difference in protein expression in the progression of pulp pathogenesis, as well as to describe the biological functions of proteins identified in pulp tissue. Samples were obtained from six patients treated at the Araçatuba School of Dentistry and were divided into three groups: normal pulp - from teeth extracted for orthodontic indication; inflamed pulp and necrotic pulp - from patients diagnosed with irreversible pulpitis and chronic apical periodontitis, respectively. After previous proteomic preparation, dental pulp samples were processed for label-free quantitative proteomic analysis in a nanoACQUITY UPLC-Xevo QTof MS system. The difference in expression between the groups was calculated using the Protein Lynx Global Service software using the Monte Carlo algorithm. A total of 465 human proteins were identified in all groups. The most expressed proteins in the inflamed pulp group in relation to the normal pulp group were hemoglobin, peroxiredoxins and immunoglobulins, whereas the less expressed were the tubulins. Expression levels of albumins, immunoglobulins and alpha-2-macroglobulin were higher in the necrotic pulp group than in the inflamed pulp group. As for the qualitative analysis, the most prevalent protein functions in the normal pulp group were metabolic and energetic pathways; in the inflamed pulp group: cellular communication and signal transduction; and regulation and repair of DNA/RNA, while in the necrotic pulp group proteins were associated with the immune response. Thus, proteomic analysis showed quantitative and qualitative differences in protein expression in different types of pulp conditions.

Prevalence of the Genus Propionibacterium in Primary and Persistent Endodontic Lesions: A Systematic Review

Propionibacterium are anaerobic/aero-tolerant rod Gram-positive bacteria, and numerous studies are associated with primary and secondary endodontic infections. The data in the literature on the prevalence of Propionibacterium are conflicting, and there are studies that report conflicting data on the prevalence in primary and secondary endodontic infections. This review aims to clarify the prevalence of bacteria of the genus Propionibacterium in endodontic lesions. The present systematic review work was performed on the basis of the Prisma protocol. A search was carried out on the PubMed and Scopus databases with the use of keywords. The research produced 410 records, which, after the elimination of the overlaps and the application of the inclusion and exclusion criteria, led to a number of 36 included articles divided by the three outcomes. The first outcome concerns prevalence of bacteria of the genus Propionibacterium in primary and secondary endodontic lesions. The secondary outcome, differences in the prevalence of bacteria of the genus Propionibacterium between primary endodontic infections and secondary endodontic infections. The tertiary outcome, differences in the prevalence of Propionibacterium Acnes compared to Propionibacterium propionicum in endodontic infections. The results of the meta-analysis show that the genus Propionibacterium bacteria are more prevalent in secondary endodontic infections and that P. Acnes has a higher prevalence than P. propionicum.