Human Exoproteome in Acute Apical Abscesses

The Hidden World Within: Microbial Dynamics in Root Canal Systems

Several hundred different microbial taxa have made the oral cavity their home because of their evolution in multiple species communities within the special ecosystem. On the other hand, the dental pulp or internal tissue of the tooth is a connective tissue that is physiologically sterile and where any microbial infiltration is a harmful indication. It causes the pulp tissue to become inflamed, which leads to the death of the pulp and diffuses infection with inflammation to the peri-radicular tissues. Comprehending the biology of biofilms, the microbial makeup, and the host's reaction to infections in the pathobiology of root canal infections has received a lot of attention throughout the last few decades. Such comprehensive knowledge is required to design preventive medicines as well as clinically effective treatment regimens. Surprisingly, clinical approaches have concentrated more on radiographically perfecting channel preparation than on debridement of these intricate root canal systems, despite the clear realization that root canal infections are biofilm mediated. Since the present comprehension of the microbial etiopathogenesis of apical periodontitis highlights the significance of focusing on procedures such as "canal cleaning" and chemo-mechanical disinfection, the exclusive purpose of endodontic therapy is mainly missed while discussing "canal shaping." We thoroughly examine the state of our knowledge of the composition and functional traits of the root canal microbiome in this review. We also go into the difficulties with root canal disinfection and the cutting-edge approaches that try to solve these difficulties. In conclusion, we present essential guidance for prospective research areas, underscoring their significance as crucial considerations in the field of frontiers in oral health.

Ferroptosis of macrophages facilitates bone loss in apical periodontitis via NRF2/FSP1/ROS pathway

Apical periodontitis (AP) is an infectious disease that causes periapical tissue inflammation and bone destruction. Ferroptosis, a novel type of regulated cell death, is closely associated with inflammatory diseases and the regulation of bone homeostasis. However, the exact involvement of ferroptosis in the bone loss of AP is not fully understood. In this study, human periapical tissues were collected, and a mouse model was established to investigate the role of ferroptosis in AP. Colocalization staining revealed that ferroptosis in macrophages contributes to the inflammatory bone loss associated with AP. A cell model was constructed using RAW 264.7 cells stimulated with LPS to further explore the mechanism underlying ferroptosis in macrophages upon inflammatory conditions, which exhibited ferroptotic characteristics. Moreover, downregulation of NRF2 was observed in ferroptotic macrophages, while overexpression of NRF2 upregulated the level of FSP1, leading to a reduction in reactive oxygen species (ROS) in macrophages. Additionally, ferroptotic macrophages released TNF-α, which activated the p38 MAPK signaling pathway and further increased ROS accumulation in macrophages. In vitro co-culture experiments demonstrated that the osteogenic ability of mouse bone marrow stromal cells (BMSCs) was suppressed with the stimulation of TNF-α from ferroptotic macrophages. These findings suggest that the TNF-α autocrine-paracrine loop in ferroptotic macrophages can inhibit osteogenesis in BMSCs through the NRF2/FSP1/ROS signaling pathway, leading to bone loss in AP. This study highlights the potential therapeutic value of targeting ferroptosis in the treatment of inflammatory bone diseases.

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.

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.

The multifaceted roles of antimicrobial peptides in oral diseases

Antimicrobial peptides are naturally occurring protein molecules with antibacterial, antiviral and/or antifungal activity. Some antimicrobial peptides kill microorganisms through direct binding with negatively charged microbial surfaces. This action disrupts the cytoplasmic membrane and leads to the leakage of the cytoplasm. In addition, they are involved in the innate immune response. Antimicrobial peptides play an important role in oral health, as natural antimicrobial peptides are the first line of host defence in response to microbial infection. The level of natural antimicrobial peptides increases during severe disease conditions and play a role in promoting the healing of oral tissues. However, they are insufficient for eliminating pathogenic micro-organisms. The variability of the oral environment can markedly reduce the effect of natural antimicrobial peptides. Thus, researchers are developing synthetic antimicrobial peptides with promising stability and biocompatibility. Synthetic antimicrobial peptides are a potential alternative to traditional antimicrobial therapy. Pertinent to oral diseases, the deregulation of antimicrobial peptides is involved in the pathogenesis of dental caries, periodontal disease, mucosal disease and oral cancer, where they can kill pathogenic microorganisms, promote tissue healing, serve as biomarkers and inhibit tumor cells. This narrative review provides an overview of the multifaceted roles of antimicrobial peptides in oral diseases.

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.

Proteomic analysis of human dental pulp in different clinical diagnosis

OBJECTIVES

The present study aimed to identify proteins obtained from pulp tissue and correlate with each clinical diagnosis (healthy pulp, inflamed pulp, and necrotic pulp).

MATERIALS AND METHODS

A total of forty-five molars were used. Three biological replicas were evaluated. Lysis and sonication were used for protein extraction. Protein quantification was assessed by using the Bradford technique, and shotgun proteome analysis was performed by nanoUPLC-MS^E using a Synapt G2 mass spectrometer. Mass spectra data were processed using the Waters PLGS software, and protein identification was done using the human Uniprot database appended to the PLGS search engine.

RESULTS

A total of 123 different proteins were identified in all evaluated pulp conditions. Among these, 66 proteins were observed for healthy pulp, 66 for inflamed pulp, and 91 for necrotic pulp. Most protein identification was related to immune response, multi-organism process, platelet activation, and stress in inflamed pulp samples compared to healthy pulp. Proteins related to cellular component organization or biogenesis, developmental process, growth, immune response, multi-organism process, response to stimulus, signaling, stress, and transport were identified in cases of apical periodontitis compared to inflamed pulp.

CONCLUSIONS

The progression of the disease to inflamed pulp promoted a high abundance of proteins related to the immune system and stress. Comparing the necrotic pulp with inflamed pulp conditions, a high abundance of proteins was noticed related to metabolism, transport, and response between organisms.

CLINICAL RELEVANCE

This finding may assist in future studies of new markers, understanding of tissue engineering, and development of future products.

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.