The immune landscape in apical periodontitis: From mechanism to therapy.

Apical periodontitis (AP) is featured by a persistent inflammatory response and alveolar bone resorption initiated by microorganisms, posing risks to both dental and systemic health. Nonsurgical endodontic treatment is the recommended treatment plan for AP with a high success rate, but in some cases, periapical lesions may persist despite standard endodontic treatment. Better comprehension of the AP inflammatory microenvironment can help develop adjunct therapies to improve the outcome of endodontic treatment. This review presents an overview of the immune landscape in AP, elucidating how microbial invasion triggers host immune activation and shapes the inflammatory microenvironment, ultimately impacting bone homeostasis. The destructive effect of excessive immune activation on periapical tissues is emphasized. This review aimed to systematically discuss the immunological basis of AP, the inflammatory bone resorption and the immune cell network in AP, thereby providing insights into potential immunotherapeutic strategies such as targeted therapy, antioxidant therapy, adoptive cell therapy and cytokine therapy to mitigate AP-associated tissue destruction.

Gut microbiota changes in patients with Alzheimer's disease spectrum based on 16S rRNA sequencing: a systematic review and meta-analysis.

Background: The gut microbiota (GM) is hypothesized to play roles in Alzheimer's disease (AD) pathogenesis. In recent years, many GM composition and abundance investigations in AD patients have been conducted; however, despite this work, some results remain controversial. Therefore, we conducted a systematic review and meta-analysis using 16S ribosomal RNA (16S rRNA) sequencing to explore GM alterations between patients with AD spectrum and healthy controls (HCs). Methods: A systematic and comprehensive literature search of PubMed, Web of Science, Embase, the Cochrane Library, China National Knowledge Infrastructure, China Biology Medicine disc database, WanFang database and Social Sciences Citation Index databases was conducted from inception to January 2023. Inclusion and exclusion criteria were strictly defined, and two researchers independently screened and extracted information from selected studies. Data quality were evaluated according to the "Cochrane system evaluator manual" and pooled data were comprehensively analyzed using Stata 14 software with standardized mean differences (SMDs) and 95% confidence intervals (95% CIs) used to measure effect sizes. Also, geographical heterogeneity effects (related to cohorts) on GM abundance were examined based on subgroup meta-analyses if sufficient studies reported outcomes. Finally, publication bias was assessed using funnel plots. Results: Out of 1566 articles, 13 studies involving 581 patients with AD spectrum and 445 HCs were deemed eligible and included in our analysis. In summary, a decreased microbiota alpha diversity and a significantly distinct pattern of clustering with regard to beta diversity were observed in AD spectrum patients when compared with HCs. Comparative analyses revealed a decreased Ruminococcus, Faecalibacterium, Lachnospira, Dialister, Lachnoclostridium, and Roseburia abundance in AD spectrum patients while Phascolarctobacterium, Lactobacillus, and Akkermansia muciniphila were more enriched in patients when compared to HCs. Furthermore, regional variations may have been in play for intestinal microbes such as Bacteroides, Bifidobacterium, and Alistipes. Conclusion: Our meta-analysis identified alterations in GM abundance in patients with AD spectrum, with 12 genera from four major phyla significantly associated with AD. Moreover, we provided evidence for region-specific alterations in Bacteroides, Bifidobacterium, and Alistipes abundance. These findings may have profound implications for the development of innovative GM-based strategies to prevent and treat AD. Systematic review registration: https://doi.org/10.37766/inplasy2024.6.0067, identifier INPLASY202460067.

Interplay of RUNX2 and KLF4 in initial commitment of odontoblast differentiation.

Odontoblast differentiation is a key process in dentin formation. Mouse dental papilla cells (mDPCs) are pivotal in dentinogenesis through their differentiation into odontoblasts. Odontoblast differentiation is intricately controlled by transcription factors (TFs) in a spatiotemporal manner. Previous research explored the role of RUNX2 and KLF4 in odontoblast lineage commitment, respectively. Building on bioinformatics analysis of our previous ATAC-seq profiling, we hypothesized that KLF4 potentially collaborates with RUNX2 to exert its biological role. To investigate the synergistic effect of multiple TFs in odontoblastic differentiation, we first examined the spatiotemporal expression patterns of RUNX2 and KLF4 in dental papilla at the bell stage using immunostaining techniques. Notably, RUNX2 and KLF4 demonstrated colocalization in preodontoblast. Further, immunoprecipitation and proximity ligation assays verified the interaction between RUNX2 and KLF4 in vitro. Specifically, the C-terminus of RUNX2 was identified as the interacting domain with KLF4. Functional implications of this interaction were investigated using small hairpin RNA-mediated knockdown of Runx2, Klf4, or both. Western blot analysis revealed a marked decrease in DSPP expression, an odontoblast differentiation marker, particularly in the double knockdown condition. Additionally, alizarin red S staining indicated significantly reduced mineralized nodule formation in this group. Collectively, our findings highlight the synergistic interaction between RUNX2 and KLF4 in promoting odontoblast differentiation from mDPCs. This study contributes to a more comprehensive understanding of the regulatory network of TFs governing odontoblast differentiation.

A magnetic beads-based ligand fishing method Coupled with UHPLC-QTOF MS for screening and identification of α-glucosidase inhibitors from Houttuynia cordata Thunb.

In this study, a method for the screening and identification of α-glucosidase inhibitors from natural products was developed. The α-glucosidase was immobilized on carboxyl terminated magnetic beads to form a ligand fishing system to screen the potential inhibitors. A total of 9 compounds were fishing out from the crude Houttuynia cordata Thunb. extract. Meanwhile, ultra-high performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-QTOF MS) was used for the identification of the chemical structures, including 3 chlorogenic acid isomers, 2 flavone C-glycosides and 4 flavone O-glycosides. The combination of enzyme immobilization magnetic beads and UHPLC-QTOF MS could be used for the screening of bioactive multi-components from herbs with appropriate targets. Taking the advantage of the specificity of enzyme binding and the convenience of magnetic separation, the method has great potential for rapid screening of α-glucosidase inhibitors from complicated natural product extracts.

Sensitive label-free detection of the biomarker phosphorylated tau-217 protein in Alzheimer's disease using a graphene-based solution-gated field effect transistor.

Alzheimer's disease (AD) is generally diagnosed using advanced imaging, but recent research suggests early screening using biomarkers in peripheral blood is feasible; among them, plasma tau proteins phosphorylated at threonine 231, threonine 181, and threonine 217 (p-tau217) are potential targets. A recent study indicates that the p-tau217 protein is the most efficacious biomarker. However, a clinical study found a pg/ml threshold for AD screening beyond standard detection methods. A biosensor with high sensitivity and specificity p-tau217 detection has not yet been reported. In this study, we developed a label-free solution-gated field effect transistor (SGFET)-based biosensor featuring a graphene oxide/graphene (GO/G) layered composite. The top layer of bilayer graphene grown using chemical vapor deposition was functionalized with oxidative groups serving as active sites for forming covalent bonds with the biorecognition element (antibodies); the bottom G could act as a transducer to respond to the attachment of the target analytes onto the top GO conjugated with the biorecognition element via π-π interactions between the GO and G layers. With this unique atomically layered G composite, we obtained a good linear electrical response in the Dirac point shift to p-tau217 protein concentrations in the range of 10 fg/ml to 100 pg/ml. The biosensor exhibited a high sensitivity of 18.6 mV/decade with a high linearity of 0.991 in phosphate-buffered saline (PBS); in human serum albumin, it showed approximately 90% of the sensitivity (16.7 mV/decade) in PBS, demonstrating high specificity. High stability of the biosensor was also displayed in this study.

Phosphorylation of ATF2 promotes odontoblastic differentiation via intrinsic HAT activity.

Mouse dental papilla cells (mDPCs) are cranial neural crest-derived dental mesenchymal cells that give rise to dentin-secreting odontoblasts after the bell stage during odontogenesis. The odontoblastic differentiation of mDPCs is spatiotemporally regulated by transcription factors (TFs). Our previous work reveals that chromatin accessibility was correlated with the occupation of the basic leucine zipper TF family during odontoblastic differentiation. However, the detailed mechanism by which TFs regulate the initiation of odontoblastic differentiation remains elusive. Here, we report that phosphorylation of ATF2 (p-ATF2) is particularly increased during odontoblastic differentiation in vivo and in vitro. ATAC-seq and p-ATF2 CUT&Tag experiments further demonstrate a high correlation between p-ATF2 localization and increased chromatin accessibility of regions near mineralization-related genes. Knockdown of Atf2 inhibits the odontoblastic differentiation of mDPCs, while overexpression of p-ATF2 promotes odontoblastic differentiation. ATAC-seq after overexpression of p-ATF2 reveals that p-ATF2 increases the chromatin accessibility of regions adjacent to genes associated with matrix mineralization. Furthermore, we find that p-ATF2 physically interacts with and promotes H2BK12 acetylation. Taken together, our findings reveal a mechanism that p-ATF2 promotes odontoblastic differentiation at initiation via remodeling chromatin accessibility and emphasize the role of the phosphoswitch model of TFs in cell fate transitions.

Chromatin Accessibility Predetermines Odontoblast Terminal Differentiation.

Embryonic development and stem cell differentiation are orchestrated by changes in sequential binding of regulatory transcriptional factors to their motifs. These processes are invariably accompanied by the alternations in chromatin accessibility, conformation, and histone modification. Odontoblast lineage originates from cranial neural crest cells and is crucial in dentinogenesis. Our previous work revealed several transcription factors (TFs) that promote odontoblast differentiation. However, it remains elusive as to whether chromatin accessibility affects odontoblast terminal differentiation. Herein, integration of single-cell RNA-seq and bulk RNA-seq revealed that in vitro odontoblast differentiation using dental papilla cells at E18.5 was comparable to the crown odontoblast differentiation trajectory of OC (osteocalcin)-positive odontogenic lineage. Before in vitro odontoblast differentiation, ATAC-seq and H3K27Ac CUT and Tag experiments demonstrated high accessibility of chromatin regions adjacent to genes associated with odontogenic potential. However, following odontoblastic induction, regions near mineralization-related genes became accessible. Integration of RNA-seq and ATAC-seq results further revealed that the expression levels of these genes were correlated with the accessibility of nearby chromatin. Time-course ATAC-seq experiments further demonstrated that odontoblast terminal differentiation was correlated with the occupation of the basic region/leucine zipper motif (bZIP) TF family, whereby we validated the positive role of ATF5 in vitro. Collectively, this study reports a global mapping of open chromatin regulatory elements during dentinogenesis and illustrates how these regions are regulated via dynamic binding of different TF families, resulting in odontoblast terminal differentiation. The findings also shed light on understanding the genetic regulation of dentin regeneration using dental mesenchymal stem cells.

Epigallocatechin-3-Gallate Promotes Osteo-/Odontogenic Differentiation of Stem Cells from the Apical Papilla through Activating the BMP-Smad Signaling Pathway.

Stem cells from apical papilla (SCAPs) are desirable sources of dentin regeneration. Epigallocatechin-3-gallate (EGCG), a natural component of green tea, shows potential in promoting the osteogenic differentiation of bone mesenchymal stem cells. However, whether EGCG regulates the odontogenic differentiation of SCAPs and how this occurs remain unknown. SCAPs from immature human third molars (16-20 years, n = 5) were treated with a medium containing different concentrations of EGCG or bone morphogenic protein 2 (BMP2), with or without LDN193189 (an inhibitor of the canonical BMP pathway). Cell proliferation and migration were analyzed using a CCK-8 assay and wound-healing assay, respectively. Osteo-/odontogenic differentiation was evaluated via alkaline phosphatase staining, alizarin red S staining, and the expression of osteo-/odontogenic markers using qPCR and Western blotting. We found that EGCG (1 or 10 µM) promoted the proliferation of SCAPs, increased alkaline phosphatase activity and mineral deposition, and upregulated the expression of osteo-/odontogenic markers including dentin sialophosphoprotein (Dspp), dentin matrix protein-1 (Dmp-1), bone sialoprotein (Bsp), and Type I collagen (Col1), along with the elevated expression of BMP2 and phosphorylation level of Smad1/5/9 (p < 0.01). EGCG at concentrations below 10 µM had no significant influence on cell migration. Moreover, EGCG-induced osteo-/odontogenic differentiation was significantly attenuated via LDN193189 treatment (p < 0.01). Furthermore, EGCG showed the ability to promote mineralization comparable with that of recombinant BMP2. Our study demonstrated that EGCG promotes the osteo-/odontogenic differentiation of SCAPs through the BMP-Smad signaling pathway.

BMP2-dependent gene regulatory network analysis reveals Klf4 as a novel transcription factor of osteoblast differentiation.

Transcription factors (TFs) regulate the expression of target genes, inducing changes in cell morphology or activities needed for cell fate determination and differentiation. The BMP signaling pathway is widely regarded as one of the most important pathways in vertebrate skeletal biology, of which BMP2 is a potent inducer, governing the osteoblast differentiation of bone marrow stromal cells (BMSCs). However, the mechanism by which BMP2 initiates its downstream transcription factor cascade and determines the direction of differentiation remains largely unknown. In this study, we used RNA-seq, ATAC-seq, and animal models to characterize the BMP2-dependent gene regulatory network governing osteoblast lineage commitment. Sp7-Cre; Bmp2fx/fx mice (BMP2-cKO) were generated and exhibited decreased bone density and lower osteoblast number (n > 6). In vitro experiments showed that BMP2-cKO mouse bone marrow stromal cells (mBMSCs) had an impact on osteoblast differentiation and deficient cell proliferation. Osteogenic medium induced mBMSCs from BMP2-cKO mice and control were subjected to RNA-seq and ATAC-seq analysis to reveal differentially expressed TFs, along with their target open chromatin regions. Combined with H3K27Ac CUT&Tag during osteoblast differentiation, we identified 2338 BMP2-dependent osteoblast-specific active enhancers. Motif enrichment assay revealed that over 80% of these elements were directly targeted by RUNX2, DLX5, MEF2C, OASIS, and KLF4. We deactivated Klf4 in the Sp7 + lineage to validate the role of KLF4 in osteoblast differentiation of mBMSCs. Compared to the wild-type, Sp7-Cre; Klf4fx/+ mice (KLF4-Het) were smaller in size and had abnormal incisors resembling BMP2-cKO mice. Additionally, KLF4-Het mice had fewer osteoblasts and decreased osteogenic ability. RNA-seq and ATAC-seq revealed that KLF4 mainly "co-bound" with RUNX2 to regulate downstream genes. Given the significant overlap between KLF4- and BMP2-dependent NFRs and enriched motifs, our findings outline a comprehensive BMP2-dependent gene regulatory network specifically governing osteoblast differentiation of the Sp7 + lineage, in which Klf4 is a novel transcription factor.

SALL1 regulates commitment of odontoblast lineages by interacting with RUNX2 to remodel open chromatin regions.

Mouse dental papilla cells (mDPCs) derive from cranial neural crest cells and maintain mesenchymal stem cell characteristics. The differentiation of neural crest cells into odontoblasts is orchestrated by transcription factors regulating the expression of genes whose enhancers are initially inaccessible. However, the identity of the transcription factors driving the emergence of odontoblast lineages remains elusive. In this study, we identified SALL1, a transcription factor that was particularly expressed in preodontoblasts, polarizing odontoblasts, and secretory odontoblasts in vivo. Knockdown of Sall1 in mDPCs inhibited their odontoblastic differentiation. In order to identify the regulatory network of Sall1, RNA sequencing and an assay for transposase-accessible chromatin with high-throughput sequencing were performed to analyze the genome-wide direct regulatory targets of SALL1. We found that inhibition of Sall1 expression could decrease the accessibility of some chromatin regions associated with odontoblast lineages at embryonic day 16.5, whereas these regions remained unaffected at postnatal day 0.5, suggesting that SALL1 regulates the fate of mDPCs by remodeling open chromatin regions at the early bell stage. Specifically, we found that SALL1 could directly increase the accessibility of cis-regulatory elements near Tgf-ß2 and within the Runx2 locus. Moreover, coimmunoprecipitation and proximal ligation assays showed that SALL1 could establish functional interactions with RUNX2. Taken together, our results demonstrated that SALL1 positively regulates the commitment of odontoblast lineages by interacting with RUNX2 and directly activating Tgf-ß2 at an early stage.

RUNX2 co-operates with EGR1 to regulate osteogenic differentiation through Htra1 enhancers.

Runt-related transcription factor 2 (Runx2) has been shown to regulate osteoblast differentiation by directly or indirectly regulating numerous osteoblast-related genes. However, our understanding of the transcriptional mechanisms of RUNX2 is mainly restricted to its transactivation, while the mechanism underlying its inhibitory effect during osteoblast differentiation remains largely unknown. Here, we incorporated the anti-RUNX2 chromatin immunoprecipitation (ChIP) sequencing in MC3T3-E1 cells and RNA-sequencing of parietal bone from Runx2 heterozygous mutant mice, to identify the putative genes negatively regulated by RUNX2. We identified HtrA serine peptidase 1 (Htra1) as a target gene and found ten candidate Htra1 enhancers potentially regulated by RUNX2, among which seven were verified by dual-luciferase assays. Furthermore, we investigated the motifs in the vicinity of RUNX2-binding sites and identified early growth response 1 (EGR1) as a potential partner transcription factor (TF) potentially regulating Htra1 expression, which was subsequently confirmed by Re-ChIP assays. RUNX2 and EGR1 co-repressed Htra1 and increased the expression levels of other osteoblast marker genes, such as osterix, osteocalcin, and osteoprotegerin at the messenger RNA and protein level. Moreover, Alizarin red staining combined with alkaline phosphatase (ALP) staining showed decreased calcified nodules and ALP activity in the siRUNX2+siEGR1 group compared with siRUNX2 group. Our findings revealed the detailed mechanism of the inhibitory function of RUNX2 towards its downstream genes, along with its partner TFs, to promote osteoblast differentiation.

Coordinated expression of p300 and HDAC3 upregulates histone acetylation during dentinogenesis.

Cellular differentiation is caused by highly controlled modifications in the gene expression but rarely involves a change in the DNA sequence itself. Histone acetylation is a major epigenetic factor that adds an acetyl group to histone proteins, thus altering their interaction with DNA and nuclear proteins. Illumination of the histone acetylation during dentinogenesis is important for odontoblast differentiation and dentinogenesis. In the current study, we aimed to discover the roles and regulation of acetylation at histone 3 lysine 9 (H3K9ac) and H3K27ac during dentinogenesis. We first found that both of these modifications were enhanced during odontoblast differentiation and dentinogenesis. These modifications are dynamically catalyzed by histone acetyltransferases (HATs) and deacetylases (HDACs), among which HDAC3 was decreased while p300 increased during odontoblast differentiation. Moreover, overexpression of HDAC3 or knockdown p300 inhibited odontoblast differentiation in vitro, and inhibition of HDAC3 and p300 with trichostatin A or C646 regulated odontoblast differentiation. Taken together, the results of our present study suggest that histone acetylation is involved in dentinogenesis and coordinated expression of p300- and HDAC3-regulated odontoblast differentiation through upregulating histone acetylation.

Structural and Fluorine Plasma Etching Behavior of Sputter-Deposition Yttrium Fluoride Film.

Yttrium fluoride (YF3) films were grown on sapphire substrate by a radio frequency magnetron using a commercial ceramic target in a vacuum chamber. The structure, composition, and plasma etching behavior of the films were systematically investigated. The YF3 film was deposited at a working pressure of 5 mTorr and an RF power of 150 W. The substrate-heating temperature was increased from 400 to 700 °C in increments of 100 °C. High-resolution transmission electron microscopy (HRTEM) and X-ray diffraction results confirmed an orthorhombic YF3 structure was obtained at a substrate temperature of 700 °C for 2 h. X-ray photoelectron spectroscopy revealed a strongly fluorinated bond (Y⁻F bond) on the etched surface of the YF3 films. HRTEM analysis also revealed that the YF3 films became yttrium-oxyfluorinated after exposure to fluorocarbon plasma. The etching depth was three times lower on YF3 film than on Al2O3 plate. These results showed that the YF3 films have excellent erosion resistance properties compared to Al2O3 plates.

miR-3065-5p regulates mouse odontoblastic differentiation partially through bone morphogenetic protein receptor type II.

Illumination of the molecular mechanisms regulating odontoblastic differentiation of dental papilla cells is of great significance for proper dentinogenesis and dental pulp regeneration. In this study, we discovered that microRNA (miR)-3065-5p is up-regulated during odontoblastic differentiation. Overexpression of miR-3065-5p promoted odontoblastic differentiation in vitro. Dual luciferase report assay verified that miR-3065-5p could bind to the 3'UTR of bone morphogenetic protein receptor type II (BMPR2), which dramatically increased in the beginning of odontoblastic differentiation but decreased in the terminal differentiation stage. Inhibition of Bmpr2 in the early stage retarded odontoblastic differentiation while knockdown of Bmpr2 in the terminal stage enhanced odontoblastic differentiation, resembling the effect of miR-3065-5p. Taken together, our present study suggests that miR-3065-5p positively regulates odontoblastic differentiation by directly binding to Bmpr2 in the terminal differentiation stage.