Molecular mechanisms linking peri-implantitis and type 2 diabetes mellitus revealed by transcriptomic analysis

Is 26S proteasome non-ATPase regulatory subunit 6 a potential molecular target for intrahepatic cholangiocarcinoma?

In this editorial we comment on the article by Tang et al published in the recent issue of World Journal of Hepatology. Drug therapy of intrahepatic cholangiocarcinoma (iCCA) poses an enormous challenge since only a small proportion of patients demonstrate beneficial responses to therapeutic agents. Thus, there has been a sustained search for novel molecular targets for iCCA. The study by Tang et al evaluated the role of 26S proteasome non-ATPase regulatory subunit 6 (PSMD6), a 19S regulatory subunit of the proteasome, in human iCCA cells and specimens. The authors employed clustered regularly interspaced short palindromic repeat (CRISPR) knockout screening technology integrated with the computational CERES algorithm, and analyzed the human protein atlas (THPA) database and tissue microarrays. The results show that PSMD6 is a gene essential for the proliferation of 17 iCCA cell lines, and PSMD6 protein was overexpressed in iCCA tissues without a significant correlation with the clinicopathological parameters. The authors conclude that PSMD6 may play a promoting role in iCCA. The major limitations and defects of this study are the lack of detailed information of CRISPR knockout screening, in vivo experiments, and a discussion of plausible mechanistic cues, which, therefore, dampen the significance of the results. Further studies are required to verify PSMD6 as a molecular target for developing novel therapeutics for iCCA. In addition, the editorial article summarizes the latest advances in molecular targeted drugs and recently emerging immunotherapy in the clinical management of iCCA, development of proteasome inhibitors for cancer therapy, and advantages of CRISPR screening technology, computational methods, and THPA database as experimental tools for fighting cancer. We hope that these comments may provide some clues for those engaged in the field of basic and clinical research into iCCA.

Naringin and temozolomide combination suppressed the growth of glioblastoma cells by promoting cell apoptosis: network pharmacology, in-vitro assays and metabolomics based study

Introduction: Glioblastoma, which affects a large number of patients every year and has an average overall lifespan of around 14.6 months following diagnosis stands out as the most lethal primary invasive brain tumor. Currently, surgery, radiation, and chemotherapy with temozolomide (TMZ) are the three major clinical treatment approaches. However, the ability to treat patients effectively is usually limited by TMZ resistance. Naringin, a bioflavonoid with anti-cancer, antioxidant, metal-chelating, and lipid-lowering effects, has emerged as a promising therapeutic option. Methods: To explore the targets and pathways of naringin and TMZ in glioblastoma network pharmacology, cell line-based ELISA, flow cytometry, immunocytochemistry, western blotting, and LC-HRMS based metabolomics study were used. Results: The findings through the network pharmacology suggested that the key targets of naringin in the chemosensitization of glioblastoma would be Poly [ADP-ribose] polymerase 1 (PARP-1), O-6-Methylguanine-DNA Methyltransferase (MGMT), and caspases. The functional enrichment analysis revealed that these targets were significantly enriched in important pathways such as p53 signaling, apoptosis, and DNA sensing. Further, the results of the in-vitro study in U87-MG and T98-G glioblastoma cells demonstrated that TMZ and naringin together significantly reduced the percentage of viability and inhibited the DNA repair enzymes PARP-1 and MGMT, and PI3K/AKT which led to chemosensitization and, in turn, induced apoptosis, which was indicated by increased p53, caspase-3 expression and decreased Bcl2 expression. Additionally, a metabolomics study in T98-G glioblastoma cells using liquid chromatography high-resolution mass spectrometry (LC-HRMS) revealed downregulation of C8-Carnitine (-2.79), L-Hexanoylcarnitine (-4.46), DL-Carnitine (-2.46), Acetyl-L-carnitine (-3.12), Adenine (-1.3), Choline (-2.07), Propionylcarnitine (-1.69), Creatine (-1.33), Adenosine (-0.84), Spermine (-1.42), and upregulation of Palmitic Acid (+1.03) and Sphingosine (+0.89) in the naringin and TMZ treatment groups. Discussion: In conclusion, it can be said that naringin in combination with TMZ chemosensitized TMZ antiglioma response and induced apoptosis in tumor cells.

Effectiveness of two photosensitizer-mediated photodynamic therapy for treating moderate peri-implant infections in type-II diabetes mellitus patients: A randomized clinical trial

PURPOSE

This study evaluated the impact of Fox Green (FG) against methylthioninium chloride (MTC)-facilitated photodynamic therapy (PDT) as an adjunctive to manual scaling (MS) on the peri‑implant clinical and cytokine parameters in type-2 diabetes mellitus (DM) patients with peri‑implantitis.

METHODS

Patients were divided into group-A comprising 13 patients who received adjunctive FG-PDT using a diode laser (wavelength: 810 nm; irradiation power: 300 mW; irradiation time: 30 s; fluence: 56 Jcm-2), group-B comprising 12 patients who received adjunctive MTC-PDT using a diode laser (wavelength: 660 nm; irradiation power: 100 mW; irradiation time: 120 s/site; fluence: 30 Jcm-2), and group-C comprising 13 patients who received MS alone [control group]). After diagnosing the diabetics with peri‑implantitis (established on eligibility criteria), a structured questionnaire was used to gather the information of the participants. Plaque (PS) and bleeding scores (BS), along with peri‑implant probing scores (PPS) and peri‑implant bone loss (PIBL), together with immunological variables (interleukin [IL]-6, tumor necrosis factor-alpha [TNF-α], and advanced glycation end products [AGEs]) were measured in all study group participants at baseline, 3-month, and 6-month follow-ups.

RESULTS

A significant reduction was observed for PS, BS, and PPS within all tested groups at each follow-up visits compared from their baseline values (p<0.05). However, a substantial decrease in PIBL was observed in all study group patients at 6-month follow-up as compared to 3-month follow-up (p<0.05). Regarding the levels of IL-6 and TNF-α, a substantial reduction was observed in all study groups until 6-month from their baseline scores (p<0.05). However, no changes were observed in the levels of AGEs in any group at either visit (p>0.05).

CONCLUSION

In DM patients with periimplantitis, adjunctive FG-PDT and MTC-PDT exhibited comparable outcomes in terms of peri‑implant clinical as well as pro-inflammatory characteristics than MS alone among peri‑implantitis patients with DM.

Current Molecular, Cellular and Genetic Aspects of Peri-Implantitis Disease: A Narrative Review

(1) Background: Peri-implantitis is a multi-factorial disease with an inflammatory background that occurs in both soft and hard tissues surrounding implants. In recent years, the understanding of the cellular, molecular and genetic background of peri-implantitis has broadened. This study aims to summarize the currently available articles on the subject and highlight the most recent advances over the last 20 years. (2) Methods: For this study, the Embase and PubMed libraries were searched using the keywords: ("peri-implantitis" AND "cytokine" OR "genetics" OR "cellular") and ("peri-implantitis" AND "cytokine" OR "genetics" OR "cellular" AND "risk factors"). The search revealed a total of 3013 articles (992 from PubMed, 2021 from Embase). Following screening of the titles and abstracts and full-text reads, 55 articles were included. (3) Results: In peri-implantitis IL-6, IL-1β, TNF-α, MMP-8 and their genetic variations appear to be the most important cytokines in relation to not only pathogenesis, but also their potential diagnostic capabilities. Epithelial and inflammatory cells, along with those of the bone lineage, are prime cellular elements found in peri-implantitis. (4) Conclusions: A wide array of cells stand behind peri-implantitis, as well as cytokines and their genetic variations that take part in the process. However, the growing interest in this topic has led to the introduction of specific new diagnostic tools to enable a better understanding of patients' responses to treatment and, in turn, to even enable prediction of the risk of developing peri-implant disease.

Chloro-aluminum phthalocyanine-mediated photodynamic therapy improves peri-implant parameters and crevicular fluid cytokine levels in cigarette smokers with chronic hyperglycemia

PURPOSE

This clinical trial aimed to evaluate the effectiveness of chloroaluminum phthalocyanine-mediated photodynamic therapy (CAPC-PDT) as an adjunct to peri-implant mechanical debridement (PID) in the treatment of peri-implantitis in patients with chronic hyperglycemia and cigarette smoking.

METHODS

The selected participants with peri-implantitis were divided into two groups: Group I (n=15) included hyperglycemic patients with no history of smoking and Group II (n=15) included hyperglycemic patients with a history of smoking cigarettes. Both groups were further divided into two subgroups based on the type of therapy provided: PDT+PID and PID alone. Peri-implant bleeding on probing (PiBOP), peri-implant pocket depth (PiPD), peri-implant plaque scores (PiPS), and crestal bone loss (CBL) were assessed. Peri-implant crevicular fluid (PICF) was sampled for quantification of interleukin (IL)-1β and tumor necrosis factor-alpha (TNF-α) using an enzyme-linked immunosorbent assay. All assessments were performed at baseline and at three and six months.

RESULTS

PDT+PID showed a higher reduction in PiBOP than PID alone in hyperglycemic/non-smoking participants (p<0.01). PDT+PID and PID show a significant reduction in PiBOP in smokers only at 6 months (p<0.05), with comparable differences between PDT+PID and PID (p>0.05). PDT+PID significantly reduced PiPD hyperglycemic/smoking patients at 3 and 6 months (p<0.05), whereas PID only produced a significant reduction in PiPD at 6 months in smoking patients (p<0.05). CBL alone with PDT+PID in both smokers and non-smokers showed a statistically significant reduction at 6 months follow-up (p<0.05). IL-1β was significantly reduced in hyperglycemic/non-smoking participants at 6 months follow-up with both PDT+PID and PID alone (p<0.01). This trend was also observed in cigarette smokers, with an additional short-term reduction in IL-1β at 3 months with PDT+PID (p<0.05). Only the PDT+PID group showed a significant reduction in TNF-a among cigarette smoking patients with chronic hyperglycemia at 6 months follow-up (p<0.05) CONCLUSION: Chloroaluminum phthalocyanine-mediated PDT proved effective in improving peri-implant clinical outcomes and reducing cytokine levels in smoking patients with chronic hyperglycemia.

Impact of local predisposing/precipitating factors and systemic drivers on peri‐implant diseases

BACKGROUND

Strong evidence suggests the infectious nature of peri-implant diseases occurring in susceptible hosts. Epidemiological reports, though, indicate that peri-implantitis is a site-specific entity. Hence, the significance of local factors that may predispose/precipitate plaque accumulation and the impact of systemic drivers that alter the immune response are relevant in the prevention and management of peri-implant disorders.

PURPOSE

The purpose of the present review is to shed light on the significance of local and systemic factors on peri-implant diseases, making special emphasis on the associations with peri-implantitis.

METHODS

The biologic plausibility and supporting evidence aiming at providing a concluding remark were explored in the recent scientific literature for local predisposing/precipitating factors and systemic drivers related to peri-implant diseases.

RESULTS

Local predisposing factors such as soft tissue characteristics, implant position and prosthetic design proved being strongly associated with the occurrence of peri-implant diseases. Hard tissue characteristics, however, failed to demonstrate having a direct association with peri-implant diseases. Robust data points toward the strong link between residual sub-mucosal cement and peri-implant diseases, while limited data suggests the impact of residual sub-mucosal floss and peri-implantitis. Systemic drivers/habits such as hyperglycemia and smoking showed a strong negative impact on peri-implantitis. However, there is insufficient evidence to claim for any link between metabolic syndrome, atherosclerotic cardiovascular disease, and obesity and peri-implant diseases.

CONCLUSION

Local predisposing/precipitating factors and systemic drivers may increase the risk of peri-implant diseases. Therefore, comprehensive anamnesis of the patients, educational/motivational programs and exhaustive prosthetically-driven treatment planning must be fostered aiming at reducing the rate of biological complications in implant dentistry.

Integrated strategy of RNA-sequencing and network pharmacology for exploring the protective mechanism of Shen-Shi-Jiang-Zhuo formula in rat with non-alcoholic fatty liver disease

CONTEXT

Shen-Shi-Jiang-Zhuo formula (SSJZF) exhibits a definite curative effect in the clinical treatment of non-alcoholic fatty liver disease (NAFLD).

OBJECTIVE

To explore the therapeutic effect and mechanism of SSJZF on NAFLD.

MATERIALS AND METHODS

Sprague Dawley rats were randomly divided into control, NAFLD, positive drug (12 mg/kg/day), SSJZF high-dose (200 mg/kg/day), SSJZF middle-dose (100 mg/kg/day), and SSJZF low-dose (50 mg/kg/day) groups. After daily intragastric administration of NAFLD rats for 8 weeks, lipid metabolism and hepatic fibrosis were evaluated by biochemical indices and histopathology. Then we uncovered the main active compounds and mechanism of SSJZF against NAFLD by integrating RNA-sequencing and network pharmacology, and PI3K/AKT pathway activity was verified by western blot.

RESULTS

High dose SSJZF had the best inhibitory effect on hepatic lipid accumulation and fibrosis in rats with NAFLD, which significantly down-regulated total triglycerides (58%), cholesterol (62%), aspartate aminotransferase (57%), alanine aminotransferase (41%) andγ-glutamyl transpeptidase (36%), as well as the expression of ACC (5.3-fold), FAS (12.1-fold), SREBP1C (2.3-fold), and CD36 (4.4-fold), and significantly reduced collagen deposition (67%). Then we identified 23 compounds of SSJZF that acted on 25 key therapeutic targets of NAFLD by integrating RNA-sequencing and network pharmacology. Finally, we also confirmed that high dose SSJZF increased p-PI3K/PI3K (1.6-fold) and p-AKT/AKT (1.6-fold) in NAFLD rats.

DISCUSSION AND CONCLUSION

We found for first time that SSJZF improved NAFLD in rats by activating the PI3K/Akt pathway. These findings provide scientific support for SSJZF in the clinical treatment of NAFLD and contribute to the development of new NAFLD drugs.

Similarity and Potential Relation Between Periimplantitis and Rheumatoid Arthritis on Transcriptomic Level: Results of a Bioinformatics Study

Background

This bioinformatics study aimed to reveal potential cross-talk genes, related pathways, and transcription factors between periimplantitis and rheumatoid arthritis (RA).

Methods

The datasets GSE33774 (seven periimplantitis and eight control samples) and GSE106090 (six periimplantitis and six control samples) were included from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO). A differential expression analysis (p < 0.05 and |logFC (fold change)| ≥ 1) and a functional enrichment analysis (p < 0.05) were performed. Based on this, a protein-protein interaction (PPI) network was constructed by Cytoscape. RA-related genes were extracted from DisGeNET database, and an overlap between periimplantitis-related genes and these RA-related genes was examined to identify potential cross-talk genes. Gene expression was merged between two datasets, and feature selection was performed by Recursive Feature Elimination (RFE) algorithm. For the feature selection cross-talk genes, support vector machine (SVM) models were constructed. The expression of these feature genes was determined from GSE93272 for RA. Finally, a network including cross-talk genes, related pathways, and transcription factors was constructed.

Results

Periimplantitis datasets included 138 common differentially expressed genes (DEGs) including 101 up- and 37 downregulated DEGs. The PPI interwork of periimplantitis comprised 1,818 nodes and 2,517 edges. The RFE method selected six features, i.e., MERTK, CD14, MAPT, CCR1, C3AR1, and FCGR2B, which had the highest prediction. Out of these feature genes, CD14 and FCGR2B were most highly expressed in periimplantitis and RA. The final activated pathway-gene network contained 181 nodes and 360 edges. Nuclear factor (NF) kappa B signaling pathway and osteoclast differentiation were identified as potentially relevant pathways.

Conclusions

This current study revealed FCGR2B and CD14 as the most relevant potential cross-talk genes between RA and periimplantitis, which suggests a similarity between RA and periimplantitis and can serve as a theoretical basis for future research.

Levels of SERPIN family proteins in peri-implant crevicular fluid in patients with peri-implantitis

Purpose

Serine protease inhibitors (SERPINs) family has been discovered in many disorders with proteolysis mechanisms. Our study determined the SERPINBs protein expression via public‐based GEO databases and further validated by peri‐implant crevicular fluid (PICF) of peri‐implantitis patients and healthy recruiters.

Methods

This study is a retrospective analysis. A total of 123 participants of Fujian Medical University Fujian Stomatological Hospital, consisting of 58 cases of peri‐implantitis and 65 samples of healthy control were retrospectively analyzed by ELISA assays and explored the gene enrichment pathways and clinical significance of SERPINBs expression accompanied by two different cytokines (IL‐6 and TNF‐α). Moreover, the clinical significance of SERPINBs was evaluated in peri‐implantitis patients with PICF samples by the receiver operating curve (ROC) using the area under the curve (AUC).

Results

KEGG database showed that Starch and sucrose metabolism, Retrograde endocannabinoid signaling, Prion diseases, Pentose phosphate pathways, and Olfactory pathways are up‐regulated; GO database showed that synapse organization, synapse assembly, sequestering of triglyceride, sensory perception of smell, and regulation of synapse organization pathways are up‐regulated. SERPINBs were overexpressed in peri‐implant tissues and peri‐implantitis patients with PICF. SERPINBs was positively correlated to IL‐6 and TNF‐α in peri‐implantitis patients with PICF. The ROC‐AUCs of SERPINBs achieved a significantly higher range from 0.895 to 0.939 in peri‐implantitis patients with PICF. Therefore, certain SERPINBs expressions were not only perceived through PICF and peri‐implant tissues but also showed potential significance in peri‐implantitis.

Conclusion

SERPINBs play an influential role in the pathogenesis of peri‐implantitis via binding with other inflammatory cytokines.

Effect of Titanium and Zirconium Oxide Microparticles on Pro-Inflammatory Response in Human Macrophages under Induced Sterile Inflammation: An In Vitro Study

The wear-debris particles released by shearing forces during dental implant insertion may contribute to inflammatory reactions or osteolysis associated with peri-implantitis by stimulating inflammasome-activation. The study aim was to examine cytotoxic and pro-inflammatory effects of titanium (TiO₂) and zirconia (ZrO₂) particles in macrophages regarding their nature/particle concentration over time under sterile lipopolysaccharide (LPS) inflammation. Macrophages were exposed to TiO₂ and ZrO₂ particles (≤5 µm) in cell culture. Dental glass was used as inert control and LPS (1 μg/mL) was used to promote sterile inflammation. Cytotoxicity was determined using MTT assays and cytokine expression of TNF-α, IL-1β and IL-6 was evaluated by qRT-PCR. Data were analyzed using Student's t-test and ANOVA (p ≤ 0.05). Cytotoxicity was significantly increased when exposed to higher concentrations of glass, TiO₂ and ZrO₂ (≥10⁷ particles/mL) compared to controls (p ≤ 0.05). Macrophages challenged with TiO₂ particles expressed up to ≈3.5-fold higher upregulation than ZrO₂ from 12 to 48 h. However, when exposed to LPS, TiO₂ and ZrO₂ particle-induced pro-inflammatory gene expression was further enhanced (p ≤ 0.05). Our data suggest that ZrO₂ particles produce less toxicity/inflammatory cytokine production than TiO₂. The present study shows that the biological reactivity of TiO₂ and ZrO₂ depends on the type and concentration of particles in a time-dependent manner.

A Network Pharmacology Approach to Explore the Mechanism of HuangZhi YiShen Capsule for Treatment of Diabetic Kidney Disease

BACKGROUND AND OBJECTIVE

HuangZhi YiShen Capsule (HZYS) is a Chinese patent herbal drug that protects kidney function in diabetic kidney disease (DKD) patients. However, the pharmacologic mechanisms of HZYS remain unclear. This study would use network pharmacology to explore the pharmacologic mechanisms of HZYS.

METHODS

Chemical constituents of HZYS were obtained through the Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and literature search. Potential targets of HZYS were identified by using the TCMSP and the SwissTarget Prediction databases. DKD-related target genes were collected by using the Online Mendelian Inheritance in Man, Therapeutic Target Database, GeneCards, DisGeNET, and Drugbank databases. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out to further explore the mechanisms of HZYS in treating DKD. Molecular docking was conducted to verify the potential interactions between the prime compounds and the hub genes.

RESULTS

179 active compounds and 620 target genes were obtained, and 571 common targets were considered potential therapeutic targets. The top 10 main active compounds of HZYS were heparin, quercetin, kaempferol, luteolin, methyl14-methylpentadecanoate, methyl (Z)-11-hexadecenoate, 17-hydroxycorticosterone, 4-pregnene-17α, 20β, 21-triol-3, 11-dione, wogonin, and hydroxyecdysone. Hub signaling pathways by which HZYS treating DKD were PI3K-Akt, MAPK, AGE-RAGE in diabetic complications, TNF, and apoptosis. The top 10 target genes associated with these pathways were IL6, MAPK1, AKT1, RELA, BCL2, JUN, MAPK3, MAP2K1, CASP3, and TNF. Quercetin and Luteolin were verified to have good binding capability with the hub potential targets IL6, MAPK1, AKT1 through molecular docking.

CONCLUSION

HZYS appeared to treat DKD by regulating the inflammatory, oxidative stress, apoptotic, and fibrosis signaling pathways. This study provided a novel perspective for further research of HZYS.

Development of a rat model for type 2 diabetes mellitus peri-implantitis: A preliminary study

OBJECTIVE

To develop an in vivo model to simulate the complex internal environment of diabetic peri-implantitis (T2DM-PI) model for a better understanding of peri-implantitis in type 2 diabetic patients.

MATERIALS AND METHODS

Maxillary first molars were extracted in Sprague-Dawley (SD) rats, and customized cone-shaped titanium implants were installed in the extraction sites. Thereafter, implants were uncovered and customized abutments were screwed into implants. A high-fat diet and a low-dose injection of streptozotocin were utilized to induce T2DM. Finally, LPS was locally injected in implant sulcus to induce peri-implantitis.

RESULTS

In the present study, T2DM-PI model has been successfully established. Imaging analysis revealed that abundant inflammatory cells infiltrated in the soft tissue in T2DM-PI group with concomitant excessive secretion of inflammatory cytokines. Moreover, higher expression of MMP and increased number of osteoclasts led to collagen disintegration and bone resorption in T2DM-PI group.

CONCLUSIONS

These results describe a novel rat model which stimulate T2DM-PI in vivo, characterized by overwhelming inflammatory response and bone resorption. This model has a potential to be used for investigation of initiation, progression and interventional therapy of T2DM-PI.

Identification and integrated analysis of differentially expressed long non-coding RNAs associated with periodontitis in humans

Background and Objective

Long non‐coding RNAs (lncRNAs) can act as competing endogenous RNAs (ceRNAs) to compete for micro‐RNAs (miRNAs) in regulation of downstream genes, various biological functions and diseases. Yet, the expression and regulation of lncRNAs in periodontitis are not fully understood. The objective of the study was to identify potential genes (lncRNA, messenger RNA [mRNA] and miRNA) involved in periodontitis, construct lncRNA‐miRNA‐mRNA ceRNA networks, explore gene functions and validate gene expressions.

Material and Methods

The data sets for the lncRNA, mRNA and miRNA expression profiles in gingival samples from periodontally healthy subjects and chronic periodontitis patients were obtained from the Gene Expression Omnibus. The differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) were identified, and ceRNA networks were then constructed. The expression of DElncRNAs and DEmRNAs was examined by quantitative real‐time polymerase chain reaction (qPCR). Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed for exploring the potential functions and biological pathways.

Results

The GSE80715 and GSE54710 data sets were retrieved. Subsequently, 26 DElncRNAs, 436 DEmRNAs and 12 DEmiRNAs were identified (|fold change| ≥2, adjusted p < 0.05). Further bioinformatics analysis contributed to establishment of the ceRNA networks, which consisted of 10 DElncRNAs, 11 DEmiRNAs and 83 DEmRNAs. Notably, the qPCR results showed a marked decrease in the expression of lncRNA H19 and two mRNAs (NOS1 and MAPT) which further supported the identified ceRNA network. The GO results revealed that the up‐regulated mRNAs were significantly enriched in inflammatory processes, whilst the down‐regulated mRNAs were enriched in cellular potentials.

Conclusion

Non‐coding RNAs are critically involved in the regulatory mechanisms in the pathogenesis of periodontitis. Further study is warranted to investigate the specific underlying genetic traits and networks.

qPCR Analysis Reveals Association of Differential Expression of SRR, NFKB1, and PDE4B Genes With Type 2 Diabetes Mellitus

BACKGROUND

Type 2 diabetes mellitus (T2DM) is a heterogeneous, metabolic, and chronic condition affecting vast numbers of the world's population. The related variables and T2DM associations have not been fully understood due to their diverse nature. However, functional genomics can facilitate understanding of the disease. This information will be useful in drug design, advanced diagnostic, and prognostic markers.

AIM

To understand the genetic causes of T2DM, this study was designed to identify the differentially expressed genes (DEGs) of the disease.

METHODS

We investigated 20 publicly available disease-specific cDNA datasets from Gene Expression Omnibus (GEO) containing several attributes including gene symbols and clone identifiers, GenBank accession numbers, and phenotypic feature coordinates. We analyzed an integrated system-level framework involving Gene Ontology (GO), protein motifs and co-expression analysis, pathway enrichment, and transcriptional factors to reveal the biological information of genes. A co-expression network was studied to highlight the genes that showed a coordinated expression pattern across a group of samples. The DEGs were validated by quantitative PCR (qPCR) to analyze the expression levels of case and control samples (50 each) using glyceraldehyde 3-phosphate dehydrogenase (GAPDH) as the reference gene.

RESULTS

From the list of 50 DEGs, we ranked three T2DM-related genes (p < 0.05): SRR, NFKB1, and PDE4B. The enriched terms revealed a significant functional role in amino acid metabolism, signal transduction, transmembrane and intracellular transport, and other vital biological functions. DMBX1, TAL1, ZFP161, NFIC (66.7%), and NR1H4 (33.3%) are transcriptional factors associated with the regulatory mechanism. We found substantial enrichment of insulin signaling and other T2DM-related pathways, such as valine, leucine and isoleucine biosynthesis, serine and threonine metabolism, adipocytokine signaling pathway, P13K/Akt pathway, and Hedgehog signaling pathway. The expression profiles of these DEGs verified by qPCR showed a substantial level of twofold change (FC) expression (2-ΔΔCT) in the genes SRR (FC ≤ 0.12), NFKB1 (FC ≤ 1.09), and PDE4B (FC ≤ 0.9) compared to controls (FC ≥ 1.6). The downregulated expression of these genes is associated with pathophysiological development and metabolic disorders.

CONCLUSION

This study would help to modulate the therapeutic strategies for T2DM and could speed up drug discovery outcomes.

Hygiene Recall in Diabetic and Nondiabetic Patients: A Periodic Prognostic Factor in the Protection Against Peri-Implantitis?

PURPOSE

Diabetes mellitus is associated with an increased risk of poor outcomes with dental implant placement. This study aims to identify if frequency of hygiene visits is a protective factor for the development of peri-implantitis in diabetic patients.

METHODS

A retrospective cohort design was conducted on patients presenting for dental implant placement at the Philadelphia Veterans Affairs (VA) Medical Center from 2006 to 2012. The primary predictor variable was hygiene frequency, recorded as either infrequent, annual (7-12 month recall), or biannual (≤6-month recall). The number of months between implant placement and the presence of peri-implantitis was the primary outcome (time-to-peri-implantitis) variable, which was assessed on a subject level and adjusted for clustered, correlated multiple implants on the same subject. Additional variables were greater than or equal to 60 years of age, male gender, smokers, short implant length, diabetes, uncontrolled diabetes, and removable prostheses. Descriptive, univariate, and Cox proportional hazards regression statistics were computed to measure associations with peri-implantitis with P ≤ .05 used to define statistical significance.

RESULTS

The study sample was composed of 286 patients. In total, 748 implants were placed. Subjects greater than or equal to 60 years of age were 2 times more likely to develop peri-implantitis (hazards ratio (HR) = 2.015, 95% Cl (0.985-4.119), P = .0549). Subjects receiving implant-supported removable prostheses were 2.3 times more likely to develop peri-implantitis (HR = 2.315, 95% CI (1.006-5.327), P = .0485). With each hygiene visit, patients' risk of developing peri-implantitis decreased 20% (HR = 0.805, 95% Cl (0.394-1.647), P = .5528). In addition, diabetic patients were 49% more likely to develop peri-implantitis (HR = 1.491, 95% CI (0.758-2.936), P = .2475) than nondiabetic patients.

CONCLUSIONS

Diabetic patients may be at increased risk for the development of peri-implantitis and an increased frequency of hygiene visits may reduce peri-implant diseases.

Differential Gene Expression Changes in Human Primary Dental Pulp Cells Treated with Biodentine and TheraCal LC Compared to MTA

This study aimed to analyze the effects of pulp capping materials on gene expression changes in primary tooth-derived dental pulp cells using next-generation sequencing. Dental pulp cells were extracted and treated with mineral trioxide aggregate (MTA), Biodentine (BD), or TheraCal LC (TC). Cell viability assays were performed. Total RNA was extracted and analyzed through mRNA sequencing. Bioinformatic analysis of differential gene expression in dental pulp cells exposed to BD or TC versus MTA was performed. MTA, BD, and TC exposure had no significant effect on pulp cell viability (p > 0.05). Gene sets associated with inflammatory response (p = 2.94 × 10⁻⁵) and tumor necrosis factor alpha (TNF-α) signaling via the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) pathway (p = 2.94 × 10⁻⁵) were enriched in all materials. In BD-treated cells, Wnt/β-catenin signaling (p = 3.15 × 10⁻⁴) gene sets were enriched, whereas enrichment of interferon gamma (IFN-γ) response (p = 3 × 10⁻³) was observed in TC-treated cells. In gene plot analysis, marked increases in receptor activator of nuclear factor kappa-Β ligand (RANKL) expression were seen in TC-treated cells over time. Despite the similar cell viabilities exhibited among MTA-, BD-, and TC-treated cells, patterns of gene networks differed, suggesting that diverse functional gene differences may be associated with treatment using these materials.

Integrated Analysis to Study the Relationship between Tumor-Associated Selenoproteins: Focus on Prostate Cancer

Selenoproteins are proteins that contain selenium within selenocysteine residues. To date, twenty-five mammalian selenoproteins have been identified; however, the functions of nearly half of these selenoproteins are unknown. Although alterations in selenoprotein expression and function have been suggested to play a role in cancer development and progression, few detailed studies have been carried out in this field. Network analyses and data mining of publicly available datasets on gene expression levels in different cancers, and the correlations with patient outcome, represent important tools to study the correlation between selenoproteins and other proteins present in the human interactome, and to determine whether altered selenoprotein expression is cancer type-specific, and/or correlated with cancer patient prognosis. Therefore, in the present study, we used bioinformatics approaches to (i) build up the network of interactions between twenty-five selenoproteins and identify the most inter-correlated proteins/genes, which are named HUB nodes; and (ii) analyze the correlation between selenoprotein gene expression and patient outcome in ten solid tumors. Then, considering the need to confirm by experimental approaches the correlations suggested by the bioinformatics analyses, we decided to evaluate the gene expression levels of the twenty-five selenoproteins and six HUB nodes in androgen receptor-positive (22RV1 and LNCaP) and androgen receptor-negative (DU145 and PC3) cell lines, compared to human nontransformed, and differentiated, prostate epithelial cells (EPN) by RT-qPCR analysis. This analysis confirmed that the combined evaluation of some selenoproteins and HUB nodes could have prognostic value and may improve patient outcome predictions.

Identifying potential active components of walnut leaf that action diabetes mellitus through integration of UHPLC-Q-Orbitrap HRMS and network pharmacology analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Walnut leaf (WL) is a hypoglycemic herbal medication with blood glucose-lowering activity that can affect diabetes mellitus (DM). However, the active components of WL and the mechanisms by which these compounds affect DM are unclear.

AIM OF STUDY

This study aimed to determine these effective ingredients and elucidate the potential mechanisms by which they affect DM via ultra-high performance liquid chromatography-hybrid quadrupole-Orbitrap high-resolution mass spectrometry (UHPLC-Q-Orbitrap HRMS) coupled with network pharmacology analysis.

MATERIALS AND METHODS

First, UHPLC-Q-Orbitrap HRMS was utilized to identify components of WL. Second, the putative targets of the components were identified and predicted based on chemical similarity and online databases. Third, the key candidate targets and potential active components were identified through topological analysis of a component-disease target interaction network. Finally, interactions between active components and therapeutic targets were confirmed by molecular docking analysis.

RESULTS

One hundred and thirty components were identified in WL, among which 38 were considered potentially bioactive, as they showed hypoglycemic effects. Among these 38, 8 key active components possessed high similarities and shared 4 targets with approved drugs. These findings were confirmed by molecular docking analysis.

CONCLUSION

The approach combining UHPLC-Q-Orbitrap HRMS with network pharmacology analysis is a rapid and effective tool to identify potentially bioactive constituents in medicinal plants and prescriptions.

Quantitative Proteomics and Weighted Correlation Network Analysis of Tear Samples in Type 2 Diabetes Patients Complicated with Dry Eye

PURPOSE

Diabetic patients are more likely to experience dry eye (DE). TMT-based proteomics and WGCNA are used to identify the differentially expressed proteins in tear proteome of type 2 diabetes with DE. The aim is to provide a molecular basis for exploring possible mechanisms underlying the pathogenesis of diabetic DE.

EXPERIMENTAL DESIGN

Subjects are divided into four groups (ten in each): type 2 diabetes with DE; type 2 diabetes without DE; non-diabetes with DE and normal controls. All subjects undergo DE tests. Total proteins are extracted and quantitatively labeled with TMT, then analyzed using liquid chromatography-mass spectrometry. WGCNA is used to identify the hub genes. Finally, differentially expressed proteins are validated by ELISA.

RESULTS

A total of 1922 proteins are identified, of which 1814 contain quantitative information. Ultimately, 650 of these proteins yield quantitative values. WGCNA performed on these 650 proteins reveal four distinct hub genes of diabetic DE.

CONCLUSIONS AND CLINICAL RELEVANCE

DE is associated with the differential expression of tear proteins in type 2 diabetes. Inflammation, immune factors, and lipid metabolism may play a role in the development of diabetic DE. LTF, LYZ, ZAG, and DNAJC3 have the potential to be the biomarkers of DE in diabetes.

Uncovering the Mechanism of Astragalus membranaceus in the Treatment of Diabetic Nephropathy Based on Network Pharmacology

BACKGROUND

Diabetic nephropathy (DN), characterized by hyperglycemia, hypertension, proteinuria, and edema, is a unique microvascular complication of diabetes. Traditional Chinese medicine (TCM) Astragalus membranaceus (AM) has been widely used for DN in China while the pharmacological mechanisms are still unclear. This work is aimed at undertaking a network pharmacology analysis to reveal the mechanism of the effects of AM in DN. Materials and Methods. In this study, chemical constituents of AM were obtained via Traditional Chinese Medicine Systems Pharmacology Database (TCMSP), and the potential targets of AM were identified using the Therapeutic Target Database (TTD). DisGeNET and GeneCards databases were used to collect DN-related target genes. DN-AM common target protein interaction network was established by using the STRING database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were carried out to further explore the DN mechanism and therapeutic effect of AM. The network diagrams of the active component-action target and protein-protein interaction (PPI) networks were constructed using Cytoscape software.

RESULTS

A total of 16 active ingredients contained and 78 putative identified target genes were screened from AM, of which 42 overlapped with the targets of DN and were considered potential therapeutic targets. The analysis of the network results showed that the AM activity of component quercetin, formononetin, calycosin, 7-O-methylisomucronulatol, and quercetin have a good binding activity with top ten screened targets, such as VEGFA, TNF, IL-6, MAPK, CCL3, NOS3, PTGS2, IL-1β, JUN, and EGFR. GO and KEGG analyses revealed that these targets were associated with inflammatory response, angiogenesis, oxidative stress reaction, rheumatoid arthritis, and other biological process.

CONCLUSIONS

This study demonstrated the multicomponent, multitarget, and multichannel characteristics of AM, which provided a novel approach for further research of the mechanism of AM in the treatment of DN.

Mangiferin alleviates experimental peri-implantitis via suppressing interleukin-6 production and Toll-like receptor 2 signaling pathway

BACKGROUND

TLR2 (Toll-like receptor 2) signaling and its downstream proinflammatory cytokines are considered to be important in the progression of peri-implantitis. A natural medicine, mangiferin has exhibited modulatory effect on TLR2 signaling and anti-inflammatory effects on different diseases. The objective of the present study is to investigate the effect of mangiferin on peri-implantitis and the potential mechanisms by administering this drug to an experimental peri-implantitis mouse model.

METHODS

Maxillary left first, second, and third molars of mice were extracted, and dental implants were placed in the region of the maxillary left second molars. Then, peri-implantitis was induced by tying ligatures around implants, and mangiferin was given orally to the mice. After 6-week mangiferin treatment, bone loss around the implants was detected using micro-computerized tomography (micro-CT). Alveolar bone and inflammatory infiltrate in peri-implant tissues were examined using hematoxylin and eosin (H&E) staining. Production of interleukin-6 (IL6), a TLR2 downstream proinflammatory cytokine, in the tissue surrounding implants was measured using quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) analysis. IL6 protein expression and TLR2 signaling pathway activation in peri-implant tissues were detected using western blot analysis.

RESULTS

Micro-CT demonstrated reduced bone loss in peri-implantitis upon mangiferin administration. Additionally, H&E staining showed more alveolar bone and less inflammatory infiltrate in peri-implant tissues after mangiferin application. Moreover, qRT-PCR analysis demonstrated lower levels of IL6 gene expression, and western blot analysis showed decreased protein expression of IL6 and TLR2, and suppressed phosphorylation of TLR2 downstream nuclear factor-κB, p38 mitogen-activated protein kinase, and c-Jun N-terminal kinase after mangiferin treatment.

CONCLUSIONS

These results suggest the suppressive effect of mangiferin on bone damage and inflammatory infiltrate in peri-implantitis. These therapeutic effects may be associated with inhibited IL6 production and reduced TLR2 signaling activation in peri-implant tissues.