Medication-Related Osteonecrosis of the Jaw: A Systematic Review and a Bioinformatic Analysis.

The objective was to evaluate the current evidence regarding the etiology of medication-related osteonecrosis of the jaw (MRONJ). This study systematically reviewed the literature by searching PubMed, Web of Science, and ProQuest databases for genes, proteins, and microRNAs associated with MRONJ from the earliest records through April 2023. Conference abstracts, letters, review articles, non-human studies, and non-English publications were excluded. Twelve studies meeting the inclusion criteria involving exposure of human oral mucosa, blood, serum, saliva, or adjacent bone or periodontium to anti-resorptive or anti-angiogenic agents were analyzed. The Cochrane Collaboration risk assessment tool was used to assess the quality of the studies. A total of 824 differentially expressed genes/proteins (DEGs) and 22 microRNAs were extracted for further bioinformatic analysis using Cytoscape, STRING, BiNGO, cytoHubba, MCODE, and ReactomeFI software packages and web-based platforms: DIANA mirPath, OmicsNet, and miRNet tools. The analysis yielded an interactome consisting of 17 hub genes and hsa-mir-16-1, hsa-mir-21, hsa-mir-23a, hsa-mir-145, hsa-mir-186, hsa-mir-221, and hsa-mir-424. A dominance of cytokine pathways was observed in both the cluster of hub DEGs and the interactome of hub genes with dysregulated miRNAs. In conclusion, a panel of genes, miRNAs, and related pathways were found, which is a step toward understanding the complexity of the disease.

Experimental Analysis of Tear Fluid and Its Processing for the Diagnosis of Multiple Sclerosis.

A pilot analysis of the tear fluid of patients with multiple sclerosis (MS) collected by glass microcapillary was performed using various experimental methods: liquid chromatography-mass spectrometry, Raman spectroscopy, infrared spectroscopy, and atomic-force microscopy. Infrared spectroscopy found no significant difference between the tear fluid of MS patients and the control spectra; all three significant peaks were located at around the same positions. Raman analysis showed differences between the spectra of the tear fluid of MS patients and the spectra of healthy subjects, which indicated a decrease in tryptophan and phenylalanine content and changes in the relative contributions of the secondary structures of the polypeptide chains of tear proteins. Atomic-force microscopy exhibited a surface fern-shaped dendrite morphology of the tear fluid of patients with MS, with less roughness on both oriented silicon (100) and glass substrates compared to the tear fluid of control subjects. The results of liquid chromatography-mass spectrometry showed downregulation of glycosphingolipid metabolism, sphingolipid metabolism, and lipid metabolism. Proteomic analysis identified upregulated proteins in the tear fluid of patients with MS such as cystatine, phospholipid transfer protein, transcobalamin-1, immunoglobulin lambda variable 1-47, lactoperoxidase, and ferroptosis suppressor protein 1; and downregulated proteins such as haptoglobin, prosaposin, cytoskeletal keratin type I pre-mRNA-processing factor 17, neutrophil gelatinase-associated lipocalin, and phospholipase A2. This study showed that the tear proteome in patients with MS is modified and can reflect inflammation. Tear fluid is not a commonly used biological material in clinico-biochemical laboratories. Experimental proteomics has the potential to become a promising contemporary tool for personalized medicine, and it might be applied in clinical practice by providing a detailed analysis of the tear-fluid proteomic profile of patients with MS.

Differential Urinary Proteomic Analysis of High-Risk Cervical Intraepithelial Neoplasia.

Human papillomavirus (HPV)-associated lesions and malignancies exhibit alterations in the composition and functionality of the extracellular matrix (ECM) that represent the complex molecular pathways present between infection and disease. A total of 20 urine samples were used, including from 10 patients with cervical intraepithelial neoplasia grade 3 (CIN3) and 10 healthy controls to perform the label-free quantitative analysis using the nano-HPLC and ESI-MS ion trap mass analyzer and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF/MS) fast screening. Among 476 identified/quantified proteins, 48 were significantly changed (log2-fold change ≥1.0 or ≤-1.0, -log10 (bbinominal, p-value ≥ 1.3), of which were 40 proteins (down-regulated) and 8 proteins (up-regulated) in CIN3, in comparison to healthy controls. The biological function and key pathway enrichment of the gene set using gen set enrichment analysis (GSEA) were analyzed. The ECM-receptor interaction pathway (NES = -1.64, p = 0.026) was down-regulated by 13 proteins (HSPG2, COL6A1, COL6A3, SPP1, THBS1, TNC, DAG1, FN1, COMP, GP6, VTN, SDC1, and CD44; log2 FC range from -0.03 to -1.48) for the CIN3 group in the KEGG database. The MALDI-TOF/MS screening showed the difference of protein profiles between the control and CIN3 groups, i.e., using the scatter plot with a well-separated shape, as well as effectively distinguishing both groups (control and CIN3) using genetic algorithms (GA) with cross-validation (51.56%) and recognition capability (95.0%). Decreased levels of ECM-receptor interaction proteins may cause disturbances in the interactions of cells with the ECM and play an important role in the development and progression of cervical cancer.

MALDI-TOF/MS Profiling of Whole Saliva and Gingival Crevicular Fluid in Patients with the Invisalign System and Fixed Orthodontic Appliances.

The movement of teeth by orthodontic treatment with the Invisalign (IN) system and fixed orthodontic appliances (FOA) is characterized by the reconstruction of periodontal ligaments, alveolar bone, and gingiva. A reflection of these phenomena can be found in the composition of gingival crevicular fluid (GCF). A total of 90 samples from 45 participants (45 whole saliva and 45 GCF), including 15 patients with FOA, 15 patients with IN, and 15 patients with oral health, were subjected to matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF/MS) analysis. Mass fingerprints were generated for each sample. Three models were tested: a quick classifier (QC), a genetic algorithm (GA), and a supervised neural network (SNN). For both groups of samples (saliva and GCF), the GA model showed the highest recognition abilities of 88.89% (saliva) and 95.56% (GCF). Differences between the treated (FOA and IN) groups and the control group in saliva and GCF samples were determined using cluster analysis. In addition, we monitored the effect of long-term orthodontic treatment (after 6 months) in the lag phase of orthodontic tooth movement. The results show increased levels of inflammatory markers (α-defensins), which may indicate an ongoing inflammatory process even after 21 days from force application.

Dichloroacetate as a metabolic modulator of heart mitochondrial proteome under conditions of reduced oxygen utilization.

Myocardial compensatory mechanisms stimulated by reduced oxygen utilization caused by streptozotocin-induced diabetes mellitus (DM) and treated with dichloroacetate (DCA) are presumably associated with the regulation of mitochondria. We aimed to promote the understanding of key signaling pathways and identify effectors involved in signal transduction. Proteomic analysis and fluorescence spectroscopy measurements revealed significantly decreased membrane potential and upregulated protein amine oxidase [flavin-containing] A (AOFA) in DM mitochondria, indicative of oxidative damage. DCA in diabetic animals (DM + DCA) downregulated AOFA, increased membrane potential, and stimulated thioredoxin-dependent peroxide reductase, a protein with antioxidant function. Furthermore, the DM condition was associated with mitochondrial resistance to calcium overload through mitochondrial permeability transition pores (mPTPs) regulation, despite an increased protein level of voltage-dependent anion-selective protein (VDAC1). In contrast, DM + DCA influenced ROS levels and downregulated VDAC1 and VDAC3 when compared to DM alone. The diabetic myocardium showed an identical pattern of mPTP protein interactions as in the control group, but the interactions were attenuated. Characterization of the combined effect of DM + DCA is a novel finding showing that DCA acted as an effector of VDAC protein interactions, calcium uptake regulation, and ROS production. Overall, DM and DCA did not exhibit an additive effect, but an individual cardioprotective pathway.

Tear fluid biomarkers in major depressive disorder: Potential of spectral methods in biomarker discovery.

Spectroscopic methods represent a group of analytical methods that demonstrate high potential in providing clinically relevant diagnostic information, such as biochemical, functional or structural changes of macromolecular complexes that might occur due to pathological processes or therapeutic intervention. Although application of these methods in the field of psychiatric research is still relatively recent, the preliminary results show that they have the capacity to detect subtle neurobiological abnormalities in major depressive disorder (MDD). Methods of mass spectrometry (MALDI-TOF MS), zymography, synchronous fluorescence spectroscopy (SFS), circular dichroism (CD) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy and atomic force microscopy (AFM) were used to analyze the human tear fluid of subjects with MDD. Using MALDI-TOF MS, two diagnostically significant peaks (3747 and 16 411 m/z) were identified with an AUC value of 0.89 and 0.92 in tear fluid of subjects with MDD vs controls, respectively. We also identified various forms of matrix metalloproteinase 9 in subjects with MDD using zymography and synchronous fluorescence spectra (SFS) showed a significant increase in fluorescence intensity at 280 nm. CD spectra were redshifted in tear fluid of subjects with MDD vs healthy controls. FTIR spectroscopy showed changes in the positions of peaks for amide A, I, II in tear fluid of subjects with MDD vs controls. Moreover, atomic force microscopy (AFM) showed different pattern in the crystal structures of tear fluid components in subjects with MDD. SFS, CD, FTIR spectroscopy, AFM and MALDI-TOF MS confirmed, that the human tear fluid proteome could be helpful in discriminating between the group of subjects with MDD and healthy controls. These preliminary findings suggest that spectral methods could represent a useful tool in clinical psychiatry, especially in establishing differential diagnosis, monitoring illness progression and the effect of psychiatric treatment.

Microchip isotachophoresis coupled to surface-enhanced Raman spectroscopy for pharmaceutical analysis.

A novel online coupling of microchip isotachophoresis (µITP) with surface-enhanced Raman spectroscopy (SERS) for the analysis of complex samples is presented. Polymeric microchip with coupled channels was used for µITP-SERS analysis of four structurally similar Raman active synthetic dyes (brilliant black BN, carmoisine, ponceau 4R, and sunset yellow FCF) in pharmaceuticals. The µITP separation and simultaneous pre-concentration of the analytes were performed in the first channel of the microchip at pH 6.0 with the aid of non-Raman active discrete spacers (acetate, butyrate, glutarate, pantothenate, and valerate). Silver nanoparticles used for Raman enhancement were present in the second channel, and individual SERS spectra of the dyes were acquired by a mini Raman spectrometer operating at 532 nm. The analytical enhancement factors for silver nanoparticles were 1-5 × 104. The microchip with coupled channels enabled independent µITP separation and SERS detection, and eliminated any adverse impact of nanoparticles on the separation. The developed approach allowed reliable online SERS identification and detection of dyes with limits of detection ranging from 12 to 62 nM. Synthetic dyes were successfully separated, identified, and quantified in pharmaceutical preparations within 7 min without the need for complex or time-consuming sample pretreatment. The results were in good agreement with those obtained by an independent analytical method reported for studied dyes. Graphical abstract.

mPTP Proteins Regulated by Streptozotocin-Induced Diabetes Mellitus Are Effectively Involved in the Processes of Maintaining Myocardial Metabolic Adaptation.

Mitochondrial permeability transition pores (mPTPs) have become an important topic in investigating the initiation and signaling pathways involved in cardioprotection. Experimental streptozotocin-induced diabetes mellitus (D) was shown to provide sufficient protection to the myocardium via compensatory mechanisms enabling mitochondria to produce energy under pathological conditions during the acute phase. The hypothesized involvement of mPTPs in these processes prompted us to use liquid chromatography and mass spectrometry-based proteomic analysis to investigate the effects of the acute-phase D condition on the structural and regulatory components of this multienzyme complex and the changes caused by compensation events. We detected ADT1, ATP5H, ATPA, and ATPB as the most abundant mPTP proteins. The between-group differences in protein abundance of the mPTP complex as a whole were significantly upregulated in the D group when compared with the control (C) group (p = 0.0106), but fold changes in individual protein expression levels were not significantly altered except for ATP5H, ATP5J, and KCRS. However, none of them passed the criterion of a 1.5-fold change in differential expression for biologically meaningful change. Visualization of the (dis-)similarity between the C and D groups and pairwise correlations revealed different patterns of protein interactions under the C and D conditions which may be linked to endogenous protective processes, of which beneficial effects on myocardial function were previously confirmed.

Proteomic analysis of the vitamin C effect on the doxorubicin cytotoxicity in the MCF-7 breast cancer cell line.

PURPOSE: Doxorubicin is an anthracycline drug which inhibits the growth of breast cancer cell lines. However, a major factor limiting its use is a cumulative, dose-dependent cardiotoxicity, resulting in a permanent loss of cardiomyocytes. Vitamin C was found to potentiate the cytotoxic effects of a variety of chemotherapeutic drugs including doxorubicin. The aim of the study was to describe the changes in protein expression and proliferation of the MCF-7 cells induced by the vitamin C applied with doxorubicin. METHODS: Label-free quantitative proteomics and real-time cell analysis methods were used to search for proteome and cell proliferation changes. These changes were induced by the pure DOX and by DOX combined with vitamin C applied on the MCF-7 cell line. RESULTS: From the real-time cell analysis experiments, it is clear that the highest anti-proliferative effect occurs with the addition of 200 µM of vitamin C to 1 µM of doxorubicin. By applying both the label-free protein quantification method and total ion current assay, we found statistically significant changes (p ≤ 0.05) of 26 proteins induced by the addition of vitamin C to doxorubicin on the MCF-7 cell line. These differentially expressed proteins are involved in processes such as structural molecule activity, transcription and translation, immune system process and antioxidant, cellular signalling and transport. CONCLUSION: The detected proteins may be capable of predicting response to DOX therapy. This is a key tool in the treatment of breast cancer, and the combination with vit C seems to be of particular interest due to the fact that it can potentiate anti-proliferative effect of DOX.

Delayed bradykinin postconditioning modulates intrinsic neuroprotective enzyme expression in the rat CA1 region after cerebral ischemia: a proteomic study.

Pyramidal cells in the CA1 brain region exhibit an ischemic tolerance after delayed postconditioning; therefore, this approach seems to be a promising neuroprotective procedure in cerebral postischemic injury improvement. However, little is known about the effect of postconditioning on protein expression patterns in the brain, especially in the affected hippocampal neurons after global cerebral ischemia. This study is focused on the examination of the ischemia-vulnerable CA1 neuronal layer and on the acquisition of protection from delayed neuronal death after ischemia. Ischemic-reperfusion injury was induced in Wistar rats and bradykinin was applied 2 days after the ischemic insult in an attempt to overcome delayed cell death. Analysis of complex peptide CA1 samples was performed by automated two dimensional liquid chromatography (2D-LC) fractionation coupled to tandem matrix assisted laser desorption/ionization time-of-flight (MALDI TOF/TOF) mass spectrometry instrumentation. We devoted our attention to differences in protein expression mapping in ischemic injured CA1 neurons in comparison with equally affected neurons, but with bradykinin application. Proteomic analysis identified several proteins occurring only after postconditioning and control, which could have a potentially neuroprotective influence on ischemic injured neurons. Among them, the prominent position occupies a regulator of glutamate level aspartate transaminase AATC, a scavenger of glutamate in brain neuroprotection after ischemia-reperfusion. We identified this enzyme in controls and after postconditioning, but AATC presence was not detected in the ischemic injured CA1 region. This finding was confirmed by two-dimensional differential electrophoresis followed by MALDI-TOF/TOF MS identification. Results suggest that bradykinin as delayed postconditioning may be associated with modulation of protein expression after ischemic injury and thus this procedure can be involved in neuroprotective metabolic pathways.

Comparative TOF-SIMS and MALDI TOF-MS analysis on different chromatographic planar substrates.

A comparison is made between two high resolution, surface-based, mass spectrometric methods: time-of-flight secondary ion mass spectrometry (TOF-SIMS) and matrix-assisted laser desorption/ionisation mass spectrometry (MALDI TOF-MS) in indication of abietic and gibberellic acids molecular profiles on different chromatographic thin layers. The analytes were applied to silica gel chromatographic thin layers with SIMS on-line interfacing channel, monolithic silica gel ultra-thin layers, and thin layers specifically designed for direct Raman spectroscopic analysis. Two MALDI matrices were used in this research: ferulic acid and 2,5-dihydroxybenzoic acid. The silica gel SIMS-interfacing channel strongly supported formation of numerous different MALDI MS fragments with abietic and gibberellic acids, and ferulic acid matrix. The most intense fragments belonged to [M-OH](+) and [M](+) ions from ferulic acid. Intense conjugates were detected with gibberellic acid. The MALDI MS spectrum from the monolithic silica gel surface showed very low analyte signal intensity and it was not possible to obtain MALDI spectra from a Raman spectroscopy treated chromatographic layer. The MALDI TOF MS gibberellic acid fragmentation profile was shielded by the matrix used and was accompanied by poor analyte identification. The most useful TOF-SIMS analytical signal response was obtained from analytes separated on monolithic silica gel and a SIMS-interfacing modified silica gel surface. New horizons with nanostructured surfaces call for high resolution MS methods (which cannot readily be miniaturised like many optical and electrochemical methods) to be integrated in chip and nanoscale detection systems.