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BACKGROUND: Breast cancer (BC) is one of the most life-threatening cancer types among women. Despite major developments in medical sciences and technologies, the incidence and mortality rates of BC cases are still increasing. One of the reasons for this increase is the absence of an easy to perform early-diagnostic tool. Although there are defined BC biomarkers routinely used for diagnostic and prognostic purposes, none of these biomarkers is useful for early diagnosis. Therefore, early diagnosis of BC remains an important challenge and there is a great need for the early-diagnostic biomarker(s). OBJECTIVE: In this study, we aimed to evaluate the diagnostic and prognostic values of glycerol-3-phosphate dehydrogenase (GPD1) and monoacylglycerol lipase (MAGL) proteins as non-invasive serum biomarkers. METHODS: GPD1 and MAGL serum levels were determined by ELISA for BC patients (n= 100) from five different subtypes, and healthy controls (n= 20), and a comparative analysis was performed to determine statistically significant expression differences among the groups. RESULTS: The results provided evidence that GPD1 acted as a diagnostic biomarker in distinguishing triple-negative breast cancer (TNBC) patients from other subtypes, and MAGL acted as a diagnostic biomarker in distinguishing healthy individuals from BC patients. CONCLUSION: GPD1 and MAGL might be proposed as non-invasive diagnostic biomarkers for BC with high sensitivity and specificity.

High-fat diet-induced obesity adversely affects the female reproductive system. The metabolic changes that the high-fat diet causes on the ovaries have not been elucidated. Herein, to understand the molecular and cellular mechanisms underlying the effects of long-term high-fat diet-fed, the changes in the global proteomic profile of the rat ovaries were investigated. The female rats were randomly divided into two groups based on their diets: the ones that were fed with the high-fat diet and the other ones that were fed with the control diet for 18 weeks. To identify differentially expressed proteins, the changes in ovary proteomes were investigated by two-dimensional electrophoresis coupled to matrix-assisted laser desorption/ionization-time-of-flight/time-of-flight and label-free quantification with nano-high performance liquid chromatography to tandem mass spectrometry (nHPLC-MS/MS). A total of 80 proteins were differentially regulated. The upregulated proteins were involved in responses to chemical and organic substances, cytokines, external stimuli, and lipids. These proteins were particularly associated with vesicles, microbodies, and cell surface proteins. The downregulated proteins were involved in biological processes associated with cellular respiration. Those proteins created a network consisting of proteins involved in aerobic respiration and energy generation. Our results demonstrated that the mechanisms related to energy production in the ovary tissue were particularly affected by the high-fat diet.

Variation in the mitochondrial tRNALys gene at position 8296 was previously found to be associated with maternally inherited diabetes mellitus and deafness, hypertrophic cardiomyopathy, myoclonic epilepsy with ragged-red fibers and mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes. The pathogenicity of the m.8296A>G variation is unclear. In this study, we aimed to analyze the mitochondrial proteome in a patient with m.8296A>G variation to elucidate the effects of this mutation at the protein level. Whole-exome sequencing and mitochondrial genome analysis were performed in a patient with sensorineural hearing impairment, cognitive impairment, leukodystrophy, migraine-like headaches, and gastrointestinal dysmotility. Mitochondrial genome analysis identified a homoplasmic m.8296A>G variation in the mitochondrial tRNALys gene in the proband and unaffected mother. Global mitochondrial proteome analysis was carried out in the muscle mitochondria of the index patient and a control subject. Comparative muscle mitochondrial proteome analysis revealed a total of 13 nuclear-encoded mitochondrial proteins differently expressed with respect to the control. Ten of the 13 proteins were downregulated. Most of the proteins were involved in ATP synthesis and Krebs cycle and have strong interactions with each other. We considered the m.8296A>G variation to be pathogenic with variable penetrance for our patient’s phenotype, and this variation led to different expressions of nuclear-encoded proteins involved in energy metabolism.

Background Green Fluorescent Protein is widely used as a cellular marker tool, but its potential influence on cells has been questioned. Although the potential off-target effects of GFP on tumor cells have been studied to some extent, the findings at the molecular level are insufficient to explain the effect of GFP expression on the tumorigenic capacity of cancer cells. Here, we aimed to investigate the effect of GFP expression on the tumorigenicity of PC3 prostate cancer cells. Methods and Results Using GFP-expressing and wild-type PC3 cells, xenograft models were generated in athymic BALB/C mice. To identify differentially expressed proteins, the change in the proteome of cells was investigated by label‐free quantification with nano‐high performance liquid chromatography to tandem mass spectrometry (nHPLC‐MS/MS). The proteins that showed significantly altered expression levels were evaluated using the bioinformatics tools. The results showed that GFP-expressing cells, in contrast to the wild-type cells, failed to develop tumor. Label-free quantification revealed a total of 216 differentially regulated proteins, of which 98 were upregulated and 117 were downregulated. Conclusion Upon GFP expression, the immune system, translational machinery, energy metabolism, elements of cytoskeletal and VEGF signaling pathway were regulated. Alterations in these cellular events caused attenuated tumorigenicity. Therefore, ultimate care should be taken into account to prevent reporting deceitful mechanisms generated from studies utilizing GFP.

Phylogenetic analysis (PA) is used for elucidation of relationships among different species and provides information about their evolution. BLM protein (BLM RecQ like helicase) is responsible for the repair of stalled replication fork during double-strand break repair by homologous recombination. In the current study, phylogenetic analysis was performed using BLM protein sequences, sequences of its homologs and its putative homologs from 34 species including covering the genera of Bacteria, Archaea and Eukaryotes. This study was carried out for the purpose of (1) illustrating and comparing relationships among eukaryotic BLM proteins, their homologs (ATP-dependent DNA helicase RecQs in Bacteria) and their potential putative homologs (ATP-dependent DNA helicase Hel308s in Archaea), (2) evaluating how BLM protein evolution took place, what it brought to the organisms by acquiring functional changes and how future potential changes would occur and (3) gaining the general perspective in the evolution of BLM protein. All analyzed species in Bacteria, Archaea and Eukaryota formed a clear inter-species cluster, except for P. sinensis (Reptilia). The results supported that Hjm helicase may be one of the candidate potential ancestors of the BLM proteins and their homologs. Moreover, especially two domains which are Helicase ATP-binding and Helicase C-terminal domain were encountered in the all analyzed species and seem to be strictly conserved in the future. Repair related-highly sophisticated interaction network of BLM indicated that its functional evolution reaches a certain level and it appears to have taken an important place in maintaining genomic stability. However, it should be taken into account that BLM may acquire additional functions or become a cornerstone in different pathways in the future depending on its participation in various metabolic roads.

Small cell lung carcinoma (SCLC) is a highly aggressive cancer with low survival rate. Although initial response to chemotherapy in SCLC patients is well-rated, the treatments applied after the disease relapses are not successful. Drug resistance is accepted to be one of the main reasons for this failure. Therefore, there is an urgent need for new treatment strategies for SCLC. Meclofenamic acid, a nonsteroidal anti-inflammatory drug, has been shown to have anticancer effects on various types of cancers via different mechanisms. The aim of this study was to investigate the alterations that meclofenamic acid caused on a SCLC cell line, DMS114 using the tools of proteomics namely two-dimensional gel electrophoresis coupled to MALDI-TOF/TOF and nHPLC coupled to LC-MS/MS. Among the proteins identified by both methods, those showing significantly altered expression levels were evaluated using bioinformatics databases, PANTHER and STRING. The key altered metabolism upon meclofenamic acid treatment appeared to the cellular energy metabolism. Glycolysis was suppressed, whereas mitochondrial activity and oxidative phosphorylation were boosted. The cells underwent metabolic reprogramming to adapt into their new environment for survival. Metabolic reprogramming is known to cause drug resistance in several cancer types including SCLC. The identified differentially regulated proteins in here associated with energy metabolism hold value as the potential targets to overcome drug resistance in SCLC treatment.

Three siblings born to Turkish parents from the same village had normal brain development until acute neurological deterioration between 12 months and 8 years of age. Consequent loss of all acquired motor, social, and language functions following infections was associated with a pontine cyst, calcification, and cerebellar atrophy. Exome sequencing revealed a homozygous c.1297G>A (p.Gly433Ser) alteration in BEND4, which was predicted to be deleterious in in silico analysis tools and segregated in multiple affected individuals in the family. BEND4 has not been associated with any existing disease. Immunofluorescence microscopy analysis of wild-type and mutant BEND4 expressing Vero cells showed nuclear and cytoplasmic localization. Wild-type BEND4 displayed a network-like distribution, whereas mutant BEND4 showed a juxtanuclear distribution pattern. Differential proteome analysis of Vero cells expressing BEND4 revealed that mutant BEND4 expression caused selective increase in reticulocalbin-1 and endoplasmic reticulum resident protein-29. Both proteins are associated with the endoplasmic reticulum and are primarily involved in protein processing and folding pathways. Any defect or stress in protein folding creates stress on cells and may cause chronic damage. This is the first study showing that pathogenic BEND4 variants may lead to an infection-induced acute necrotizing encephalopathy as demonstrated in characteristic neuroimaging findings.

Prostate cancer is the most common type of cancer among men, and there is still no definitively effective drug treatment. Thus, the search for novel drug agents that may be used for the effective treatment continues. Meclofenamic acid (MA), a non-steroidal anti-inflammatory drug, with anti-tumor effects in various types of cancers was used to investigate its effects on LNCaP cells, a prostate cancer cell line, at the proteome level. The cells were treated with 80 µM MA for 24 h and a comparative proteomic analysis was performed with their untreated control cells. Proteins were extracted from the cells and then were subjected to two-dimensional gel electrophoresis. Protein spots displaying changes in their regulation ratios for more than two-fold were excised from the gels and identified with MALDI-TOF/TOF mass spectrometry. Bioinformatics analysis of the differentially regulated proteins that we identified showed that they were all associated with and took part in related pathways. Glycolytic pathway, cytoskeletal formation, transport activity, protein metabolism, and most notably an mRNA processing pathway were affected by the MA treatment. In addition to presenting a detailed information for what is happening inside the cells upon MA treatment, the proteins affected by MA treatment hold the potential to be novel targets for prostate cancer treatment provided that further in vivo experiments are carried out.

Idiopathic Granulomatous Mastitis (IGM) is a disease that clinically mimics breast cancers with symptoms of pain, edema, erythema, nipple discharge, nipple retraction, and fistula. Although IGM is considered to be formed by autoimmune responses or infections, the molecular mechanism behind formation and progress is unknown. Therefore, in this study, we aimed to investigate molecular mechanisms underlying IGM formation, progress, and recurrence by monitoring the changes at the proteome level. Protein extracts prepared from IGM (n = 15) and within-control tissues (n = 15) were subjected to nHPLC followed by LC-MS/MS proteomic analysis. Label-free quantitation analysis revealed that sixty differentially regulated between the two groups. Those proteins were classified based on their role in metabolic pathways using bioinformatics tools. Based on DAVID analysis, 16 of the differently regulated proteins were associated with the immune system, while 17 proteins were involved in cancer metabolism. STRING analysis showed that five of the differentially regulated proteins were associated with combined immune deficiency which were PNP, TAP1, ITGAL, PRKDC, and PTPRC while the other proteins were involved in insulin response and neutrophil degranulation. This study is one of the very few studies that investigated the changes in protein expressions of IGM tissues compared to controls. For the first time, we have shown the relationship of IGM with the immune system at the protein level and also underlined the cancer-like behavior of the disease. Furthermore, the proteins that were pointed out as combined immune deficiency-related proteins may have value as diagnostic markers for idiopathic granulomatous mastitis although further studies are needed to shed more light on the pathogenesis of the disease.

Objective: Fat mass and obesity associated (FTO) protein is an RNA-demethylase which is employed in various metabolic functions such as post-transcriptional modifications, DNA repair and fatty acid utilization. Fat mass and obesity associated protein was initially found to be closely associated with obesity and increased body-mass-index and later studies have established association of FTO with neurological diseases and cancer. The aim of this study was to investigate the effect of R316Q FTO mutation on soluble proteome in SH-SY5Y cells.Methods: SH-SY5Y cells stably expressing the wild-type (WT) and the mutant FTO proteins under the control of Tet-promoter were used to study changes in overall proteome using two-dimentional Difference Gel Electrophoresis approach. More than 500 protein spots were compared in samples that overexpressed the WT-FTO or the mutant-FTO protein according to 2-fold-criteria. Spots displaying differences were cut from the gels and identified by MALDI-TOF/TOF. Results: In overall, the expression of neither the WT nor the mutant FTO caused major changes in the soluble proteome. However, we observed some minor changes in six protein spots. Three of those protein spots belonged to Hsp70 and were up-regulated in the mutant-FTO-expressing cells. This indicated that Hsp70 was not only up-regulated but also post-translationally modified. The other proteins regulated were phosphoglycerate kinase-1, calmodulin and keratin. Conclusion: These results indicated that FTO appear to be associated with energy metabolism and might induce the cellular stress. In addition, FTO might affect to the Wnt signalling pathway. In overall, our study highlighted the multifaceted properties of the FTO and reflected onto the changes occurring in the proteome of neuroblastoma cells.

Background/aim During the last two decades, Parkinson's disease (PD)-associated genes have been associated with cancer; however, a shared pathogenic mechanism has yet to be discovered. Parkin, an E3 ubiquitin ligase that is involved in early-onset Parkinson's disease, has also been reported to exert tumor suppressor activity. However, the details about the role of Parkin in cancer remain unknown. The present study aimed at identifying differentially regulated nuclear proteins and nuclear phosphoproteins whose levels were affected by Parkin expression. Materials and methods SHS-SY5Y cells expressing either wild-type Parkin or its mutant under tetracycline control were used in this study; cells not expressing Parkin served as control. Nuclear proteins were enriched from Parkin-expressing and control cells to perform a comparative proteomics study using two-dimensional gel electrophoresis (2D) coupled to matrix assisted laser desorption/ionisation-time of flight (MALDI-TOF/TOF) mass spectrometry analysis. Changes in phosphoproteome and nuclear phosphoproteome were also studied by staining the 2D gels with ProQ diamond phosphoprotein stain. The identified proteins were subjected to bioinformatics analysis to elucidate the reactomes and relevant pathways. Results Six nuclear proteins, namely NCL, DDIT3, PARP1, HMGB1, TCTP and TPI were shown to be differentially regulated in cells expressing Parkin protein. Regulations in phosphorylation levels of ENPL, PRDX4, ECHM, ALDOA SET, DHSA, RCC1 and DULRD were also detected. Bioinformatics analysis of differentially regulated proteins highlighted the involvement of Parkin in DNA repair. Conclusion Several nuclear protein candidates whose expression or phosphorylation levels were altered in cells expressing Parkin. Bioinformatics analysis of these proteins indicated that the nuclear form of Parkin may play a significant role in DNA repair and contribute to prevention of tumorogenesis via maintaining DNA integrity.

Objective: Proteomic approaches, have been used in monitoring the disease processes and identification of biomarkers. Biological samples used in the field of proteomics include biological fluids and solid samples. In this context, pre-analytical processes e.g., tissue sample quality, sampling site accuracy and sample transfer time to the site of proteomic laboratory are very important. In this study, the proteome profiles of samples taken from two different regions within a tumor tissue were compared to show tumor heterogeneity.Material and Methods: Proteins obtained from two different regions of adrenocortical tumor tissue (adenoma and intra-adenoma) and healthy tissue of a patient who was operated on with the diagnosis of Cushing's syndrome were separated by 2DE and subjected to comparative analysis. The number of differentially regulated proteins among the samples was determined and identified by MALDI-TOF/TOF mass spectrometry. Results: Seventeen and thirteen proteins were differentially regulated in the adenoma and intra adenoma regions compared to the control tissue, respectively. These proteins mostly associated with energy metabolism, cytoskeletal organization, and cellular stress. Conclusion: This study showed to what extent the sample area in the tumor tissue affects the proteome profile. The samples taken from two different regions of a same tumor tissue displayed serious differences in the expressions of some proteins, mostly those associated with energy metabolism. This highlights the need to be careful in interpreting proteomic findings, especially in studies where biomarkers are sought. To minimize sample variation, as many samples as possible should be studied in proteomic studies., Amaç: Birçok hastalığın ve kanserlerin biyolojik mekanizmalarının incelenmesinde yaygın olarak kullanılan proteomik yaklaşımlar, hastalık sürecinin izlenmesinde, biyobelirteçlerin ve potansiyel terapötik hedeflerin tanımlanmasında kullanılagelmektedir. Proteomik alanında kullanılan biyolojik örnekler arasında serum gibi biyolojik sıvılar ve doku gibi katı örnekler sayılabilir. Bu bağlamda analiz edilen doku örneklerinin kalitesi, örneğin alındığı bölgenin doğruluğu ve hatta örneğin alınmasından sonra proteomik araştırma laboratuarına ulaşıncaya kadar geçen süre gibi pre-analitik süreçler çok önemlidir. Biz bu çalışmamızda, tümör dokusu içerisinde iki farklı bölgeden alınan örneklerin çözünür proteom profillerini karşılaştırmayı ve varsa tümör heterojenitesini göstermeyi amaçladık.Gereç ve Yöntemler: Cushing sendromu tanısı ile opere edilen bir hastanın adrenokortikal tümör dokusunun iki farklı bölgesinden (adenoma ve adenoma içi) ve sağlıklı dokusundan elde edilen proteinler 2DE yöntemi ile ayrıştırılarak karşılaştırmalı analize tabi tutulmuştur. Örnekler arasında regülasyon düzeyinde farklılık görülen protein sayısı belirlenmiş ve jellerden kesilerek MALDI-TOF/TOF kütle spektrometresi aracılığı ile tanımlanmıştır. Bulgular: Kontrol dokusuna göre adenom bölgesinde 17 protein, adenom içi bölgede ise 13 proteinin seviyelerinde regülasyon tespit edilmiştir. Bu proteinler çoğu enerji metabolizması, hücre iskeleti organizasyonu ve hücresel stres ile ilişkili proteinlerdir. Sonuç: Bu çalışma tümör dokusu içerisinde örneğin alındığı bölgenin proteom profilini ne ölçüde etkilediğini göstermiştir. Tümör dokusundan iki farklı bölgeden aldığımız örneklerde daha çok enerji metabolizması ile ilişkili proteinler olmak üzere bazı proteinlerin ifadelerinde ciddi farklılıklar görülmüştür. Bu durum özellikle biyobelirteç arayışlarının olduğu çalışmalarda proteomik bulgularının yorumlanmasında dikkat edilmesi gerektiği ve proteomik çalışmalarında örnek sayısının mümkün olduğunca fazla tutulması gerektiğini vurgulamaktadır.

Serum contains proteins that possess important information about diseases and their progression. Unfortunately, these proteins, which carry the information in the serum are in low abundance and are masked by other serum proteins that are in high abundance. Such masking prevents their identification and quantification. Therefore, removal of high abundance proteins is required to enrich, identify, and quantify the low abundance proteins. Immunodepletion methods are often used for this purpose, but there are limitations in their use because of off-target effects and high costs. Here we presented a robust, reproducible and cost-effective experimental workflow to remove immunoglobulins and albumin from serum with high efficiency. The workflow did not suffer from such limitations and enabled identification of 681 low abundance proteins that were otherwise undetectable in the serum. The identified low abundance proteins belonged to 21 different protein classes, namely the immunity-related proteins, modulators of protein-binding activity, and protein-modifying enzymes. They also played roles in various metabolic events, such as integrin signalling, inflammation-mediated signalling, and cadherin signalling. The presented workflow can be adapted to remove abundant proteins from other types of biological material and to provide considerable enrichment for low-abundance proteins.

In diabetic retinopathy patients, intravitreal bevacizumab (IVB) injections are widely used to facilitate dissection of retinal fibrovascular membranes during surgery, reduce the rate of perioperative hemorrhage, and prevent recurrent neovascularization. Previous studies have shown that IVB may worsen fibrosis and thereby impair vision. The aim of this study was to determine which markers are associated with fibrosis.Twenty-three patients with proliferative diabetic retinopathy (PDR) underwent pars plana vitrectomy (PPV) with IVB pretreatment for intraocular hemorrhage (IOH) and/or tractional retinal detachment (TRD). Vitreous samples were obtained at the time of IVB injection and again at the beginning of PPV, about a week later. Using Western blot analysis, the concentrations of vascular endothelial growth factor (VEGF), placental growth factor (PIGF), insulin like growth factor-1 (IGF-1), angiogenin-1 (Ang-1), and vascular endothelial cadherin (VE-cadherin) were measured in vitreous samples.After treatment with IVB, VEGF, PIGF, and VE-cadherin concentrations in the vitreous significantly decreased (p 0.001, p 0.001, and p = 0.001, respectively), whereas the concentrations of IGF-1 increased (p = 0.001). There were no significant changes in Ang-1 concentrations in the vitreous after IVB injection (p = 0.732). There were no statistically significant differences in VEGF-A, PIGF, VE-cadherin, IGF, and Ang-1 levels before and after IVB injection when the IOH and TRD groups underwent subgroup analysis (p = 0.696, p = 0.516, p = 0.498, p = 0.188, and p = 0.243, respectively).The levels of VEGF and other cytokines changed in the vitreous after IVB. The adverse effects associated with IVB, such as fibrosis, may result from modulation of vitreous cytokine concentrations. In the treatment of PDR, drugs that optimize the effects of PIGF, IGF-1, and VE-cadherin to reduce these side effects may be useful.

Behçet's syndrome (BS) is a systemic inflammatory disorder with unknown etiology. Investigation of proteome profiles of disease specific cells facilitates our understanding of the processes and related molecular pathways, especially in disorders like BS with complex inheritance pattern and clinical heterogeneity. In the current study, we evaluated the peripheral blood mononuclear cells (PBMCs) proteome of 59 patients with BS (33 in active and 26 in inactive phases) and of 28 healthy controls using two-dimensional fluorescence difference gel electrophoresis (2D-DIGE). Differentially expressed protein spots with at least twofold and/or statistically significant change (p ≤ 0.05) between active BS vs inactive BS, and also active BS vs healthy controls were identified by mass spectrometry (MALDI-TOF/TOF). Bioinformatic analyses revealed 16 differentially expressed proteins (12 of them in active vs inactive BS comparison, whereas 11 of them for active BS vs healthy control comparison) belonging to glycolysis, cytoskeleton organization, protein folding, and regulation of blood coagulation pathways. Stathmin (active BS vs inactive BS; fourfold, active BS vs healthy control; 4.7-fold) and WD repeat-containing protein-1 (active BS vs inactive BS; 2.7-fold, active BS vs healthy control; 2.7-fold), which are cytoskeleton-related proteins, were found to be lower in active patients compared to inactive patients and healthy control. Decreased levels of calreticulin (active BS vs inactive BS; 1.29-fold) and heat shock 70 kDa protein 8 (active BS vs healthy control; 1.5-fold) which are involved in protein folding and endoplasmic reticulum (ER) stress process, were observed in patients with active phase of BS. Down-regulation of protein folding and ER stress process proteins in BS patients may further support the involvement of ER stress in BS.

Plasma membrane proteins perform a variety of important tasks in the cells. These tasks can be diverse as carrying nutrients across the plasma membrane, receiving chemical signals from outside the cell, translating them into intracellular action, and anchoring the cell in a particular location. When these crucial roles of plasma membrane proteins are considered, the need for their characterization becomes inevitable. Certain characteristics of plasma membrane proteins such as hydrophobicity, low solubility, and low abundance limit their detection by proteomic analyses. Here, we presented a comparative proteomics study in which the most commonly used plasma membrane protein enrichment methods were evaluated. The methods that were utilized include biotinylation, selective CyDye labeling, temperature-dependent phase partition, and density-gradient ultracentrifugation. Western blot analysis was performed to assess the level of plasma membrane protein enrichment using plasma membrane and cytoplasmic protein markers. Quantitative evaluation of the level of enrichment was performed by two-dimensional electrophoresis (2-DE) and benzyldimethyl-n-hexadecylammonium chloride/sodium dodecyl sulfate polyacrylamide gel electrophoresis (16-BAC/SDS-PAGE) from which the protein spots were cut and identified. Results from this study demonstrated that density-gradient ultracentrifugation method was superior when coupled with 16-BAC/SDS-PAGE. This work presents a valuable contribution and provides a future direction to the membrane sub-proteome research by evaluating commonly used methods for plasma membrane protein enrichment. TUBITAKTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [113S868] WOS:000492416500007 31346646 Q3

Background/aim Breast cancer (BC) incidence and mortality rates have been increasing due to the lack of appropriate diagnostic tools for early detection. Proteomics-based studies may provide novel targets for early diagnosis and efficient treatment. The aim of this study was to investigate the global changes occurring in protein profiles in breast cancer tissues to discover potential diagnostic or prognostic biomarkers. Materials and methods BC tissues and their corresponding healthy counterparts were collected, subtyped, and subjected to comparative proteomics analyses using two-dimensional gel electrophoresis (2-DE) and two-dimensional electrophoresis fluorescence difference gel (DIGE) coupled to matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF/TOF) to explore BC metabolism at the proteome level. Western blot analysis was used to verify changes occurring at the protein levels. Results Bioinformatics analyses performed with differentially regulated proteins highlighted the changes occurring in triacylglyceride (TAG) metabolism, and directed our attention to TAG metabolism-associated proteins, namely glycerol-3-phosphate dehydrogenase 1 (GPD1) and monoacylglycerol lipase (MAGL). These proteins were down-regulated in tumor groups in comparison to controls. Conclusion GPD1 and MAGL might be promising tissue-based protein biomarkers with a predictive potential for BC.

Background: To investigate the protein content in patients with age-related macular degeneration (AMD) with the aim of revealing the pathogenesis of the disease. Methods: Two groups were formed: 13 patients as the AMD group and 11 patients as the healthy control group. Vitreous samples were taken from both groups under sterile conditions and sent to the proteomics laboratory for proteomics analysis. In this study, we evaluated the proteome of vitreous samples of AMD and control groups using two-dimensional gel electrophoresis (2DE) coupled with MALDI-TOF/TOF.Results: We detected 11 proteins differentially regulated in the vitreous of AMD patients relative to healthy controls. The only protein that was up-regulated was Apolipoprotein E. We observed that Alpha 1-acid glycoprotein (AAG), Leucine-rich alpha-2-glycoprotein (LRG-1), Alpha-2-HS-glycoprotein, Haptoglobin, Alpha-Crystalline A Chain, Alpha- Crystalline B Chain, Immunoglobulin kappa constant, Beta-crystallin B2, Beta-crystallin A3, Beta-crystallin S levels were significantly decreased in patients with AMD. Conclusion: The detected proteins are related to biological regulation, retinal protection, and regulation of inflammation and angiogenesis processes. We believe that investigating these proteins will help to reveal the pathological mechanisms of AMD.

Serum is a valuable biomarker source and serum biomarkers can tell us a lot about an organisms current health status. For many human diseases, however, there is no serum biomarker available. Those biomarkers are still waiting to be discovered. Herein we presented a protocol that allowed depletion of immunoglobulins and reduction of albumin from human serum with high efficiency to unveil potential serum biomarkers. The protocol involved the use of protein G column and preperative gel electrophporesis. Unlike other protocols that are currently in use, the protocol developed in here prevented off-target affects caused by the albumin. In overall, more than 2.5-fold increase was achieved in identification of potential biomarker proteins.

We aimed to identify proteins that were differentially regulated in spermatozoal samples collected from fertile healthy men (FHM) and infertile patients with varicocele (IFPV) before and after varicocelectomy. Seminal samples were collected from 20 IFPV before and after varicocelectomy and from 14 FHM as controls. Samples underwent seminal examination and proteomic analysis. Extracted spermatozoal proteins were analysed using two-dimensional gel electrophoresis, and differentially regulated spermatozoal proteins (DRSPs) were identified. In particular, attention was placed on those DRSPs in which the concentration changed after varicocelectomy and corrected to approximate levels observed in FHM. Varicocelectomy significantly improved the sperm count and concentration in IFPV (p < 0.05). Proteomic analysis showed that 11 DRSPs were identified when comparisons were made among the three groups. Among these 11 proteins, change in the SERPIN A5 concentrations was notable because it was 100-fold downregulated in pre-operative IFPV samples and nearly resembled to control concentrations following varicocelectomy. Western blot analysis using an anti-SERPIN antibody validated the changes observed in SERPIN A5 levels before and after varicocelectomy operation. Increase in SERPIN A5 after varicocelectomy may be due to improvement in semen quality, suggesting that SERPIN A5 is a potential seminal biomarker for assessment of semen quality in varicocele-related infertility.

Graves' disease (GD) and toxic multinodular goitre (TMNG) are the most common thyroid diseases which mainly lead to thyrotoxicosis, however, the underlying mechanism of distinct clinical presentations remains unclear. Protein extracts from the thyroid tissue specimens of the patients with GD and TMNG were subjected to Difference Gel Electrophoresis (DIGE). Differentially regulated protein spots were determined by image analysis, and the spots displaying statistically significant differences were identified by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometer (MALDI-TOF) followed by MASCOT search. Western blot analysis was used to verify changes occurring at the protein levels. The identified proteins were classified based on their functions in metabolic pathways using bioinformatics algorithms. Fifteen proteins showed significant alterations in abundance between the two disease groups. Bioinformatic analysis revealed the differentially regulated proteins were particularly related to catabolism, oxidative stress and especially energy utilization pathways, including glycolysis, proteolysis, ketone body catabolism and other energy metabolism-related pathways. SIGNIFICANCE OF THE STUDY: Previously, GD has been the subject of many studies that performed the proteomics approaches in the orbital tissue samples or tear. This is one of the very few studies that investigate the changes in the proteome of thyroid tissue in GD. We demonstrated mainly the upregulation of catabolic activity-related proteins in patients with GD compared to TMNG. Although it remains to be elucidated, some of these proteins can be used as markers for GD or have a role in the pathogenesis of the disease. Our study contributes the increasing data over time by providing new biomarker candidates for GD.

One of the drawbacks preventing the use of mesenchymal stem cells (MSCs) in clinical practice is the heterogeneous nature of their cultures. MSC cultures are not homogeneously formed by the MSCs and may contain non-mesenchymal cell types. Therefore, prior to use in clinics or research, complete characterization of MSCs should be performed to demonstrate the existence or absence of proper stem cell markers, many of which are happened to be cell-surface proteins. Unfortunately, the success of MSC characterization studies is limited due to the low specificity of the currently available cell-surface markers. Therefore, in this study, we aimed to investigate the plasma membrane (PM) proteins of MSCs isolated from human dental pulp (DP), adipose tissue (AT), bone marrow (BM), and hair follicle (HF) with the hope of proposing novel putative specific MSC markers. Differential-velocity centrifugation was used to enrich PM proteins. The isolated proteins were then identified by nLC-MS/MS and subjected to bioinformatics analysis. Proteins that were unique to each MSC type (CD9, CD10, CD63 for DP-MSCs; CD26, CD81, CD201, CD364 for AT-MSCs; Cd49a, CD49d for HF-MSCs; CD49e, CD56, CD92, CD97, CD156b, CD156c, CD220, CD221, CD298, CD315 for BM-MSCs) and common to all four MSC types (CD13, CD29, CD44, CD51, CD59, CD73, CD90) were identified. Uncharacterized proteins that have transmembrane (TM) domains were also detected. Some of the proteins identified in this study were the putative cell-surface markers that might be used for characterization of MSCs. WOS:000670167600001 34230997 Q4

Neuronal autoantibodies and favorable response to immunosuppressive treatment have been described in patients with chronic epilepsy of unknown cause, suggesting autoimmune etiology. Our aim was to identify novel epilepsy-specific autoantibodies reactive with neuronal surface antigens.Sera of 172 epilepsy patients with unknown cause and 30 healthy controls were screened with indirect immunofluorescence to identify IgG reacting with primary rat neuronal cultures. Putative target autoantigens were investigated with immunoprecipitation (IP) and liquid chromatography-mass/mass spectrometry (LC-MS/MS) studies using SH-SY5Y cells. Validation of LC-MS/MS results was carried out by IP and immunocytochemistry assays.Antibodies to neuronal cell surface antigens were detected in 18 epilepsy patients. LC-MS/MS analysis identified voltage-gated potassium channel modifier subfamily F member 1 (KCNF1, Kv5.1) as the single common cell surface antigen in 4 patients with Lennox-Gastaut syndrome (n = 2), focal epilepsy of unknown cause (n = 1) and mesial temporal lobe epilepsy with hippocampal sclerosis (n = 1). These patients had the common features of early seizure onset and treatment-resistance. IP assays and co-localization (serum IgG and commercial Kv5.1-antibody) studies done with non-fixed Kv5.1-transfected HEK293 cells and primary neuronal cultures confirmed the presence of Kv5.1-antibody in 4 epilepsy patients identified by LC-MS/MS. Similar findings were not obtained by sera of other patients with epilepsy, patients with autoimmune encephalitis and healthy controls.The herein described novel neuronal surface antibody to Kv5.1 appears to be associated with treatment-resistant epilepsy of unknown cause. Exact clinical and pathogenic significance of this antibody remains to be elucidated.

The SARS-CoV-2 virus caused the most severe pandemic around the world, and vaccine development for urgent use became a crucial issue. Inactivated virus formulated vaccines such as Hepatitis A, oral polio vaccine, and smallpox proved to be reliable approaches for immunization for prolonged periods. During the pandemic, we produced an inactivated SARS-CoV-2 vaccine candidate, having the advantages of being manufactured rapidly and tested easily in comparison with recombinant vaccines. In this study, an inactivated virus vaccine that includes a gamma irradiation process for the inactivation as an alternative to classical chemical inactivation methods so that there is no extra purification required has been optimized. The vaccine candidate (OZG-38.61.3) was then applied in mice by employing the intradermal route, which decreased the requirement of a higher concentration of inactivated virus for proper immunization, unlike most of the classical inactivated vaccine treatments. Hence, the novelty of our vaccine candidate (OZG-38.61.3) is that it is a non-adjuvant added, gamma-irradiated, and intradermally applied inactive viral vaccine. Efficiency and safety dose (either 1013 or 1014 viral copy per dose) of OZG-38.61.3 was initially determined in Balb/c mice. This was followed by testing the immunogenicity and protective efficacy of OZG-38.61.3. Human ACE2-encoding transgenic mice were immunized and then infected with a dose of infective SARS-CoV-2 virus for the challenge test. Findings of this study show that vaccinated mice have lower SARS-CoV-2 viral copy number in oropharyngeal specimens along with humoral and cellular immune responses against the SARS-CoV-2, including the neutralizing antibodies similar to those shown in Balb/c mice without substantial toxicity. Subsequently, plans are being made for the commencement of Phase 1 clinical trial of the OZG-38.61.3 vaccine for the COVID-19 pandemic.

Talazoparib (TAL) has been effectively used for the treatment of gBRCA1/2-mutated HER2-negative metastatic breast cancer. However, acquired resistance to TAL remains a major challenge that impedes the clinical success of TAL treatment. Therefore, elucidation of proteins and pathways that contribute to or are affected by the TAL resistance is urgently needed to improve the treatment response and provide novel treatment strategies for advanced metastatic breast cancers. Herein, we aimed to investigate the altered protein signatures in TAL-resistant triple-negative breast cancer (TNBC) cells by comparing with the TNBC parental cell line via proteomic analysis. After validation of TAL-resistance by WST-1 and Annexin V analysis, two-dimensional gel electrophoresis (2DE)-based proteomic analysis coupled to matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF) mass spectrometry was performed to identify differentially regulated proteins. The findings revealed the identities of 10 differentially regulated proteins in TAL-resistant TNBC cells whose bioinformatic analysis predicted changes in EGF/FGF signaling pathways as well as in the AMPK signaling pathway. In addition, phosphorylation/dephosphorylation dynamics were predicted to be altered in TAL-resistant cells. The proteins identified in this study might be the targets to overcome TAL resistance for the treatment of TNBC.

In this study, we aimed to compare DNA fragmentation ratios, centrosomal protein concentrations (centrin and tubulin) and numerical chromosomal abnormalities between four groups including asthenozoospermia, teratozoospermia, oligoasthenozoospermia and normozoospermia patients, and to emphasize the necessity of investigating genetic and protein content of the spermatozoa also in patients with a semen analysis within normal reference range. Evaluation of semen analysis of the patients was performed based on WHO 2010 criteria. As a result of the statistical analysis, it was observed that the sperm DNA fragmentation rate in the normozoospermia group (6.50 ± 3.46%) was significantly lower than those in the teratozoospermia (19.69 ± 9.86%) and oligoasthenoteratozoospermia group (32.47± 14.13%) (p

Purpose The aim of this study was to monitor inflammatory, proliferative and progressive effects of proliferative vitreoretinopathy (PVR) and aflibercept treatment in dispase induced PVR rat model by proteomic analysis. Material and methods A total of 35 male Long Evans pigmented rats were divided into three groups, namely, PVR (dispase+saline), PVR+aflibercept (dispase+aflibercept) and control. The PVR group received 2 μl of 0.03 IU/μl dispase and 2 μl saline, the PVR+aflibercept group received 2 μl of 0.03 IU/μl and 2 μl of 40 mg/ml aflibercept at the first day of the experiment. At the end of the 6th week all retina and vitreous specimens were collected by evisceration and transferred to the proteomics laboratory for analysis. Proteomic analysis by 2D gel electrophoresis coupled with MALDI-TOF/TOF was performed. Results In the PVR and PVR+aflibercept group 16 different proteins that were identified to be differentially regulated in comparison to the control group. In the PVR+aflibercept group, ENO1, ENO2, LDH-B, PEBP-1 and GS levels were higher than the PVR group. In addition, the association of proteins such as UCHL, PEBP1, PDHB and ENO1 with PVR has been demonstrated for the first time. Conclusion STRING analysis elucidated the functional protein-protein interaction among the differentially regulated proteins and highlighted that those proteins mainly played roles in carbon and nucleotide metabolisms. Functional analysis of the differentially regulated proteins indicated the presence of inflammation, gliosis and retinal damage in the PVR group. Aflibercept treatment had pronounced effect on prevention of inflammation and retinal damage while causing a slight increase in gliosis. However, aflibercept treatment was not effective enough to normalize the levels of differentially regulated proteins of the PVR group. Therefore, we predict that the treatment dose of aflibercept used in this study was below of its ideal concentration and should be increased in the future studies. The differential regulation of these structural proteins in this study should shed some light to the mechanism of glial wound formation in the retina and guide future treatment modalities.

Introduction The origin and content of prolonged wound drainage (PWD) after arthroplasty remain uncertain. In this study, we performed the biochemical, biological and advanced proteomic analysis of the drainage fluid collected from PWD patients following hip hemiarthroplasty (HA). Methods Data of 28 patients who developed PWD after HA were prospectively analyzed. After examining the biochemical content of the drainage fluid collected on postoperative day 6, to find out if the drainage fluid was transudate or exudate, it was compared with the patient's serum values according to the Light criteria. Subsequently, biological and proteomic analyzes of both drainage fluid and serum were performed. The similarities and differences in terms of protein concentrations, protein identities were examined. In the drainage fluid, we analyzed lymph-specific proteins. Results 16 patients with PWD were male (61.1%), 12 were female (38.9%), and the mean age of all patients was 79.64 ± 8.44 (65-95). Biochemical test results of the drainage fluid / serum were as follows: Total protein: 2.1 / 5.2 g/dl, albumin: 1.3 / 3.1 g/dl, lactate dehydrogenase (LDH): 121/324 U/l, cholesterol: 28/160 mg/dl, triglyceride: 37/122 mg/dl, sodium (Na): 140/ 140mg/dl, potassium (K): 4.1/ 4.1 mg/dl. pH of the drainage fluid was 7.6. According to these biochemical values, drainage fluid was classified as transudate. As a result of protein identification, fibrinogen beta chain, keratin type 1, creatine kinase M-type protein were detected in drainage fluid. Subsequent western analysis revealed that, gliseraldehyde-3-phosphate dehydrogenase (GAPDH) and beta actin antibody were detected in the drainage fluid but not in serum. Conclusion Despite the similarity in serum and transudative PWD fluid in terms of biochemical content, we found that when we carried out further proteomic analysis, PWD contains lymph-specific proteins. Unlike PWD, these proteins were not determined in serum. PWD fluid can be also called as lymphorrhea. PWD fluid with abundant proteins may also provide an appropriate environment for the growth of microorganisms.

Objective Investigating the molecular basis of bipolar disorder (BD) is crucial in terms of developing effective treatment strategies as well as objective laboratory-based diagnostic tools for the disease. Methods We examined the urine samples of BD patients both in manic episode and after remission and compared their urinary protein profiles with the controls. Twelve patients and twelve controls (C group) included to the study. Urinary samples of patients were first collected during manic episode (M group) and then after remission (R group). Two-dimensional gel electrophoresis (2-DE) coupled to MALDI-TOF/TOF massspectrometry approach and Western blot analysis were used. Results Alpha-1-microglobulin and bukinin precursor (AMBP), Mannan-binding lectine serin protease-2 (MASP-2), and Ig gamma-1-chain displayed significant increases in their abundance in the urine protein pool of M group in comparison to the C and R groups. Alpha-1B glycoprotein and prostaglandin-H2 D-isomerase (PGD2) levels were significantly higher in the urine protein pool of the M and R groups in comparison to the C group. Annexin A1 was downregulated significantly in the urine protein pool of the M group in comparison to the C group. Conclusion Intensities of MASP-2 and AMBP proteins discriminated manic episode from remission period and healthy controls indicating that these proteins may be candidate biomarkers for manic episode. The decrease in Annexin A1 and increase in Ig gamma-1 chain levels appeared to be associated with "Manic Episode" while the increase in PGD2 and alpha-1B glycoprotein levels appeared to be associated with "Bipolar Disorder".

PubMed: 32682359 2-s2.0-85098783154 Background/aim: Thermopsis turcica is a perennial species endemic to Turkey and different extracts of T. turcica have an antiproliferative effect on cancer cells, but there has not been any report on HeLa (human cervical cancer) cells. Materials and methods: To get a better understanding of the molecular mechanism of anticancer activity of methanolic extracts of leaves (LE) and flowers (FE) of T. turcica, we employed 2-DE-based proteomics to explore the proteins involved in anticancer activity in HeLa cells. Results: T. turcica extracts showed a potent cytotoxic effect on HeLa cells with the IC50 values of 1.75 mg/mL for LE and 3.25 mg/mL for FE. The induction of apoptosis by LE and FE was also consistent with increased expression of caspase mRNAs and DNA fragmentation. In terms of the proteomic approach, 27 differentially expressed proteins were detected and identified through MALDI-TOF/TOF mass spectrometry. These altered proteins were involved in cytoskeleton organization and movement, protein folding, proteolysis and translation, cell cycle and proliferation, signal transduction, cell redox homeostasis, and metabolism. Conclusion: Up-regulation of protein disulfide isomerases and down-regulation of Rho GDP-dissociation inhibitor, heterogeneous nuclear ribonucleoproteins, and heat shock proteins may contribute to the induction of apoptosis and arresting of the cell cycle in HeLa cells. © TÜBİTAK. Afyon Kocatepe Üniversitesi: TEMAT?K.01 This work was supported by Afyon Kocatepe University Scientific Research Projects Coordination Unit (project number: 15.TEMATİK.01). The authors also wish to thank Afyon Kocatepe University’s Foreign Language Support Unit for language editing. This work was supported by Afyon Kocatepe University Scientific Research Projects Coordination Unit (project number: 15.TEMAT?K.01). The authors also wish to thank Afyon Kocatepe University?s Foreign Language Support Unit for language editing.

Background/purpose: It is well-known that diverse types of blood proteins contribute to healing process via different mechanisms. Presence and potential involvements of blood-derived abundant proteins in the platelet-rich fibrin (PRF) to its regenerative capacity have not been sufficiently emphasized in the literature. The aim of this paper was to analyze the abundant proteome content of PRF and summarize previously reported effects of identified proteins on wound healing via a literature review. Materials and methods: The PRF samples obtained from non-smoking, systemically healthy volunteers were subjected to 2D gel electrophoresis after extracting the proteins from fibrin matrices. All matching spots were excised from the gels and identified by MALDI TOF/TOF MS/MS analysis. A literature review was conducted to reveal possible contributions of identified proteins to wound healing. Results: Totally, thirty-five blood proteins were commonly identified among all studied samples. These proteins included serine protease inhibitors, such as alpha-1-antitrypsin, alpha-1-antichymotrypsin, alpha-1-acid glycoprotein, inter-alpha-trypsin-inhibitor, protease C1 inhibitor, and complement proteins. In addition, abundant presence of immunoglobulin G was observed. The abundance of albumin, haptoglobin, ceruloplasmin vitronectin, fetuin-A, ficolin-3 and transthyretin was also detected. Conclusion: The results of this study indicated that PRF abundantly contains blood-origin actors which were previously reported for their direct contribution to wound healing. Further studies exploring the protein content of PRF are needed to reveal its undisclosed potential roles in the healing process. Keywords: Platelet-rich fibrin, Proteomics, MALDI, Blood proteins

Tetracycline regulated protein expression in mammalian cells is a powerful tool to predict the physiological function, cellular localization, and stability of a protein. In addition, to predict metabolic networks affected by the expression of wild-type or mutant forms of proteins, researchers generally produce a single mammalian cell clone that can express the protein of interest under tetracycline control and study the changes occurring in overall proteome before and after expression of a protein of interest. One limitation of tetracycline regulated clonal cell creation, however, is that it sometimes creates clones with changed protein levels even without the expression of the protein of interest due to the nonspecific insertion of the gene encoding the protein of interest into the genome or disruption of a metabolic pathway due to insertional silencing or activation. The aim of this study was to demonstrate the limitation of tetracycline regulated gene expression by creating clonal cell lines expressing the wild-type or the mutant forms of Fat mass and obesity-associated protein. Comparative proteome analysis of the protein extracts by two-dimensional gel electrophoresis coupled to MALDI-TOF/TOF revealed the presence of eight proteins subjected to differential regulation even in the absence of induction. The identified proteins were 14-3-3 protein Epsilon, Vimentin, Heterogeneous nuclear ribonucleoprotein K, Tubulin beta-2C chain, Heat shock protein HSP 90-alpha, Heat shock protein HSP 90-beta, Alpha-enolase, TATA-binding protein-associated factor 2N. An ultimate care should be taken to prevent reporting of deceitful proteins generated from studies utilizing tetracycline regulated gene expression systems.

To elucidate the metabolic processes playing roles in the formation of keratoconus (KC). Tears samples were collected using capillary glass tubes without stimulation and without prior anesthesia from 17 patients and 16 controls. Proteomic analysis by fluorescent 2D gel electrophoresis (DIGE) coupled with MALDI-TOF/TOF was performed. The identified proteins that were differentially regulated were subjected to Ingenuity Pathway Analysis (IPA). Corneal topography analyses with Sirius topography system (Costruzioni Strumenti Oftalmici, Florence, Italy) were performed on all participants. The steepest keratometry index was lower than 50 diopters in all keratoconus patients. DIGE analysis showed changes in abundance of nine proteins. Six of these proteins, namely serum albumin, Keratin Type II Cytoskeletal 1, IgG gamma chain-1, GAPDH, alpha-1 antitrypsin and ApoA-I, were down-regulated in the KC samples in comparison with the controls. In addition, we detected up-regulation of lysozyme C, keratin type I cytoskeletal 10 and lipocalin. The subsequent IPA predicted that NADH repair pathway is activated in the KC patients. This pathway involves generation of NADHX as a by-product via catalysis by GAPDH. NADHX is an inhibitor of several dehydrogenases and must be removed. The involvement of NADHX repair pathway in KC should be investigated, since preliminary clues obtained in this study point to that direction. In particular, showing the presence of ATP-dependent NAD(P)H-hydrate dehydratase that eliminates NADHX would strengthen our findings and would be a major step toward understanding KC.

The objective of this study is to perform proteomic analysis of pleomorphic adenoma (PA) in the human parotid gland (PG) with comparison of normal PG. This is an individual prospective randomized controlled trial. This study was performed in a tertiary referral center. Tissue samples of PG and PA were taken after surgical excision of PG from 13 patients. Protein extracts were prepared and protein pools created from the soluble extracts were subjected to 2D-DIGE analysis. Proteins displaying regulation in their abundance were determined and identified using MALDIT-OF/TOF analysis. The identified proteins were subjected to STRING analysis for classification of the proteins based on their biological roles in metabolic pathways. Fifteen proteins, carbonic anhydrase 1, carbonic anhydrase 2, fibrinogen beta chain, alpha-amylase 1, heats hock protein hsp 90-alpha, clusterin, 78 kDa glucose-regulated protein, endoplasmin, alpha-amylase 2b, ATP synthase subunit alpha (mitochondrial), elongation factor 1-gamma, malate dehydrogenase, cytoplasmic, triosephosphate isomerase, receptor of activated protein c kinase 1, and aconitate hydratase, mitochondrial were down-regulated, whereas 11 proteins including ig kappa chain c region, serotransferrin, vimentin, annexin a5, glial fibrillary acidic protein, calreticulin, cartilage oligomeric matrix protein, microfibril-associated glycoprotein 4, 14-3-3 protein epsilon, fibulin-5, and f-box only protein 2 were up-regulated in PA samples in comparison to healthy parotid tissue. This study described the differences observed in protein expression patterns of the PA and normal PG. The results may provide new insights into the pathogenesis and diagnosis of PA in human PG. Level of evidence: 1b.

Background/Aim: To unveil the pathophysiology of primary hyperparathyroidism, molecular details of parathyroid hyperplasia and adenoma have to be revealed. Such details will provide the tools necessary for differentiation of these two look-alike diseases. Therefore, in the present study, a comparative proteomic study using postoperative tissue samples from the parathyroid adenoma and parathyroid hyperplasia patients was performed. Materials and Methods: Protein extracts were prepared from tissue samples (n=8 per group). Protein pools were created for each group and subjected to DIGE and conventional 2DE. Following image analysis, spots representing the differentially regulated proteins were excised from the and used for identification via MALDI-TOF/TOF analysis. Results: The identities of 40 differentially-expressed proteins were revealed. Fourteen of these proteins were over-expressed in the hyperplasia while 26 of them were over-expressed in the adenoma. Conclusion: Most proteins found to be over-expressed in the hyperplasia samples were mitochondrial, underlying the importance of the mitochondrial activity as a potential biomarker for differentiation of parathyroid hyperplasia from adenoma.

Gingiva is a unique tissue which protects the underlying periodontal tissues from consistent mechanical and bacterial aggressions. Molecular analysis of gingiva is likely to improve our understanding of the underlying biological processes at work. The aim of this preliminary exploratory study is to analyze the proteomic profile of healthy gingiva and to detect prominently expressed proteins. Gingival tissue samples were obtained from periodontally healthy individuals who underwent surgical crown lengthening procedure. After protein isolation, two dimensional gel electrophoresis (2DE) gels were prepared for each sample and only protein spots common to all gels were selected to eliminate the bias caused by the effect of individuals on proteomic profile. Following the 2DE; in-gel tryptic digestion and MALDI-TOF/TOF steps were performed for protein identifications. Forty-seven proteins were successfully identified. The identified proteins were classified based on their classes, molecular functions and involvements in biological processes and metabolic pathways. Among them, 14-3-3 protein sigma, Protein DJ-1, Alpha-enolase, Triosephosphate isomerase, Superoxide dismutase, Peroxiredoxin-1, Protein S100-A9, Galectin-7, Annexin A2/A4, Carbonic anhydrase 1 and chaperone proteins are worthy of attention. The proteomic profile of the gingiva reflected its highly dynamic characteristics. Despite complexity of the gingival tissue proteome, 2DE was an effective approach in studying the common protein expression profile of the gingiva. Considering the significance of gingiva in the formation of periodontal diseases, it is important to generate a detailed proteome map of gingival tissue to set up a bridge between molecular events and the disease formation. This study established an initial proteome map of the gingival tissue from healthy individuals.

Parkinson's disease (PD) is an insidious disorder affecting more than 1-2% of the population over the age of 65. Understanding the etiology of PD may create opportunities for developing new treatments. Genomic and transcriptomic studies are useful, but do not provide evidence for the actual status of the disease. Conversely, proteomic studies deal with proteins, which are real time players, and can hence provide information on the dynamic nature of the affected cells. The number of publications relating to the proteomics of PD is vast. Therefore, there is a need to evaluate the current proteomics literature and establish the connections between the past and the present to foresee the future. Areas covered: PubMed and Web of Science were used to retrieve the literature associated with PD proteomics. Studies using human samples, model organisms and cell lines were selected and reviewed to highlight their contributions to PD. Expert commentary: The proteomic studies associated with PD achieved only limited success in facilitating disease diagnosis, monitoring and progression. A global system biology approach using new models is needed. Future research should integrate the findings of proteomics with other omics data to facilitate both early diagnosis and the treatment of PD.

Comparative physiological and proteomic analysis were performed to understand the stress responses of two chickpea species (C. reticulatum and C. arietinum) against drought. Our study revealed that drought stress reduced root length, leaf water content, and enhanced free proline content in both species. Effect of drought stress appeared to be greater in

Comparative physiological and proteomic analysis were performed to understand the stress responses of two chickpea species (C. reticulatum and C. arietinum) against drought. Our study revealed that drought stress reduced root length, leaf water content, and enhanced free proline content in both species. Effect of drought stress appeared to be greater in C. arietinum compared to C. reticulatum. A total of 24 differently expressed proteins were identified by using MALDI-TOF/ TOF-MS/MS in response to drought. The proteins involved in photosynthesis and energy mechanisms were up-regulated in C. reticulatum and down-regulated in C. arietinum under drought. Our results suggest that the photosynthesis capacity of C. reticulatum is greater than that of C. arietinum under drought stress. Abundance of proline and sucrose biosynthesis related proteins, glutamine synthetase and cyctosolic fructose-bisphosphate aldolase, respectively, also increased in C. reticulatum under drought stress. The findings of this proteome analysis will help in understanding the mechanism of drought resistance in chickpea and may be also helpful in developing drought-resistant transgenic plants.