Proteomic analysis in endometrial cancer and endometrial hyperplasia tissues by 2D-DIGE technique.

OBJECTIVE: To compare the protein expression of complex atypical endometrial hyperplasia, endometrial carcinoma and healthy endometrial tissues, and by this way, to identify proteins that can be used for diagnosis, prognosis and therapeutic targets. METHODS: Histopathological examination of the D&C material had reported "benign endometrial changes", "complex atypical endometrial hyperplasia" and "endometrioid adenocarcinoma" and 30 patients ,who underwent surgery with these diagnosis, were studied. Protein profiles of the study groups were detected using 2D-DIGE technique and compared to the control group. Protein spots which showing different expression, were defined by MALDI TOF/TOF-MS method. RESULTS: In the present study, significant elevations were observed in the levels of K2C8, UAP56, ENOA, ACTB, GRP78, GSTP1, PSME1, CALR, PPIA, PDIA3 and IDHc proteins when comparisons were made among the cancer cases and the healthy and complex atypical hyperplasia cases. We determined that the induction of CALR activity may be a factor that progresses apoptosis, thus, may be a hope for postoperative new chemotherapy treatment methods. Moreover, when the expressions of the CAH1 and PPIB proteins are compared to complex atypical hyperplasia and endometrial adenocarcinoma stages, we determined that the CAH1 and PPIB levels increased in more advanced stages. Among these indicators, the proteins that had the closest relation to advanced stage cancer were determined as K2C8, UAP56 and GRP78. CONCLUSION: We think that it would be useful to determine the diagnosis, prediction of prognosis and identifying therapeutic targets of the highlighted proteins of our study that are K2C8, UAP56, GRP78 and CALR in endometrial cancer.

Vitreous IL-8 and VEGF levels in diabetic macular edema with or without subretinal fluid.

PURPOSE: To determine the cytokine levels in vitreous samples of diabetic macular edema (DME) patients in comparison with nondiabetic patients, and to evaluate the effect of subretinal fluid on the cytokine levels of vitreous samples. METHODS: In this prospective case-control study, 11 eyes of 11 patients with DME and subretinal fluid, 11 eyes of 11 patients with DME without subretinal fluid, and 14 eyes of 14 patients who had undergone vitreoretinal surgery for the epiretinal membrane or a macular hole (control group) were evaluated. The blood glycated hemoglobin (HbA1c) level, vitreous vascular endothelial growth factor (VEGF), and interleukin-8 (IL-8) levels were determined. RESULTS: The vitreous VEGF level of patients in DME groups was significantly higher than the control group (p < 0.001) without significant difference between DME patients with and without subretinal fluid (p = 0.796). The vitreous IL-8 level of DME patients with subretinal fluid was significantly higher than both control (p = 0.002) and DME without subretinal fluid groups (p = 0.019). The blood HbA1c level was significantly higher in DME group with subretinal fluid than those without subretinal fluid (8.7 ± 1.32 and 7.1 ± 1.13%, respectively, p = 0.010). The only significant correlation was between vitreous VEGF level and blood HbA1c level in DME patients without subretinal fluid (r = 0.813, p = 0.002). CONCLUSIONS: IL-8 level in vitreous samples was higher in DME patients with subretinal fluid than those without subretinal fluid, suggesting that inflammation is an important factor in the progression of DME leading to the subretinal fluid formation in diabetic patients.

Histopathologic and molecular comparative analyses of intravesical Aurora kinase-A inhibitor Alisertib with bacillus Calmette-Guérin on precancerous lesions of bladder in a rat model.

PURPOSE: Recent studies have shown that Aurora-A expression is associated with bladder cancer initiation and progression. In this study, the effects of intravesical Aurora-A inhibitor Alisertib (ALS) and bacillus Calmette-Guérin (BCG) were compared on bladder carcinogenesis. METHODS: Two mg N-Methyl-N-nitrosourea was administered intravesically to forty of Wistar-albino rats every other week for 8 weeks. At week 10, rats were divided into four groups (10/group): No-treatment (vehicle), ALS-alone, BCG-alone, and ALS + BCG. The intravesical treatment of ALS, BCG, and ALS plus BCG was performed once a week for 6 weeks. At week 16, bladders were collected for immunohistopathological and Western blot analysis. The cell cycle regulators p53, p21, Aurora-A, phosphorylated Aurora-A (p-Aurora-A), and apoptotic marker cleavage of poly [ADP-ribose] polymerase (c-PARP) were determined by Western blot. RESULTS: Histopathologically relatively healthy urothelium was observed in ALS + BCG group (87.5%) compared to the ALS-alone (50%) and the BCG-alone (50%) groups. The lowest expression of p21 and p53 was detected in the BCG-alone, while the highest level of expression was evident in no-treatment group. The ALS treatment alone caused a slight decrease in Aurora-A while there was a dramatic decrease in p-Aurora-A in comparison to no-treatment group. In overall combined treatment with ALS + BCG significantly increased c-PARP compared to all mono-treatments, and decreased all cell cycle parameters compared to no-treatment group. CONCLUSIONS: Although intravesical ALS treatment has similar antiproliferative effects like BCG, ALS + BCG combined treatment led to a best histopathologic and apoptotic response. Consequently, BCG combined with Aurora-A inhibition may provide a new intravesical treatment modality in the prevention of bladder carcinogenesis.

The prominent proteins expressed in healthy gingiva: a pilot exploratory tissue proteomics study.

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.

Monitoring the response of urothelial precancerous lesions to Bacillus Calmette-Guerin at the proteome level in an in vivo rat model.

Intravesical Bacillus Calmette-Guerin (BCG) is the best treatment modality for progression of non-muscle invasive bladder cancer. We aimed to monitor changes at the proteome level to identify putative protein biomarkers associated with the response of urothelial precancerous lesions to intravesical BCG treatment. The rats were divided into three groups (n = 10/group): control, non-treated, and BCG-treated groups. The non-treated and BCG-treated groups received N-methyl-N-nitrosourea intravesically. BCG Tice-strain was instilled into bladder in BCG-treated group. At the endpoint of experiment, all surviving rat bladders were collected and equally divided into two portions vertically from dome to neck. Half of each bladder was assessed immunohistopathologically and the other half was used for 2D-based comparative proteomic analysis. Differentially expressed proteins were validated by Western blot analysis. Precancerous lesions of bladder cancer were more common in non-treated group (77.8%) than in BCG-treated group (50%) and the control group (0%). Greater than twofold changes occurred in the expression of a number of proteins. Among them, Rab-GDIß, aldehyde dehydrogenase 2 (ALDH2) and 14-3-3 zeta/delta were important since they were previously reported to be associated with cancer and their expression levels were found to be lower in BCG-treated group in comparison to the non-treated group. ALDH2 and 14-3-3 zeta/delta were also found to be highly expressed in the non-treated group compared to the control group. The down-regulation of these proteins and Rab-GDIß was achieved with BCG; this result indicates that they may be used as putative biomarkers for monitoring changes in bladder carcinogenesis in response to BCG immunotherapy.

Comparative proteomic analysis of amnion membrane transplantation and cross-linking treatments in an experimental alkali injury model.

PURPOSE: In this study, by using a two-dimensional (2D) electrophoresis-based experimental approach, we aimed at understanding the nature of alkali injuries and the underlying mechanisms. A secondary aim was to compare the effects of cross-linking (CXL) and amnion membrane transplantation (AMT) on corneal protein compositions at the end of the early repair phase after injured with alkali. METHOD: The right corneas of 24 rabbits were injured with a 1 N solution of NaOH. Groups were formed based on the adjuvant therapies as (1) healthy group, (2) control group, (3) CXL group, (4) AMT group. In addition to the therapies, a conventional medical treatment was applied to all groups. Left eyes were used as within-subject healthy corneas (1). The corneas were excised at day 21, and a comparative proteomic analysis was performed using 2D gel electrophoresis coupled with MALDI-TOF/TOF. RESULT: 2D gel electrophoresis revealed the presence seven protein spots whose abundance changed among the groups. Those proteins were SH3 domain-binding protein, plant homeodomain finger protein 23, S100 calcium binding protein A-11(S100 A11), keratin type 2 cytoskeletal 1 and 2, transketolase and glyceraldehyde 3-phosphate dehydrogenase. Ingenuity pathway analysis predicted that the observed changes may be linked to a central metabolic pathway, transforming growth factor beta 1. Canonical pathway analysis focused our attention to two different pathways, namely nicotinamide adenine dinucleotide repair pathway and non-oxidative branch of pentose phosphate pathway. CONCLUSION: Our results shed some light onto the molecular mechanisms affected by alkali injury and adjuvant treatments. Further research is needed to propose medically significant target molecules that may be used for novel drug developments for alkali injury.

Comparative proteome analysis of the tear samples in patients with low-grade keratoconus.

PURPOSE: To elucidate the metabolic processes playing roles in the formation of keratoconus (KC). METHODS: 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. RESULTS: 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. CONCLUSION: 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.

Exogenous Expressions of FTO Wild-Type and R316Q Mutant Proteins Caused an Increase in HNRPK Levels in 3T3-L1 Cells as Demonstrated by DIGE Analysis.

Fat mass and obesity-associated protein is an enzyme that oxidatively demethylates DNA. Although there are numerous studies regarding the catalytic function of FTO, the overall existence or absence of FTO on cellular proteome has not been investigated. This study investigated the changes in the soluble proteome of 3T3-L1 cells upon expression of the WT and the mutant (R316Q) FTO proteins. Protein extracts prepared from 3T3-L1 cells expressing either the WT or the mutant FTO proteins were used in DIGE experiments. Analysis of the data revealed the number of spots matched to every member and there were 350 ± 20 spots with 30.5% overall mean coefficient of variation. Eleven regulated protein spots were excised from the gels and identified by MALDI-TOF/TOF. One of the identified proteins was heterogeneous nuclear ribonucleoprotein K, which displayed more than 2.6- and 3.7-fold increases in its abundance in the WT and the mutant FTO expressing cells, respectively. Western blot analysis validated these observations. This is the first study revealing the presence of a parallel increase in expressions of FTO and HNRNPK proteins. This increase may codictate the metabolic changes occurring in the cell and may attribute a significance to HNRNPK in FTO-associated transformations.

Linking a compound-heterozygous Parkin mutant (Q311R and A371T) to Parkinson's disease by using proteomic and molecular approaches.

Parkin is an E3-protein ubiquitin ligase, which plays an important role as a scavenger in cell metabolism. Since the discovery of the link between Parkin and Parkinson's disease, Parkin was placed in the center of Parkinson's disease research. Previously, we isolated a mutant form of the Parkin protein (Q311R and A371T) from a Parkinson's disease patient. In this study, we aimed at characterizing this mutant Parkin protein by using biochemical and proteomic approaches. We used neuroblastoma cells (SH-SY5Y) as our model and created two inducible cell lines that expressed the wild type and the mutant Parkin proteins. We first investigated the effect of expressing both the wild type and the mutant Parkin proteins on the overall proteome by using 2D-DIGE approach. The experiments yielded the identification of 22 differentially regulated proteins, of which 13 were regulated in the mutant Parkin expressing cells. Classification of the identified proteins based on biological process and molecular function revealed that the majority of the regulated proteins belonged to protein folding and energy metabolism. Ingenuity Pathway Analysis predicted the presence of a link between the regulated proteins of the mutant Parkin expressing cells and Parkinson's disease. We also performed biochemical characterization studies on the wild type and the mutant Parkin proteins to make sense out of the differences observed at the proteome level. Both proteins displayed biological activity, had similar stabilities and localized similarly to the cytoplasm and the nucleus in SH-SY5Y cells. The mutant protein, however, was cut by a protease and subjected to a post-translational modification. The observed differences at the proteome level might be due to the differences in processing of the mutant Parkin protein. Overall, we were able to create a possible link between a pair of Parkin mutations to its pertinent disease by using 2D-DIGE in combination with biochemical and molecular approaches.