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  • PROTEOMICS  (5)
  • 1
    Keywords: brain ; COMBINATION ; Germany ; GENERATION ; SYSTEM ; liver ; PROTEIN ; PROTEINS ; HEART ; COMPLEX ; COMPLEXES ; MECHANISM ; RAT ; PHOSPHORYLATION ; TARGET ; RAT-LIVER ; SUBUNIT ; MEMBRANE ; STRESS ; MODULATION ; MITOCHONDRIA ; OXYGEN ; antioxidants ; PROTEOMICS ; reactive oxygen species ; glutathione-S-transferase ; GENE-EXPRESSION PROFILE ; ageing ; GEL-ELECTROPHORESIS ; assembly ; proteome ; REACTIVE OXYGEN ; ROS ; CALORIE RESTRICTION ; SHORT-TERM ; COMPLEX-I ; MEMBRANE-PROTEINS ; CYTOCHROME-C-OXIDASE ; DIGE ; Species ; ROS PRODUCTION ; SHIFT ; RESPIRATORY-CHAIN
    Abstract: Mitochondria being the major source and target of reactive oxygen species (ROS) play a crucial role during ageing. We analyzed ageing and calorie restriction (CR)-induced changes in abundance of rat liver mitochondrial proteins to understand key aspects behind the age-retarding mechanism of CR. The combination of blue-native (BN) gel system with fluorescence Difference Gel Electrophoresis (DIGE) facilitated an efficient analysis of soluble and membrane proteins, existing as monomers or multi-protein assemblies. Changes in abundance of specific key subunits of respiratory chain complexes I, IV and V, critical for activity and/or assembly of the complexes were identified. CR lowered complex I assembly and complex IV activity, which is discussed as a molecular mechanism to minimize ROS production at mitochondria. Notably, the antioxidant system was found to be least affected. The GSH:GSSG couple could be depicted as a rapid mean to handle the fluctuations in ROS levels led by reversible metabolic shifts. We evaluated the relative significance of ROS generation against quenching. We also observed parallel and unidirectional changes as effect of ageing and CR, in subunits of ATP synthase, cytochrome P450 and glutathione S-transferase. This is the first report on such 'putatively hormetic' ageing-analogous effects of CR, besides the age-retarding ones
    Type of Publication: Journal article published
    PubMed ID: 19894137
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  • 2
    Keywords: CANCER ; EXPRESSION ; INHIBITOR ; tumor ; carcinoma ; CELL ; Germany ; CLASSIFICATION ; DIAGNOSIS ; RISK ; PROTEIN ; SAMPLES ; PATIENT ; BIOLOGY ; ASSOCIATION ; FIELD ; ALPHA ; STAGE ; IDENTIFICATION ; IN-SITU ; immunohistochemistry ; genetics ; ABERRATIONS ; MASS-SPECTROMETRY ; ONCOGENE ; HUMAN-PAPILLOMAVIRUS ; SQUAMOUS-CELL CARCINOMA ; HEAD ; NECK ; RISK ASSESSMENT ; heredity ; BIOPSY ; protein expression ; PROTEOMICS ; PROTEOMIC ANALYSIS ; NECK-CANCER ; CELL CARCINOMA ; ONCOLOGY ; TUMORIGENESIS ; ARRAY ; HNSCC ; LYMPH-NODE METASTASIS ; development ; analysis ; PROFILES ; EVENTS ; protein biomarkers ; HISTOLOGY ; FRAGMENT ; SELDI-TOF-MS ; BIOPSIES ; CLINICAL-IMPLICATIONS ; aberration ; comparison ; acyl-CoA-binding protein ; CANCERIZATION ; field cancerization ; GENETICALLY ALTERED FIELDS ; HUMAN NEUTROPHIL PEPTIDE-1 ; TUMOR-DISTANT EPITHELIA
    Abstract: Development of head and necksquamous cell carcinoma (HNSCC) is a multistep process and in many cases involves a phenomenon coined 'field cancerization'. In order to identify changes in protein expression occurring at different stages of tumorigenesis and field cancerization, we analysed 113 HNSCCs and 73 healthy, 99 tumor-distant and 18 tumor-adjacent squamous mucosae by SELDI-TOF-MS on IMAC30 ProteinChip Arrays. Forty-eight protein peaks were differentially expressed between healthy mucosa and HNSCC. Calgizarrin (S100A11), the Cystein proteinase inhibitor Cystatin A, Acyl-CoA-binding protein, Stratifin (14-3-3 sigma), Histone H4, alpha- and beta-Hemoglobin, a C-terminal fragment of beta-hemoglobin and the alpha-defensins 1-3 were identified by mass spectrometry. The alpha-defensins showed various alterations in expression as validated by immunohistochemistry (IHC). Supervised prediction analysis revealed excellent classification of healthy mucosa (94.5% correctly classified) and tumor samples (92.9% correctly classified). Application of this classifier to the tumor-adjacent and tumor-distant mucosa samples disclosed dramatic changes: only 59.6% of the tumor-distant biopsies were classified as normal, 27.3% were predicted as aberrant or HNSCC. Strikingly, 72% of the tumor-adjacent mucosae were predicted as aberrant. These data provide evidence for the existence of genetically altered fields with inconspicuous histology. Comparison of the protein profiles in the tumor-distant-samples with clinical outcome of 32 patients revealed a significant association between aberrant profiles with tumor relapse events (P = 0.018; Fisher's exact test, two-tailed). We conclude that proteomic pro. ling in conjunction with protein identification greatly outperforms histopathological diagnosis and may have significant predictive power for clinical outcome and personalized risk assessment
    Type of Publication: Journal article published
    PubMed ID: 16819514
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  • 3
    Keywords: CELLS ; EXPRESSION ; carcinoma ; FACTOR RECEPTOR ; IN-VIVO ; PROTEIN ; HEAD ; NECK ; pancreatic cancer ; PROTEOMICS ; EPIDERMAL-GROWTH-FACTOR ; SERUM ; biomarker ; exosome ; METASTATIC BREAST-CANCER ; TARGETED THERAPY ; EGFR forms ; Secretome ; TUMOR AGGRESSIVENESS
    Abstract: Aims: Members of the epidermal growth factor receptor (EGFR) family represent validated targets for anticancer therapy and EGFR inhibitors have also shown efficacy in pancreatic carcinoma. We here described in detail molecular forms of the EGF receptor released by pancreatic cancer cells. We found peptides specific for the EGER in the secretomes of five pancreatic cancer cell lines. Secretomes from cultured cancer cells are widely used as sources for serum biomarker discovery. Main methods: The detailed analysis of EGFR forms in secretomes of human pancreatic cancer cells is a compilation of results from mass spectrometry (MS) and Western blotting with intracellular and extracellular domain specific antibodies. Key findings: Pancreatic cancer cells secrete a 110 kDa soluble form of the EGFR (sEGFR) representing the ligand binding extracellular EGFR domains and presumably released by ectodomain shedding. At the same time, as constituents of exosomes, the EGFR is released as full-length intact receptor (170 kDa) and as a 65 kDa processed form, the C-terminal remnant fragment that corresponds to the intracellular kinase domain. Significance: The detailed characterization of diverse EGER forms released by pancreatic cancer cells in vitro and presumably in vivo bears important implications for functional studies, for the validation of soluble EGFR as a serum biomarker and for the design of targeted therapies.
    Type of Publication: Journal article published
    PubMed ID: 21763319
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  • 4
    Keywords: EXPRESSION ; Germany ; MODEL ; INFORMATION ; SYSTEM ; GENE ; GENE-EXPRESSION ; GENOME ; PROTEIN ; PROTEINS ; RESOLUTION ; MECHANISM ; FAMILY ; DOMAIN ; mechanisms ; TOLERANCE ; CYCLE ; SEQUENCE ; IDENTIFICATION ; gene expression ; HEAT-SHOCK ; mass spectrometry ; SPECTROMETRY ; DATABASE ; MASS-SPECTROMETRY ; PROJECT ; PROTEOMICS ; PROTEIN IDENTIFICATION ; ARABIDOPSIS-THALIANA ; HIGH-RESOLUTION ; ANNOTATION ; SCIENCE ; LIFE ; MOLECULAR-MECHANISMS ; GLUTATHIONE S-TRANSFERASES ; Genetic ; protein extraction ; MILNESIUM-TARDIGRADUM ; RICHTERSIUS-CORONIFER ; ARTEMIA-FRANCISCANA ; DESICCATION TOLERANCE ; EST ; Sequence information ; Molecular mechanisms ; BRINE SHRIMP ; TREHALOSE
    Abstract: Background: Tardigrades are small, multicellular invertebrates which are able to survive times of unfavourable environmental conditions using their well-known capability to undergo cryptobiosis at any stage of their life cycle. Milnesium tardigradum has become a powerful model system for the analysis of cryptobiosis. While some genetic information is already available for Milnesium tardigradum the proteome is still to be discovered. Principal Findings: Here we present to the best of our knowledge the first comprehensive study of Milnesium tardigradum on the protein level. To establish a proteome reference map we developed optimized protocols for protein extraction from tardigrades in the active state and for separation of proteins by high resolution two-dimensional gel electrophoresis. Since only limited sequence information of M. tardigradum on the genome and gene expression level is available to date in public databases we initiated in parallel a tardigrade EST sequencing project to allow for protein identification by electrospray ionization tandem mass spectrometry. 271 out of 606 analyzed protein spots could be identified by searching against the publicly available NCBInr database as well as our newly established tardigrade protein database corresponding to 144 unique proteins. Another 150 spots could be identified in the tardigrade clustered EST database corresponding to 36 unique contigs and ESTs. Proteins with annotated function were further categorized in more detail by their molecular function, biological process and cellular component. For the proteins of unknown function more information could be obtained by performing a protein domain annotation analysis. Our results include proteins like protein member of different heat shock protein families and LEA group 3, which might play important roles in surviving extreme conditions. Conclusions: The proteome reference map of Milnesium tardigradum provides the basis for further studies in order to identify and characterize the biochemical mechanisms of tolerance to extreme desiccation. The optimized proteomics workflow will enable application of sensitive quantification techniques to detect differences in protein expression, which are characteristic of the active and anhydrobiotic states of tardigrades
    Type of Publication: Journal article published
    PubMed ID: 20224743
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  • 5
    Keywords: EXPRESSION ; QUANTIFICATION ; GENES ; PROTEOMICS ; QUANTITATIVE MASS-SPECTROMETRY
    Abstract: Quantitative proteomics has increasingly gained impact in life science research as a tool to describe changes in protein expression between different cellular states. Stable isotope labeling by amino acids in cell culture (SILAC) is a powerful technique for relative quantification of proteins. However, the accuracy of quantification is impaired by the metabolic conversion of arginine to proline resulting in additional heavy labeled proline peptide satellites. Here we reinvestigated the addition of unlabeled proline during cell cultivation under SILAC conditions considering several thousand peptides and demonstrated that the arginine-to-proline conversion is prevented independent of the cell line used.
    Type of Publication: Journal article published
    PubMed ID: 21241653
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