@article{ArltBiehlTayloretal.2011, author = {Arlt, Wiebke and Biehl, Michael and Taylor, Angela E. and Hahner, Stefanie and Lib{\´e}, Rossella and Hughes, Beverly A. and Schneider, Petra and Smith, David J. and Stiekema, Han and Krone, Nils and Porfiri, Emilio and Opocher, Giuseppe and Bertherat, Jer{\^o}me and Mantero, Franco and Allolio, Bruno and Terzolo, Massimo and Nightingale, Peter and Shackleton, Cedric H. L. and Bertagna, Xavier and Fassnacht, Martin and Stewart, Paul M.}, title = {Urine Steroid Metabolomics as a Biomarker Tool for Detecting Malignancy in Adrenal Tumors}, series = {The Journal of Clinical Endocrinology \& Metabolism}, volume = {96}, journal = {The Journal of Clinical Endocrinology \& Metabolism}, number = {12}, doi = {10.1210/jc.2011-1565}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-154682}, pages = {3775 -- 3784}, year = {2011}, abstract = {Context: Adrenal tumors have a prevalence of around 2\% in the general population. Adrenocortical carcinoma (ACC) is rare but accounts for 2-11\% of incidentally discovered adrenal masses. Differentiating ACC from adrenocortical adenoma (ACA) represents a diagnostic challenge in patients with adrenal incidentalomas, with tumor size, imaging, and even histology all providing unsatisfactory predictive values. Objective: Here we developed a novel steroid metabolomic approach, mass spectrometry-based steroid profiling followed by machine learning analysis, and examined its diagnostic value for the detection of adrenal malignancy. Design: Quantification of 32 distinct adrenal derived steroids was carried out by gas chromatography/mass spectrometry in 24-h urine samples from 102 ACA patients (age range 19-84 yr) and 45 ACC patients (20-80 yr). Underlying diagnosis was ascertained by histology and metastasis in ACC and by clinical follow-up [median duration 52 (range 26-201) months] without evidence of metastasis in ACA. Steroid excretion data were subjected to generalized matrix learning vector quantization (GMLVQ) to identify the most discriminative steroids. Results: Steroid profiling revealed a pattern of predominantly immature, early-stage steroidogenesis in ACC. GMLVQ analysis identified a subset of nine steroids that performed best in differentiating ACA from ACC. Receiver-operating characteristics analysis of GMLVQ results demonstrated sensitivity = specificity = 90\% (area under the curve = 0.97) employing all 32 steroids and sensitivity = specificity = 88\% (area under the curve = 0.96) when using only the nine most differentiating markers. Conclusions: Urine steroid metabolomics is a novel, highly sensitive, and specific biomarker tool for discriminating benign from malignant adrenal tumors, with obvious promise for the diagnostic work-up of patients with adrenal incidentalomas.}, language = {en} } @article{SbirkovKwokBhamraetal.2017, author = {Sbirkov, Yordan and Kwok, Colin and Bhamra, Amandeep and Thompson, Andrew J. and Gil, Veronica and Zelent, Arthur and Petrie, Kevin}, title = {Semi-quantitative mass spectrometry in AML cells identifies new non-genomic targets of the EZH2 methyltransferase}, series = {International Journal of Molecular Sciences}, volume = {18}, journal = {International Journal of Molecular Sciences}, number = {7}, issn = {1422-0067}, doi = {10.3390/ijms18071440}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-285541}, year = {2017}, abstract = {Alterations to the gene encoding the EZH2 (KMT6A) methyltransferase, including both gain-of-function and loss-of-function, have been linked to a variety of haematological malignancies and solid tumours, suggesting a complex, context-dependent role of this methyltransferase. The successful implementation of molecularly targeted therapies against EZH2 requires a greater understanding of the potential mechanisms by which EZH2 contributes to cancer. One aspect of this effort is the mapping of EZH2 partner proteins and cellular targets. To this end we performed affinity-purification mass spectrometry in the FAB-M2 HL-60 acute myeloid leukaemia (AML) cell line before and after all-trans retinoic acid-induced differentiation. These studies identified new EZH2 interaction partners and potential non-histone substrates for EZH2-mediated methylation. Our results suggest that EZH2 is involved in the regulation of translation through interactions with a number of RNA binding proteins and by methylating key components of protein synthesis such as eEF1A1. Given that deregulated mRNA translation is a frequent feature of cancer and that eEF1A1 is highly expressed in many human tumours, these findings present new possibilities for the therapeutic targeting of EZH2 in AML.}, language = {en} } @article{BergerDemolombeHemetal.2022, author = {Berger, Nathalie and Demolombe, Vincent and Hem, Sonia and Rofidal, Val{\´e}rie and Steinmann, Laura and Krouk, Gabriel and Crabos, Amandine and Nacry, Philippe and Verdoucq, Lionel and Santoni, V{\´e}ronique}, title = {Root membrane ubiquitinome under short-term osmotic stress}, series = {International Journal of Molecular Sciences}, volume = {23}, journal = {International Journal of Molecular Sciences}, number = {4}, issn = {1422-0067}, doi = {10.3390/ijms23041956}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-284003}, year = {2022}, abstract = {Osmotic stress can be detrimental to plants, whose survival relies heavily on proteomic plasticity. Protein ubiquitination is a central post-translational modification in osmotic-mediated stress. In this study, we used the K-Ɛ-GG antibody enrichment method integrated with high-resolution mass spectrometry to compile a list of 719 ubiquitinated lysine (K-Ub) residues from 450 Arabidopsis root membrane proteins (58\% of which are transmembrane proteins), thereby adding to the database of ubiquitinated substrates in plants. Although no ubiquitin (Ub) motifs could be identified, the presence of acidic residues close to K-Ub was revealed. Our ubiquitinome analysis pointed to a broad role of ubiquitination in the internalization and sorting of cargo proteins. Moreover, the simultaneous proteome and ubiquitinome quantification showed that ubiquitination is mostly not involved in membrane protein degradation in response to short osmotic treatment but that it is putatively involved in protein internalization, as described for the aquaporin PIP2;1. Our in silico analysis of ubiquitinated proteins shows that two E2 Ub-conjugating enzymes, UBC32 and UBC34, putatively target membrane proteins under osmotic stress. Finally, we revealed a positive role for UBC32 and UBC34 in primary root growth under osmotic stress.}, language = {en} } @article{SangesScheuermannZahedietal.2012, author = {Sanges, C. and Scheuermann, C. and Zahedi, R. P. and Sickmann, A. and Lamberti, A. and Migliaccio, N. and Baljuls, A. and Marra, M. and Zappavigna, S. and Reinders, J. and Rapp, U. and Abbruzzese, A. and Caraglia, M. and Arcari, P.}, title = {Raf kinases mediate the phosphorylation of eukaryotic translation elongation factor 1A and regulate its stability in eukaryotic cells}, series = {Cell Death and Disease}, volume = {3}, journal = {Cell Death and Disease}, number = {e276}, doi = {10.1038/cddis.2012.16}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-124149}, year = {2012}, abstract = {We identified eukaryotic translation elongation factor 1A (eEF1A) Raf-mediated phosphorylation sites and defined their role in the regulation of eEF1A half-life and of apoptosis of human cancer cells. Mass spectrometry identified in vitro S21 and T88 as phosphorylation sites mediated by B-Raf but not C-Raf on eEF1A1 whereas S21 was phosphorylated on eEF1A2 by both B- and C-Raf. Interestingly, S21 belongs to the first eEF1A GTP/GDP-binding consensus sequence. Phosphorylation of S21 was strongly enhanced when both eEF1A isoforms were preincubated prior the assay with C-Raf, suggesting that the eEF1A isoforms can heterodimerize thus increasing the accessibility of S21 to the phosphate. Overexpression of eEF1A1 in COS 7 cells confirmed the phosphorylation of T88 also in vivo. Compared with wt, in COS 7 cells overexpressed phosphodeficient (A) and phospho-mimicking (D) mutants of eEF1A1 (S21A/D and T88A/D) and of eEF1A2 (S21A/D), resulted less stable and more rapidly proteasome degraded. Transfection of S21 A/D eEF1A mutants in H1355 cells increased apoptosis in comparison with the wt isoforms. It indicates that the blockage of S21 interferes with or even supports C-Raf induced apoptosis rather than cell survival. Raf-mediated regulation of this site could be a crucial mechanism involved in the functional switching of eEF1A between its role in protein biosynthesis and its participation in other cellular processes.}, language = {en} } @article{SangesScheuermannZahedietal.2012, author = {Sanges, C. and Scheuermann, C. and Zahedi, R. P. and Sickmann, A. and Lamberti, A. and Migliaccio, N. and Baljuls, A. and Marra, M. and Zappavigna, S. and Rapp, U. and Abbruzzese, A. and Caraglia, M. and Arcari, P.}, title = {Raf kinases mediate the phosphorylation of eukaryotic translation elongation factor 1A and regulate its stability in eukaryotic cells}, series = {Cell Death \& Disease}, volume = {3}, journal = {Cell Death \& Disease}, number = {e276}, doi = {10.1038/cddis.2012.16}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-134673}, year = {2012}, abstract = {We identified eukaryotic translation elongation factor 1A (eEF1A) Raf-mediated phosphorylation sites and defined their role in the regulation of eEF1A half-life and of apoptosis of human cancer cells. Mass spectrometry identified in vitro S21 and T88 as phosphorylation sites mediated by B-Raf but not C-Raf on eEF1A1 whereas S21 was phosphorylated on eEF1A2 by both B-and C-Raf. Interestingly, S21 belongs to the first eEF1A GTP/GDP-binding consensus sequence. Phosphorylation of S21 was strongly enhanced when both eEF1A isoforms were preincubated prior the assay with C-Raf, suggesting that the eEF1A isoforms can heterodimerize thus increasing the accessibility of S21 to the phosphate. Overexpression of eEF1A1 in COS 7 cells confirmed the phosphorylation of T88 also in vivo. Compared with wt, in COS 7 cells overexpressed phosphodeficient (A) and phospho-mimicking (D) mutants of eEF1A1 (S21A/D and T88A/D) and of eEF1A2 (S21A/D), resulted less stable and more rapidly proteasome degraded. Transfection of S21 A/D eEF1A mutants in H1355 cells increased apoptosis in comparison with the wt isoforms. It indicates that the blockage of S21 interferes with or even supports C-Raf induced apoptosis rather than cell survival. Raf-mediated regulation of this site could be a crucial mechanism involved in the functional switching of eEF1A between its role in protein biosynthesis and its participation in other cellular processes.}, language = {en} } @article{MacintyreZhangViegelmannetal.2014, author = {Macintyre, Lynsey and Zhang, Tong and Viegelmann, Christina and Martinez, Ignacio Juarez and Cheng, Cheng and Dowdells, Catherine and Abdelmohsen, Usama Ramadan and Gernert, Christine and Hentschel, Ute and Edrada-Ebel, RuAngelie}, title = {Metabolomic Tools for Secondary Metabolite Discovery from Marine Microbial Symbionts}, series = {Marine Drugs}, volume = {12}, journal = {Marine Drugs}, number = {6}, issn = {1660-3397}, doi = {10.3390/md12063416}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-116097}, pages = {3416-3448}, year = {2014}, abstract = {Marine invertebrate-associated symbiotic bacteria produce a plethora of novel secondary metabolites which may be structurally unique with interesting pharmacological properties. Selection of strains usually relies on literature searching, genetic screening and bioactivity results, often without considering the chemical novelty and abundance of secondary metabolites being produced by the microorganism until the time-consuming bioassay-guided isolation stages. To fast track the selection process, metabolomic tools were used to aid strain selection by investigating differences in the chemical profiles of 77 bacterial extracts isolated from cold water marine invertebrates from Orkney, Scotland using liquid chromatography-high resolution mass spectrometry (LC-HRMS) and nuclear magnetic resonance (NMR) spectroscopy. Following mass spectrometric analysis and dereplication using an Excel macro developed in-house, principal component analysis (PCA) was employed to differentiate the bacterial strains based on their chemical profiles. NMR H-1 and correlation spectroscopy (COSY) were also employed to obtain a chemical fingerprint of each bacterial strain and to confirm the presence of functional groups and spin systems. These results were then combined with taxonomic identification and bioassay screening data to identify three bacterial strains, namely Bacillus sp. 4117, Rhodococcus sp. ZS402 and Vibrio splendidus strain LGP32, to prioritize for scale-up based on their chemically interesting secondary metabolomes, established through dereplication and interesting bioactivities, determined from bioassay screening.}, language = {en} } @article{SchmitzKodererElMeseryetal.2021, author = {Schmitz, Werner and Koderer, Corinna and El-Mesery, Mohamed and Gobik, Sebastian and Sampers, Rene and Straub, Anton and K{\"u}bler, Alexander Christian and Seher, Axel}, title = {Metabolic fingerprinting of murine L929 fibroblasts as a cell-based tumour suppressor model system for methionine restriction}, series = {International Journal of Molecular Sciences}, volume = {22}, journal = {International Journal of Molecular Sciences}, number = {6}, issn = {1422-0067}, doi = {10.3390/ijms22063039}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259198}, year = {2021}, abstract = {Since Otto Warburg reported in 1924 that cancer cells address their increased energy requirement through a massive intake of glucose, the cellular energy level has offered a therapeutic anticancer strategy. Methionine restriction (MetR) is one of the most effective approaches for inducing low-energy metabolism (LEM) due to the central position in metabolism of this amino acid. However, no simple in vitro system for the rapid analysis of MetR is currently available, and this study establishes the murine cell line L929 as such a model system. L929 cells react rapidly and efficiently to MetR, and the analysis of more than 150 different metabolites belonging to different classes (amino acids, urea and tricarboxylic acid cycle (TCA) cycles, carbohydrates, etc.) by liquid chromatography/mass spectrometry (LC/MS) defines a metabolic fingerprint and enables the identification of specific metabolites representing normal or MetR conditions. The system facilitates the rapid and efficient testing of potential cancer therapeutic metabolic targets. To date, MS studies of MetR have been performed using organisms and yeast, and the current LC/MS analysis of the intra- and extracellular metabolites in the murine cell line L929 over a period of 5 days thus provides new insights into the effects of MetR at the cellular metabolic level.}, language = {en} } @article{VollandKauppSchmitzetal.2022, author = {Volland, Julian Manuel and Kaupp, Johannes and Schmitz, Werner and W{\"u}nsch, Anna Chiara and Balint, Julia and M{\"o}llmann, Marc and El-Mesery, Mohamed and Frackmann, Kyra and Peter, Leslie and Hartmann, Stefan and K{\"u}bler, Alexander Christian and Seher, Axel}, title = {Mass spectrometric metabolic fingerprinting of 2-Deoxy-D-Glucose (2-DG)-induced inhibition of glycolysis and comparative analysis of methionine restriction versus glucose restriction under perfusion culture in the murine L929 model system}, series = {International Journal of Molecular Sciences}, volume = {23}, journal = {International Journal of Molecular Sciences}, number = {16}, issn = {1422-0067}, doi = {10.3390/ijms23169220}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-286007}, year = {2022}, abstract = {All forms of restriction, from caloric to amino acid to glucose restriction, have been established in recent years as therapeutic options for various diseases, including cancer. However, usually there is no direct comparison between the different restriction forms. Additionally, many cell culture experiments take place under static conditions. In this work, we used a closed perfusion culture in murine L929 cells over a period of 7 days to compare methionine restriction (MetR) and glucose restriction (LowCarb) in the same system and analysed the metabolome by liquid chromatography mass spectrometry (LC-MS). In addition, we analysed the inhibition of glycolysis by 2-deoxy-D-glucose (2-DG) over a period of 72 h. 2-DG induced very fast a low-energy situation by a reduced glycolysis metabolite flow rate resulting in pyruvate, lactate, and ATP depletion. Under perfusion culture, both MetR and LowCarb were established on the metabolic level. Interestingly, over the period of 7 days, the metabolome of MetR and LowCarb showed more similarities than differences. This leads to the conclusion that the conditioned medium, in addition to the different restriction forms, substantially reprogramm the cells on the metabolic level.}, language = {en} } @article{KodererSchmitzWuenschetal.2022, author = {Koderer, Corinna and Schmitz, Werner and W{\"u}nsch, Anna Chiara and Balint, Julia and El-Mesery, Mohamed and Volland, Julian Manuel and Hartmann, Stefan and Linz, Christian and K{\"u}bler, Alexander Christian and Seher, Axel}, title = {Low energy status under methionine restriction is essentially independent of proliferation or cell contact inhibition}, series = {Cells}, volume = {11}, journal = {Cells}, number = {3}, issn = {2073-4409}, doi = {10.3390/cells11030551}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-262329}, year = {2022}, abstract = {Nonlimited proliferation is one of the most striking features of neoplastic cells. The basis of cell division is the sufficient presence of mass (amino acids) and energy (ATP and NADH). A sophisticated intracellular network permanently measures the mass and energy levels. Thus, in vivo restrictions in the form of amino acid, protein, or caloric restrictions strongly affect absolute lifespan and age-associated diseases such as cancer. The induction of permanent low energy metabolism (LEM) is essential in this process. The murine cell line L929 responds to methionine restriction (MetR) for a short time period with LEM at the metabolic level defined by a characteristic fingerprint consisting of the molecules acetoacetate, creatine, spermidine, GSSG, UDP-glucose, pantothenate, and ATP. Here, we used mass spectrometry (LC/MS) to investigate the influence of proliferation and contact inhibition on the energy status of cells. Interestingly, the energy status was essentially independent of proliferation or contact inhibition. LC/MS analyses showed that in full medium, the cells maintain active and energetic metabolism for optional proliferation. In contrast, MetR induced LEM independently of proliferation or contact inhibition. These results are important for cell behaviour under MetR and for the optional application of restrictions in cancer therapy.}, language = {en} } @phdthesis{Tribl2005, author = {Tribl, Florian}, title = {Isolierung und Charakterisierung Neuromelanin-assoziierter Proteine aus Neuromelanin-Granula des menschlichen Gehirns mittels subzellul{\"a}rer Proteomanalyse}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-16117}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2005}, abstract = {Im Mittelpunkt dieser Arbeit stehen Untersuchungen zur Bildung des Pigments Neuromelanin, das die Ursache f{\"u}r die dunkle Farbgebung der humanen Substantia nigra pars compacta ist. Eine Beteiligung von Neuromelanin an den pathobiochemischen Ereignissen bei Parkinson-Krankheit erkl{\"a}rt das klinische Interesse an Neuromelanin. Die Untersuchungsm{\"o}glichkeiten von Neuromelanin sind limitiert: einerseits ist eine chemische Strukturaufkl{\"a}rung aufgrund der Unl{\"o}slichkeit dieses amorphen Polymers kaum zu bewerkstelligen, andererseits wird mangels geeigneter biologischer Testsysteme ein Einblick in die Biogenese von Neuromelanin verwehrt. Zurzeit wird die Bildung von Neuromelanin anhand der beiden konkurrierenden Hypothesen als Autoxidation von Dopamin oder durch Beteiligung eines Enzyms („Tyrosinase-Konzept") erkl{\"a}rt. In dieser Arbeit wurden beide hypothetischen Ans{\"a}tze bearbeitet, wobei einer enzymatischen Biogenese von Neuromelanin die Pr{\"a}ferenz gegeben wird. Zur globalen Untersuchung von Neuromelanin-Granula wurde nun erstmals eine Isolierung der Pigment-haltigen Organelle vorgestellt, die die Basis f{\"u}r eine umfassende Proteomanalyse mittels 1-D-SDS-PAGE und ESI-Tandem-Massenspektrometrie bildete. Mit diesem methodischen Ansatz wurden ingesamt 73 Proteinen identifiziert. Diese waren vor allem lysosomalen Proteinen zuordenbar, z.B. charakteristischen Membranproteinen (LAMP-1), s{\"a}mtlichen Proteasen, Proteinen des Metabolismus von (Glyco-)Lipiden und Glycoproteinen, aber auch Proteinen des Cytosols und des vesikul{\"a}ren Verkehrs. Entscheidend war die Anwesenheit von Proteinen des Endoplasmatischen Reticulums (ER); Calnexin gilt als ein melanogenes Chaperon, das nicht in Lysosomen vorkommt, dagegen aber in Lysosomen-verwandten Organellen. Im Vergleich mit bereits existierenden Proteinprofilen von Lysosomen und Lysosomen-verwandten Organellen zeigten die in Neuromelanin-Granula identifizierten lysosomalen Proteine und Proteine des ER, dass diese Organellen der humanen Substantia nigra keine konventionellen Lysosomen sind, sondern mit hoher Wahrscheinlichkeit der Gruppe der Lysosomen-verwandten Organellen zuzuordnen sind.}, subject = {Melanin}, language = {de} } @article{BerghoffKonzerManketal.2013, author = {Berghoff, Bork A. and Konzer, Anne and Mank, Nils N. and Looso, Mario and Rische, Tom and F{\"o}rstner, Konrad U. and Kr{\"u}ger, Marcus and Klug, Gabriele}, title = {Integrative "Omics"-Approach Discovers Dynamic and Regulatory Features of Bacterial Stress Responses}, series = {PLOS Genetics}, volume = {9}, journal = {PLOS Genetics}, number = {6}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1003576}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-127587}, pages = {e1003576}, year = {2013}, abstract = {Bacteria constantly face stress conditions and therefore mount specific responses to ensure adaptation and survival. Stress responses were believed to be predominantly regulated at the transcriptional level. In the phototrophic bacterium Rhodobacter sphaeroides the response to singlet oxygen is initiated by alternative sigma factors. Further adaptive mechanisms include post-transcriptional and post-translational events, which have to be considered to gain a deeper understanding of how sophisticated regulation networks operate. To address this issue, we integrated three layers of regulation: (1) total mRNA levels at different time-points revealed dynamics of the transcriptome, (2) mRNAs in polysome fractions reported on translational regulation (translatome), and (3) SILAC-based mass spectrometry was used to quantify protein abundances (proteome). The singlet oxygen stress response exhibited highly dynamic features regarding short-term effects and late adaptation, which could in part be assigned to the sigma factors RpoE and RpoH2 generating distinct expression kinetics of corresponding regulons. The occurrence of polar expression patterns of genes within stress-inducible operons pointed to an alternative of dynamic fine-tuning upon stress. In addition to transcriptional activation, we observed significant induction of genes at the post-transcriptional level (translatome), which identified new putative regulators and assigned genes of quorum sensing to the singlet oxygen stress response. Intriguingly, the SILAC approach explored the stress-dependent decline of photosynthetic proteins, but also identified 19 new open reading frames, which were partly validated by RNA-seq. We propose that comparative approaches as presented here will help to create multi-layered expression maps on the system level ("expressome"). Finally, intense mass spectrometry combined with RNA-seq might be the future tool of choice to re-annotate genomes in various organisms and will help to understand how they adapt to alternating conditions.}, language = {en} } @phdthesis{Carstensen2018, author = {Carstensen, Anne Carola}, title = {Identification of novel N-MYC interacting proteins reveals N-MYC interaction with TFIIIC}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-143658}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2018}, abstract = {N-MYC is a member of the human MYC proto-oncogene family, which comprises three transcription factors (C-, N- and L-MYC) that function in multiple biological processes. Deregulated expression of MYC proteins is linked to tumour initiation, maintenance and progression. For example, a large fraction of neuroblastoma displays high N-MYC levels due to an amplification of the N-MYC encoding gene. MYCN-amplified neuroblastoma depend on high N-MYC protein levels, which are maintained by Aurora-A kinase. Aurora-A interaction with N-MYC interferes with degradation of N-MYC via the E3 ubiquitin ligase SCFFBXW7. However, the underlying mechanism of Aurora-A-mediated stabilisation of N-MYC remains to be elucidated. To identify novel N-MYC interacting proteins, which could be involved in N-MYC stabilisation by Aurora-A, a proteomic analysis of purified N-MYC protein complexes was conducted. Since two alanine mutations in MBI of N-MYC, T58A and S62A (N-MYC mut), disable Aurora-A-mediated stabilisation of N-MYC, N-MYC protein complexes from cells expressing either N-MYC wt or mut were analysed. Proteomic analysis revealed that N-MYC interacts with two deubiquitinating enzymes, USP7 and USP11, which catalyse the removal of ubiquitin chains from target proteins, preventing recognition by the proteasome and subsequent degradation. Although N-MYC interaction with USP7 and USP11 was confirmed in subsequent immunoprecipitation experiments, neither USP7, nor USP11 was shown to be involved in the regulation of N-MYC stability. Besides USP7/11, proteomic analyses identified numerous additional N-MYC interacting proteins that were not described to interact with MYC transcription factors previously. Interestingly, many of the identified N-MYC interaction partners displayed a preference for the interaction with N-MYC wt, suggesting a MBI-dependent interaction. Among these were several proteins, which are involved in three-dimensional organisation of chromatin domains and transcriptional elongation by POL II. Not only the interaction of N-MYC with proteins functioning in elongation, such as the DSIF component SPT5 and the PAF1C components CDC73 and CTR9, was validated in immunoprecipitation experiments, but also with the POL III transcription factor TFIIIC and topoisomerases TOP2A/B. ChIP-sequencing analysis of N-MYC and TFIIIC subunit 5 (TFIIIC5) revealed a large number of joint binding sites in POL II promoters and intergenic regions, which are characterised by the presence of a specific motif that is highly similar to the CTCF motif. Additionally, N-MYC was shown to interact with the ring-shaped cohesin complex that is known to bind to CTCF motifs and to assist the insulator protein CTCF. Importantly, individual ChIP experiments demonstrated that N-MYC, TFIIIC5 and cohesin subunit RAD21 occupy joint binding sites comprising a CTCF motif. Collectively, the results indicate that N-MYC functions in two biological processes that have not been linked to MYC biology previously. Furthermore, the identification of joint binding sites of N-MYC, TFIIIC and cohesin and the confirmation of their interaction with each other suggests a novel function of MYC transcription factors in three-dimensional organisation of chromatin.}, subject = {Biologie}, language = {en} } @phdthesis{JakobRodamer2014, author = {Jakob-Rodamer, Verena}, title = {Development and validation of LC-MS/MS methods to determine PK/PD parameters of anti-infectives}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-109215}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2014}, abstract = {In the present thesis the development and validation of bioanalytical LC-MS/MS methods for the quantification of erythromycin A, erythromycin ethylsuccinate, roxithromycin, clarithromycin, 14 hydroxy clarithromycin, flucloxacillin, piperacillin and moxifloxacin in human plasma and human urine (piperacillin) is introduced. All methods were applied to analyze human plasma and urine samples from clinical trials and therefore, have been validated according to international guidelines. The methods were reliable in these studies and fulfilled all regulatory requirements known at the time of the study conduct. Moreover, the validation data of the macrolides were compared on three different mass spectrometers (API III Plus, API 3000™, API 5000™). The new innovations in the ion source (horizontal versus vertical electrospray), the ionpath (skimmer, QJet) and the diameter of the orifice resulted in better sensitivity and a larger linearity range for the majority of the analytes. Sensitivity was improved up to a factor of 12 (for clarithromycin) between API III Plus to API 3000™ and up to a factor of 8 (for erythromycin and roxithromycin) between API 3000™ and API 5000™, keeping the accuracy and precision data at about the same level. The high sensitivity was a benefit for example for the flucloxacillin study, because concentrations from all subject samples were detectable up to approximately eight half-lives, i.e. no concentrations needed to be reported below the quantification limit. Also the linearity range were extended from two orders of magnitude to up to four orders of magnitude, which increases the likelihood to allow to analyze all samples from a pharmacokinetic study in the same run. This is especially useful if a large concentration range needs to be analysed, for example, if the method shall be applied in an ascending dose study. Then, all low concentrations from the beginning of the study can be determined, as well as all high concentrations, without the need to dilute and analyse single samples repeatedly. The pharmacokinetic data were compared to previously reported literature data and correlated graphically with MIC values of popular microorganisms which might be a starting point for further PK/PD investigations. The PK/PD theory is a very helpful tool for prediction of the efficacy of given drugs against certain micro-organisms. Depending on the pharmacodynamic processes, e. g. the mode of action, three classes of drugs have been identified. In the same way this applies to adverse effects, which need to be minimised by reducing plasma concentrations. These coherences are not well-investigated, yet, and are not discussed further in this thesis. Still, a lot of research has to be done in this interdisciplinary field to minimise uncertainty in single values, like an AUC/MIC. These include: Improve accuracy and precision of bioanalytical methods determining total and free concentration data in biological matrices for calculation of AUC and Cmax These parameters are related to the MIC in pharmacodynamic considerations. Since the determination of the MIC often underlies significant variations and also differences between microbiological laboratories, the determination of concentrations of anti-infectives is particular important, being achievable by scientific exact techniques. Finally, from the volume of distribution of antibiotics can be used to derive information about intracellular concentrations and effectivity of antiinfectives.}, subject = {Antimikrobieller Wirkstoff}, language = {en} } @phdthesis{Simon2006, author = {Simon, Karoline}, title = {Development and Evaluation of a Generic HPLC-Tandem MS Screening Method for the Detection of Potential Biomarkers for Reactive Intermediates}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-21916}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {Conjugation of reactive intermediates of drugs with proteins or DNA may result in toxic effects such as hepatotoxicity, agranulocytosis, allergies, tumors, etc. From 1975 to 1999, 2.9\% of drugs were withdrawn from the market due to such severe adverse drug reactions. Thus, formation of chemically reactive intermediates is a widely discussed problem in drug development processes. Early detection of potentially toxic compounds is required for drug discovery and drug development. Conjugation of such electrophilic compounds with glutathione (GSH) is one of the most important detoxifying reactions in vivo. Processing of these GSH-conjugates ultimately leads to the formation of renally cleared mercapturic acids, which may also be oxidized to sulfoxides. Thus, mercapturic acids may be generated and detected in vitro and non-invasively in vivo in urine to assess the reactivity of a compound in early stages of drug development processes. Therefore, the aim of this work was to develop and evaluate a HPLC-MS/MS screening method for simple and rapid detection and characterization of known and unknown mercapturic acids and application of the method to several different matrices. Based on the common constant neutral loss (CNL) of 129 Da of all mercapturic acids tested (in negative ion mode), a CNL survey scan was performed using a linear ion trap instrument and was combined with two enhanced product ion (EPI) scans with different collision energies to characterize the detected signals. The CNL resulted from the cleavage between the sulfur and the carbon atom in the N-acetyl-L-cysteine moiety. After optimization of the experimental parameters, the detection limits of the reference substances in rat urine ranged from 0.3 to 15.5 pmol on column (i.e. 20 ng/ml to 800 ng/ml). For in vitro evaluation of the method, the model compounds acetaminophen, diclofenac, bifonazole, clozapine, troglitazone, carbamazepine, and bisphenol A were screened for formation of reactive intermediates and, hence, detection of the corresponding mercapturic acids. To determine possible species- and tissue-specific toxicities, the model compounds were incubated with stimulated neutrophils and with liver microsomes from rats and humans. Species-specific differences were observed in incubations of acetaminophen and diclofenac with rat and human hepatic microsomes. Tissue-specific differences in biotransformation of the model compounds in incubations with human neutrophils and human liver microsomes were observed for diclofenac, carbamazepine, clozapine, and bifonazole. The developed HPLC-MS/MS method was also evaluated in vivo by analysis of rat and human urine. Drug-related mercapturic acids were detected in urine of rats orally treated with acetaminophen (20 mg/kg and 640 mg/kg b.w.) or diclofenac (10 mg/kg and 20 mg/kg b.w.). Human urine samples were analyzed before and after oral administration of a clinically used dose of 500 mg and 50 mg of acetaminophen. Besides detection of the mercapturic acid of N-acetylbenzoquinoneimine (AAP-MA), a second mercapturic acid with m/z 327 occurred dose-dependently in rat and human urine samples after administration of acetaminophen. Further investigations on identification of this metabolite using authentic compounds and comparing their MS/MS mass spectra demonstrated oxidation of AAP-MA to stereoisomeric sulfoxides in vivo. For diclofenac, a novel mercapturic acid with m/z 441 was detected in rat urine samples that was identical to a metabolite obtained in incubations with human neutrophils before. The in vivo formation of this diclofenac metabolite is described here for the first time. In addition, three endogenously formed mercapturic acids were detected and identified. In conclusion, the results of the in vitro and in vivo evaluation demonstrate the advantages of the rapid and generic HPLC-MS/MS screening method for the detection of mercapturic acids, that can be obtained with a minimum of sample preparation and a high throughput in diverse matrices.}, subject = {Acetylcysteinderivate}, language = {en} } @article{SchmitzRiesKodereretal.2021, author = {Schmitz, Werner and Ries, Elena and Koderer, Corinna and V{\"o}lter, Maximilian Friedrich and W{\"u}nsch, Anna Chiara and El-Mesery, Mohamed and Frackmann, Kyra and K{\"u}bler, Alexander Christian and Linz, Christian and Seher, Axel}, title = {Cysteine restriction in murine L929 fibroblasts as an alternative strategy to methionine restriction in cancer therapy}, series = {International Journal of Molecular Sciences}, volume = {22}, journal = {International Journal of Molecular Sciences}, number = {21}, issn = {1422-0067}, doi = {10.3390/ijms222111630}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-265486}, year = {2021}, abstract = {Methionine restriction (MetR) is an efficient method of amino acid restriction (AR) in cells and organisms that induces low energy metabolism (LEM) similar to caloric restriction (CR). The implementation of MetR as a therapy for cancer or other diseases is not simple since the elimination of a single amino acid in the diet is difficult. However, the in vivo turnover rate of cysteine is usually higher than the rate of intake through food. For this reason, every cell can enzymatically synthesize cysteine from methionine, which enables the use of specific enzymatic inhibitors. In this work, we analysed the potential of cysteine restriction (CysR) in the murine cell line L929. This study determined metabolic fingerprints using mass spectrometry (LC/MS). The profiles were compared with profiles created in an earlier work under MetR. The study was supplemented by proliferation studies using D-amino acid analogues and inhibitors of intracellular cysteine synthesis. CysR showed a proliferation inhibition potential comparable to that of MetR. However, the metabolic footprints differed significantly and showed that CysR does not induce classic LEM at the metabolic level. Nevertheless, CysR offers great potential as an alternative for decisive interventions in general and tumour metabolism at the metabolic level.}, language = {en} } @phdthesis{Deubel2006, author = {Deubel, Alexandra}, title = {Charakterisierung des Verunreinigungsprofils von Erythromycin mittels chromatographischer Methoden und massenspektrometrischer Detektion}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-20160}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2006}, abstract = {Im Rahmen der vorliegenden Arbeit wurden analytische Methoden zur Bestimmung des Verunreinigungsprofils von Erythromycin entwickelt, die der bestehenden Ph.Eur.-Methode {\"u}berlegen sind. Die neue HPLC-Methode ist in der Lage, alle verwandten Verbindungen mit angemessener Pr{\"a}zision nachzuweisen und zu quantifizieren. Mit Hilfe der Massenspektrometrie konnten alle Hauptkomponenten und verwandten Verbindungen der Base, ihrer Ester und Salze eindeutig identifiziert und quantifiziert werden. Zudem konnten zwei neue verwandte Verbindungen von Erythromycin gefunden und als N,N-Didemethylerythromycin A und Anhydroerythromycin F identifiziert werden.}, subject = {Erythromycin}, language = {de} } @phdthesis{Boerner2010, author = {B{\"o}rner, Juliane}, title = {Charakterisierung der Phosphorylierungsstellen der Guanylyl Cyklase A, dem Rezeptor f{\"u}r das atriale natriuretische Peptid, mittels Massenspektrometrie}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51914}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {Das ANP/GC-A-System spielt durch die Produktion des sekund{\"a}ren Botenstoffs cGMP eine wichtige Rolle bei der Regulation des Blutdruckes und des Blutvolumens. Bei Patienten mit Herzhypertrophie oder Herzinsuffizienz sind die ANP-Plasmakonzentrationen erh{\"o}ht, aber die GC-A-vermittelten Effekte stark reduziert, was auf einen Defekt des Signalsystems hinweist. Studien an metabolisch markierten GC-A-{\"u}berexprimierenden HEK 293-Zellen zeigten, dass der GC-A-Rezeptor im basalen Zustand stark phosphoryliert und die homologe bzw. heterologe Desensitisierung wahrscheinlich mit einer Dephosphorylierung verbunden ist. Die Desensitisierung stellt einen Mechanismus dar, der in vivo zu einem Funktionsverlust des Rezeptors beitragen k{\"o}nnte. Im Rahmen dieser Arbeit konnten mittels Massenspektrometrie sieben Phosphorylierungsstellen in der Kinasehomologen Dom{\"a}ne aus FLAG-GC-A exprimierenden HEK 293-Zellen detektiert werden: Ser487, Ser497, Thr500, Ser502, Ser506, Ser510 und Thr513. Die massenspektrometrische relative Quantifizierung basierend auf der Multiple-Reaction-Monitoring (MRM)-Methode zeigte bei ANP-induzierter, homologer Desensitisierung eine Dephosphorylierung der Phosphorylierungsstellen Ser497, Thr500, Ser502, Ser506, Ser510 und Thr513, was mit bereits publizierten Daten {\"u}bereinstimmt, und einen starken Anstieg der Phosphorylierung an Ser487. Nach Inkubation mit Angiotensin II, welches eine heterologe Desensitisierung hervorruft, wurde eine Reduzierung aller Phosphorylierungen verzeichnet, die zudem st{\"a}rker ausgepr{\"a}gt war als bei der ANP-abh{\"a}ngigen Desensitisierung. Die Funktion der neu identifizierten Phosphorylierung an Ser487 wurde mittels Mutagenese analysiert. Die Substitution des Serins durch Alanin, welche den unphosphorylierten Zustand nachstellt, resultierte in einer Rezeptoraktivit{\"a}t und desensitisierung vergleichbar zum GC-A Wildtyp-Rezeptor. Wurde hingegen Serin gegen Glutamat getauscht, um den phosphorylierten Zustand zu imitieren, konnte der Rezeptor weder aktiviert noch desensitisiert werden. Diese Ergebnisse best{\"a}tigen vorherige Studien, dass die GC-A-Rezeptorantwort auf ANP durch die Phosphorylierungen reguliert wird. Allerdings scheint bei der homologen Desensitisierung die Phosphorylierung an der Position Ser487 eine Rolle zu spielen, da sie die Aktivit{\"a}t des Rezeptors inhibiert. Die Identifizierung und Charakterisierung dieser Phosphorylierungsstelle tr{\"a}gt zum Verst{\"a}ndnis des Mechanismus der homologen Desensitierung bei. Zus{\"a}tzlich konnten einige der beschriebenen Phosphorylierungen in Zellsystemen detektiert werden, die die GC-A endogen exprimieren. Dadurch sind unter physiologischen Bedingungen Analysen der Mechanismen m{\"o}glich, die bei der Aktivierung und Deaktivierung der GC-A involviert sind und somit wichtige pathophysiologische Konsequenzen haben k{\"o}nnen.}, subject = {Guanylatcyclase}, language = {de} } @phdthesis{Nuwal2010, author = {Nuwal, Tulip}, title = {Characterization of Synapsin, Tubulin-Binding Chaperone E-like, And Their Putative Interactions With Synapse Associated Protein Of 47 kDa In Drosophila melanogaster}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51683}, school = {Universit{\"a}t W{\"u}rzburg}, year = {2010}, abstract = {In this thesis we have used Drosophila melanogaster as a model organism to investigate proteins and their putative interacting partners that are directly or indirectly involved in the release of neurotransmitters at the synapse. We have used molecular techniques to investigate conserved synaptic proteins, synapsin and synapse associated protein of 47 kD (SAP47), and a putative interaction partner of SAP47, tubulin binding chaperone E-like (TBCEL). SAP47 and synapsins are highly conserved synaptic vesicle associated proteins in Drosophila melanogaster. To further investigate the role and function of Sap47 and Syn genes, we had earlier generated the null mutants by P-element mutagenesis (Funk et al., 2004; Godenschwege et al., 2004). Western blots and ELISA of brain homogenates from Sap47156 null mutants showed the presence of up-regulated phospho-synapsin in comparison to wild-type (CS) and the presence of up-regulated phospho-synapsin was partially abolished when a pan-neuronal rescue of SAP47 was performed by the Gal4- UAS technique. Thus, the results suggest a qualitative and quantitative modulation of synapsin by SAP47. At the transcript level, we did not observe any difference in content of Syn transcript in Sap47156 and wild-type CS flies. The question of a direct molecular interaction between SAP47 and synapsin was investigated by co-immunoprecipitation (Co-IP) experiments and we did not find any stable interactions under the several IP conditions we tested. The possibility of Sap47 as a modifier of Syn at the genetic level was investigated by generating and testing homozygous double null mutants of Sap47 and Syn. The Syn97, Sap47156 double mutants are viable but have a reduced life span and decreased locomotion when compared to CS. In 2D-PAGE analysis of synapsins we identified trains of spots corresponding to synapsins, suggesting that synapsin has several isoforms and each one of them is posttranslationally modified. In an analysis by Blue native-SDS-PAGE (BN-SDS-2D- PAGE) and Western blot we observed synapsin and SAP47 signals to be present at 700-900 kDa and 200-250 kDa, respectively, suggesting that they are part of large but different complexes. We also report the possibility of Drosophila synapsin forming homo- and heteromultimers, which has also been reported for synapsins of vertebrates. In parallel to the above experiments, phosphorylation of synapsins in Drosophila was studied by IP techniques followed by 1D-SDS gel electrophoresis and mass spectrometry (in collaboration with S. Heo and G. Lubec). We identified and verified 5 unique phosphorylation sites in Drosophila synapsin from our MS analysis. Apart from phosphorylation modifications we identified several other PTMs which have not been verified. The significance of these phosphorylations and other identified PTMs needs to be investigated further and their implications for synapsin function and Drosophila behavior has to be elucidated by further experiments. In a collaborative project with S. Kneitz and N. Nuwal, we investigated the effects of Sap156 and Syn97 mutations by performing a whole Drosophila transcriptome microarray analysis of the individual null mutants and the double mutants (V2 and V3). We obtained several candidates which were significantly altered in the mutants. These genes need to be investigated further to elucidate their interactions with Sap47 and Syn. In another project, we investigated the role and function of Drosophila tubulin- binding chaperone E-like (Tbcel, CG12214). The TBCEL protein has high homology to vertebrate TBCE-like (or E-like) which has high sequence similarity to tubulin-binding chaperone E (TBCE) (hence the name TBCE-Like). We generated an anti-TBCEL polyclonal antiserum (in collaboration with G. Krohne). According to flybase, the Tbcel gene has only one exon and codes for two different transcripts by alternative transcription start sites. The longer transcript RB is present only in males whereas the shorter transcript RA is present only in females. In order to study the gene function we performed P- element jump-out mutagenesis to generate deletion mutants. We used the NP4786 (NP) stock which has a P(GawB) insertion in the 5' UTR of the Tbcel gene. NP4786 flies are homozygous lethal due to a second-site lethality as the flies are viable over a deficiency (Df) chromosome (a deletion of genomic region spanning the Tbcel gene and other upstream and downstream genes). We performed the P-element mutagenesis twice. In the first trial we obtained only revertants and the second experiment is still in progress. In the second attempt, jump-out was performed over the deficiency chromosome to prevent homologous chromosome mediated double stranded DNA repair. During the second mutagenesis an insertion stock G18151 became available. These flies had a P-element insertion in the open reading frame (ORF) of the Tbcel gene but was homozygous viable. Western blots of fresh tissue homogenates of NP/Df and G18151 flies probed with anti-TBCEL antiserum showed no TBCEL signal, suggesting that these flies are Tbcel null mutants. We used these flies for further immunohistochemical analyses and found that TBCEL is specifically expressed in the cytoplasm of cyst cells of the testes and is associated with the tubulin of spermatid tails in wild-type CS, whereas in NP/Df and G18151 flies the TBCEL staining in the cyst cells was absent and there was a disruption of actin investment cones. We also found enrichment of TBCEL staining around the actin investment cone. These results are also supported by the observation that the enhancer trap expression of the NP4786 line is localised to the cyst cells, similar to TBCEL expression. Also, male fertility of NP/Df and G18151 flies was tested and they were found to be sterile with few escapers. Thus, these results suggest that TBCEL is involved in Drosophila spermatogenesis with a possible role in the spermatid elongation and individualisation process.}, subject = {Taufliege}, language = {en} } @incollection{DasZografakisOeljeklausetal.2023, author = {Das, Hirakjyoti and Zografakis, Alexandros and Oeljeklaus, Silke and Warscheid, Bettina}, title = {Analysis of Yeast Peroxisomes via Spatial Proteomics}, series = {Peroxisomes}, booktitle = {Peroxisomes}, edition = {accepted version}, publisher = {Springer}, doi = {10.1007/978-1-0716-3048-8_2}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-327532}, publisher = {Universit{\"a}t W{\"u}rzburg}, pages = {13-31}, year = {2023}, abstract = {Peroxisomes are ubiquitous organelles with essential functions in numerous cellular processes such as lipid metabolism, detoxification of reactive oxygen species and signaling. Knowledge of the peroxisomal proteome including multi-localized proteins and, most importantly, changes of its composition induced by altering cellular conditions or impaired peroxisome biogenesis and function is of paramount importance for a holistic view on peroxisomes and their diverse functions in a cellular context. In this chapter, we provide a spatial proteomics protocol specifically tailored to the analysis of the peroxisomal proteome of baker's yeast that enables the definition of the peroxisomal proteome under distinct conditions and to monitor dynamic changes of the proteome including the relocation of individual proteins to a different cellular compartment. The protocol comprises subcellular fractionation by differential centrifugation followed by Nycodenz density gradient centrifugation of a crude peroxisomal fraction, quantitative mass spectrometric measurements of subcellular and density gradient fractions and advanced computational data analysis, resulting in the establishment of organellar maps on a global scale.}, language = {en} }