New hybrid guanidine-quinoline copper complexes and their use in atom transfer radical polymerization

In this thesis, the synthesis and characterization of a family of seven new guanidine-quinoline hybrid ligands and their six CuI and seven CuII complexes is presented. The catalytic activities of the copper complexes in atom transfer radical polymerization (ATRP) reactions were studied and their electrochemical potentials, ATRP equilibria and reaction rate constants were determined. The molecular structures of the CuBr complexes showed bischelate tetrahedral coordination of the electron-rich ligands and a trigonal-planar geometry for the electron-poor ligands. Similar, the CuII halide complexes exhibited distorted bischelate trigonal-bipyramidal coordination for the electron-rich ligands and monochelate distorted square-pyramidal coordination for electronpoor CuCl2 complexes. All catalysts were found to polymerize styrene in high polymerization rates under controlled conditions. The use of copper complexes with electron-rich ligands resulted in faster catalysis and the [Cu(TMG6Methoxyqu)2]Br complex led to outstandingly fast ATRP reactions, yielding two to five times higher rate constants kp than other investigated catalysts. Electrochemical examinations of the CuBr2 complexes revealed that they exhibited increasing negative potentials for complexes with stronger electron-donating substituents. The potentials ranged from −0.439V to −0.545V (vs. Fc/Fc+). For the CuBr complexes, an increase of the electrochemical potential was found to lie in between 10mV and 35mV and the potentials of the CuCl2 complexes were found to be 40mV to 60mV lower than their CuBr2 counterparts. Most of the electrochemical potentials showed strong correlations with the data from polymerization studies. In correlation with the determined polymerization rates and electrochemical data, the KATRP values of the CuBr complexes were found to be larger for ligands bearing more electron-donating substituents. Our UV/Vis measurements afforded KATRP values ranging from 3.6 × 10-8 to 3.6 × 10-7. After addition of TEMPO to the equilibrium reaction, the kact values were determined to lie between 0.34 s-1 and 2.33 s-1 and values for kdeact were found to range from 5.9 × 106 s-1 to 1.3 × 107 s-1. The data further indicated, that the electron-rich ligands TMG6dmaqu and TMG6dbaqu form bidentate ATRP catalysts with the highest KATRP values known in the literature. The values are increased by one order of magnitude compared to 4,4’-dinonyl-2,2’-bipyridine (dNbpy) complexes

RNAi-based validation of antibodies for reverse phase protein arrays

<p>Abstract</p> <p>Background</p> <p>Reverse phase protein arrays (RPPA) have been demonstrated to be a useful experimental platform for quantitative protein profiling in a high-throughput format. Target protein detection relies on the readout obtained from a single detection antibody. For this reason, antibody specificity is a key factor for RPPA. RNAi allows the specific knockdown of a target protein in complex samples and was therefore examined for its utility to assess antibody performance for RPPA applications.</p> <p>Results</p> <p>To proof the feasibility of our strategy, two different anti-EGFR antibodies were compared by RPPA. Both detected the knockdown of EGFR but at a different rate. Western blot data were used to identify the most reliable antibody. The RNAi approach was also used to characterize commercial anti-STAT3 antibodies. Out of ten tested anti-STAT3 antibodies, four antibodies detected the STAT3-knockdown at 80-85%, and the most sensitive anti-STAT3 antibody was identified by comparing detection limits. Thus, the use of RNAi for RPPA antibody validation was demonstrated to be a stringent approach to identify highly specific and highly sensitive antibodies. Furthermore, the RNAi/RPPA strategy is also useful for the validation of isoform-specific antibodies as shown for the identification of AKT1/AKT2 and CCND1/CCND3-specific antibodies.</p> <p>Conclusions</p> <p>RNAi is a valuable tool for the identification of very specific and highly sensitive antibodies, and is therefore especially useful for the validation of RPPA-suitable detection antibodies. On the other hand, when a set of well-characterized RPPA-antibodies is available, large-scale RNAi experiments analyzed by RPPA might deliver useful information for network reconstruction.</p

Analyse von Signalproteinen in Zelllinien und Tumorgewebe mit Reverse Phase Proteinarrays

Krebs ist eine der häufigsten Todesursachen weltweit, wobei Lungen- und Prostatakrebs bei Männern die am weitesten verbreiteten Krebsarten sind. Dabei unterscheiden sich beide Krebsarten grundlegend. Während Lungenkrebs stark abhängig von umweltbedingten Risikofaktoren ist, zeigt Prostatakrebs eine ausgeprägte molekulare Heterogenität sowie ein altersbedingt steigendes Risiko. Der molekulare Hintergrund von Lungenkrebs ist häufig eine Deregulation der Rezeptor-Tyrosin-Kinase-Signalwege, speziell des AKT- und MAPK-Signalweges. Daher sind spezifische Kinase-Inhibitoren vielversprechende Wirkstoffe für die individuelle Therapie von Lungenkrebspatienten. Zur Beurteilung der Reaktion auf eine Behandlung mit solchen Inhibitoren sollte in einem Set von 84 Lungenkrebszelllinen nach Proteinexpressionsprofilen gesucht werden, die mit deren Wirksamkeit korrelieren. Als maßgebliche Grundlage zur Behandlung von Prostatakrebspatienten dient der in der Histopathologie bestimmte Gleasonwert der Biopsieproben. Jedoch führt dieser nicht immer zu einer angemessenen Therapieentscheidung, da die prognostische Aussage des Gleasonwertes nur unzureichend ist. Daher sollten zur Verbesserung der Prognose in einem Set von Tumorproben Markerproteine gefunden werden, die einerseits die Aggressivität der Tumore berücksichtigen sowie mit dem Auftreten des TMPRSS:ERG-Fusionsgens assoziiert sind. Zur Beantwortung dieser Fragen wurde auf die Reverse Phase Proteinarray-Technologie zurückgegriffen, die zunächst im Hinblick auf Durchsatz, Sensitivität und Robustheit weiterentwickelt wurde. Eine antikörperbasierte Signalamplifikation wurde zur Steigerung der Sensitivität entwickelt, um auch die Detektion gering exprimierter Proteine zu ermöglichen. Die Validierung von Antikörpern mittels RNAi wurde etabliert, um die Datenqualität zu verbessern und die isoformspezifische Detektion von Proteinen sicherzustellen. Nach erfolgreicher Optimierung der RPPA-Technologie wurde in der statistischen Umgebung R ein Analysewerkzeug programmiert, das flexibel eingesetzt werden kann, um RPPA-Daten einzulesen, zu normalisieren und zu visualisieren. Die Verwendung der experimentellen Verbesserungen wie auch der entwickelten Datenanalysewerkzeuge in einem miRNA-Screening bestätigte die hohe Leistungsfähigkeit und Robustheit zum Einsatz in Hochdurchsatzproteomanalysen. Die Analyse der Lungenkrebszelllinien ergab für jeden Wirkstoff sechs bis acht potentielle Markerproteine, wobei vor allem Proteine des AKT-Signalweges als mögliche Resistenzmarker identifiziert wurden. Als Ergebnis der Analyse des RPPA-basierenden Proteomprofilings von Prostatatumoren konnte eine erhöhte Aktivierung von p38 mit geringen Gleasonwerten korreliert werden. Die TMPSS:ERG-fusionsgenpositiven Prostatatumore zeigten eine reduzierte Expression der onkogenen Proteine ERK, PI3K p110 und CDK6, was auf eine Assoziation mit weniger aggressiven Tumoren hinweist. Es konnte zudem gezeigt werden, dass die formale Begriffsanalyse zur Datenintegration für kleine Probensätze sinnvoll eingesetzt werden kann. So wurde eine Korrelation des TMPRSS:ERG-Fusionsgens mit geringen Gleasonwerten beobachtet. Darüber hinaus zeigte sich eine gegensätzliche Regulation der p38- und ERK-Signalwege. In Proben hohen Gleasonwertes ist p38 gering aktiviert bei gleichzeitig hoher Expression und starker Aktivierung von ERK

Evaluation of reverse phase protein array (RPPA)-based pathway-activation profiling in 84 non-small cell lung cancer (NSCLC) cell lines as platform for cancer proteomics and biomarker discovery

AbstractThe reverse phase protein array (RPPA) approach was employed for a quantitative analysis of 71 cancer-relevant proteins and phosphoproteins in 84 non-small cell lung cancer (NSCLC) cell lines and by monitoring the activation state of selected receptor tyrosine kinases, PI3K/AKT and MEK/ERK1/2 signaling, cell cycle control, apoptosis, and DNA damage. Additional information on NSCLC cell lines such as that of transcriptomic data, genomic aberrations, and drug sensitivity was analyzed in the context of proteomic data using supervised and non-supervised approaches for data analysis. First, the unsupervised analysis of proteomic data indicated that proteins clustering closely together reflect well-known signaling modules, e.g. PI3K/AKT- and RAS/RAF/ERK-signaling, cell cycle regulation, and apoptosis. However, mutations of EGFR, ERBB2, RAF, RAS, TP53, and PI3K were found dispersed across different signaling pathway clusters. Merely cell lines with an amplification of EGFR and/or ERBB2 clustered closely together on the proteomic, but not on the transcriptomic level. Secondly, supervised data analysis revealed that sensitivity towards anti-EGFR drugs generally correlated better with high level EGFR phosphorylation than with EGFR abundance itself. High level phosphorylation of RB and high abundance of AURKA were identified as candidates that can potentially predict sensitivity towards the aurora kinase inhibitor VX680. Examples shown demonstrate that the RPPA approach presents a useful platform for targeted proteomics with high potential for biomarker discovery. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge

Increasing the sensitivity of reverse phase protein arrays by antibody-mediated signal amplification

<p>Abstract</p> <p>Background</p> <p>Reverse phase protein arrays (RPPA) emerged as a useful experimental platform to analyze biological samples in a high-throughput format. Different signal detection methods have been described to generate a quantitative readout on RPPA including the use of fluorescently labeled antibodies. Increasing the sensitivity of RPPA approaches is important since many signaling proteins or posttranslational modifications are present at a low level.</p> <p>Results</p> <p>A new antibody-mediated signal amplification (AMSA) strategy relying on sequential incubation steps with fluorescently-labeled secondary antibodies reactive against each other is introduced here. The signal quantification is performed in the near-infrared range. The RPPA-based analysis of 14 endogenous proteins in seven different cell lines demonstrated a strong correlation (r = 0.89) between AMSA and standard NIR detection. Probing serial dilutions of human cancer cell lines with different primary antibodies demonstrated that the new amplification approach improved the limit of detection especially for low abundant target proteins.</p> <p>Conclusions</p> <p>Antibody-mediated signal amplification is a convenient and cost-effective approach for the robust and specific quantification of low abundant proteins on RPPAs. Contrasting other amplification approaches it allows target protein detection over a large linear range.</p

Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer

BACKGROUND: Tri- and tetra-nucleotide repeats in mammalian genomes can induce formation of alternative non-B DNA structures such as triplexes and guanine (G)-quadruplexes. These structures can induce mutagenesis, chromosomal translocations and genomic instability. We wanted to determine if proteins that bind triplex DNA structures are quantitatively or qualitatively different between colorectal tumor and adjacent normal tissue and if this binding activity correlates with patient clinical characteristics. METHODS: Extracts from 63 human colorectal tumor and adjacent normal tissues were examined by gel shifts (EMSA) for triplex DNA-binding proteins, which were correlated with clinicopathological tumor characteristics using the Mann-Whitney U, Spearman’s rho, Kaplan-Meier and Mantel-Cox log-rank tests. Biotinylated triplex DNA and streptavidin agarose affinity binding were used to purify triplex-binding proteins in RKO cells. Western blotting and reverse-phase protein array were used to measure protein expression in tissue extracts. RESULTS: Increased triplex DNA-binding activity in tumor extracts correlated significantly with lymphatic disease, metastasis, and reduced overall survival. We identified three multifunctional splicing factors with biotinylated triplex DNA affinity: U2AF65 in cytoplasmic extracts, and PSF and p54nrb in nuclear extracts. Super-shift EMSA with anti-U2AF65 antibodies produced a shifted band of the major EMSA H3 complex, identifying U2AF65 as the protein present in the major EMSA band. U2AF65 expression correlated significantly with EMSA H3 values in all extracts and was higher in extracts from Stage III/IV vs. Stage I/II colon tumors (p = 0.024). EMSA H3 values and U2AF65 expression also correlated significantly with GSK3 beta, beta-catenin, and NF- B p65 expression, whereas p54nrb and PSF expression correlated with c-Myc, cyclin D1, and CDK4. EMSA values and expression of all three splicing factors correlated with ErbB1, mTOR, PTEN, and Stat5. Western blots confirmed that full-length and truncated beta-catenin expression correlated with U2AF65 expression in tumor extracts. CONCLUSIONS: Increased triplex DNA-binding activity in vitro correlates with lymph node disease, metastasis, and reduced overall survival in colorectal cancer, and increased U2AF65 expression is associated with total and truncated beta-catenin expression in high-stage colorectal tumors

A pro-inflammatory signalome is constitutively activated by C33Y mutant TNF receptor 1 in TNF receptor-associated periodic syndrome (TRAPS)

Mutations in TNFRSF1A encoding TNF receptor 1 (TNFR1) cause the autosomal dominant TNF receptor-associated periodic syndrome (TRAPS): a systemic autoinflammatory disorder. Misfolding, intracellular aggregation, and ligand-independent signaling by mutant TNFR1 are central to disease pathophysiology. Our aim was to understand the extent of signaling pathway perturbation in TRAPS. A prototypic mutant TNFR1 (C33Y), and wild-type TNFR1 (WT), were expressed at near physiological levels in an SK-Hep-1 cell model. TNFR1-associated signaling pathway intermediates were examined in this model, and in PBMCs from C33Y TRAPS patients and healthy controls. In C33Y-TNFR1-expressing SK-Hep-1 cells and TRAPS patients' PBMCs, a subtle, constitutive upregulation of a wide spectrum of signaling intermediates and their phosphorylated forms was observed; these were associated with a proinflammatory/antiapoptotic phenotype. In TRAPS patients' PBMCs, this upregulation of proinflammatory signaling pathways was observed irrespective of concurrent treatment with glucocorticoids, anakinra or etanercept, and the absence of overt clinical symptoms at the time that the blood samples were taken. This study reveals the pleiotropic effect of a TRAPS-associated mutant form of TNFR1 on inflammatory signaling pathways (a proinflammatory signalome), which is consistent with the variable and limited efficacy of cytokine-blocking therapies in TRAPS. It highlights new potential target pathways for therapeutic intervention