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McWeeney S.K.,Oregon Health And Science University | Pemberton L.C.,Oregon Health And Science University | Pemberton L.C.,Northumbria University | Loriaux M.M.,Oregon Health And Science University | And 17 more authors.
Blood | Year: 2010

In chronic-phase chronic myeloid leukemia (CML) patients, the lack of a major cytogenetic response (< 36% Ph+ metaphases) to imatinib within 12 months indicates failure and mandates a change of therapy. To identify biomarkers predictive of imatinib failure, we performed gene expression array profiling of CD34+ cells from 2 independent cohorts of imatinib-naive chronic-phase CML patients. The learning set consisted of retrospectively selected patients with a complete cytogenetic response or more than65%Ph + metaphases within 12 months of imatinib therapy.Basedonanalysis of varianceP less than .1 and fold difference 1.5 or more, we identified 885 probe sets with differential expression between responders and nonre-sponders, from which we extracted a 75-probe set minimal signature (classifier) that separated the 2 groups. On application to a prospectively accrued validation set, the classifier correctly predicted 88% of responders and83% of nonresponders. Bioinformatics analysis and comparison with published studies revealed overlap of classifier genes withCMLprogression signatures and implicated β-catenin in their regulation, suggesting that chronic-phase CML patients destined to fail imatinib have more advanced disease than evident by morphologic criteria. Our classifier may allow directing more aggressive therapy upfront to the patients most likely to benefit while sparing good-risk patients from unnecessary toxicity. © 2010 by The American Society of Hematology. Source

Song O.R.,Institute Pasteur Korea | Kim T.-H.,Institute Pasteur Korea | Kim T.-H.,Yonsei University | Perrodon X.,Institute Pasteur Korea | And 8 more authors.
Journal of Biomolecular Screening | Year: 2010

Rapid mixing in microplates is still an underappreciated challenge in screening assay development, particularly with the use of noncontact nanoliter liquid handlers. In high-content/throughput screening (HC/TS), fast and efficient mixing between compounds and cell culture medium is even more critical as biological kinetics dictates speed of mixing, usually within a few minutes. Moreover, mixing in HC/TS should be gentle enough, to avoid any negative disruption in. cell layer. Here the authors introduce a method to accurately quantify drop diffusion into a microplate well, independently of buffer, liquid han-dler, or dispensing protocol. This method was used to determine the effect of various mixing methods on the diffusion of a nanoliter drop of pure DMSO in aqueous buffer in 384-well plates. Rapid plate shaking and additional buffer addition were shown to be the most efficient and effective mixing methods for HC/TS. However, efficient mixing by plate shaking is lim-ited by assay volume. Bulk addition shows fast and efficient mixing, without negative effects on cells. Moreover, this simple, fast, and inexpensive method can be easily adapted on any platform. © 2010 Society for Biomolecular Sciences. Source

Sharma K.,Max Planck Institute of Biochemistry | Sharma K.,Research and Development Center | Kumar C.,Max Planck Institute of Biochemistry | Kumar C.,Lilly Singapore Center for Drug Discovery | And 5 more authors.
Journal of Proteome Research | Year: 2010

The innate immune system senses invariant microbial components via toll-like receptors (TLRs) to elicit a host defense program against invading pathogens. Lipopolysaccharide (LPS), a constituent of Gram-negative bacteria, is recognized by TLR4 and triggers protein kinase signaling to orchestrate immune responses such as inflammatory cytokine production. To analyze kinase-proximal signaling in murine macrophages, we performed prefractionation experiments with immobilized kinase inhibitors to enrich for protein kinases and their interaction partners. In conjunction with SILAC-based quantitative mass spectrometry and phosphopeptide enrichment, we recorded five time point profiles for more than 850 distinct phosphorylation events on protein kinases and copurifying factors. More than 15% exhibited significant changes and many of those mapped to LPS-regulated kinase networks. We identified many unreported TLR signaling events including LPS-triggered phosphorylations of Akt substrates, which point to previously unknown molecular mechanisms in innate immune response. We further detected extensive phosphoregulation of TANK-binding kinase 1, inhibitor of nuclear factor-κB kinase ε and their associating scaffolding factors, and none of these events were known despite the key roles of these proteins in LPS signaling. Thus, our data expands previous knowledge for functional analyses of innate immune response. © 2010 American Chemical Society. Source

Yang C.-S.,Duke University | Thomenius M.J.,Duke University | Gan E.C.,Duke University | Gan E.C.,Lilly Singapore Center for Drug Discovery | And 6 more authors.
EMBO Journal | Year: 2010

Apoptosis ensures tissue homeostasis in response to developmental cues or cellular damage. Recently reported genome-wide RNAi screens have suggested that several metabolic regulators can modulate caspase activation in Drosophila. Here, we establish a previously unrecognized link between metabolism and Drosophila apoptosis by showing that cellular NADPH levels modulate the initiator caspase Dronc through its phosphorylation at S130. Depletion of NADPH removed this inhibitory phosphorylation, resulting in the activation of Dronc and subsequent cell death. Conversely, upregulation of NADPH prevented Dronc-mediated apoptosis upon DIAP1 RNAi or cycloheximide treatment. Furthermore, this CaMKII-mediated phosphorylation of Dronc hindered Dronc activation, but not its catalytic activity. Blockade of NADPH production aggravated the death-inducing activity of Dronc in specific neurons, but not in the photoreceptor cells of the eyes of transgenic flies; similarly, non-phosphorylatable Dronc was more potent than wild type in triggering specific neuronal apoptosis. Our observations reveal a novel regulatory circuitry in Drosophila apoptosis, and, as NADPH levels are elevated in cancer cells, also provide a genetic model to understand aberrations in cancer cell apoptosis resulting from metabolic alterations. © 2010 European Molecular Biology Organization. Source

Olsen J.V.,Max Planck Institute of Biochemistry | Olsen J.V.,Novo Nordisk AS | Vermeulen M.,Max Planck Institute of Biochemistry | Vermeulen M.,University Utrecht | And 14 more authors.
Science Signaling | Year: 2010

Eukaryotic cells replicate by a complex series of evolutionarily conserved events that are tightly regulated at defined stages of the cell division cycle. Progression through this cycle involves a large number of dedicated protein complexes and signaling pathways, and deregulation of this process is implicated in tumorigenesis. We applied high-resolution mass spectrometry-based proteomics to investigate the proteome and phosphoproteome of the human cell cycle on a global scale and quantified 6027 proteins and 20,443 unique phosphorylation sites and their dynamics. Co-regulated proteins and phosphorylation sites were grouped according to their cell cycle kinetics and compared to publicly available messenger RNA microarray data. Most detected phosphorylation sites and more than 20% of all quantified proteins showed substantial regulation, mainly in mitotic cells. Kinase-motif analysis revealed global activation during S phase of the DNA damage response network, which was mediated by phosphorylation by ATM or AT or DNA-dependent protein kinases. We determined site-specific stoichiometry of more than 5000 sites and found that most of the up-regulated sites phosphorylated by cyclin-dependent kinase 1 (CDK1) or CDK2 were almost fully phosphorylated in mitotic cells. In particular, nuclear proteins and proteins involved in regulating metabolic processes have high phosphorylation site occupancy in mitosis. This suggests that these proteins may be inactivated by phosphorylation in mitotic cells. Copyright 2008 by the American Association for the Advancement of Science; all rights reserved. Source

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