Juan-Carlos Rodriguez-Prados

Publications (9) View all

• Article: Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors

  Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodriguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas
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  ABSTRACT: BACKGROUND: Tumor classification based on their predicted responses to kinase inhibitors is a major goal for advancing targeted personalized therapies. Here, we used a phosphoproteomic approach to investigate biological heterogeneity across hematological cancer cell lines including acute myeloid leukemia, lymphoma and multiple myeloma. RESULTS: Mass spectrometry was used to quantify 2,000 phosphorylation sites across three acute myeloid leukemia, three lymphoma and three multiple myeloma cell lines in six biological replicates. The intensities of the phosphorylation sites grouped these cancer cell lines according to their tumor type. In addition, a phosphoproteomic analysis of seven acute myeloid leukemia cell lines revealed a battery of phosphorylation sites whose combined intensities correlated with the growth-inhibitory responses to three kinase inhibitors with remarkable correlation coefficients and fold changes (>100 between the most resistant and sensitive cells). Modeling based on regression analysis indicated that a subset of phosphorylation sites could be used to predict response to the tested drugs. Quantitative analysis of phosphorylation motifs indicated that resistant and sensitive cells differed in their patterns of kinase activities, but, interestingly, phosphorylations correlating with responses were not on members of the pathway being targeted; instead, these mainly were on parallel kinase pathways. CONCLUSION: This study reveals that the information on kinase activation encoded in phosphoproteomics data correlates remarkably well with the phenotypic responses of cancer cells to compounds that target kinase signaling and could be useful for the identification of novel markers of resistance or sensitivity to drugs that target the signaling network.
  Genome Biology 04/2013; · 9.04 Impact Factor
• Article: Kinase-substrate enrichment analysis provides insights into the heterogeneity of signaling pathway activation in leukemia cells.

  Pedro Casado, Juan-Carlos Rodriguez-Prados, Sabina C Cosulich, Sylvie Guichard, Bart Vanhaesebroeck, Simon Joel, Pedro R Cutillas
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  ABSTRACT: Kinases determine the phenotypes of many cancer cells, but the frequency with which individual kinases are activated in primary tumors remains largely unknown. We used a computational approach, termed kinase-substrate enrichment analysis (KSEA), to systematically infer the activation of given kinase pathways from mass spectrometry-based phosphoproteomic analysis of acute myeloid leukemia (AML) cells. Experiments conducted in cell lines validated the approach and, furthermore, revealed that DNA-dependent protein kinase (DNA-PK) was activated as a result of inhibiting the phosphoinositide 3-kinase (PI3K)-mammalian target of rapamycin (mTOR) signaling pathway. Application of KSEA to primary AML cells identified PI3K, casein kinases (CKs), cyclin-dependent kinases (CDKs), and p21-activated kinases (PAKs) as the kinase substrate groups most frequently enriched in this cancer type. Substrates phosphorylated by extracellular signal-regulated kinase (ERK) and cell division cycle 7 (CDC7) were enriched in primary AML cells that were resistant to inhibition of PI3K-mTOR signaling, whereas substrates of the kinases Abl, Lck, Src, and CDK1 were increased in abundance in inhibitor-sensitive cells. Modeling based on the abundances of these substrate groups accurately predicted sensitivity to a dual PI3K and mTOR inhibitor in two independent sets of primary AML cells isolated from patients. Thus, our study demonstrates KSEA as an untargeted method for the systematic profiling of kinase pathway activities and for increasing our understanding of diseases caused by the dysregulation of signaling pathways.
  Science Signaling 01/2013; 6(268):rs6. · 7.50 Impact Factor
• Article: Global profiling of protein kinase activities in cancer cells by mass spectrometry.

  Luisa Beltran, Pedro Casado, Juan-Carlos Rodríguez-Prados, Pedro R Cutillas
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  ABSTRACT: Protein kinases have important functions in the control of cell biology and are implicated in several diseases including cancer. Here we describe a technique to quantify protein kinase activity in a global fashion and without preconception of the kinases that may be active in the cell or tissue under investigation. In Global Kinase Activity Profiling (GKAP), protein kinases present in experimental cell lysates phosphorylate endogenous substrates, also present in the lysate, under defined conditions. Reaction products are then quantified using standard phosphoproteomic techniques based on LC-MS/MS. The technique thus allows measuring the combined activities of kinases targeting common substrates, which are detected as phosphopeptides by LC-MS/MS. Almost four hundred kinase reactions could be quantified in a human epithelial cell line, 177 of which increased in response to EGF treatment while others decreased in cells exposed to the kinase inhibitors LY294002 or U0126. GKAP also detected marked differences in the patterns of kinase activities in human leukemia cell lines with different sensitivities to kinase inhibitors. These results reveal that GKAP detects and quantifies hundreds of kinase activities modulated by growth factors or pharmacological inhibitors, and that these activities correlate with the phenotypes of cancer cells and their responses to kinase inhibitors.
  Journal of proteomics 10/2012; · 5.07 Impact Factor
• Article: Relevance of the MEK/ERK signaling pathway in the metabolism of activated macrophages: a metabolomic approach.

  Paqui G Través, Pedro de Atauri, Silvia Marín, María Pimentel-Santillana, Juan-Carlos Rodríguez-Prados, Igor Marín de Mas, Vitaly A Selivanov, Paloma Martín-Sanz, Lisardo Boscá, Marta Cascante
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  ABSTRACT: The activation of immune cells in response to a pathogen involves a succession of signaling events leading to gene and protein expression, which requires metabolic changes to match the energy demands. The metabolic profile associated with the MAPK cascade (ERK1/2, p38, and JNK) in macrophages was studied, and the effect of its inhibition on the specific metabolic pattern of LPS stimulation was characterized. A [1,2-[(13)C](2)]glucose tracer-based metabolomic approach was used to examine the metabolic flux distribution in these cells after MEK/ERK inhibition. Bioinformatic tools were used to analyze changes in mass isotopomer distribution and changes in glucose and glutamine consumption and lactate production in basal and LPS-stimulated conditions in the presence and absence of the selective inhibitor of the MEK/ERK cascade, PD325901. Results showed that PD325901-mediated ERK1/2 inhibition significantly decreased glucose consumption and lactate production but did not affect glutamine consumption. These changes were accompanied by a decrease in the glycolytic flux, consistent with the observed decrease in fructose-2,6-bisphosphate concentration. The oxidative and nonoxidative pentose phosphate pathways and the ratio between them also decreased. However, tricarboxylic acid cycle flux did not change significantly. LPS activation led to the opposite responses, although all of these were suppressed by PD325901. However, LPS also induced a small decrease in pentose phosphate pathway fluxes and an increase in glutamine consumption that were not affected by PD325901. We concluded that inhibition of the MEK/ERK cascade interferes with central metabolism, and this cross-talk between signal transduction and metabolism also occurs in the presence of LPS.
  The Journal of Immunology 12/2011; 188(3):1402-10. · 5.79 Impact Factor
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  Available from: Juan-Carlos Rodriguez-Prados

  Article: Characterization of a TiO₂ enrichment method for label-free quantitative phosphoproteomics.

  Alex Montoya, Luisa Beltran, Pedro Casado, Juan-Carlos Rodríguez-Prados, Pedro R Cutillas
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  ABSTRACT: Phosphorylation is a protein post-translational modification with key roles in the regulation of cell biochemistry and signaling. In-depth analysis of phosphorylation using mass spectrometry is permitting the investigation of processes controlled by phosphorylation at the system level. A critical step of these phosphoproteomics methods involves the isolation of phosphorylated peptides from the more abundant unmodified peptides produced by the digestion of cell lysates. Although different techniques to enrich for phosphopeptides have been reported, there are limited data on their suitability for direct quantitative analysis by MS. Here we report a TiO(2) based enrichment method compatible with large-scale and label-free quantitative analysis by LC-MS/MS. Starting with just 500 μg of protein, the technique reproducibly isolated hundreds of peptides, >85% of which were phosphorylated. These results were obtained by using relatively short LC-MS/MS gradient runs (45 min) and without any previous separation step. In order to characterize the performance of the method for quantitative analyses, we employed label-free LC-MS/MS using extracted ion chromatograms as the quantitative readout. After normalization, phosphopeptides were quantified with good precision (coefficient of variation was 20% on average, n=900 phosphopeptides), linearity (correlation coefficients >0.98) and accuracy (deviations <20%). Thus, phosphopeptide ion signals correlated with the concentration of the respective phosphopeptide in samples, making the approach suitable for in-depth relative quantification of phosphorylation by label-free LC-MS/MS.
  Methods 02/2011; 54(4):370-8. · 4.01 Impact Factor