Research Topics
Genomes and Genes
| John M AsaraSummaryAffiliation: Harvard University Country: USA Publications
| Collaborators
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Detail Information
Publications
Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometryJohn M Asara
Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Science 316:280-5. 2007....- In-Gel Stable-Isotope Labeling (ISIL): a strategy for mass spectrometry-based relative quantificationJohn M Asara
Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
J Proteome Res 5:155-63. 2006..An advantage of ISIL is that visualization of gel differences can be used as a first quantification step followed by accurate and sensitive protein level stable-isotope labeling and mass spectrometry-based relative quantification... - A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screenJohn M Asara
Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Proteomics 8:994-9. 2008.... - In-gel stable isotope labeling for relative quantification using mass spectrometryJohn M Asara
Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
Nat Protoc 1:46-51. 2006..This protocol should take approximately 24-26 h to complete, including the incubation time for proteolytic digestion. Additional time will be needed for data analysis and interpretation... - Proteomic screening method for phosphopeptide motif binding proteins using peptide librariesHeather R Christofk
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
J Proteome Res 10:4158-64. 2011.... - Inhibition of pyruvate kinase M2 by reactive oxygen species contributes to cellular antioxidant responsesDimitrios Anastasiou
Beth Israel Deaconess Medical Center, Department of Medicine Division of Signal Transduction, Boston, MA 02115, USA
Science 334:1278-83. 2011..Besides promoting metabolic changes required for proliferation, the regulatory properties of PKM2 may confer an additional advantage to cancer cells by allowing them to withstand oxidative stress... - Phosphorylation of the tumor suppressor CYLD by the breast cancer oncogene IKKepsilon promotes cell transformationJessica E Hutti
Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
Mol Cell 34:461-72. 2009..Together, these observations define IKKepsilon and CYLD as an oncogene-tumor suppressor network that participates in tumorigenesis... - Proteomic and functional genomic landscape of receptor tyrosine kinase and ras to extracellular signal-regulated kinase signalingAdam A Friedman
Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
Sci Signal 4:rs10. 2011.... - Evidence for an alternative glycolytic pathway in rapidly proliferating cellsMatthew G Vander Heiden
Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
Science 329:1492-9. 2010.... - Regulation of oxysterol-binding protein Golgi localization through protein kinase D-mediated phosphorylationSokha Nhek
Departments of Pathology and Signal Transduction, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
Mol Biol Cell 21:2327-37. 2010..Instead, phosphorylation attenuates OSBP Golgi localization in response to 25-hydroxycholesterol and cholesterol depletion, impairs CERT Golgi localization, and promotes Golgi fragmentation... - IkappaB kinase beta phosphorylates the K63 deubiquitinase A20 to cause feedback inhibition of the NF-kappaB pathwayJessica E Hutti
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
Mol Cell Biol 27:7451-61. 2007..Phosphorylation of A20 by IKKbeta thus represents part of a novel feedback loop that regulates the duration of NF-kappaB signaling following activation of innate immune signaling pathways... - Phosphoglycerate dehydrogenase diverts glycolytic flux and contributes to oncogenesisJason W Locasale
Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
Nat Genet 43:869-74. 2011..Our findings show that the diversion of glycolytic flux into a specific alternate pathway can be selected during tumor development and may contribute to the pathogenesis of human cancer... - Oncogenic B-RAF negatively regulates the tumor suppressor LKB1 to promote melanoma cell proliferationBin Zheng
Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Mol Cell 33:237-47. 2009..Our findings provide a molecular linkage between the LKB1-AMPK and the RAF-MEK-ERK pathways and suggest that suppression of LKB1 function by B-RAF V600E plays an important role in B-RAF V600E-driven tumorigenesis... - Characterization of Rictor phosphorylation sites reveals direct regulation of mTOR complex 2 by S6K1Christian C Dibble
Department of Genetics and Complex Diseases, Harvard School of Public Health, 665 Huntington Ave, SPH2 117, Boston, MA 02115, USA
Mol Cell Biol 29:5657-70. 2009..We provide evidence that Rictor-T1135 phosphorylation acts in parallel with other mTORC1-dependent feedback mechanisms, such as those affecting IRS-1 signaling to PI3K, to regulate the response of Akt to insulin... - The role of the transcription factor SIM2 in prostate cancerBin Lu
Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS ONE 6:e28837. 2011..This study was designed to elucidate the role of SIM2 in prostate cancer using a shRNA-based approach in the PC3 prostate cancer cell line... - A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissueMin Yuan
1 Division of Signal Transduction Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA 2
Nat Protoc 7:872-81. 2012..The procedure takes ?12 h from metabolite extraction to peak integration for a data set containing 15 total samples (?6 h for a single sample)... - Using tandem mass spectrometry in targeted mode to identify activators of class IA PI3K in cancerXuemei Yang
Beth Israel Deaconess Medical Center, Division of Signal Transduction, Boston, Massachusetts 02115, USA
Cancer Res 71:5965-75. 2011..Using this technique to define the pathways that activate PI3K signaling in a given tumor could help inform clinical decision making by helping guide personalized therapeutic strategies for different patients... - Metabolic regulation of protein N-alpha-acetylation by Bcl-xL promotes cell survivalCaroline H Yi
Department of Cell Biology, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
Cell 146:607-20. 2011..We propose that acetyl-CoA serves as a signaling molecule that couples apoptotic sensitivity to metabolism by regulating protein N-alpha-acetylation... - mTOR drives its own activation via SCF(?TrCP)-dependent degradation of the mTOR inhibitor DEPTORDaMing Gao
Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
Mol Cell 44:290-303. 2011.... - Regulation and identification of Na,K-ATPase alpha1 subunit phosphorylation in rat parotid acinar cellsStephen P Soltoff
Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, USA
J Biol Chem 285:36330-8. 2010.... - Ubiquitination of K-Ras enhances activation and facilitates binding to select downstream effectorsAtsuo T Sasaki
1Division of Signal Transduction, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
Sci Signal 4:ra13. 2011..Thus, monoubiquitination could enhance GTP loading on K-Ras and increase its affinity for specific downstream effectors, providing a previously unidentified mechanism for Ras activation... - Essential role for the prolyl isomerase Pin1 in Toll-like receptor signaling and type I interferon-mediated immunityAdrian Tun-Kyi
Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
Nat Immunol 12:733-41. 2011..Given the critical role of aberrant activation of IRAK1 and type I interferons in various immune diseases, controlling IRAK1 activation via inhibition of Pin1 may represent a useful therapeutic approach... - The holo-apoptosome: activation of procaspase-9 and interactions with caspase-3Shujun Yuan
Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118 2526, USA
Structure 19:1084-96. 2011..These binding sites may play a role in pc-3 activation and could allow the formation of hybrid apoptosomes with pc-9 and caspase-3 proteolytic activities... - Polymerase I and transcript release factor regulates lipolysis via a phosphorylation-dependent mechanismNabila Aboulaich
Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
Diabetes 60:757-65. 2011..Polymerase I and transcript release factor (PTRF) is a protein highly expressed in adipose tissue and is an integral structural component of caveolae. Here, we report on a novel role of PTRF in lipid mobilization... - Phosphoinositide 3-kinase pathway activation in phosphate and tensin homolog (PTEN)-deficient prostate cancer cells is independent of receptor tyrosine kinases and mediated by the p110beta and p110delta catalytic subunitsXinnong Jiang
Hematology Oncology, Department ofMedicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, USA
J Biol Chem 285:14980-9. 2010..Increased p110beta expression in PCa may be required for RTK-independent PI3K pathway activation in adult prostate epithelium with genetic or epigenetic PTEN down-regulation... - Use of a label-free quantitative platform based on MS/MS average TIC to calculate dynamics of protein complexes in insulin signalingXuemei Yang
Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
J Biomol Tech 20:272-7. 2009..The MS strategy showed excellent coverage of known components in addition to potentially novel interactions... - Pilot proteomic profile of differentially regulated proteins in right atrial appendage before and after cardiac surgery using cardioplegia and cardiopulmonary bypassRichard T Clements
Division of Cardiothoracic Surgery, Beth Israel Deaconess Medical Center, LMOB 2A, 110 Francis St, Boston, MA 02215, USA
Circulation 118:S24-31. 2008..Acute changes in myocardial contractile activity are likely regulated via protein modifications. We performed the following study to determine changes in the protein profile of human myocardium following CP/CPB... - Determining in vivo phosphorylation sites using mass spectrometrySusanne B Breitkopf
Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts
Curr Protoc Mol Biol . 2012..One can also immunoprecipitate only phosphotyrosine peptides using a pTyr antibody followed by LC-MS/MS. Curr. Protoc. Mol. Biol. 98:18.19.1-18.19.27. © 2012 by John Wiley & Sons, Inc... - The Crohn's disease protein, NOD2, requires RIP2 in order to induce ubiquitinylation of a novel site on NEMODerek W Abbott
Division of Gastrointestinal Pathology, Department of Pathology, Brigham and Women s Hospital, Harvard Medical School, Boston, MA, USA
Curr Biol 14:2217-27. 2004..NOD2 can both strongly activate and negatively attenuate NF-kB signaling. The biochemical mechanism for this dual function of NOD2 is unknown... - Serum proteomics and biomarkers in hepatocellular carcinoma and chronic liver diseaseNoah T Zinkin
Liver Center, Department of Gastroenterology and Hepatology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02115, USA
Clin Cancer Res 14:470-7. 2008.... - Metabolomic profiling from formalin-fixed, paraffin-embedded tumor tissue using targeted LC/MS/MS: application in sarcomaAndrew D Kelly
Division of Hematology Oncology, Sarcoma Program, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
PLoS ONE 6:e25357. 2011..Our study supports the notion that reliable and broadly informative metabolomic data may be acquired from FFPE soft tissue sarcoma specimens, a finding that is likely to be extended to other malignancies... - An automated method for the analysis of stable isotope labeling data in proteomicsXiang Zhang
Beyond Genomics Inc, Waltham, Massachusetts, USA
J Am Soc Mass Spectrom 16:1181-91. 2005..The experimental results correlated well with known mixing ratios... - Data pre-processing in liquid chromatography-mass spectrometry-based proteomicsXiang Zhang
Bindley Bioscience Center, Purdue University West Lafayette, IN, USA
Bioinformatics 21:4054-9. 2005..It is necessary to develop a data mining system to perform peak quantification, peak alignment and data quality assurance... - Analyses of soft tissue from Tyrannosaurus rex suggest the presence of proteinMary Higby Schweitzer
Department of Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC 27695, USA
Science 316:277-80. 2007..The presence of endogenous protein in dinosaur bone may validate hypotheses about evolutionary relationships, rates, and patterns of molecular change and degradation, as well as the chemical stability of molecules over time... - Interpreting sequences from mastodon and T. rexJohn M Asara
Science 317:1324-5. 2007 - Molecular phylogenetics of mastodon and Tyrannosaurus rexChris L Organ
Harvard University, Cambridge, MA 02138, USA
Science 320:499. 2008..rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable... - Pyruvate kinase M2 is a phosphotyrosine-binding proteinHeather R Christofk
Department of Systems Biology
Nature 452:181-6. 2008..Collectively, our results indicate that expression of this phosphotyrosine-binding form of pyruvate kinase is critical for rapid growth in cancer cells... - Insulin-stimulated phosphorylation of a Rab GTPase-activating protein regulates GLUT4 translocationHiroyuki Sano
Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
J Biol Chem 278:14599-602. 2003..These findings strongly indicate that insulin-stimulated phosphorylation of AS160 is required for GLUT4 translocation and that this phosphorylation signals translocation through inactivation of the Rab GAP function... - Identification of immunoreactive material in mammoth fossilsMary Schweitzer
Department of Microbiology, Montana State University, Bozeman, MT 59717, USA
J Mol Evol 55:696-705. 2002..Although the presence of peptides and amino acids was demonstrated, the exact nature of the antigenic material was not fully clarified. This report demonstrates that antibodies may be used to obtain information from the fossil record... - A method to identify serine kinase substrates. Akt phosphorylates a novel adipocyte protein with a Rab GTPase-activating protein (GAP) domainSusan Kane
Department of Biochemistry, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
J Biol Chem 277:22115-8. 2002..Insulin treatment of adipocytes caused AS160 to redistribute from the low density microsomes to the cytosol...