1
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Roth Flach RJ, Bollinger E, Reyes AR, Laforest B, Kormos BL, Liu S, Reese MR, Martinez Alsina LA, Buzon L, Zhang Y, Bechle B, Rosado A, Sahasrabudhe PV, Knafels J, Bhattacharya SK, Omoto K, Stansfield JC, Hurley LD, Song L, Luo L, Breitkopf SB, Monetti M, Cunio T, Tierney B, Geoly FJ, Delmore J, Siddall CP, Xue L, Yip KN, Kalgutkar AS, Miller RA, Zhang BB, Filipski KJ. Small molecule branched-chain ketoacid dehydrogenase kinase (BDK) inhibitors with opposing effects on BDK protein levels. Nat Commun 2023; 14:4812. [PMID: 37558654 PMCID: PMC10412597 DOI: 10.1038/s41467-023-40536-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 07/25/2023] [Indexed: 08/11/2023] Open
Abstract
Branched chain amino acid (BCAA) catabolic impairments have been implicated in several diseases. Branched chain ketoacid dehydrogenase (BCKDH) controls the rate limiting step in BCAA degradation, the activity of which is inhibited by BCKDH kinase (BDK)-mediated phosphorylation. Screening efforts to discover BDK inhibitors led to identification of thiophene PF-07208254, which improved cardiometabolic endpoints in mice. Structure-activity relationship studies led to identification of a thiazole series of BDK inhibitors; however, these inhibitors did not improve metabolism in mice upon chronic administration. While the thiophenes demonstrated sustained branched chain ketoacid (BCKA) lowering and reduced BDK protein levels, the thiazoles increased BCKAs and BDK protein levels. Thiazoles increased BDK proximity to BCKDH-E2, whereas thiophenes reduced BDK proximity to BCKDH-E2, which may promote BDK degradation. Thus, we describe two BDK inhibitor series that possess differing attributes regarding BDK degradation or stabilization and provide a mechanistic understanding of the desirable features of an effective BDK inhibitor.
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Affiliation(s)
- Rachel J Roth Flach
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA.
| | - Eliza Bollinger
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Allan R Reyes
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Brigitte Laforest
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Bethany L Kormos
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Shenping Liu
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | - Matthew R Reese
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | | | - Leanne Buzon
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | - Yuan Zhang
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | - Bruce Bechle
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | - Amy Rosado
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | | | - John Knafels
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | | | - Kiyoyuki Omoto
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - John C Stansfield
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Liam D Hurley
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - LouJin Song
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Lina Luo
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | | | - Mara Monetti
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Teresa Cunio
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Brendan Tierney
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | - Frank J Geoly
- Pfizer Worldwide Research, Development & Medical, Groton, CT, 06340, USA
| | - Jake Delmore
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - C Parker Siddall
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Liang Xue
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Ka N Yip
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Amit S Kalgutkar
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Russell A Miller
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Bei B Zhang
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA
| | - Kevin J Filipski
- Pfizer Worldwide Research, Development & Medical, Cambridge, MA, 02139, USA.
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2
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Flaherty SE, Bezy O, Zheng W, Yan D, Li X, Jagarlapudi S, Albuquerque B, Esquejo RM, Peloquin M, Semache M, Mancini A, Kang L, Drujan D, Breitkopf SB, Griffin JD, Jean Beltran PM, Xue L, Stansfield J, Pashos E, Shakey Q, Pehmøller C, Monetti M, Birnbaum MJ, Fortin JP, Wu Z. Chronic UCN2 treatment desensitizes CRHR2 and improves insulin sensitivity. Nat Commun 2023; 14:3953. [PMID: 37402735 DOI: 10.1038/s41467-023-39597-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/21/2023] [Indexed: 07/06/2023] Open
Abstract
Urocortin 2 (UCN2) acts as a ligand for the G protein-coupled receptor corticotropin-releasing hormone receptor 2 (CRHR2). UCN2 has been reported to improve or worsen insulin sensitivity and glucose tolerance in vivo. Here we show that acute dosing of UCN2 induces systemic insulin resistance in male mice and skeletal muscle. Inversely, chronic elevation of UCN2 by injection with adenovirus encoding UCN2 resolves metabolic complications, improving glucose tolerance. CRHR2 recruits Gs in response to low concentrations of UCN2, as well as Gi and β-Arrestin at high concentrations of UCN2. Pre-treating cells and skeletal muscle ex vivo with UCN2 leads to internalization of CRHR2, dampened ligand-dependent increases in cAMP, and blunted reductions in insulin signaling. These results provide mechanistic insights into how UCN2 regulates insulin sensitivity and glucose metabolism in skeletal muscle and in vivo. Importantly, a working model was derived from these results that unifies the contradictory metabolic effects of UCN2.
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Affiliation(s)
- Stephen E Flaherty
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Olivier Bezy
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Wei Zheng
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Dong Yan
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Xiangping Li
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Srinath Jagarlapudi
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Bina Albuquerque
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Ryan M Esquejo
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Matthew Peloquin
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | | | | | - Liya Kang
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Doreen Drujan
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Susanne B Breitkopf
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - John D Griffin
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Pierre M Jean Beltran
- Machine Learning and Computational Sciences, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Liang Xue
- Machine Learning and Computational Sciences, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - John Stansfield
- Biostatistics, Early Clinical Development, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Evanthia Pashos
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Quazi Shakey
- Biomedicine design, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Christian Pehmøller
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Mara Monetti
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Morris J Birnbaum
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Jean-Philippe Fortin
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA
| | - Zhidan Wu
- Internal Medicine Research Unit, Pfizer Inc., 1 Portland Street, Cambridge, MA, USA.
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3
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Chen M, Zhang J, Sampieri K, Clohessy JG, Mendez L, Gonzalez-Billalabeitia E, Liu XS, Lee YR, Fung J, Katon JM, Menon AV, Webster KA, Ng C, Palumbieri MD, Diolombi MS, Breitkopf SB, Teruya-Feldstein J, Signoretti S, Bronson RT, Asara JM, Castillo-Martin M, Cordon-Cardo C, Pandolfi PP. An aberrant SREBP-dependent lipogenic program promotes metastatic prostate cancer. Nat Genet 2018; 50:206-218. [PMID: 29335545 DOI: 10.1038/s41588-017-0027-2] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 12/01/2017] [Indexed: 12/15/2022]
Abstract
Lipids, either endogenously synthesized or exogenous, have been linked to human cancer. Here we found that PML is frequently co-deleted with PTEN in metastatic human prostate cancer (CaP). We demonstrated that conditional inactivation of Pml in the mouse prostate morphs indolent Pten-null tumors into lethal metastatic disease. We identified MAPK reactivation, subsequent hyperactivation of an aberrant SREBP prometastatic lipogenic program, and a distinctive lipidomic profile as key characteristic features of metastatic Pml and Pten double-null CaP. Furthermore, targeting SREBP in vivo by fatostatin blocked both tumor growth and distant metastasis. Importantly, a high-fat diet (HFD) induced lipid accumulation in prostate tumors and was sufficient to drive metastasis in a nonmetastatic Pten-null mouse model of CaP, and an SREBP signature was highly enriched in metastatic human CaP. Thus, our findings uncover a prometastatic lipogenic program and lend direct genetic and experimental support to the notion that a Western HFD can promote metastasis.
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Affiliation(s)
- Ming Chen
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jiangwen Zhang
- School of Biological Sciences, University of Hong Kong, Hong Kong, China
| | - Katia Sampieri
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,GSK Vaccines, Antigen Identification and Molecular Biology, Siena, Italy
| | - John G Clohessy
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.,Preclinical Murine Pharmacogenetics Facility and Mouse Hospital, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Lourdes Mendez
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Enrique Gonzalez-Billalabeitia
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xue-Song Liu
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yu-Ru Lee
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jacqueline Fung
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jesse M Katon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Archita Venugopal Menon
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Kaitlyn A Webster
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Christopher Ng
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Maria Dilia Palumbieri
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Moussa S Diolombi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Julie Teruya-Feldstein
- Department of Pathology, Sloan-Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sabina Signoretti
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Roderick T Bronson
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Mireia Castillo-Martin
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Champalimaud Center for the Unknown, Lisbon, Portugal
| | - Carlos Cordon-Cardo
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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4
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Breitkopf SB, Taveira MDO, Yuan M, Wulf GM, Asara JM. Serial-omics of P53-/-, Brca1-/- Mouse Breast Tumor and Normal Mammary Gland. Sci Rep 2017; 7:14503. [PMID: 29109428 PMCID: PMC5674068 DOI: 10.1038/s41598-017-15132-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/20/2017] [Indexed: 12/28/2022] Open
Abstract
This study demonstrates a liquid-liquid extraction for the sequential tandem mass spectrometry (LC-MS/MS) analysis of non-polar lipids, polar metabolites, proteins and phosphorylation sites from a single piece of tissue. Extraction of 10 mg BRCA-/-, p53-/- breast tumor tissue or normal mammary gland tissue with methyl-tert-butyl ether (MTBE) results in three phases: an upper non-polar phase containing 1,382 lipids, a lower polar phase with 805 metabolites and a precipitated protein pellet with 4,792 proteins with 1,072 phosphorylation sites. Comparative analysis revealed an activated AKT-mTOR pathway in tumors. Tumors also showed a reduction of phosphorylation sites involved in transcription and RNA splicing and decreased abundance of enzymes in lipid synthesis. Analysis of polar metabolites revealed a reduction in glycolysis, pentose phosphate pathway, polyamines and nucleotides, but an increase in TCA and urea cycle intermediates. Analysis of lipids revealed a shift from high triglycerides in mammary gland to high phospholipid levels in tumors. The data were integrated into a model showing breast tumors exhibit features on the proteomic, lipidomic and metabolomic level that are distinct from normal breast tissue. Our integrative technique lends itself to samples such as tumor biopsies, dried blood spots and fluids including urine and CSF to develop biomarkers of disease.
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Affiliation(s)
- Susanne B Breitkopf
- Beth Israel Deaconess Medical Center, Division of Signal Transduction, Boston, MA, USA
- Harvard Medical School, Department of Medicine, Boston, MA, USA
| | - Mateus De Oliveira Taveira
- Harvard Medical School, Department of Medicine, Boston, MA, USA
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Min Yuan
- Beth Israel Deaconess Medical Center, Division of Signal Transduction, Boston, MA, USA
| | - Gerburg M Wulf
- Harvard Medical School, Department of Medicine, Boston, MA, USA
- Division of Hematology and Oncology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - John M Asara
- Beth Israel Deaconess Medical Center, Division of Signal Transduction, Boston, MA, USA.
- Harvard Medical School, Department of Medicine, Boston, MA, USA.
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5
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Bowden JA, Heckert A, Ulmer CZ, Jones CM, Koelmel JP, Abdullah L, Ahonen L, Alnouti Y, Armando AM, Asara JM, Bamba T, Barr JR, Bergquist J, Borchers CH, Brandsma J, Breitkopf SB, Cajka T, Cazenave-Gassiot A, Checa A, Cinel MA, Colas RA, Cremers S, Dennis EA, Evans JE, Fauland A, Fiehn O, Gardner MS, Garrett TJ, Gotlinger KH, Han J, Huang Y, Neo AH, Hyötyläinen T, Izumi Y, Jiang H, Jiang H, Jiang J, Kachman M, Kiyonami R, Klavins K, Klose C, Köfeler HC, Kolmert J, Koal T, Koster G, Kuklenyik Z, Kurland IJ, Leadley M, Lin K, Maddipati KR, McDougall D, Meikle PJ, Mellett NA, Monnin C, Moseley MA, Nandakumar R, Oresic M, Patterson R, Peake D, Pierce JS, Post M, Postle AD, Pugh R, Qiu Y, Quehenberger O, Ramrup P, Rees J, Rembiesa B, Reynaud D, Roth MR, Sales S, Schuhmann K, Schwartzman ML, Serhan CN, Shevchenko A, Somerville SE, St John-Williams L, Surma MA, Takeda H, Thakare R, Thompson JW, Torta F, Triebl A, Trötzmüller M, Ubhayasekera SJK, Vuckovic D, Weir JM, Welti R, Wenk MR, Wheelock CE, Yao L, Yuan M, Zhao XH, Zhou S. Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J Lipid Res 2017; 58:2275-2288. [PMID: 28986437 DOI: 10.1194/jlr.m079012] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/02/2017] [Indexed: 12/22/2022] Open
Abstract
As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a commercially available reference material. The interlaboratory study comprised 31 diverse laboratories, with each laboratory using a different lipidomics workflow. A total of 1,527 unique lipids were measured across all laboratories and consensus location estimates and associated uncertainties were determined for 339 of these lipids measured at the sum composition level by five or more participating laboratories. These evaluated lipids detected in SRM 1950 serve as community-wide benchmarks for intra- and interlaboratory quality control and method validation. These analyses were performed using nonstandardized laboratory-independent workflows. The consensus locations were also compared with a previous examination of SRM 1950 by the LIPID MAPS consortium. While the central theme of the interlaboratory study was to provide values to help harmonize lipids, lipid mediators, and precursor measurements across the community, it was also initiated to stimulate a discussion regarding areas in need of improvement.
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Affiliation(s)
- John A Bowden
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Alan Heckert
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| | - Candice Z Ulmer
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Christina M Jones
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Jeremy P Koelmel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Linda Ahonen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Yazen Alnouti
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - Aaron M Armando
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA
| | - Takeshi Bamba
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Gerald Bronfman Department of Oncology McGill University, Montreal, Quebec, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Joost Brandsma
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Tomas Cajka
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Antonio Checa
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michelle A Cinel
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Romain A Colas
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Serge Cremers
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Edward A Dennis
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | | | - Alexander Fauland
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA.,Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Michael S Gardner
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Katherine H Gotlinger
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | | | - Aveline Huipeng Neo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | | | - Yoshihiro Izumi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Hongfeng Jiang
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Houli Jiang
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jiang Jiang
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Maureen Kachman
- Metabolomics Core, BRCF, University of Michigan, Ann Arbor, MI
| | | | | | | | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Johan Kolmert
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Grielof Koster
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Zsuzsanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Irwin J Kurland
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Michael Leadley
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Karen Lin
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Krishna Rao Maddipati
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
| | - Danielle McDougall
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | | | - Cian Monnin
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Renu Nandakumar
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Matej Oresic
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rainey Patterson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Jason S Pierce
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Martin Post
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Anthony D Postle
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Rebecca Pugh
- Chemical Sciences Division, Environmental Specimen Bank Group, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Oswald Quehenberger
- Departments of Medicine and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Parsram Ramrup
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jon Rees
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Barbara Rembiesa
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Denis Reynaud
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Mary R Roth
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Charles N Serhan
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stephen E Somerville
- Hollings Marine Laboratory, Medical University of South Carolina, Charleston, SC
| | - Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | | | - Hiroaki Takeda
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Rhishikesh Thakare
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | | | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jacquelyn M Weir
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Ruth Welti
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Libin Yao
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Xueqing Heather Zhao
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Senlin Zhou
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
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Breitkopf SB, Ricoult SJH, Yuan M, Xu Y, Peake DA, Manning BD, Asara JM. A relative quantitative positive/negative ion switching method for untargeted lipidomics via high resolution LC-MS/MS from any biological source. Metabolomics 2017; 13:30. [PMID: 28496395 PMCID: PMC5421409 DOI: 10.1007/s11306-016-1157-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Advances in high-resolution mass spectrometry have created renewed interest for studying global lipid biochemistry in disease and biological systems. OBJECTIVES Here, we present an untargeted 30 min. LC-MS/MS platform that utilizes positive/negative polarity switching to perform unbiased data dependent acquisitions (DDA) via higher energy collisional dissociation (HCD) fragmentation to profile more than 1000-1500 lipid ions mainly from methyl-tert-butyl ether (MTBE) or chloroform:methanol extractions. METHODS The platform uses C18 reversed-phase chromatography coupled to a hybrid QExactive Plus/HF Orbitrap mass spectrometer and the entire procedure takes ~10 h from lipid extraction to identification/quantification for a data set containing 12 samples (~4 h for a single sample). Lipids are identified by both accurate precursor ion mass and fragmentation features and quantified using Lipid-Search and Elements software. RESULTS Using this approach, we are able to profile intact lipid ions from up to 18 different main lipid classes and 66 subclasses. We show several studies from different biological sources, including cultured cancer cells, resected tissues from mice such as lung and breast tumors and biological fluids such as plasma and urine. CONCLUSIONS Using mouse embryonic fibroblasts, we showed that TSC2-/- KD significantly abrogates lipid biosynthesis and that rapamycin can rescue triglyceride (TG) lipids and we show that SREBP-/- shuts down lipid biosynthesis significantly via mTORC1 signaling pathways. We show that in mouse EGFR driven lung tumors, a large number of TGs and phosphatidylmethanol (PMe) lipids are elevated while some phospholipids (PLs) show some of the largest decrease in lipid levels from ~ 2000 identified lipid ions. In addition, we identified more than 1500 unique lipid species from human blood plasma.
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Affiliation(s)
- Susanne B Breitkopf
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Stéphane J H Ricoult
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Min Yuan
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Ying Xu
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - David A Peake
- Thermo Fisher Scientific, 355 River Oaks Pkwy, San Jose, CA 95134, USA
| | - Brendan D Manning
- Department of Genetics and Complex Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction/Mass Spectrometry Core, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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Breitkopf SB, Yuan M, Helenius KP, Lyssiotis CA, Asara JM. Triomics Analysis of Imatinib-Treated Myeloma Cells Connects Kinase Inhibition to RNA Processing and Decreased Lipid Biosynthesis. Anal Chem 2015; 87:10995-1006. [PMID: 26434776 PMCID: PMC5585869 DOI: 10.1021/acs.analchem.5b03040] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The combination of metabolomics, lipidomics, and phosphoproteomics that incorporates triple stable isotope labeling by amino acids in cell culture (SILAC) protein labeling, as well as (13)C in vivo metabolite labeling, was demonstrated on BCR-ABL-positive H929 multiple myeloma cells. From 11 880 phosphorylation sites, we confirm that H929 cells are primarily signaling through the BCR-ABL-ERK pathway, and we show that imatinib treatment not only downregulates phosphosites in this pathway but also upregulates phosphosites on proteins involved in RNA expression. Metabolomics analyses reveal that BCR-ABL-ERK signaling in H929 cells drives the pentose phosphate pathway (PPP) and RNA biosynthesis, where pathway inhibition via imatinib results in marked PPP impairment and an accumulation of RNA nucleotides and negative regulation of mRNA. Lipidomics data also show an overall reduction in lipid biosynthesis and fatty acid incorporation with a significant decrease in lysophospholipids. RNA immunoprecipitation studies confirm that RNA degradation is inhibited with short imatinib treatment and transcription is inhibited upon long imatinib treatment, validating the triomics results. These data show the utility of combining mass spectrometry-based "-omics" technologies and reveals that kinase inhibitors may not only downregulate phosphorylation of their targets but also induce metabolic events via increased phosphorylation of other cellular components.
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Affiliation(s)
- Susanne B. Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
| | - Katja P. Helenius
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology and Division of Gastroenterology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts 02115, United States
- Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, United States
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Bordoli MR, Yum J, Breitkopf SB, Thon JN, Italiano JE, Xiao J, Worby C, Wong SK, Lin G, Edenius M, Keller TL, Asara JM, Dixon JE, Yeo CY, Whitman M. A secreted tyrosine kinase acts in the extracellular environment. Cell 2015; 158:1033-1044. [PMID: 25171405 DOI: 10.1016/j.cell.2014.06.048] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 05/06/2014] [Accepted: 06/20/2014] [Indexed: 11/17/2022]
Abstract
Although tyrosine phosphorylation of extracellular proteins has been reported to occur extensively in vivo, no secreted protein tyrosine kinase has been identified. As a result, investigation of the potential role of extracellular tyrosine phosphorylation in physiological and pathological tissue regulation has not been possible. Here, we show that VLK, a putative protein kinase previously shown to be essential in embryonic development, is a secreted protein kinase, with preference for tyrosine, that phosphorylates a broad range of secreted and ER-resident substrate proteins. We find that VLK is rapidly and quantitatively secreted from platelets in response to stimuli and can tyrosine phosphorylate coreleased proteins utilizing endogenous as well as exogenous ATP sources. We propose that discovery of VLK activity provides an explanation for the extensive and conserved pattern of extracellular tyrosine phosphophorylation seen in vivo, and extends the importance of regulated tyrosine phosphorylation into the extracellular environment.
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Affiliation(s)
- Mattia R Bordoli
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Jina Yum
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jonathan N Thon
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Joseph E Italiano
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Vascular Biology Program, Department of Surgery, Children's Hospital, Boston, MA 02115, USA
| | - Junyu Xiao
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Carolyn Worby
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Swee-Kee Wong
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Grace Lin
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Maja Edenius
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Tracy L Keller
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Jack E Dixon
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92031, USA
| | - Chang-Yeol Yeo
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA; Department of Life Science and Global Top5 Research Program, Ewha Womans University, Seoul 120-750, Republic of Korea.
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA 02115, USA.
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Abstract
Phosphorylation is the most studied protein post-translational modification (PTM) in biological systems, since it controls cell growth, proliferation, survival, and other processes. High-resolution/high mass accuracy mass spectrometers are used to identify protein phosphorylation sites due to their speed, sensitivity, selectivity, and throughput. The protocols described here focus on two common strategies: (1) identifying phosphorylation sites from individual proteins and small protein complexes, and (2) identifying global phosphorylation sites from whole-cell and tissue extracts. For the first, endogenous or epitope-tagged proteins are typically immunopurified from cell lysates, purified via gel electrophoresis or precipitation, and enzymatically digested into peptides. Samples can be optionally enriched for phosphopeptides using immobilized metal affinity chromatography (IMAC) or titanium dioxide (TiO(2)) and then analyzed by microcapillary liquid chromatography/tandem mass spectrometry (LC-MS/MS). Global phosphorylation site analyses that capture pSer/pThr/pTyr sites from biological sources sites are more resource and time consuming and involve digesting the whole-cell lysate, followed by peptide fractionation by strong cation-exchange chromatography, phosphopeptide enrichment by IMAC or TiO(2), and LC-MS/MS. Alternatively, the protein lysate can be fractionated by SDS-PAGE, followed by digestion, phosphopeptide enrichment, and LC-MS/MS. One can also immunoprecipitate only phosphotyrosine peptides using a pTyr antibody followed by LC-MS/MS.
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Affiliation(s)
- Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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Kelly AD, Breitkopf SB, Yuan M, Goldsmith J, Spentzos D, Asara JM. Metabolomic profiling from formalin-fixed, paraffin-embedded tumor tissue using targeted LC/MS/MS: application in sarcoma. PLoS One 2011; 6:e25357. [PMID: 21984915 PMCID: PMC3184969 DOI: 10.1371/journal.pone.0025357] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 09/01/2011] [Indexed: 01/23/2023] Open
Abstract
The relatively new field of onco-metabolomics attempts to identify relationships between various cancer phenotypes and global metabolite content. Previous metabolomics studies utilized either nuclear magnetic resonance spectroscopy or gas chromatography/mass spectrometry, and analyzed metabolites present in urine and serum. However, direct metabolomic assessment of tumor tissues is important for determining altered metabolism in cancers. In this respect, the ability to obtain reliable data from archival specimens is desirable and has not been reported to date. In this feasibility study, we demonstrate the analysis of polar metabolites extracted directly from ten formalin-fixed, paraffin-embedded (FFPE) specimens, including five soft tissue sarcomas and five paired normal samples. Using targeted liquid chromatography-tandem mass spectrometry (LC/MS/MS) via selected reaction monitoring (SRM), we detect an average of 106 metabolites across the samples with excellent reproducibility and correlation between different sections of the same specimen. Unsupervised hierarchical clustering and principal components analysis reliably recovers a priori known tumor and normal tissue phenotypes, and supervised analysis identifies candidate metabolic markers supported by the literature. In addition, we find that diverse biochemical processes are well-represented in the list of detected metabolites. 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.
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Affiliation(s)
- Andrew D. Kelly
- Division of Hematology/Oncology, Sarcoma Program, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susanne B. Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Jeffrey Goldsmith
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Dimitrios Spentzos
- Division of Hematology/Oncology, Sarcoma Program, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - John M. Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail:
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Breitkopf SB, Oppermann FS, Kéri G, Grammel M, Daub H. Proteomics Analysis of Cellular Imatinib Targets and their Candidate Downstream Effectors. J Proteome Res 2010; 9:6033-43. [DOI: 10.1021/pr1008527] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Susanne B. Breitkopf
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Vichem Chemie Ltd., Herman Ottó u. 15., Budapest, 1022, Hungary, Pathobiochemistry Research Group of the Hungarian Academy of Science, Semmelweis University, Puskin u. 9., Budapest, 1088, Hungary, and Kinaxo Biotechnologies GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany
| | - Felix S. Oppermann
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Vichem Chemie Ltd., Herman Ottó u. 15., Budapest, 1022, Hungary, Pathobiochemistry Research Group of the Hungarian Academy of Science, Semmelweis University, Puskin u. 9., Budapest, 1088, Hungary, and Kinaxo Biotechnologies GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany
| | - György Kéri
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Vichem Chemie Ltd., Herman Ottó u. 15., Budapest, 1022, Hungary, Pathobiochemistry Research Group of the Hungarian Academy of Science, Semmelweis University, Puskin u. 9., Budapest, 1088, Hungary, and Kinaxo Biotechnologies GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany
| | - Markus Grammel
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Vichem Chemie Ltd., Herman Ottó u. 15., Budapest, 1022, Hungary, Pathobiochemistry Research Group of the Hungarian Academy of Science, Semmelweis University, Puskin u. 9., Budapest, 1088, Hungary, and Kinaxo Biotechnologies GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany
| | - Henrik Daub
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany, Vichem Chemie Ltd., Herman Ottó u. 15., Budapest, 1022, Hungary, Pathobiochemistry Research Group of the Hungarian Academy of Science, Semmelweis University, Puskin u. 9., Budapest, 1088, Hungary, and Kinaxo Biotechnologies GmbH, Am Klopferspitz 19, 82152 Martinsried, Germany
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Sharma K, Kumar C, Kéri G, Breitkopf SB, Oppermann FS, Daub H. Quantitative Analysis of Kinase-Proximal Signaling in Lipopolysaccharide-Induced Innate Immune Response. J Proteome Res 2010; 9:2539-49. [DOI: 10.1021/pr901192p] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Schreiber TB, Mäusbacher N, Breitkopf SB, Grundner-Culemann K, Daub H. Quantitative phosphoproteomics--an emerging key technology in signal-transduction research. Proteomics 2008; 8:4416-32. [PMID: 18837465 DOI: 10.1002/pmic.200800132] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Protein phosphorylation is the most important type of reversible post-translational modification involved in the regulation of cellular signal-transduction processes. In addition to controlling normal cellular physiology on the molecular level, perturbations of phosphorylation-based signaling networks and cascades have been implicated in the onset and progression of various human diseases. Recent advances in mass spectrometry-based proteomics helped to overcome many of the previous limitations in protein phosphorylation analysis. Improved isotope labeling and phosphopeptide enrichment strategies in conjunction with more powerful mass spectrometers and advances in data analysis have been integrated in highly efficient phosphoproteomics workflows, which are capable of monitoring up to several thousands of site-specific phosphorylation events within one large-scale analysis. Combined with ongoing efforts to define kinase-substrate relationships in intact cells, these major achievements have considerable potential to assess phosphorylation-based signaling networks on a system-wide scale. Here, we provide an overview of these exciting developments and their potential to transform signal-transduction research into a technology-driven, high-throughput science.
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Affiliation(s)
- Thiemo B Schreiber
- Department of Molecular Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
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