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Volumn 114, Issue 25, 2017, Pages 6581-6586

Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas

Author keywords

Biomarkers; CRISPR screen; Lymphoma; Proteomics; RNA seq

Indexed keywords

ANAPLASTIC LYMPHOMA KINASE; ARYLDIALKYLPHOSPHATASE 2; CD19 ANTIGEN; CD2 ANTIGEN; CD22 ANTIGEN; CD3 ANTIGEN; CD4 ANTIGEN; CD5 ANTIGEN; CD7 ANTIGEN; CD79A ANTIGEN; CD79B ANTIGEN; CYTOKINE RECEPTOR; GLYCOPROTEIN; GUIDE RNA; HERMES ANTIGEN; INTERLEUKIN 2; INTERLEUKIN 22; INTERLEUKIN 31 RECEPTOR BETA; INTERLEUKIN 6; JANUS KINASE 1; JANUS KINASE 2; N GLYCOPROTEIN; NUCLEOPHOSMIN; ONCOSTATIN M; STAT1 PROTEIN; STAT3 PROTEIN; STAT5 PROTEIN; STAT5B PROTEIN; TRANSCRIPTOME; TUMOR MARKER; UNCLASSIFIED DRUG; PROTEIN TYROSINE KINASE;

EID: 85021116647     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1701263114     Document Type: Article
Times cited : (38)

References (35)
  • 1
    • 78651105000 scopus 로고    scopus 로고
    • Mass spectrometry based glycoproteomics-from a proteomics perspective
    • 003251
    • Pan S, Chen R, Aebersold R, Brentnall TA (2011) Mass spectrometry based glycoproteomics-from a proteomics perspective. Mol Cell Proteomics 10:R110. 003251.
    • (2011) Mol Cell Proteomics , vol.10 , pp. R110
    • Pan, S.1    Chen, R.2    Aebersold, R.3    Brentnall, T.A.4
  • 2
    • 0038699625 scopus 로고    scopus 로고
    • Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry
    • Zhang H, Li XJ, Martin DB, Aebersold R (2003) Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry. Nat Biotechnol 21:660-666.
    • (2003) Nat Biotechnol , vol.21 , pp. 660-666
    • Zhang, H.1    Li, X.J.2    Martin, D.B.3    Aebersold, R.4
  • 3
    • 0036462601 scopus 로고    scopus 로고
    • Protein N-glycosylation along the secretory pathway: Relationship to organelle topography and function, protein quality control, and cell interactions
    • Roth J (2002) Protein N-glycosylation along the secretory pathway: Relationship to organelle topography and function, protein quality control, and cell interactions. Chem Rev 102:285-303.
    • (2002) Chem Rev , vol.102 , pp. 285-303
    • Roth, J.1
  • 4
    • 78650275183 scopus 로고    scopus 로고
    • Immunohistochemical analysis of HLDA9 Workshop antibodies against cell-surface molecules in reactive and neoplastic lymphoid tissues
    • Ramos-Medina R, et al. (2011) Immunohistochemical analysis of HLDA9 Workshop antibodies against cell-surface molecules in reactive and neoplastic lymphoid tissues. Immunol Lett 134:150-156.
    • (2011) Immunol Lett , vol.134 , pp. 150-156
    • Ramos-Medina, R.1
  • 5
    • 44649184200 scopus 로고    scopus 로고
    • Combination of the anti-CD30-auristatin-E antibody-drug conjugate (SGN-35) with chemotherapy improves antitumour activity in Hodgkin lymphoma
    • Oflazoglu E, Kissler KM, Sievers EL, Grewal IS, Gerber HP (2008) Combination of the anti-CD30-auristatin-E antibody-drug conjugate (SGN-35) with chemotherapy improves antitumour activity in Hodgkin lymphoma. Br J Haematol 142:69-73.
    • (2008) Br J Haematol , vol.142 , pp. 69-73
    • Oflazoglu, E.1    Kissler, K.M.2    Sievers, E.L.3    Grewal, I.S.4    Gerber, H.P.5
  • 6
    • 0028057250 scopus 로고
    • Depletion of B cells in vivo by a chimeric mouse human monoclonal antibody to CD20
    • Reff ME, et al. (1994) Depletion of B cells in vivo by a chimeric mouse human monoclonal antibody to CD20. Blood 83:435-445.
    • (1994) Blood , vol.83 , pp. 435-445
    • Reff, M.E.1
  • 7
    • 0642312825 scopus 로고    scopus 로고
    • Rituximab (monoclonal anti-CD20 antibody): Mechanisms of action and resistance
    • Smith MR (2003) Rituximab (monoclonal anti-CD20 antibody): Mechanisms of action and resistance. Oncogene 22:7359-7368.
    • (2003) Oncogene , vol.22 , pp. 7359-7368
    • Smith, M.R.1
  • 8
    • 83055168476 scopus 로고    scopus 로고
    • Chimeric antigen receptor therapy for B-cell malignancies
    • Porter DL, Kalos M, Zheng Z, Levine B, June C (2011) Chimeric antigen receptor therapy for B-cell malignancies. J Cancer 2:331-332.
    • (2011) J Cancer , vol.2 , pp. 331-332
    • Porter, D.L.1    Kalos, M.2    Zheng, Z.3    Levine, B.4    June, C.5
  • 9
    • 84947471999 scopus 로고    scopus 로고
    • Identification and characterization of essential genes in the human genome
    • Wang T, et al. (2015) Identification and characterization of essential genes in the human genome. Science 350:1096-1101.
    • (2015) Science , vol.350 , pp. 1096-1101
    • Wang, T.1
  • 10
    • 34547800600 scopus 로고    scopus 로고
    • Isolation of N-linked glycopeptides from plasma
    • Zhou Y, Aebersold R, Zhang H (2007) Isolation of N-linked glycopeptides from plasma. Anal Chem 79:5826-5837.
    • (2007) Anal Chem , vol.79 , pp. 5826-5837
    • Zhou, Y.1    Aebersold, R.2    Zhang, H.3
  • 11
    • 79953062776 scopus 로고    scopus 로고
    • Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis
    • Fermin D, Basrur V, Yocum AK, Nesvizhskii AI (2011) Abacus: A computational tool for extracting and pre-processing spectral count data for label-free quantitative proteomic analysis. Proteomics 11:1340-1345.
    • (2011) Proteomics , vol.11 , pp. 1340-1345
    • Fermin, D.1    Basrur, V.2    Yocum, A.K.3    Nesvizhskii, A.I.4
  • 12
    • 84874762979 scopus 로고    scopus 로고
    • The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013
    • Vizcaíno JA, et al. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: Status in 2013. Nucleic Acids Res 41:D1063-D1069.
    • (2013) Nucleic Acids Res , vol.41 , pp. D1063-D1069
    • Vizcaíno, J.A.1
  • 13
    • 0031826040 scopus 로고    scopus 로고
    • SOSUI: Classification and secondary structure prediction system for membrane proteins
    • Hirokawa T, Boon-Chieng S, Mitaku S (1998) SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics 14:378-379.
    • (1998) Bioinformatics , vol.14 , pp. 378-379
    • Hirokawa, T.1    Boon-Chieng, S.2    Mitaku, S.3
  • 14
    • 27944499451 scopus 로고    scopus 로고
    • An iterative statistical approach to the identification of protein phosphorylationmotifs from large-scale data sets
    • Schwartz D, Gygi SP (2005) An iterative statistical approach to the identification of protein phosphorylationmotifs from large-scale data sets. Nat Biotechnol 23:1391-1398.
    • (2005) Nat Biotechnol , vol.23 , pp. 1391-1398
    • Schwartz, D.1    Gygi, S.P.2
  • 17
    • 76749118059 scopus 로고    scopus 로고
    • Genomic and gene expression profiling defines indolent forms of mantle cell lymphoma
    • Fernàndez V, et al. (2010) Genomic and gene expression profiling defines indolent forms of mantle cell lymphoma. Cancer Res 70:1408-1418.
    • (2010) Cancer Res , vol.70 , pp. 1408-1418
    • Fernàndez, V.1
  • 18
    • 84879071011 scopus 로고    scopus 로고
    • Crizotinib versus chemotherapy in advanced ALK-positive lung cancer
    • Shaw AT, et al. (2013) Crizotinib versus chemotherapy in advanced ALK-positive lung cancer. N Engl J Med 368:2385-2394.
    • (2013) N Engl J Med , vol.368 , pp. 2385-2394
    • Shaw, A.T.1
  • 19
    • 84874271270 scopus 로고    scopus 로고
    • NCBI GEO: Archive for functional genomics data sets-update
    • Barrett T, et al. (2013) NCBI GEO: Archive for functional genomics data sets-update. Nucleic Acids Res 41:D991-D995.
    • (2013) Nucleic Acids Res , vol.41 , pp. D991-D995
    • Barrett, T.1
  • 20
    • 27344435774 scopus 로고    scopus 로고
    • Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
    • Subramanian A, et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 102: 15545-15550.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 15545-15550
    • Subramanian, A.1
  • 21
    • 84907269780 scopus 로고    scopus 로고
    • Proteogenomic characterization of human colon and rectal cancer
    • NCI CPTAC
    • Zhang B, et al.; NCI CPTAC (2014) Proteogenomic characterization of human colon and rectal cancer. Nature 513:382-387.
    • (2014) Nature , vol.513 , pp. 382-387
    • Zhang, B.1
  • 22
    • 0030916177 scopus 로고    scopus 로고
    • Signaling of type II oncostatin M receptor
    • Auguste P, et al. (1997) Signaling of type II oncostatin M receptor. J Biol Chem 272: 15760-15764.
    • (1997) J Biol Chem , vol.272 , pp. 15760-15764
    • Auguste, P.1
  • 23
    • 20944435271 scopus 로고    scopus 로고
    • Stat3 is required for ALK-mediated lymphomagenesis and provides a possible therapeutic target
    • Chiarle R, et al. (2005) Stat3 is required for ALK-mediated lymphomagenesis and provides a possible therapeutic target. Nat Med 11:623-629.
    • (2005) Nat Med , vol.11 , pp. 623-629
    • Chiarle, R.1
  • 25
    • 77449122863 scopus 로고    scopus 로고
    • Trans-proteomic pipeline: A pipeline for proteomic analysis
    • Pedrioli PG (2010) Trans-proteomic pipeline: A pipeline for proteomic analysis. Methods Mol Biol 604:213-238.
    • (2010) Methods Mol Biol , vol.604 , pp. 213-238
    • Pedrioli, P.G.1
  • 26
    • 0037108887 scopus 로고    scopus 로고
    • Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search
    • Keller A, Nesvizhskii AI, Kolker E, Aebersold R (2002) Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. Anal Chem 74:5383-5392.
    • (2002) Anal Chem , vol.74 , pp. 5383-5392
    • Keller, A.1    Nesvizhskii, A.I.2    Kolker, E.3    Aebersold, R.4
  • 27
    • 0042338362 scopus 로고    scopus 로고
    • A statistical model for identifying proteins by tandem mass spectrometry
    • Nesvizhskii AI, Keller A, Kolker E, Aebersold R (2003) A statistical model for identifying proteins by tandem mass spectrometry. Anal Chem 75:4646-4658.
    • (2003) Anal Chem , vol.75 , pp. 4646-4658
    • Nesvizhskii, A.I.1    Keller, A.2    Kolker, E.3    Aebersold, R.4
  • 28
    • 34247642450 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors
    • Paoletti AC, et al. (2006) Quantitative proteomic analysis of distinct mammalian Mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci USA 103:18928-18933.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 18928-18933
    • Paoletti, A.C.1
  • 29
    • 84914179053 scopus 로고    scopus 로고
    • (F Foundation for Statistical Reporting, Vienna). Accessed February 8, 2016
    • R Core Team (2014) R: A Language and Environment for Statistical Computing (F Foundation for Statistical Reporting, Vienna). Available at www.R-project.org/. Accessed February 8, 2016.
    • (2014) R: A Language and Environment for Statistical Computing
  • 30
    • 84871809302 scopus 로고    scopus 로고
    • STAR: Ultrafast universal RNA-seq aligner
    • Dobin A, et al. (2013) STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29:15-21.
    • (2013) Bioinformatics , vol.29 , pp. 15-21
    • Dobin, A.1
  • 31
    • 84941051170 scopus 로고    scopus 로고
    • STRING v10: Protein-protein interaction networks, integrated over the tree of life
    • Szklarczyk D, et al. (2015) STRING v10: Protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res 43:D447-D452.
    • (2015) Nucleic Acids Res , vol.43 , pp. D447-D452
    • Szklarczyk, D.1
  • 32
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon P, et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498-2504.
    • (2003) Genome Res , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 33
    • 84875978905 scopus 로고    scopus 로고
    • ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens
    • Shao DD, et al. (2013) ATARiS: Computational quantification of gene suppression phenotypes from multisample RNAi screens. Genome Res 23:665-678.
    • (2013) Genome Res , vol.23 , pp. 665-678
    • Shao, D.D.1
  • 34
    • 84955328286 scopus 로고    scopus 로고
    • The Molecular Signatures Database (MSigDB) hallmark gene set collection
    • Liberzon A, et al. (2015) The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst 1:417-425.
    • (2015) Cell Syst , vol.1 , pp. 417-425
    • Liberzon, A.1
  • 35
    • 33644875050 scopus 로고    scopus 로고
    • The HUGO gene nomenclature database, 2006 updates
    • Eyre TA, et al. (2006) The HUGO Gene Nomenclature Database, 2006 updates. Nucleic Acids Res 34:D319-D321.
    • (2006) Nucleic Acids Res , vol.34 , pp. D319-D321
    • Eyre, T.A.1


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