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Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S. Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins. PLoS One 2015; 10:e0139695. [PMID: 26437229 PMCID: PMC4593582 DOI: 10.1371/journal.pone.0139695] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [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: 06/23/2015] [Accepted: 09/16/2015] [Indexed: 01/18/2023] Open
Abstract
We developed and optimized a high-throughput project workflow to generate renewable recombinant antibodies to human proteins involved in epigenetic signalling. Three different strategies to produce phage display compatible protein antigens in bacterial systems were compared, and we found that in vivo biotinylation through the use of an Avi tag was the most productive method. Phage display selections were performed on 265 in vivo biotinylated antigen domains. High-affinity Fabs (<20nM) were obtained for 196. We constructed and optimized a new expression vector to produce in vivo biotinylated Fabs in E. coli. This increased average yields up to 10-fold, with an average yield of 4 mg/L. For 118 antigens, we identified Fabs that could immunoprecipitate their full-length endogenous targets from mammalian cell lysates. One Fab for each antigen was converted to a recombinant IgG and produced in mammalian cells, with an average yield of 15 mg/L. In summary, we have optimized each step of the pipeline to produce recombinant antibodies, significantly increasing both efficiency and yield, and also showed that these Fabs and IgGs can be generally useful for chromatin immunoprecipitation (ChIP) protocols.
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Affiliation(s)
- Nan Zhong
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Mani Ravichandran
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Maria Fenner
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Harshika Jain
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Anandi Bhattacharya
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Ashley Hutchinson
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Marcin Paduch
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Vincent Lu
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Michal Olszewski
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Anthony A. Kossiakoff
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Evan Dowdell
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Akiko Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, Knapp Center for Biomedical Discovery, University of Chicago, 900 East 57th St., Chicago, IL 60637, United States of America
| | - Haiming Huang
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Vincent Nadeem
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Sachdev S. Sidhu
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Jack F. Greenblatt
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
- Department of Molecular Genetics, University of Toronto, 1 Kings College Circle, MSB-4180, Toronto, ON M5S 1A8, Canada
| | - Edyta Marcon
- Terrence Donnelly Center for Cellular & Biomolecular Research, University of Toronto, 160 College Street, Toronto, ON M5S 3E1, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
| | - Susanne Gräslund
- Structural Genomics Consortium, University of Toronto, MaRS South tower, 101 College street, Toronto, ON M5G 1L7, Canada
- * E-mail:
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2
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Huang H, Economopoulos NO, Liu BA, Uetrecht A, Gu J, Jarvik N, Nadeem V, Pawson T, Moffat J, Miersch S, Sidhu SS. Selection of recombinant anti-SH3 domain antibodies by high-throughput phage display. Protein Sci 2015; 24:1890-900. [PMID: 26332758 DOI: 10.1002/pro.2799] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 07/03/2015] [Accepted: 08/26/2015] [Indexed: 01/01/2023]
Abstract
Antibodies are indispensable tools in biochemical research and play an expanding role as therapeutics. While hybridoma technology is the dominant method for antibody production, phage display is an emerging technology. Here, we developed and employed a high-throughput pipeline that enables selection of antibodies against hundreds of antigens in parallel. Binding selections using a phage-displayed synthetic antigen-binding fragment (Fab) library against 110 human SH3 domains yielded hundreds of Fabs targeting 58 antigens. Affinity assays demonstrated that representative Fabs bind tightly and specifically to their targets. Furthermore, we developed an efficient affinity maturation strategy adaptable to high-throughput, which increased affinity dramatically but did not compromise specificity. Finally, we tested Fabs in common cell biology applications and confirmed recognition of the full-length antigen in immunoprecipitation, immunoblotting and immunofluorescence assays. In summary, we have established a rapid and robust high-throughput methodology that can be applied to generate highly functional and renewable antibodies targeting protein domains on a proteome-wide scale.
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Affiliation(s)
- Haiming Huang
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Nicolas O Economopoulos
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Bernard A Liu
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Andrea Uetrecht
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Jun Gu
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Nick Jarvik
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Vincent Nadeem
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Tony Pawson
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Jason Moffat
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Shane Miersch
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
| | - Sachdev S Sidhu
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada, M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3E1
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3
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Sampson PB, Liu Y, Forrest B, Cumming G, Li SW, Patel NK, Edwards L, Laufer R, Feher M, Ban F, Awrey DE, Mao G, Plotnikova O, Hodgson R, Beletskaya I, Mason JM, Luo X, Nadeem V, Wei X, Kiarash R, Madeira B, Huang P, Mak TW, Pan G, Pauls HW. The discovery of Polo-like kinase 4 inhibitors: identification of (1R,2S).2-(3-((E).4-(((cis).2,6-dimethylmorpholino)methyl)styryl). 1H.indazol-6-yl)-5'-methoxyspiro[cyclopropane-1,3'-indolin]-2'-one (CFI-400945) as a potent, orally active antitumor agent. J Med Chem 2015; 58:147-169. [PMID: 25723005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Previous publications from our laboratory have introduced novel inhibitors of Polo-like kinase 4 (PLK4), a mitotic kinase identified as a potential target for cancer therapy. The search for potent and selective PLK4 inhibitors yielded (E)-3-((1Hindazol-6-yl)methylene)indolin-2-ones, which were superseded by the bioisosteric 2-(1H-indazol-6-yl)spiro[cyclopropane-1,3'-indolin]-2'-ones, e.g., 3. The later scaffold confers improved drug-like properties and incorporates two stereogenic centers. This work reports the discovery of a novel one-pot double SN2 displacement reaction for the stereoselective installation of the desired asymmetric centers and confirms the stereochemistry of the most potent stereoisomer, e.g., 44. Subsequent work keys on the optimization of the oral exposure of nanomolar PLK4 inhibitors with potent cancer cell growth inhibitory activity. A short list of compounds with superior potency and pharmacokinetic properties in rodents and dogs was studied in mouse models of tumor growth. We conclude with the identification of compound 48 (designated CFI-400945) as a novel clinical candidate for cancer therapy.
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4
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Sampson PB, Liu Y, Forrest B, Cumming G, Li SW, Patel NK, Edwards L, Laufer R, Feher M, Ban F, Awrey DE, Mao G, Plotnikova O, Hodgson R, Beletskaya I, Mason JM, Luo X, Nadeem V, Wei X, Kiarash R, Madeira B, Huang P, Mak TW, Pan G, Pauls HW. The Discovery of Polo-Like Kinase 4 Inhibitors: Identification of (1R,2S)-2-(3-((E)-4-(((cis)-2,6-Dimethylmorpholino)methyl)styryl)-1H-indazol-6-yl)-5′-methoxyspiro[cyclopropane-1,3′-indolin]-2′-one (CFI-400945) as a Potent, Orally Active Antitumor Agent. J Med Chem 2014; 58:130-46. [DOI: 10.1021/jm5005336] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Peter B. Sampson
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Yong Liu
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Bryan Forrest
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Graham Cumming
- Celtic Catalysts, 1-03 Nova Centre, Belfield, Dublin 4, Ireland
| | - Sze-Wan Li
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Narendra Kumar Patel
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Louise Edwards
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Radoslaw Laufer
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Miklos Feher
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Fuqiang Ban
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Donald E. Awrey
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Guodong Mao
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Olga Plotnikova
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Richard Hodgson
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Irina Beletskaya
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Jacqueline M. Mason
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Xunyi Luo
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Vincent Nadeem
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Xin Wei
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Reza Kiarash
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Brian Madeira
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Ping Huang
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Tak W. Mak
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Guohua Pan
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
| | - Henry W. Pauls
- Campbell Family
Institute for Breast Cancer Research, University Health Network, TMDT
East Tower, MaRS Centre, 101 College Street, Toronto, Ontario MG5 1L7, Canada
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5
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Zaugg K, Yao Y, Reilly PT, Kannan K, Kiarash R, Mason J, Huang P, Sawyer SK, Fuerth B, Faubert B, Kalliomäki T, Elia A, Luo X, Nadeem V, Bungard D, Yalavarthi S, Growney JD, Wakeham A, Moolani Y, Silvester J, Ten AY, Bakker W, Tsuchihara K, Berger SL, Hill RP, Jones RG, Tsao M, Robinson MO, Thompson CB, Pan G, Mak TW. Carnitine palmitoyltransferase 1C promotes cell survival and tumor growth under conditions of metabolic stress. Genes Dev 2011; 25:1041-51. [PMID: 21576264 DOI: 10.1101/gad.1987211] [Citation(s) in RCA: 355] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Tumor cells gain a survival/growth advantage by adapting their metabolism to respond to environmental stress, a process known as metabolic transformation. The best-known aspect of metabolic transformation is the Warburg effect, whereby cancer cells up-regulate glycolysis under aerobic conditions. However, other mechanisms mediating metabolic transformation remain undefined. Here we report that carnitine palmitoyltransferase 1C (CPT1C), a brain-specific metabolic enzyme, may participate in metabolic transformation. CPT1C expression correlates inversely with mammalian target of rapamycin (mTOR) pathway activation, contributes to rapamycin resistance in murine primary tumors, and is frequently up-regulated in human lung tumors. Tumor cells constitutively expressing CPT1C show increased fatty acid (FA) oxidation, ATP production, and resistance to glucose deprivation or hypoxia. Conversely, cancer cells lacking CPT1C produce less ATP and are more sensitive to metabolic stress. CPT1C depletion via siRNA suppresses xenograft tumor growth and metformin responsiveness in vivo. CPT1C can be induced by hypoxia or glucose deprivation and is regulated by AMPKα. Cpt1c-deficient murine embryonic stem (ES) cells show sensitivity to hypoxia and glucose deprivation and altered FA homeostasis. Our results indicate that cells can use a novel mechanism involving CPT1C and FA metabolism to protect against metabolic stress. CPT1C may thus be a new therapeutic target for the treatment of hypoxic tumors.
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Affiliation(s)
- Kathrin Zaugg
- The Campbell Family Institute for Breast Cancer Research, University of Toronto, Toronto, Ontario, Canada
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6
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Masih-Khan E, Trudel S, Heise C, Li Z, Paterson J, Nadeem V, Wei E, Roodman D, Claudio JO, Bergsagel PL, Stewart AK. MIP-1alpha (CCL3) is a downstream target of FGFR3 and RAS-MAPK signaling in multiple myeloma. Blood 2006; 108:3465-71. [PMID: 16849642 DOI: 10.1182/blood-2006-04-017087] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [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: 01/07/2023] Open
Abstract
Overexpression of fibroblast growth factor receptor 3 (FGFR3) is a hallmark of t(4;14) multiple myeloma (MM). To dissect the mechanism of FGFR3 oncogenesis in MM, we used 3 FGFR selective kinase inhibitors-CHIR258, PD173074, and SU5402-and FGFR3-specific siRNA to modulate FGFR3 activity. Conversely, the ligand FGF was used to stimulate FGFR3 function in human MM cells. The transcriptional response to FGFR3 modification was recorded, and gene expression changes common to all 5 modifiers were documented. Ten genes were commonly regulated. Macrophage inflammatory protein-1 alpha (MIP-1alpha) was the single most differentially altered gene. MIP-1 alpha promoter function, gene expression, and protein secretion were each down-regulated following inhibition of FGFR3 signaling. Down-regulation of MIP-1 alpha was not, however, observed following FGFR3 inhibition in MM cells with RAS mutations implicating RAS-MAPK in MIP-1 alpha regulation. As confirmation, inhibition of ERK1 also down-regulated MIP-1 alpha in FGFR3 inhibitor-resistant cells harboring RAS mutations. MIP-1 alpha is implicated in the survival and proliferation of MM cells and the pathogenesis of MM bone disease. Our observation is the first to directly link an initiating IgH translocation not only to MM-cell growth and survival but also to the disease-associated bone disease.
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Affiliation(s)
- Esther Masih-Khan
- Department of Medical Oncology, Princess Margaret Hospital, University Health Network, Toronto, ON, Canada
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7
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Claudio JO, Masih-Khan E, Tang H, Gonçalves J, Voralia M, Li ZH, Nadeem V, Cukerman E, Francisco-Pabalan O, Liew CC, Woodgett JR, Stewart AK. A molecular compendium of genes expressed in multiple myeloma. Blood 2002; 100:2175-86. [PMID: 12200383 DOI: 10.1182/blood-2002-01-0008] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.9] [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: 12/11/2022] Open
Abstract
We have created a molecular resource of genes expressed in primary malignant plasma cells using a combination of cDNA library construction, 5' end single-pass sequencing, bioinformatics, and microarray analysis. In total, we identified 9732 nonredundant expressed genes. This dataset is available as the Myeloma Gene Index (www.uhnres.utoronto.ca/akstewart_lab).Predictably, the sequenced profile of myeloma cDNAs mirrored the known function of immunoglobulin-producing, high-respiratory rate, low-cycling, terminally differentiated plasma cells. Nevertheless, approximately 10% of myeloma-expressed sequences matched only entries in the database of Expressed Sequence Tags (dbEST) or the high-throughput genomic sequence (htgs) database. Numerous novel genes of potential biologic significance were identified. We therefore spotted 4300 sequenced cDNAs on glass slides creating a myeloma-enriched microarray. Several of the most highly expressed genes identified by sequencing, such as a novel putative disulfide isomerase (MGC3178), tumor rejection antigen TRA1, heat shock 70-kDa protein 5, and annexin A2, were also differentially expressed between myeloma and B lymphoma cell lines using this myeloma-enriched microarray. Furthermore, a defined subset of 34 up-regulated and 18 down-regulated genes on the array were able to differentiate myeloma from nonmyeloma cell lines. These not only include genes involved in B-cell biology such as syndecan, BCMA, PIM2, MUM1/IRF4, and XBP1, but also novel uncharacterized genes matching sequences only in the public databases. In summary, our expressed gene catalog and myeloma-enriched microarray contains numerous genes of unknown function and may complement other commercially available arrays in defining the molecular portrait of this hematopoietic malignancy. GenBank Accession numbers include BF169967-BF176369, BF185966-BF185969, and BF177280-BF177455.
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Affiliation(s)
- Jaime O Claudio
- Division of Experimental Therapeutics, Toronto General Research Institute, University Health Network, 610 University Avenue, Toronto, Ontario, M5G 2M9 Canada
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