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Tan KT, Ding LW, Sun QY, Lao ZT, Chien W, Ren X, Xiao JF, Loh XY, Xu L, Lill M, Mayakonda A, Lin DC, Yang H, Koeffler HP. Profiling the B/T cell receptor repertoire of lymphocyte derived cell lines. BMC Cancer 2018; 18:940. [PMID: 30285677 PMCID: PMC6167786 DOI: 10.1186/s12885-018-4840-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 09/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Clonal VDJ rearrangement of B/T cell receptors (B/TCRs) occurring during B/T lymphocyte development has been used as a marker to track the clonality of B/T cell populations. METHODS We systematically profiled the B/T cell receptor repertoire of 936 cancer cell lines across a variety of cancer types as well as 462 Epstein-Barr Virus (EBV) transformed normal B lymphocyte lines using RNA sequencing data. RESULTS Rearranged B/TCRs were readily detected in cell lines derived from lymphocytes, and subclonality or potential biclonality were found in a number of blood cancer cell lines. Clonal BCR/TCR rearrangements were detected in several blast phase CML lines and unexpectedly, one gastric cancer cell line (KE-97), reflecting a lymphoid origin of these cells. Notably, clonality was highly prevalent in EBV transformed B lymphocytes, suggesting either transformation only occurred in a few B cells or those with a growth advantage dominated the transformed population through clonal evolution. CONCLUSIONS Our analysis reveals the complexity and heterogeneity of the BCR/TCR rearrangement repertoire and provides a unique insight into the clonality of lymphocyte derived cell lines.
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Affiliation(s)
- Kar-Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - Qiao-Yang Sun
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Zhen-Tang Lao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Wenwen Chien
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Xi Ren
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jin-Fen Xiao
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Xin Yi Loh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Michael Lill
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - De-Chen Lin
- Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
| | - H Phillip Koeffler
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Division of Hematology/Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, USA
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Shabaneh TB, Downey SL, Goddard AL, Screen M, Lucas MM, Eastman A, Kisselev AF. Molecular basis of differential sensitivity of myeloma cells to clinically relevant bolus treatment with bortezomib. PLoS One 2013; 8:e56132. [PMID: 23460792 PMCID: PMC3584083 DOI: 10.1371/journal.pone.0056132] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2012] [Accepted: 01/05/2013] [Indexed: 01/07/2023] Open
Abstract
The proteasome inhibitor bortezomib (Velcade) is prescribed for the treatment of multiple myeloma. Clinically achievable concentrations of bortezomib cause less than 85% inhibition of the chymotrypsin-like activity of the proteasome, but little attention has been paid as to whether in vitro studies are representative of this level of inhibition. Patients receive bortezomib as an intravenous or subcutaneous bolus injection, resulting in maximum proteasome inhibition within one hour followed by a gradual recovery of activity. In contrast, most in vitro studies use continuous treatment so that activity never recovers. Replacing continuous treatment with 1 h-pulse treatment increases differences in sensitivity in a panel of 7 multiple myeloma cell lines from 5.3-fold to 18-fold, and reveals that the more sensitive cell lines undergo apoptosis at faster rates. Clinically achievable inhibition of active sites was sufficient to induce cytotoxicity only in one cell line. At concentrations of bortezomib that produced similar inhibition of peptidase activities a different extent of inhibition of protein degradation was observed, providing an explanation for the differential sensitivity. The amount of protein degraded per number of active proteasomes correlated with sensitivity to bortezomib. Thus, (i) in vitro studies of proteasome inhibitors should be conducted at pharmacologically achievable concentrations and duration of treatment; (ii) a similar level of inhibition of active sites results in a different extent of inhibition of protein breakdown in different cell lines, and hence a difference in sensitivity.
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Affiliation(s)
- Tamer B. Shabaneh
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Sondra L. Downey
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Ayrton L. Goddard
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Michael Screen
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Marcella M. Lucas
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Biology & Biochemistry, University of Bath, Bath, United Kingdom
| | - Alan Eastman
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
| | - Alexei F. Kisselev
- Norris Cotton Cancer Center, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- Department of Pharmacology and Toxicology, The Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States of America
- * E-mail:
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Gunn NM, Bachman M, Li GP, Nelson EL. Fabrication and biological evaluation of uniform extracellular matrix coatings on discontinuous photolithography generated micropallet arrays. J Biomed Mater Res A 2010; 95:401-12. [PMID: 20648537 PMCID: PMC2981065 DOI: 10.1002/jbm.a.32854] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The recent identification of rare cell populations within tissues that are associated with specific biological behaviors, for example, progenitor cells, has illuminated a limitation of current technologies to study such adherent cells directly from primary tissues. The micropallet array is a recently developed technology designed to address this limitation by virtue of its capacity to isolate and recover single adherent cells on individual micropallets. The capacity to apply this technology to primary tissues and cells with restricted growth characteristics, particularly adhesion requirements, is critically dependent on the capacity to generate functional extracellular matrix (ECM) coatings. The discontinuous nature of the micropallet array surface provides specific constraints on the processes for generating the desired ECM coatings that are necessary to achieve the full functional capacity of the micropallet array. We have developed strategies, reported herein, to generate functional coatings with various ECM protein components: fibronectin, EHS tumor basement membrane extract, collagen, and laminin-5; confirmed by evaluation for rapid cellular adherence of four dissimilar cell types: fibroblast, breast epithelial, pancreatic epithelial, and myeloma. These findings are important for the dissemination and expanded use of micropallet arrays and similar microtechnologies requiring the integrated use of ECM protein coatings to promote cellular adherence.
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Affiliation(s)
- Nicholas M. Gunn
- School of Engineering, Department of Biomedical Engineering, University of California at Irvine, Irvine, CA 92697
| | - Mark Bachman
- School of Engineering, Department of Electrical and Computer Science, University of California at Irvine, Irvine, CA 92697
- School of Engineering, Integrated Nanosystems Research Facility, University of California at Irvine, Irvine, CA 92697
- School of Engineering, California Institute for Telecommunications and Information Technology (CalIT), University of California at Irvine, Irvine, CA 92697
| | - Guann-Pyng Li
- School of Engineering, Department of Electrical and Computer Science, University of California at Irvine, Irvine, CA 92697
- School of Engineering, Integrated Nanosystems Research Facility, University of California at Irvine, Irvine, CA 92697
- School of Engineering, California Institute for Telecommunications and Information Technology (CalIT), University of California at Irvine, Irvine, CA 92697
| | - Edward L. Nelson
- School of Medicine, Department of Medicine, Division of Hematology/Oncology, University of California at Irvine, Irvine, CA 92697
- Institute for Immunology, University of California at Irvine, Irvine, CA 92697
- School of Biological Sciences, Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, CA 92697
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Peng WC, Lin X, Torres J. The strong dimerization of the transmembrane domain of the fibroblast growth factor receptor (FGFR) is modulated by C-terminal juxtamembrane residues. Protein Sci 2009; 18:450-9. [PMID: 19165726 DOI: 10.1002/pro.65] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The fibroblast growth factor receptor 3 (FGFR3) is a member of the FGFR subfamily of the receptor tyrosine kinases (RTKs) involved in signaling across the plasma membrane. Generally, ligand binding leads to receptor dimerization and activation. Dimerization involves the transmembrane (TM) domain, where mutations can lead to constitutive activation in certain cancer types and also in skeletal malformations. Thus, it has been postulated that FGFR homodimerization must be inherently weak to allow regulation, a feature reminiscent of alpha and beta integrin TM interactions. However, we show herein that in FGFR3-TM, four C-terminal residues, CRLR, have a profound destabilizing effect in an otherwise strongly dimerizing TM peptide. In the absence of these four residues, the dimerizing propensity of FGFR3-TM is comparable to glycophorin, as shown using various detergents. In addition, the expected enhanced dimerization induced by the mutation associated to the Crouzon syndrome A391E, was observed only when these four C-terminal residues were present. In the absence of these four residues, A391E was dimer-destabilizing. Finally, using site specific infrared dichroism and convergence with evolutionary conservation data, we have determined the backbone model of the FGFR3-TM homodimer in model lipid bilayers. This model is consistent with, and correlates with the effects of, most known pathological mutations found in FGFR-TM.
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Merzlyakov M, Hristova K. Forster resonance energy transfer measurements of transmembrane helix dimerization energetics. Methods Enzymol 2008; 450:107-27. [PMID: 19152858 DOI: 10.1016/s0076-6879(08)03406-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lateral interactions between hydrophobic transmembrane (TM) helices in membranes underlie the folding of multispan membrane proteins and signal transduction by receptor tyrosine kinases (RTKs). Quantitative measurements of dimerization energetics in membranes are required to uncover the physical principles behind these processes. Here, we overview how FRET measurements can be used to determine the thermodynamics of TM helix homo- and heterodimerization in vesicles and in supported bilayers. Such measurements can shed light on the molecular mechanism behind pathologies arising due to single-amino acid mutations in membrane proteins.
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Affiliation(s)
- Mikhail Merzlyakov
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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6
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Merzlyakov M, Chen L, Hristova K. Studies of receptor tyrosine kinase transmembrane domain interactions: the EmEx-FRET method. J Membr Biol 2007; 215:93-103. [PMID: 17565424 PMCID: PMC2770890 DOI: 10.1007/s00232-007-9009-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2006] [Accepted: 01/10/2007] [Indexed: 10/23/2022]
Abstract
The energetics of transmembrane (TM) helix dimerization in membranes and the thermodynamic principles behind receptor tyrosine kinase (RTK) TM domain interactions during signal transduction can be studied using Förster resonance energy transfer (FRET). For instance, FRET studies have yielded the stabilities of wild-type fibroblast growth factor receptor 3 (FGFR3) TM domains and two FGFR3 pathogenic mutants, Ala391Glu and Gly380Arg, in the native bilayer environment. To further our understanding of the molecular mechanisms of deregulated FGFR3 signaling underlying different pathologies, we determined the effect of the Gly382Asp FGFR3 mutation, identified in a multiple myeloma cell line, on the energetics of FGFR3 TM domain dimerization. We measured dimerization energetics using a novel FRET acquisition and processing method, termed "emission-excitation FRET (EmEx-FRET)," which improves the precision of thermodynamic measurements of TM helix association. The EmEx-FRET method, verified here by analyzing previously published data for wild-type FGFR3 TM domain, should have broad utility in studies of protein interactions, particularly in cases when the concentrations of fluorophore-tagged molecules cannot be controlled.
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Affiliation(s)
- Mikhail Merzlyakov
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
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7
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Li E, Hristova K. Role of receptor tyrosine kinase transmembrane domains in cell signaling and human pathologies. Biochemistry 2006; 45:6241-51. [PMID: 16700535 PMCID: PMC4301406 DOI: 10.1021/bi060609y] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Receptor tyrosine kinases (RTKs) conduct biochemical signals via lateral dimerization in the plasma membrane, and their transmembrane (TM) domains play an important role in the dimerization process. Here we present two models of RTK-mediated signaling, and we discuss the role of the TM domains within the framework of these two models. We summarize findings of single-amino acid mutations in RTK TM domains that induce unregulated signaling and, as a consequence, pathological phenotypes. We review the current knowledge of pathology induction mechanisms due to these mutations, focusing on the structural and thermodynamic basis of pathogenic dimer stabilization.
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Affiliation(s)
- Edwin Li
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore MD 21218
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore MD 21218
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Cyclin D dysregulation: an early and unifying pathogenic event in multiple myeloma. Blood 2005; 106:296-303. [PMID: 15755896 DOI: 10.1182/blood-2005-01-0034] [Citation(s) in RCA: 493] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Two oncogenic pathways have been hypothesized for multiple myeloma (MM) and premalignant monoclonal gammopathy of undetermined significance (MGUS) tumors: a nonhyperdiploid pathway associated with a high prevalence of IgH translocations and a hyperdiploid pathway associated with multiple trisomies of 8 chromosomes. Cyclin D1, D2, or D3 expression appears to be increased and/or dysregulated in virtually all MM tumors despite their low proliferative capacity. Translocations can directly dysregulate CCND1 (11q13) or CCND3 (6p21), or MAF (16q23) or MAFB (20q11) transcription factors that target CCND2. Biallelic dysregulation of CCND1 occurs in nearly 40% of tumors, most of which are hyperdiploid. Other tumors express increased CCND2, either with or without a t(4;14) translocation. Using gene expression profiling to identify 5 recurrent translocations, specific trisomies, and expression of cyclin D genes, MM tumors can be divided into 8 TC (translocation/cyclin D) groups (11q13, 6p21, 4p16, maf, D1, D1+D2, D2, and none) that appear to be defined by early, and perhaps initiating, oncogenic events. However, despite subsequent progression events, these groups have differing gene expression profiles and also significant differences in the prevalence of bone disease, frequency at relapse, and progression to extramedullary tumor.
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Keats JJ, Maxwell CA, Taylor BJ, Hendzel MJ, Chesi M, Bergsagel PL, Larratt LM, Mant MJ, Reiman T, Belch AR, Pilarski LM. Overexpression of transcripts originating from the MMSET locus characterizes all t(4;14)(p16;q32)-positive multiple myeloma patients. Blood 2005; 105:4060-9. [PMID: 15677557 PMCID: PMC1895072 DOI: 10.1182/blood-2004-09-3704] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Multiple myeloma (MM) is a B-lineage malignancy characterized by diverse genetic subtypes and clinical outcomes. The recurrent immunoglobulin heavy chain (IgH) switch translocation, t(4;14)(p16;q32), is associated with poor outcome, though the mechanism is unclear. Quantitative reverse-transcription-polymerase chain reaction (RT-PCR) for proposed target genes on a panel of myeloma cell lines and purified plasma cells showed that only transcripts originating from the WHSC1/MMSET/NSD2 gene are uniformly dysregulated in all t(4;14)POS patients. The different transcripts detected, multiple myeloma SET domain containing protein (MMSET I), MMSET II, Exon 4a/MMSET III, and response element II binding protein (RE-IIBP), are produced by alternative splicing and alternative transcription initiation events. Translation of the various transcripts, including those from major breakpoint region 4-2 (MB4-2) and MB4-3 breakpoint variants, was confirmed by transient transfection and immunoblotting. Green fluorescent protein (GFP)-tagged MMSET I and II, corresponding to proteins expressed in MB4-1 patients, localized to the nucleus but not nucleoli, whereas the MB4-2 and MB4-3 proteins concentrate in nucleoli. Cloning and localization of the Exon 4a/MMSET III splice variant, which contains the protein segment lost in the MB4-2 variant, identified a novel protein domain that prevents nucleolar localization. Kinetic studies using photobleaching suggest that the breakpoint variants are functionally distinct from wild-type proteins. In contrast, RE-IIBP is universally dysregulated and also potentially functional in all t(4;14)POS patients irrespective of fibroblast growth factor receptor 3 (FGFR3) expression or breakpoint type.
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Affiliation(s)
- Jonathan J Keats
- Department of Oncology, University of Alberta & Cross Cancer Institute, 11560 University Ave, Edmonton, AB, T6G 1Z2, Canada
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