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Ku X, Wang J, Li H, Meng C, Yu F, Yu W, Li Z, Zhou Z, Zhang C, Hua Y, Yan W, Jin J. Proteomic Portrait of Human Lymphoma Reveals Protein Molecular Fingerprint of Disease Specific Subtypes and Progression. PHENOMICS (CHAM, SWITZERLAND) 2023; 3:148-166. [PMID: 37197640 PMCID: PMC10110798 DOI: 10.1007/s43657-022-00075-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 05/19/2023]
Abstract
An altered proteome in lymph nodes often suggests abnormal signaling pathways that may be associated with diverse lymphatic disorders. Current clinical biomarkers for histological classification of lymphomas have encountered many discrepancies, particularly for borderline cases. Therefore, we launched a comprehensive proteomic study aimed to establish a proteomic landscape of patients with various lymphatic disorders and identify proteomic variations associated with different disease subgroups. In this study, 109 fresh-frozen lymph node tissues from patients with various lymphatic disorders (with a focus on Non-Hodgkin's Lymphoma) were analyzed by data-independent acquisition mass spectrometry. A quantitative proteomic landscape was comprehensively characterized, leading to the identification of featured protein profiles for each subgroup. Potential correlations between clinical outcomes and expression profiles of signature proteins were also probed. Two representative signature proteins, phospholipid-binding proteins Annexin A6 (ANXA6) and Phospholipase C Gamma 2 (PLCG2), were successfully validated via immunohistochemistry. We also evaluated the capability of acquired proteomic signatures to segregate multiple lymphatic abnormalities and identified several core signature proteins, such as Sialic Acid Binding Ig Like Lectin 1 (SIGLEC1) and GTPase of immunity-associated protein 5 (GIMAP5). In summary, the established lympho-specific data resource provides a comprehensive map of protein expression in lymph nodes during multiple disease states, thus extending the existing human tissue proteome atlas. Our findings will be of great value in exploring protein expression and regulation underlying lymphatic malignancies, while also providing novel protein candidates to classify various lymphomas for more precise medical practice. Supplementary Information The online version contains supplementary material available at 10.1007/s43657-022-00075-w.
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Affiliation(s)
- Xin Ku
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jinghan Wang
- Department of Hematology, The First Affiliated Hospital of Medical School of Zhejiang University, Hangzhou, 310003 China
- Cancer Center, Zhejiang University, Hangzhou, 310003 China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, 310003 China
| | - Haikuo Li
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240 China
- Present Address: Division of Biology & Biomedical Sciences, Washington University in St. Louis School of Medicine, St. Louis, 63130 USA
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry, Technical University of Munich, 85354 Freising, Germany
| | - Fang Yu
- Department of Pathology, The First Affiliated Hospital of Zhejiang University, Hangzhou, 310003 China
| | - Wenjuan Yu
- Department of Hematology, The First Affiliated Hospital of Medical School of Zhejiang University, Hangzhou, 310003 China
| | - Zhongqi Li
- Department of Surgical Oncology, College of Medicine, The First Affiliated Hospital, Zhejiang University, Hangzhou, 310003 China
| | - Ziqi Zhou
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Can Zhang
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Ying Hua
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Wei Yan
- Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital of Medical School of Zhejiang University, Hangzhou, 310003 China
- Cancer Center, Zhejiang University, Hangzhou, 310003 China
- Key Laboratory of Hematologic Malignancies, Diagnosis and Treatment, Hangzhou, 310003 China
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2
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ALK: Anaplastic lymphoma kinase. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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3
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Abstract
The burgeoning field of anaplastic lymphoma kinase (ALK) in cancer encompasses many cancer types, from very rare cancers to the more prevalent non-small-cell lung cancer (NSCLC). The common activation of ALK has led to the use of the ALK tyrosine kinase inhibitor (TKI) crizotinib in a range of patient populations and to the rapid development of second-generation drugs targeting ALK. In this Review, we discuss our current understanding of ALK function in human cancer and the implications for tumour treatment.
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MESH Headings
- Anaplastic Lymphoma Kinase
- Animals
- Antineoplastic Agents/therapeutic use
- Caenorhabditis elegans Proteins/physiology
- Cell Transformation, Neoplastic/genetics
- Clinical Trials as Topic
- Crizotinib
- Drosophila Proteins/physiology
- Drug Resistance, Neoplasm
- Enzyme Induction
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Neoplastic
- Humans
- Lymphoma, Large-Cell, Anaplastic/enzymology
- Lymphoma, Large-Cell, Anaplastic/genetics
- Mice
- Models, Biological
- Models, Molecular
- Mutation
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/chemistry
- Neoplasm Proteins/genetics
- Neoplasm Proteins/physiology
- Neoplasms/drug therapy
- Neoplasms/enzymology
- Neoplasms/genetics
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/physiology
- Protein Conformation
- Protein-Tyrosine Kinases/physiology
- Pyrazoles/therapeutic use
- Pyridines/therapeutic use
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptor Protein-Tyrosine Kinases/chemistry
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor Protein-Tyrosine Kinases/physiology
- Signal Transduction
- Translocation, Genetic
- Zebrafish Proteins/physiology
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Affiliation(s)
- Bengt Hallberg
- Department of Molecular Biology, Building 6L, Umeå University, Umeå S-90187, Sweden
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4
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Evolution of oncolytic adenovirus for cancer treatment. Adv Drug Deliv Rev 2012; 64:720-9. [PMID: 22212901 DOI: 10.1016/j.addr.2011.12.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 12/14/2011] [Accepted: 12/16/2011] [Indexed: 12/18/2022]
Abstract
Oncolytic adenovirus (Ad) has been used in cancer gene therapy largely due to its ability to selectively infect and replicate in tumor cells. However, because the oncolytic antitumor activity is insufficient to effectively eliminate tumors, various strategies have been devised to improve the therapeutic efficacy. Single-vector Ads "armed" with short hairpin RNA, cytokines, or matrix-modulating proteins have been developed. Two clear advantages are viral amplification of the therapeutic gene, and the additive effects of oncolytic and therapeutic gene-mediated antitumor activities. To develop systemically injectable Ad carriers, strategies to modify the Ad surface with polymers, liposomes, or nanoparticles have been shown to extend circulation time, reduce immunogenicity, and result in increased antitumor effect as well as lower accumulation and toxicity in liver. Specific targeting platforms for tumor-selective oncolytic therapies against both primary and metastatic cancers have been developed. This review will focus on updated strategies to develop potent oncolytic Ads for use in cancer treatment.
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5
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Kischel P, Waltregny D, Greffe Y, Mazzucchelli G, De Pauw E, de Leval L, Castronovo V. Identification of stromal proteins overexpressed in nodular sclerosis Hodgkin lymphoma. Proteome Sci 2011; 9:63. [PMID: 21975223 PMCID: PMC3200160 DOI: 10.1186/1477-5956-9-63] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 10/05/2011] [Indexed: 12/23/2022] Open
Abstract
Hodgkin lymphoma (HL) represents a category of lymphoid neoplasms with unique features, notably the usual scarcity of tumour cells in involved tissues. The most common subtype of classical HL, nodular sclerosis HL, characteristically comprises abundant fibrous tissue stroma. Little information is available about the protein composition of the stromal environment from HL. Moreover, the identification of valid protein targets, specifically and abundantly expressed in HL, would be of utmost importance for targeted therapies and imaging, yet the biomarkers must necessarily be accessible from the bloodstream. To characterize HL stroma and to identify potentially accessible proteins, we used a chemical proteomic approach, consisting in the labelling of accessible proteins and their subsequent purification and identification by mass spectrometry. We performed an analysis of potentially accessible proteins in lymph node biopsies from HL and reactive lymphoid tissues, and in total, more than 1400 proteins were identified in 7 samples. We have identified several extracellular matrix proteins overexpressed in HL, such as versican, fibulin-1, periostin, and other proteins such as S100-A8. These proteins were validated by immunohistochemistry on a larger series of biopsy samples, and bear the potential to become targets for antibody-based anti-cancer therapies.
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Affiliation(s)
- Philippe Kischel
- Metastasis Research Laboratory, GIGA Cancer, University of Liege, Bat. B23, CHU Sart Tilman Liège, B-4000 Liège, Belgium
| | - David Waltregny
- Metastasis Research Laboratory, GIGA Cancer, University of Liege, Bat. B23, CHU Sart Tilman Liège, B-4000 Liège, Belgium
| | - Yannick Greffe
- Metastasis Research Laboratory, GIGA Cancer, University of Liege, Bat. B23, CHU Sart Tilman Liège, B-4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liege, Bat. B6c, B-4000 Liège, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, Department of Chemistry, University of Liege, Bat. B6c, B-4000 Liège, Belgium
| | - Laurence de Leval
- Department of Pathology, University Hospital of Liege, Bat. B23, CHU Sart Tilman Liège, B-4000 Liege, Belgium
| | - Vincent Castronovo
- Metastasis Research Laboratory, GIGA Cancer, University of Liege, Bat. B23, CHU Sart Tilman Liège, B-4000 Liège, Belgium
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Colomba A, Giuriato S, Dejean E, Thornber K, Delsol G, Tronchère H, Meggetto F, Payrastre B, Gaits-Iacovoni F. Inhibition of Rac controls NPM-ALK-dependent lymphoma development and dissemination. Blood Cancer J 2011; 1:e21. [PMID: 22829165 PMCID: PMC3255265 DOI: 10.1038/bcj.2011.19] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Accepted: 04/15/2011] [Indexed: 01/16/2023] Open
Abstract
Nucleophosmin-anaplastic lymphoma kinase (NPM–ALK) is a tyrosine kinase oncogene responsible for the pathogenesis of the majority of human ALK-positive lymphomas. We recently reported that it activated the Rac1 GTPase in anaplastic large-cell lymphoma (ALCL), leading to Rac-dependent formation of active invadopodia required for invasiveness. Herein, we went further into the study of this pathway and used the inhibitor of Rac, NSC23766, to validate its potential as a molecular target in ALCL in vitro and in vivo in a xenograft model and in a conditional model of NPM–ALK transgenic mice. Our data demonstrate that Rac regulates important effectors of NPM–ALK-induced transformation such as Erk1/2, p38 and Akt. Moreover, inhibition of Rac signaling abrogates NPM–ALK-elicited disease progression and metastasis in mice, highlighting the potential of small GTPases and their regulators as additional therapic targets in lymphomas.
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Kinney MC, Higgins RA, Medina EA. Anaplastic large cell lymphoma: twenty-five years of discovery. Arch Pathol Lab Med 2011; 135:19-43. [PMID: 21204709 DOI: 10.5858/2010-0507-rar.1] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT The year 2010 commemorates the 25th year since the seminal publication by Karl Lennert and Harald Stein and others in Kiel, West Germany, describing an unusual large cell lymphoma now known as anaplastic large cell lymphoma (ALCL). Investigators at many universities and hospitals worldwide have contributed to our current in-depth understanding of this unique peripheral T-cell lymphoma, which in its systemic form, principally occurs in children and young adults. OBJECTIVE To summarize our current knowledge of the clinical and pathologic features of systemic and primary cutaneous ALCL. Particular emphasis is given to the biology and pathogenesis of ALCL. DATA SOURCES Search of the medical literature (Ovid MEDLINE In-Process & Other Non-Indexed Citations and Ovid MEDLINE: 1950 to Present [National Library of Medicine]) and more than 20 years of diagnostic experience were used as the source of data for review. CONCLUSIONS Based on immunostaining for activation antigen CD30 and the presence of dysregulation of the anaplastic lymphoma kinase gene (2p23), the diagnosis of ALCL has become relatively straightforward for most patients. Major strides have been made during the last decade in our understanding of the complex pathogenesis of ALCL. Constitutive NPM-ALK signaling has been shown to drive oncogenesis via an intricate network of redundant and interacting pathways that regulate cell proliferation, cell fate, and cytoskeletal modeling. Nevertheless, pathomechanistic, therapeutic, and diagnostic challenges remain that should be resolved as we embark on the next generation of discovery.
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Affiliation(s)
- Marsha C Kinney
- Department of Pathology, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr., San Antonio, TX 78229-3900, USA.
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8
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Yoo JY, Ryu J, Gao R, Yaguchi T, Kaul SC, Wadhwa R, Yun CO. Tumor suppression by apoptotic and anti-angiogenic effects of mortalin-targeting adeno-oncolytic virus. J Gene Med 2010; 12:586-95. [PMID: 20603860 DOI: 10.1002/jgm.1471] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Adeno-oncolytic (Adon) viruses offer an effective cancer therapeutic tool with several advantages, including wide host cell permeability, high transduction efficiency, safety, tumor selectivity, non-invasiveness, high genetic modifiability and high level of expression of the integrated transgenes. Armed Adon viruses in which the therapeutic efficacy of virus is enhanced by their coupling with cytotoxic, anti-angiogenic or anti-vascular gene products have gained importance because they engage additional mechanisms for tumor cell killing. In the present study, we selected mortalin, a stress chaperone that is tightly involved in human carcinogenesis, constructed a mortalin-targeting Adon (mot-Adon) virus and examined its therapeutic potential both in vitro and in vivo. METHODS Mortalin-targeting plasmid and viral vectors that harbored mortalin-specific small interfering RNA sequences were constructed. The therapeutic value of these vectors was investigated in vitro and in vivo by cell culture and nude mice tumor models. RESULTS We demonstrate that the mot-Adon virus has selective cytotoxicity for human cancer cells in vitro. Retrovirus-mediated overexpression of mortalin protected the cells against mot-Adon virus, confirming that mortalin silencing was the real cause of cancer cell death. Although mortalin overexpression enhanced malignant properties of cancer cells in breast xenograft models, mot-Adon virus elicited an enhanced anti-tumor effect. Immunohistochemical examination of the tumors showed that the mot-Adon virus caused enhanced apoptosis (mediated by reactivation of p53) and suppression of microvessel formation. CONCLUSIONS Mortalin is up-regulated in a large variety of tumors and hence mot-Adon virus is proposed as a candidate cancer therapeutic agent.
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Affiliation(s)
- Ji Young Yoo
- Brain Korea 21 Project for Medical Sciences, Institute for Cancer Research, Yonsei University College of Medicine, Seoul, Korea
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9
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Lagarrigue F, Dupuis-Coronas S, Ramel D, Delsol G, Tronchère H, Payrastre B, Gaits-Iacovoni F. Matrix Metalloproteinase-9 Is Upregulated in Nucleophosmin-Anaplastic Lymphoma Kinase–Positive Anaplastic Lymphomas and Activated at the Cell Surface by the Chaperone Heat Shock Protein 90 to Promote Cell Invasion. Cancer Res 2010; 70:6978-87. [DOI: 10.1158/0008-5472.can-10-0861] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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10
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Antonov AV, Dietmann S, Mewes HW. KEGG spider: interpretation of genomics data in the context of the global gene metabolic network. Genome Biol 2008; 9:R179. [PMID: 19094223 PMCID: PMC2646283 DOI: 10.1186/gb-2008-9-12-r179] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/28/2008] [Accepted: 12/18/2008] [Indexed: 12/24/2022] Open
Abstract
KEGG spider is a web-based tool for interpretation of experimentally derived gene lists in order to gain understanding of metabolism variations at a genomic level. KEGG spider implements a 'pathway-free' framework that overcomes a major bottleneck of enrichment analyses: it provides global models uniting genes from different metabolic pathways. Analyzing a number of experimentally derived gene lists, we demonstrate that KEGG spider provides deeper insights into metabolism variations in comparison to existing methods.
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Affiliation(s)
- Alexey V Antonov
- GSF National Research Centre for Environment and Health, Institute for Bioinformatics, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.
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11
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Mossuz P, Arlotto M, Hermouet S, Bouamrani A, Lippert E, Girodon F, Dobo I, Vincent P, Cahn JY, Berger F. Proteomic study of the impact of the JAK2–V617F mutation on the phenotype of essential thrombocythemia. Exp Hematol 2008; 36:1642-7. [DOI: 10.1016/j.exphem.2008.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2008] [Revised: 07/17/2008] [Accepted: 07/31/2008] [Indexed: 01/14/2023]
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The enzymatic activity of 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase is enhanced by NPM-ALK: new insights in ALK-mediated pathogenesis and the treatment of ALCL. Blood 2008; 113:2776-90. [PMID: 18845790 DOI: 10.1182/blood-2008-06-161018] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Anaplastic large cell lymphoma represents a subset of neoplasms caused by translocations that juxtapose the anaplastic lymphoma kinase (ALK) to dimerization partners. The constitutive activation of ALK fusion proteins leads to cellular transformation through a complex signaling network. To elucidate the ALK pathways sustaining lymphomagenesis and tumor maintenance, we analyzed the tyrosine-kinase protein profiles of ALK-positive cell lines using 2 complementary proteomic-based approaches, taking advantage of a specific ALK RNA interference (RNAi) or cell-permeable inhibitors. A well-defined set of ALK-associated tyrosine phosphopeptides, including metabolic enzymes, kinases, ribosomal and cytoskeletal proteins, was identified. Validation studies confirmed that vasodilator-stimulated phosphoprotein and 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine monophosphate cyclohydrolase (ATIC) associated with nucleophosmin (NPM)-ALK, and their phosphorylation required ALK activity. ATIC phosphorylation was documented in cell lines and primary tumors carrying ALK proteins and other tyrosine kinases, including TPR-Met and wild type c-Met. Functional analyses revealed that ALK-mediated ATIC phosphorylation enhanced its enzymatic activity, dampening the methotrexate-mediated transformylase activity inhibition. These findings demonstrate that proteomic approaches in well-controlled experimental settings allow the definition of informative proteomic profiles and the discovery of novel ALK downstream players that contribute to the maintenance of the neoplastic phenotype. Prediction of tumor responses to methotrexate may justify specific molecular-based chemotherapy.
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13
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Li R, Morris SW. Development of anaplastic lymphoma kinase (ALK) small-molecule inhibitors for cancer therapy. Med Res Rev 2008; 28:372-412. [PMID: 17694547 DOI: 10.1002/med.20109] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Anaplastic lymphoma kinase (ALK) is a receptor tyrosine kinase (RTK) involved in the genesis of several human cancers; indeed, ALK was initially identified in constitutively activated and oncogenic fusion forms--the most common being nucleophosmin (NPM)-ALK--in a non-Hodgkin's lymphoma (NHL) known as anaplastic large-cell lymphoma (ALCL) and subsequent studies identified ALK fusions in the human sarcomas called inflammatory myofibroblastic tumors (IMTs). In addition, two recent reports have suggested that the ALK fusion, TPM4-ALK, may be involved in the genesis of a subset of esophageal squamous cell carcinomas. While the cause-effect relationship between ALK fusions and malignancies such as ALCL and IMT is very well established, more circumstantial links implicate the involvement of the full-length, normal ALK receptor in the genesis of additional malignancies including glioblastoma, neuroblastoma, breast cancer, and others; in these instances, ALK is believed to foster tumorigenesis following activation by autocrine and/or paracrine growth loops involving the reported ALK ligands, pleiotrophin (PTN) and midkine (MK). There are no currently available ALK small-molecule inhibitors approved for clinical cancer therapy; however, recognition of the variety of malignancies in which ALK may play a causative role has recently begun to prompt developmental efforts in this area. This review provides a succinct summary of normal ALK biology, the confirmed and putative roles of ALK fusions and the full-length ALK receptor in the development of human cancers, and efforts to target ALK using small-molecule kinase inhibitors.
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Affiliation(s)
- Rongshi Li
- High-Throughput Medicinal Chemistry, ChemBridge Research Laboratories, 16981 Via Tazon, Suites K, San Diego, California 92127, USA.
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Suberbielle E, Gonzalez-Dunia D, Pont F. High reproducibility of two-dimensional liquid chromatography using pH-driven fractionation with a pressure-resistant electrode. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 871:125-9. [PMID: 18635406 DOI: 10.1016/j.jchromb.2008.06.043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Revised: 06/16/2008] [Accepted: 06/23/2008] [Indexed: 10/21/2022]
Abstract
Automated two-dimensional liquid chromatography using the PF2D system from Beckman Coulter provides a fractionation platform well suited for differential proteomic studies. To date, the reliability and reproducibility of PF2D has not been accurately tested. Here, we used an optimized software and a pressure-resistant pH electrode, allowing a precise and reproducible control of the pH limits for each fraction during PF2D. We tested the reliability of this improved system by performing several rounds of fractionation using the same protein extract. Three UV maps were generated, leading to 54 chromatograms and more than 3000 protein peaks. Using semi-automated software for peak-to-peak comparison between 2D-LC chromatograms, we demonstrate that the peak concordance is very high. The rates of concordance were higher in the second dimension repeatability tests, indicating that the limiting factors for 2D-LC reproducibility rely on the pI fractionation and sample preparation steps. The reproducibility between maps was closely related to pH curves similarities, further stressing the need of careful pH adjustment and precise electrode calibration.
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Eleuterio E, Di Giuseppe F, Sulpizio M, di Giacomo V, Rapino M, Cataldi A, Di Ilio C, Angelucci S. Proteome analysis of X-ray irradiated human erythroleukemia cells. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2008; 1784:611-20. [DOI: 10.1016/j.bbapap.2008.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2007] [Revised: 12/28/2007] [Accepted: 01/20/2008] [Indexed: 11/16/2022]
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16
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Colomba A, Courilleau D, Ramel D, Billadeau DD, Espinos E, Delsol G, Payrastre B, Gaits-Iacovoni F. Activation of Rac1 and the exchange factor Vav3 are involved in NPM-ALK signaling in anaplastic large cell lymphomas. Oncogene 2007; 27:2728-36. [PMID: 17998938 DOI: 10.1038/sj.onc.1210921] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The majority of anaplastic large cell lymphomas (ALCLs) express the nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) fusion protein, which is oncogenic due to its constitutive tyrosine kinase activity. Transformation by NPM-ALK not only increases proliferation, but also modifies cell shape and motility in both lymphoid and fibroblastic cells. We report that the Rac1 GTPase, a known cytoskeletal regulator, is activated by NPM-ALK in ALCL cell lines (Karpas 299 and Cost) and transfected cells (lymphoid Ba/F3 cells, NIH-3T3 fibroblasts). We have identified Vav3 as one of the exchange factors involved in Rac1 activation. Stimulation of Vav3 and Rac1 by NPM-ALK is under the control of Src kinases. It involves formation of a signaling complex between NPM-ALK, pp60(c-src), Lyn and Vav3, in which Vav3 associates with tyrosine 343 of NPM-ALK via its SH2 domain. Moreover, Vav3 is phosphorylated in NPM-ALK positive biopsies from patients suffering from ALCL, demonstrating the pathological relevance of this observation. The use of Vav3-specific shRNA and a dominant negative Rac1 mutant demonstrates the central role of GTPases in NPM-ALK elicited motility and invasion.
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Affiliation(s)
- A Colomba
- INSERM, U563, Centre de Physiopathologie de Toulouse Purpan, Toulouse, France
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Shiota M, Ikeda Y, Kaul Z, Itadani J, Kaul SC, Wadhwa R. Internalizing Antibody-Based Targeted Gene Delivery for Human Cancer Cells. Hum Gene Ther 2007; 18:1153-60. [DOI: 10.1089/hum.2007.087] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Maki Shiota
- National Institute of Advanced Industrial Science and Technology (ASIT), Tsukuba, Ibaraki 305-8562, Japan
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Hongo, Tokyo 113-8656, Japan
| | - Yutaka Ikeda
- National Institute of Advanced Industrial Science and Technology (ASIT), Tsukuba, Ibaraki 305-8562, Japan
| | - Zeenia Kaul
- National Institute of Advanced Industrial Science and Technology (ASIT), Tsukuba, Ibaraki 305-8562, Japan
| | - Jun Itadani
- National Institute of Advanced Industrial Science and Technology (ASIT), Tsukuba, Ibaraki 305-8562, Japan
| | - Sunil C. Kaul
- National Institute of Advanced Industrial Science and Technology (ASIT), Tsukuba, Ibaraki 305-8562, Japan
| | - Renu Wadhwa
- National Institute of Advanced Industrial Science and Technology (ASIT), Tsukuba, Ibaraki 305-8562, Japan
- Department of Chemistry and Biotechnology, School of Engineering, University of Tokyo, Hongo, Tokyo 113-8656, Japan
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Cowen EW, Liu CW, Steinberg SM, Kang S, Vonderheid EC, Kwak HS, Booher S, Petricoin EF, Liotta LA, Whiteley G, Hwang ST. Differentiation of tumour-stage mycosis fungoides, psoriasis vulgaris and normal controls in a pilot study using serum proteomic analysis. Br J Dermatol 2007; 157:946-53. [PMID: 17854367 DOI: 10.1111/j.1365-2133.2007.08185.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND Serum proteomic analysis is an analytical technique utilizing high-throughput mass spectrometry (MS) in order to assay thousands of serum proteins simultaneously. The resultant 'proteomic signature' has been used to differentiate benign and malignant diseases, enable disease prognosis, and monitor response to therapy. OBJECTIVES This pilot study was designed to determine if serum protein patterns could be used to distinguish patients with tumour-stage mycosis fungoides (MF) from patients with a benign inflammatory skin condition (psoriasis) and/or subjects with healthy skin. METHODS Serum was analysed from 45 patients with tumour-stage MF, 56 patients with psoriasis, and 47 controls using two MS platforms of differing resolution. An artificial intelligence-based classification model was constructed to predict the presence of the disease state based on the serum proteomic signature. RESULTS Based on data from an independent testing set (14-16 subjects in each group), MF was distinguished from psoriasis with 78.6% (or 78.6%) sensitivity and 86.7% (or 93.8%) specificity, while sera from patients with psoriasis were distinguished from those of nonaffected controls with 86.7% (or 93.8%) sensitivity and 75.0% (or 76.9%) specificity (depending on the MS platform used). MF was distinguished from unaffected controls with 61.5% (or 71.4%) sensitivity and 91.7% (or 92.9%) specificity. In addition, a secondary survival analysis using 11 MS peaks identified significant survival differences between two MF groups (all P-values <0.05). CONCLUSIONS Serum proteomics should be further investigated for its potential to identify patients with neoplastic skin disease and its ability to determine disease prognosis.
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Affiliation(s)
- E W Cowen
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Gez S, Crossett B, Christopherson RI. Differentially expressed cytosolic proteins in human leukemia and lymphoma cell lines correlate with lineages and functions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2007; 1774:1173-83. [PMID: 17698427 DOI: 10.1016/j.bbapap.2007.06.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2007] [Revised: 06/05/2007] [Accepted: 06/15/2007] [Indexed: 12/18/2022]
Abstract
Identification of cytosolic proteins differentially expressed between types of leukemia and lymphoma may provide a molecular basis for classification and understanding their cellular properties. Two-dimensional fluorescence difference gel electrophoresis (DIGE) and mass spectrometry have been used to identify proteins that are differentially expressed in cytosolic extracts from four human leukemia and lymphoma cell lines: HL-60 (acute promyelocytic leukemia), MEC1 (B-cell chronic lymphocytic leukemia), CCRF-CEM (T-cell acute lymphoblastic leukemia) and Raji (B-cell Burkitt's lymphoma). A total of 247 differentially expressed proteins were identified between the four cell lines. Analysis of the data by principal component analysis identified 22 protein spots (17 different protein species) differentially expressed at more than a 95% variance level between these cell lines. Several of these proteins were differentially expressed in only one cell line: HL-60 (myeloperoxidase, phosphoprotein 32 family member A, ras related protein Rab-11B, protein disulfide-isomerase, ran-specific GTPase-activating protein, nucleophosmin and S-100 calcium binding protein A4), and Raji (ezrin). Several of these proteins were differentially expressed in two cell lines: Raji and MEC1 (C-1-tetrahydrofolate synthase, elongation factor 2, alpha- and beta-tubulin, transgelin-2 and stathmin). MEC1 and CCRF-CEM (gamma-enolase), HL-60 and CCRF-CEM (ubiquitin-conjugating enzyme E2 N). The differentially expressed proteins identified in these four cell lines correlate with cellular properties and provide insights into the molecular basis of these malignancies.
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Affiliation(s)
- Swetlana Gez
- School of Molecular and Microbial Biosciences G08, University of Sydney, NSW 2006, Australia
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Sjostrom C, Seiler C, Crockett DK, Tripp SR, Elenitoba Johnson KSJ, Lim MS. Global proteome profiling of NPM/ALK-positive anaplastic large cell lymphoma. Exp Hematol 2007; 35:1240-8. [PMID: 17560012 DOI: 10.1016/j.exphem.2007.04.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 04/11/2007] [Accepted: 04/20/2007] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Constitutive overexpression of nucleophosmin/anaplastic lymphoma kinase (NPM/ALK) is a key oncogenic event in anaplastic large cell lymphomas (ALCL) that carry the t(2;5)(p23;q35) translocation. Global proteomic analysis of NPM/ALK-positive ALCL would improve understanding of the disease pathogenesis and yield new candidate targets for novel treatment and diagnostic strategies. MATERIALS AND METHODS To comprehensively determine the inventory of proteins from NPM/ALK-positive ALCL SUDHL-1 cells, the membrane, cytoplasm, and nuclear subcellular fractions were resolved by one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The MS spectra were interpreted using SEQUEST to search the electronic UniProt protein database, and analyzed by ProteinProphet and INTERACT. RESULTS A total of 623 proteins consisting of 210 membrane, 229 cytoplasm, and 184 nuclear proteins were identified with a <or=5% error rate. Extensive annotation and systematic examination of the literature for information on 209 representative proteins indicated that 19.9% were reported to be expressed in T cells and 44.7% were reported to have important function in cancers, while only 4.3% were reported to be involved in ALCL pathogenesis. Categorization of proteins into functional groups was performed using GOMiner. A subset of the identified proteins was confirmed by Western blots and immunohistochemistry of tissue samples. CONCLUSION We present an extensive catalog of proteins expressed by NPM/ALK-positive ALCL. This study illustrates the potential for novel pathogenetic discovery in NPM/ALK-positive ALCL and the utility of combining cellular subfractionation, 1D SDS-PAGE, and LC-MS/MS for the comprehensive protein analysis of lymphoma.
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Affiliation(s)
- Chris Sjostrom
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
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21
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Armstrong F, Lamant L, Hieblot C, Delsol G, Touriol C. TPM3-ALK expression induces changes in cytoskeleton organisation and confers higher metastatic capacities than other ALK fusion proteins. Eur J Cancer 2007; 43:640-6. [PMID: 17276053 DOI: 10.1016/j.ejca.2006.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 11/23/2006] [Accepted: 12/05/2006] [Indexed: 12/15/2022]
Abstract
Translocations of the anaplastic lymphoma kinase (ALK) gene result in the production of a number of oncogenic ALK fusion proteins implicated in tumour development. We have previously shown that X-ALK fusion proteins have differential effects on the proliferation, transformation, and invasion properties of NIH3T3 cells in vitro. In the present study, we have investigated the metastatic potential of various X-ALK expressing cell lines using an experimental lung metastasis assay. We have shown that TPM3-ALK expression bestows higher metastatic capacities than other X-ALK fusion proteins and in addition, that TPM3-ALK fusion protein expression specifically induces changes in cell morphology and cytoskeleton organisation. Co-immunoprecipitation studies demonstrate a specific interaction between TPM3-ALK and endogenous tropomyosin. Together the specific actions of TPM3-ALK on the cytoskeleton organisation offer an interesting hypothesis with respect to the higher cell motility and metastatic potential of this fusion protein.
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Affiliation(s)
- Florence Armstrong
- INSERM U563, Centre de Physiopathologie de Toulouse-Purpan, Department of Oncogenesis and Signalling in Haematopoietic Cells, Toulouse, France
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Lim MS, Elenitoba-Johnson KSJ. Mass Spectrometry-based Proteomic Studies of Human Anaplastic Large Cell Lymphoma. Mol Cell Proteomics 2006; 5:1787-98. [PMID: 16785248 DOI: 10.1074/mcp.r600005-mcp200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Malignant lymphomas are a diverse group of malignant neoplasms that arise as a result of a complex interplay of multiple factors including genetic aberrations, immunosuppression, and exposure to noxious agents such as ionizing radiation and chemical agents. Anaplastic large cell lymphoma (ALCL) is an aggressive T-lineage lymphoma harboring chromosomal translocations involving the anaplastic lymphoma kinase (ALK) tyrosine kinase. The most common translocation in ALCL is the t(2;5)(p23;q35). This results in the formation of a chimeric fusion kinase, nucleophosmin/ALK. Nucleophosmin/ALK activates numerous downstream signaling pathways resulting in enhanced survival and proliferation. Using a variety of mass spectrometry-driven proteomic strategies, we have studied several aspects of the ALCL proteome. In this review, we provide a summary of mass spectrometry-based proteomic studies that expands the current understanding of the molecular pathogenesis of ALCL and provides the basis for the identification of biomarkers and targets for novel therapeutic agents.
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Affiliation(s)
- Megan S Lim
- Department of Pathology and Associated Regional and University Pathologists Institute for Clinical and Experimental Pathology, University of Utah Health Sciences Center, Salt Lake City, 84132, USA.
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Duplantier MM, Lamant L, Sabourdy F, de Reynies A, Delsol G, Espinos E. Serpin A1 is overexpressed in ALK+ anaplastic large cell lymphoma and its expression correlates with extranodal dissemination. Leukemia 2006; 20:1848-54. [PMID: 16900211 DOI: 10.1038/sj.leu.2404352] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Anaplastic large cell lymphoma (ALCL) is a distinct subtype of non-Hodgkin's lymphoma. Most of ALCLs (85%) carry a chromosomal translocation involving different partners in the 5' portion, and the anaplastic lymphoma kinase (ALK) receptor kinase domain in the 3' portion. These translocations induce the ectopic expression of X-ALK proteins, thought to be involved in lymphomagenesis, through the dysregulation of cell proliferation and apoptotic pathways. In the present study, based on several ALK+ and ALK- ALCL cell lines and biopsy specimens, we showed that serpin A1, a secretory glycoprotein, was overexpressed in ALK+ ALCL cell lines and ALK+ tumors at both the transcriptional and translational levels. The crucial role of NPM-ALK in the regulation of serpin A1 expression was further demonstrated by using both ectopic expression and downregulation, by RNA interference, of the NPM-ALK oncogene. In addition, in ALK+ tumors, serpin A1 expression appeared to be correlated with the clinical status of the patients as the serpin A1 mRNA level was higher in patients presenting with extranodal dissemination. These data, together with the pattern of expression of serpin A1 we observed in ALK+ tumors, suggest that serpin A1 has an invasion-promoting effect in ALK+ ALCL.
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MESH Headings
- Adult
- Anaplastic Lymphoma Kinase
- Biopsy
- Cell Line, Tumor
- Child
- Gene Expression Regulation, Neoplastic
- Humans
- Lymph Nodes/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/physiopathology
- Neoplasm Invasiveness
- Protein Biosynthesis
- Protein-Tyrosine Kinases/genetics
- RNA, Messenger/analysis
- Receptor Protein-Tyrosine Kinases
- Transcription, Genetic
- Translocation, Genetic
- alpha 1-Antitrypsin/genetics
- alpha 1-Antitrypsin/metabolism
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Affiliation(s)
- M M Duplantier
- Department of Oncogenesis and Signaling in Hematopoietic Cells, Inserm U-563, Centre de Physiopathologie de Toulouse-Purpan, Toulouse, France
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