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Szelest M, Masternak M, Zając M, Chojnacki M, Skórka K, Zaleska J, Karczmarczyk A, Stasiak G, Wawrzyniak E, Kotkowska A, Siemieniuk-Ryś M, Purkot J, Subocz E, Cichocka E, Tomczak W, Zawirska D, Giannopoulos K. The role of NPM1 alternative splicing in patients with chronic lymphocytic leukemia. PLoS One 2022; 17:e0276674. [PMID: 36282861 PMCID: PMC9595542 DOI: 10.1371/journal.pone.0276674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/11/2022] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVES Chronic lymphocytic leukemia (CLL) is a lymphoproliferative disease with heterogeneous clinical course. Recent studies revealed a link between NOTCH1 mutation and the overexpression of MYC and MYC-related genes involved in ribosome biogenesis and protein biosynthesis, such as nucleophosmin-1 (NPM1), in CLL cells. In the present study, we aim to evaluate the impact of the NOTCH1 mutation on the MYC and MYC induced NPM1 expression in CLL cells via quantification of their transcripts. METHODS Using qRT-PCR, we analyzed the levels of MYC and three main NPM1 splice variants in 214 samples collected from CLL patients. We assessed the impact of each splice variant on CLL prognostic markers, including the IGHV, TP53, NOTCH1, SF3B1, and MYD88 mutational status, cytogenetic aberrations, and laboratory features. RESULTS Significantly higher levels of NPM1.R1 transcripts in patients with unmutated compared to mutated IGHV status were found. The median time to first treatment (TTFT) in patients with a high level of NPM1.R1 was significantly shorter compared to the group with low NPM1.R1 levels (1.5 vs 33 months, p = 0.0002). Moreover, in Multivariate Cox Proportional Hazard Regression Model NPM1.R1 splice variant provided an independent prognostic value for TTFT. CONCLUSION In conclusion, our study indicates the prognostic significance of the level of NPM1.R1 expression and suggests the importance of splicing alterations in the pathogenesis of CLL.
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Affiliation(s)
- Monika Szelest
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Marta Masternak
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
- Department of Hematology, St. John’s Cancer Centre, Lublin, Poland
| | - Małgorzata Zając
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Michał Chojnacki
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Katarzyna Skórka
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Joanna Zaleska
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | | | - Grażyna Stasiak
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Ewa Wawrzyniak
- Department of Hematology, Medical University of Lodz, Lodz, Poland
| | | | | | - Joanna Purkot
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
| | - Edyta Subocz
- Department of Hematology, Military Institute of Medicine, Warsaw, Poland
- Independent Public Health Care Center of the Ministry of Internal Affairs and Administration with the Warmian-Masurian Oncology Centre in Olsztyn, Olsztyn, Poland
| | - Edyta Cichocka
- Department of Hematology, Copernicus Hospital, Torun, Poland
| | - Waldemar Tomczak
- Department of Hematooncology and Bone Marrow Transplantation Unit, Medical University of Lublin, Lublin, Poland
| | - Daria Zawirska
- Department of Hematology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Giannopoulos
- Department of Experimental Hematooncology, Medical University of Lublin, Lublin, Poland
- Department of Hematology, St. John’s Cancer Centre, Lublin, Poland
- * E-mail:
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Mavridou D, Psatha K, Aivaliotis M. Proteomics and Drug Repurposing in CLL towards Precision Medicine. Cancers (Basel) 2021; 13:cancers13143391. [PMID: 34298607 PMCID: PMC8303629 DOI: 10.3390/cancers13143391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 11/30/2022] Open
Abstract
Simple Summary Despite continued efforts, the current status of knowledge in CLL molecular pathobiology, diagnosis, prognosis and treatment remains elusive and imprecise. Proteomics approaches combined with advanced bioinformatics and drug repurposing promise to shed light on the complex proteome heterogeneity of CLL patients and mitigate, improve, or even eliminate the knowledge stagnation. In relation to this concept, this review presents a brief overview of all the available proteomics and drug repurposing studies in CLL and suggests the way such studies can be exploited to find effective therapeutic options combined with drug repurposing strategies to adopt and accost a more “precision medicine” spectrum. Abstract CLL is a hematological malignancy considered as the most frequent lymphoproliferative disease in the western world. It is characterized by high molecular heterogeneity and despite the available therapeutic options, there are many patient subgroups showing the insufficient effectiveness of disease treatment. The challenge is to investigate the individual molecular characteristics and heterogeneity of these patients. Proteomics analysis is a powerful approach that monitors the constant state of flux operators of genetic information and can unravel the proteome heterogeneity and rewiring into protein pathways in CLL patients. This review essences all the available proteomics studies in CLL and suggests the way these studies can be exploited to find effective therapeutic options combined with drug repurposing approaches. Drug repurposing utilizes all the existing knowledge of the safety and efficacy of FDA-approved or investigational drugs and anticipates drug alignment to crucial CLL therapeutic targets, leading to a better disease outcome. The drug repurposing studies in CLL are also discussed in this review. The next goal involves the integration of proteomics-based drug repurposing in precision medicine, as well as the application of this procedure into clinical practice to predict the most appropriate drugs combination that could ensure therapy and the long-term survival of each CLL patient.
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Affiliation(s)
- Dimitra Mavridou
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
| | - Konstantina Psatha
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
| | - Michalis Aivaliotis
- Laboratory of Biochemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece;
- Functional Proteomics and Systems Biology (FunPATh)—Center for Interdisciplinary Research and Innovation (CIRI-AUTH), GR-57001 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Aristotle University of Thessaloniki, GR-54124 Thessaloniki, Greece
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology, GR-70013 Heraklion, Greece
- Correspondence: (K.P.); (M.A.)
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3
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Thurgood LA, Dwyer ES, Lower KM, Chataway TK, Kuss BJ. Altered expression of metabolic pathways in CLL detected by unlabelled quantitative mass spectrometry analysis. Br J Haematol 2019; 185:65-78. [PMID: 30656643 DOI: 10.1111/bjh.15751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/26/2018] [Indexed: 12/27/2022]
Abstract
Chronic lymphocytic leukaemia (CLL) remains the most common incurable malignancy of B cells in the western world. Patient outcomes are heterogeneous and can be difficult to predict with current prognostic markers. Here, we used a quantitative label-free proteomic technique to ascertain differences in the B-cell proteome from healthy donors and CLL patients with either mutated (M-CLL) or unmutated (UM-CLL) IGHV to identify new prognostic markers. In peripheral B-CLL cells, 349 (22%) proteins were differentially expressed between normal B cells and B-CLL cells and 189 (12%) were differentially expressed between M-CLL and UM-CLL. We also examined the proteome of proliferating CLL cells in the lymph nodes, and identified 76 (~8%) differentially expressed proteins between healthy and CLL lymph nodes. B-CLL cells show over-expression of proteins involved in lipid and cholesterol metabolism. A comprehensive lipidomic analysis highlighted large differences in glycolipids and sphingolipids. A shift was observed from the pro-apoptotic lipid ceramide towards the anti-apoptotic/chemoresistant lipid, glucosylceramide, which was more evident in patients with aggressive disease (UM-CLL). This study details a novel quantitative proteomic technique applied for the first time to primary patient samples in CLL and highlights that primary CLL lymphocytes display markers of a metabolic shift towards lipid synthesis and breakdown.
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Affiliation(s)
- Lauren A Thurgood
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Eveline S Dwyer
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Karen M Lower
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Tim K Chataway
- Flinders Proteomic Facility, Department of Human Physiology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia
| | - Bryone J Kuss
- Discipline Molecular Medicine and Pathology, College of Medicine and Public Health, Flinders University, Adelaide, South Australia, Australia.,Haematology, Molecular Medicine and Pathology, SA Pathology, Flinders Medical Centre, Adelaide, South Australia, Australia
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4
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Johnston HE, Carter MJ, Larrayoz M, Clarke J, Garbis SD, Oscier D, Strefford JC, Steele AJ, Walewska R, Cragg MS. Proteomics Profiling of CLL Versus Healthy B-cells Identifies Putative Therapeutic Targets and a Subtype-independent Signature of Spliceosome Dysregulation. Mol Cell Proteomics 2018; 17:776-791. [PMID: 29367434 PMCID: PMC5880099 DOI: 10.1074/mcp.ra117.000539] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/30/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a heterogeneous B-cell cancer exhibiting a wide spectrum of disease courses and treatment responses. Molecular characterization of RNA and DNA from CLL cases has led to the identification of important driver mutations and disease subtypes, but the precise mechanisms of disease progression remain elusive. To further our understanding of CLL biology we performed isobaric labeling and mass spectrometry proteomics on 14 CLL samples, comparing them with B-cells from healthy donors (HDB). Of 8694 identified proteins, ∼6000 were relatively quantitated between all samples (q<0.01). A clear CLL signature, independent of subtype, of 544 significantly overexpressed proteins relative to HDB was identified, highlighting established hallmarks of CLL (e.g. CD5, BCL2, ROR1 and CD23 overexpression). Previously unrecognized surface markers demonstrated overexpression (e.g. CKAP4, PIGR, TMCC3 and CD75) and three of these (LAX1, CLEC17A and ATP2B4) were implicated in B-cell receptor signaling, which plays an important role in CLL pathogenesis. Several other proteins (e.g. Wee1, HMOX1/2, HDAC7 and INPP5F) were identified with significant overexpression that also represent potential targets. Western blotting confirmed overexpression of a selection of these proteins in an independent cohort. mRNA processing machinery were broadly upregulated across the CLL samples. Spliceosome components demonstrated consistent overexpression (p = 1.3 × 10-21) suggesting dysregulation in CLL, independent of SF3B1 mutations. This study highlights the potential of proteomics in the identification of putative CLL therapeutic targets and reveals a subtype-independent protein expression signature in CLL.
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Affiliation(s)
- Harvey E Johnston
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton, UK
- §Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK
| | - Matthew J Carter
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton, UK
| | - Marta Larrayoz
- ¶Cancer Genomics, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - James Clarke
- ‖Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Spiro D Garbis
- §Centre for Proteomic Research, Institute for Life Sciences, University of Southampton, Highfield Campus, Southampton, UK
- **Clinical and Experimental Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - David Oscier
- ‡‡Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Jonathan C Strefford
- ¶Cancer Genomics, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew J Steele
- §§Leukemia and Lymphoma Molecular Mechanisms and Therapy Group, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Renata Walewska
- ¶¶Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Mark S Cragg
- From the ‡Antibody and Vaccine Group, Cancer Sciences Unit, Faculty of Medicine, General Hospital, University of Southampton, Southampton, UK;
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5
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Pozzo F, Bittolo T, Vendramini E, Bomben R, Bulian P, Rossi FM, Zucchetto A, Tissino E, Degan M, D'Arena G, Di Raimondo F, Zaja F, Pozzato G, Rossi D, Gaidano G, Del Poeta G, Gattei V, Dal Bo M. NOTCH1-mutated chronic lymphocytic leukemia cells are characterized by a MYC-related overexpression of nucleophosmin 1 and ribosome-associated components. Leukemia 2017; 31:2407-2415. [PMID: 28321119 DOI: 10.1038/leu.2017.90] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 12/24/2022]
Abstract
In chronic lymphocytic leukemia (CLL), the mechanisms controlling cell growth and proliferation in the presence of NOTCH1 mutations remain largely unexplored. By performing a gene expression profile of NOTCH1-mutated (NOTCH1-mut) versus NOTCH1 wild-type CLL, we identified a gene signature of NOTCH1-mut CLL characterized by the upregulation of genes related to ribosome biogenesis, such as nucleophosmin 1 (NPM1) and ribosomal proteins (RNPs). Activation of NOTCH1 signaling by ethylenediaminetetraacetic acid or by coculture with JAGGED1-expressing stromal cells increased NPM1 expression, and inhibition of NOTCH1 signaling by either NOTCH1-specific small interfering RNA (siRNA) or γ-secretase inhibitor reduced NPM1 expression. Bioinformatic analyses and in vitro activation/inhibition of NOTCH1 signaling suggested a role of MYC as a mediator of NOTCH1 effects over NPM1 and RNP expression in NOTCH1-mut CLL. Chromatin immunoprecipitation experiments performed on NOTCH1 intracellular domain (NICD)-transfected CLL-like cells showed the direct binding of NOTCH1 to the MYC promoter, and transfection with MYC-specific siRNA reduced NPM1 expression. In turn, NPM1 determined a proliferation advantage of CLL-like cells, as demonstrated by NPM1-specific siRNA transfection. In conclusion, NOTCH1 mutations in CLL are associated with the overexpression of MYC and MYC-related genes involved in protein biosynthesis including NPM1, which are allegedly responsible for cell growth and/or proliferation advantages of NOTCH1-mut CLL.
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Affiliation(s)
- F Pozzo
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - T Bittolo
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - E Vendramini
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - R Bomben
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - P Bulian
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - F M Rossi
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - A Zucchetto
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - E Tissino
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - M Degan
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - G D'Arena
- Department of Onco-Hematology, IRCCS 'Centro di Riferimento Oncologico della Basilicata', Rionero in Vulture, Italy
| | - F Di Raimondo
- Division of Hematology, Ferrarotto Hospital, Catania, Italy
| | - F Zaja
- Clinica Ematologica, Centro Trapianti e Terapie Cellulari 'Carlo Melzi' DISM, Azienda Ospedaliera Universitaria S Maria Misericordia, Udine, Italy
| | - G Pozzato
- Department of Internal Medicine and Hematology, Maggiore General Hospital, University of Trieste, Trieste, Italy
| | - D Rossi
- Hematology, Institute of Oncology Research and Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - G Gaidano
- Department of Translational Medicine, Division of Hematology, University of Eastern Piedmont, Novara, Italy
| | - G Del Poeta
- Division of Hematology, S Eugenio Hospital and University of Tor Vergata, Rome, Italy
| | - V Gattei
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
| | - M Dal Bo
- Clinical and Experimental Onco-Hematology Unit, Centro di Riferimento Oncologico, IRCCS, Aviano, Italy
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Sbarrato T, Horvilleur E, Pöyry T, Hill K, Chaplin LC, Spriggs RV, Stoneley M, Wilson L, Jayne S, Vulliamy T, Beck D, Dokal I, Dyer MJS, Yeomans AM, Packham G, Bushell M, Wagner SD, Willis AE. A ribosome-related signature in peripheral blood CLL B cells is linked to reduced survival following treatment. Cell Death Dis 2016; 7:e2249. [PMID: 27253413 PMCID: PMC5143378 DOI: 10.1038/cddis.2016.148] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 01/14/2023]
Abstract
We have used polysome profiling coupled to microarray analysis to examine the translatome of a panel of peripheral blood (PB) B cells isolated from 34 chronic lymphocytic leukaemia (CLL) patients. We have identified a ‘ribosome-related' signature in CLL patients with mRNAs encoding for ribosomal proteins and factors that modify ribosomal RNA, e.g. DKC1 (which encodes dyskerin, a pseudouridine synthase), showing reduced polysomal association and decreased expression of the corresponding proteins. Our data suggest a general impact of dyskerin dysregulation on the translational apparatus in CLL and importantly patients with low dyskerin levels have a significantly shorter period of overall survival following treatment. Thus, translational dysregulation of dyskerin could constitute a mechanism by which the CLL PB B cells acquire an aggressive phenotype and thus have a major role in oncogenesis.
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Affiliation(s)
- T Sbarrato
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - E Horvilleur
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - T Pöyry
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - K Hill
- The Babraham Institute, Babraham, Cambridge, UK
| | - L C Chaplin
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - R V Spriggs
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - M Stoneley
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - L Wilson
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - S Jayne
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - T Vulliamy
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, Whitechapel, London E1 2AT, UK
| | - D Beck
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - I Dokal
- Centre for Genomics and Child Health, Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, Whitechapel, London E1 2AT, UK
| | - M J S Dyer
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - A M Yeomans
- Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton, UK
| | - G Packham
- Cancer Research UK Centre, Faculty of Medicine, University of Southampton, Southampton, UK
| | - M Bushell
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
| | - S D Wagner
- Department of Cancer Studies, Ernest and Helen Scott Haematology Research Institute, University of Leicester, Lancaster Road, Leicester LE1 7H, UK
| | - A E Willis
- Medical Research Council Toxicology Unit, Hodgkin Building, PO Box 138, Lancaster Rd, Leicester LE19HN, UK
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Huang PY, Mactier S, Armacki N, Giles Best O, Belov L, Kaufman KL, Pascovici D, Mulligan SP, Christopherson RI. Protein profiles distinguish stable and progressive chronic lymphocytic leukemia. Leuk Lymphoma 2015; 57:1033-43. [DOI: 10.3109/10428194.2015.1094692] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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8
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Eagle GL, Zhuang J, Jenkins RE, Till KJ, Jithesh PV, Lin K, Johnson GG, Oates M, Park K, Kitteringham NR, Pettitt AR. Total proteome analysis identifies migration defects as a major pathogenetic factor in immunoglobulin heavy chain variable region (IGHV)-unmutated chronic lymphocytic leukemia. Mol Cell Proteomics 2015; 14:933-45. [PMID: 25645933 PMCID: PMC4390271 DOI: 10.1074/mcp.m114.044479] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Indexed: 01/07/2023] Open
Abstract
The mutational status of the immunoglobulin heavy chain variable region defines two clinically distinct forms of chronic lymphocytic leukemia (CLL) known as mutated (M-CLL) and unmutated (UM-CLL). To elucidate the molecular mechanisms underlying the adverse clinical outcome associated with UM-CLL, total proteomes from nine UM-CLL and nine M-CLL samples were analyzed by isobaric tags for relative and absolute quantification (iTRAQ)-based mass spectrometry. Based on the expression of 3521 identified proteins, principal component analysis separated CLL samples into two groups corresponding to immunoglobulin heavy chain variable region mutational status. Computational analysis showed that 43 cell migration/adhesion pathways were significantly enriched by 39 differentially expressed proteins, 35 of which were expressed at significantly lower levels in UM-CLL samples. Furthermore, UM-CLL cells underexpressed proteins associated with cytoskeletal remodeling and overexpressed proteins associated with transcriptional and translational activity. Taken together, our findings indicate that UM-CLL cells are less migratory and more adhesive than M-CLL cells, resulting in their retention in lymph nodes, where they are exposed to proliferative stimuli. In keeping with this hypothesis, analysis of an extended cohort of 120 CLL patients revealed a strong and specific association between UM-CLL and lymphadenopathy. Our study illustrates the potential of total proteome analysis to elucidate pathogenetic mechanisms in cancer.
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Affiliation(s)
- Gina L Eagle
- From the ‡Department of Molecular and Clinical Cancer Medicine
| | - Jianguo Zhuang
- From the ‡Department of Molecular and Clinical Cancer Medicine,
| | - Rosalind E Jenkins
- §MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GA, UK
| | - Kathleen J Till
- From the ‡Department of Molecular and Clinical Cancer Medicine
| | | | - Ke Lin
- ¶Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool L7 8XP, UK
| | - Gillian G Johnson
- ¶Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool L7 8XP, UK
| | - Melanie Oates
- From the ‡Department of Molecular and Clinical Cancer Medicine
| | - Kevin Park
- §MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GA, UK
| | - Neil R Kitteringham
- §MRC Centre for Drug Safety Science, Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool L69 3GA, UK
| | - Andrew R Pettitt
- From the ‡Department of Molecular and Clinical Cancer Medicine, ¶Royal Liverpool and Broadgreen University Hospitals NHS Trust, Liverpool L7 8XP, UK
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Chi HT, Ly BTK, Vu HA, Sato Y, Dung PC, Xinh PT. Down-regulated expression of NPM1 in IMS-M2 cell line by (-)-epigallocatechin-3-gallate. Asian Pac J Trop Biomed 2014; 4:570-4. [PMID: 25183279 DOI: 10.12980/apjtb.4.2014apjtb-2014-0177] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/23/2014] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVE To investigate the inhibited effect of epigallocatechin-3-gallate (EGCG) on the expression of NPM1 in IMS-M2 cells harboring the NPM1 mutations. METHODS Cell proliferation assay was performed to test the effects of EGCG on cell growth of IMS-M2 cells harboring the NPM1 mutations. Western blot analysis were performed to test the protein expression of NPM1, AKT, those associated with apoptosis. RESULTS EGCG can down-regulate the expression of NPM1 in IMS-M2 cells harboring the NPM1 mutations. Moreover, EGCG also suppressed the cell proliferation and induced apoptosis in IMS-M2 cells. CONCLUSIONS The results suggested that EGCG could be considered as a reagent for treatment of AML patients with NPM1 mutations.
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Affiliation(s)
- Hoang Thanh Chi
- Department of Molecular Cytogenetics, Hematology and Blood Transfusion Hospital in Ho Chi Minh City, Ho Chi Minh, Vietnam
| | - Bui Thi Kim Ly
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Tokyo, Japan
| | - Hoang Anh Vu
- Center for Molecular Biomedicine, The University of Medicine and Pharmacy-Ho Chi Minh City, Ho Chi Minh, Vietnam
| | - Yuko Sato
- Basic nursing science, The Japanese Red Cross College of Nursing Japan, Tokyo, Japan
| | - Phu Chi Dung
- Department of Molecular Cytogenetics, Hematology and Blood Transfusion Hospital in Ho Chi Minh City, Ho Chi Minh, Vietnam
| | - Phan Thi Xinh
- Department of Molecular Cytogenetics, Hematology and Blood Transfusion Hospital in Ho Chi Minh City, Ho Chi Minh, Vietnam ; Center for Molecular Biomedicine, The University of Medicine and Pharmacy-Ho Chi Minh City, Ho Chi Minh, Vietnam
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Mitrea DM, Grace CR, Buljan M, Yun MK, Pytel NJ, Satumba J, Nourse A, Park CG, Madan Babu M, White SW, Kriwacki RW. Structural polymorphism in the N-terminal oligomerization domain of NPM1. Proc Natl Acad Sci U S A 2014; 111:4466-71. [PMID: 24616519 PMCID: PMC3970533 DOI: 10.1073/pnas.1321007111] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleophosmin (NPM1) is a multifunctional phospho-protein with critical roles in ribosome biogenesis, tumor suppression, and nucleolar stress response. Here we show that the N-terminal oligomerization domain of NPM1 (Npm-N) exhibits structural polymorphism by populating conformational states ranging from a highly ordered, folded pentamer to a highly disordered monomer. The monomer-pentamer equilibrium is modulated by posttranslational modification and protein binding. Phosphorylation drives the equilibrium in favor of monomeric forms, and this effect can be reversed by Npm-N binding to its interaction partners. We have identified a short, arginine-rich linear motif in NPM1 binding partners that mediates Npm-N oligomerization. We propose that the diverse functional repertoire associated with NPM1 is controlled through a regulated unfolding mechanism signaled through posttranslational modifications and intermolecular interactions.
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Affiliation(s)
- Diana M. Mitrea
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Christy R. Grace
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Marija Buljan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Nicholas J. Pytel
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - John Satumba
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Amanda Nourse
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - Cheon-Gil Park
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
| | - M. Madan Babu
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; and
| | - Stephen W. White
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
| | - Richard W. Kriwacki
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163
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Abstract
An increasing number of neoplasms are associated with variably specific genetic abnormalities. This is best exemplified by hematological malignancies, in which there is a growing list of entities that are defined by their genetic lesion(s); this is not (yet) the case in mature B-cell lymphomas. However, enhanced insights into the pathogenesis of this large and diverse group of lymphomas have emerged with the ongoing unraveling of a plethora of fascinating genetic abnormalities. The purpose of this review is to synthesize well-recognized data and nascent discoveries in our understanding of the genetic basis of a spectrum of mature B-cell lymphomas, and how this may be applied to contemporary clinical practice. Despite the explosion of new and exciting knowledge in this arena, with the potential for enhanced diagnostic and prognostic strategies, it is essential to remain cognizant of the limitations (and complexity) of genetic investigations, so that assays can be developed and used both judiciously and rationally.
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12
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Boyd RS, Dyer MJ, Cain K. Proteomic analysis of B-cell malignancies. J Proteomics 2010; 73:1804-22. [DOI: 10.1016/j.jprot.2010.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 03/12/2010] [Accepted: 03/17/2010] [Indexed: 12/25/2022]
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The ratio of SRPK1/SRPK1a regulates erythroid differentiation in K562 leukaemic cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:1319-31. [PMID: 20708644 DOI: 10.1016/j.bbamcr.2010.07.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Revised: 07/19/2010] [Accepted: 07/26/2010] [Indexed: 11/22/2022]
Abstract
SRPK1, the prototype of the serine/arginine family of kinases, has been implicated in the regulation of multiple cellular processes such as pre-mRNA splicing, chromatin structure, nuclear import and germ cell development. SRPK1a is a much less studied isoform of SRPK1 that contains an extended N-terminal domain and so far has only been detected in human testis. In the present study we show that SRPK1 is the predominant isoform in K562 cells, with the ratio of the two isoforms being critical in determining cell fate. Stable overexpression of SRPK1a induces erythroid differentiation of K562 cells. The induction of globin synthesis was accompanied by a marked decrease in proliferation and a significantly reduced clonogenic potential. Small interfering RNA-mediated down-regulation of SRPK1 in K562 cells results similarly in a decrease in proliferative capacity and induction of globin synthesis. A decreased SRPK1/SRPK1a ratio is also observed upon hemin/DMSO-induced differentiation of K562 cells as well as in normal human erythroid progenitor cells. Mass spectrometric analysis of SRPK1a-associated proteins identified multiple classes of RNA-binding proteins including RNA helicases, heterogeneous nuclear ribonucleoproteins, ribosomal proteins, and mRNA-associated proteins. Several of the SRPK1a-copurifying proteins have been previously identified in ribosomal and pre-ribosomal complexes, thereby suggesting that SRPK1a may play an important role in linking ribosomal assembly and/or function to erythroid differentiation in human leukaemic cells.
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