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Bukhari A, Kalinina O, Knight KL. Death of tonsillar B cells by NETosis. Cell Death Discov 2023; 9:108. [PMID: 36997529 PMCID: PMC10063674 DOI: 10.1038/s41420-023-01402-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023] Open
Abstract
Regulating B cell death is essential for generating antibodies and maintaining immune tolerance. B cells can die by apoptosis, and we report that human tonsil B cells, but not peripheral blood B cells also die by NETosis. This cell death is density-dependent, characterized by the loss of cell and nuclear membrane integrity, release of reactive oxygen species, and chromatin decondensation. Tonsil B cells secrete high levels of TNF, and inhibiting TNF prevented chromatin decondensation. By in situ fluorescence microscopy, B cell NETosis, as identified by the hyper citrullination of Histone-3, was localized to the light zone (LZ) of germinal centers in normal tonsil and overlapped with the B cell marker CD19/IgM. We propose a model in which stimulation of B cells in the LZ induces NETosis, driven in part by TNF. We also provide evidence that NETosis of tonsil B cells may be inhibited by an unidentified factor in tonsil. The results describe a previously unidentified form of B cell death and suggest a new mechanism to maintain B cell homeostasis during immune responses.
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Affiliation(s)
- Ameera Bukhari
- Department of Microbiology and Immunology, Loyola University Chicago, 2160 S. First Ave, Maywood, IL, 60153, USA
| | - Olga Kalinina
- Department of Microbiology and Immunology, Loyola University Chicago, 2160 S. First Ave, Maywood, IL, 60153, USA
| | - Katherine L Knight
- Department of Microbiology and Immunology, Loyola University Chicago, 2160 S. First Ave, Maywood, IL, 60153, USA.
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2
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Beckmann L, Berg V, Dickhut C, Sun C, Merkel O, Bloehdorn J, Robrecht S, Seifert M, da Palma Guerreiro A, Claasen J, Loroch S, Oliverio M, Underbayev C, Vaughn L, Thomalla D, Hülsemann MF, Tausch E, Fischer K, Fink AM, Eichhorst B, Sickmann A, Wendtner CM, Stilgenbauer S, Hallek M, Wiestner A, Zahedi RP, Frenzel LP. MARCKS affects cell motility and response to BTK inhibitors in CLL. Blood 2021; 138:544-556. [PMID: 33735912 PMCID: PMC8377477 DOI: 10.1182/blood.2020009165] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/18/2021] [Accepted: 03/06/2021] [Indexed: 12/26/2022] Open
Abstract
Bruton tyrosine kinase (BTK) inhibitors are highly active drugs for the treatment of chronic lymphocytic leukemia (CLL). To understand the response to BTK inhibitors on a molecular level, we performed (phospho)proteomic analyses under ibrutinib treatment. We identified 3466 proteins and 9184 phosphopeptides (representing 2854 proteins) in CLL cells exhibiting a physiological ratio of phosphorylated serines (pS), threonines (pT), and tyrosines (pY) (pS:pT:pY). Expression of 83 proteins differed between unmutated immunoglobulin heavy-chain variable region (IGHV) CLL (UM-CLL) and mutated IGHV CLL (M-CLL). Strikingly, UM-CLL cells showed higher basal phosphorylation levels than M-CLL samples. Effects of ibrutinib on protein phosphorylation levels were stronger in UM-CLL, especially on phosphorylated tyrosines. The differentially regulated phosphopeptides and proteins clustered in pathways regulating cell migration, motility, cytoskeleton composition, and survival. One protein, myristoylated alanine-rich C-kinase substrate (MARCKS), showed striking differences in expression and phosphorylation level in UM-CLL vs M-CLL. MARCKS sequesters phosphatidylinositol-4,5-bisphosphate, thereby affecting central signaling pathways and clustering of the B-cell receptor (BCR). Genetically induced loss of MARCKS significantly increased AKT signaling and migratory capacity. CD40L stimulation increased expression of MARCKS. BCR stimulation induced phosphorylation of MARCKS, which was reduced by BTK inhibitors. In line with our in vitro findings, low MARCKS expression is associated with significantly higher treatment-induced leukocytosis and more pronounced decrease of nodal disease in patients with CLL treated with acalabrutinib.
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Affiliation(s)
- Laura Beckmann
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Valeska Berg
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Clarissa Dickhut
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Clare Sun
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Olaf Merkel
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | | | - Sandra Robrecht
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Marc Seifert
- Institute of Cell Biology (Cancer Research), Medical Faculty, University of Duisburg-Essen, Essen, Germany
| | - Alexandra da Palma Guerreiro
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Julia Claasen
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Matteo Oliverio
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Chingiz Underbayev
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Lauren Vaughn
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Daniel Thomalla
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Malte F Hülsemann
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Kirsten Fischer
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Anna Maria Fink
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Barbara Eichhorst
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
| | - Clemens M Wendtner
- Department I of Internal Medicine and
- Munich Clinic Schwabing, Academic Teaching Hospital, Ludwig Maximilian University (LMU), Munich, Germany
| | - Stephan Stilgenbauer
- Department of Internal Medicine III, Ulm University, Ulm, Germany
- Department of Internal Medicine I, Saarland University, Homburg, Germany
| | - Michael Hallek
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften (ISAS) eV, Dortmund, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute and
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, QC, Canada; and
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lukas P Frenzel
- Department I of Internal Medicine and
- Center of Integrated Oncology Aachen Bonn Cologne Dusseldorf (ABCD), University Hospital Cologne, Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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3
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Bagacean C, Iuga CA, Bordron A, Tempescul A, Pralea IE, Bernard D, Cornen M, Bergot T, Le Dantec C, Brooks W, Saad H, Ianotto JC, Pers JO, Zdrenghea M, Berthou C, Renaudineau Y. Identification of altered cell signaling pathways using proteomic profiling in stable and progressive chronic lymphocytic leukemia. J Leukoc Biol 2021; 111:313-325. [PMID: 34288092 DOI: 10.1002/jlb.4hi0620-392r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by significant biologic and clinical heterogeneity. This study was designed to explore CLL B-cells' proteomic profile in order to identify biologic processes affected at an early stage and during disease evolution as stable or progressive. Purified B cells from 11 untreated CLL patients were tested at two time points by liquid chromatography-tandem mass spectrometry. Patients included in the study evolved to either progressive (n = 6) or stable disease (n = 5). First, at an early stage of the disease (Binet stage A), based on the relative abundance levels of 389 differentially expressed proteins (DEPs), samples were separated into stable and progressive clusters with the main differentiating factor being the RNA splicing pathway. Next, in order to test how the DEPs affect RNA splicing, a RNA-Seq study was conducted showing 4217 differentially spliced genes between the two clusters. Distinct longitudinal evolutions were observed with predominantly proteomic modifications in the stable CLL group and spliced genes in the progressive CLL group. Splicing events were shown to be six times more frequent in the progressive CLL group. The main aberrant biologic processes controlled by DEPs and spliced genes in the progressive group were cytoskeletal organization, Wnt/β-catenin signaling, and mitochondrial and inositol phosphate metabolism with a downstream impact on CLL B-cell survival and migration. This study suggests that proteomic profiles at the early stage of CLL can discriminate progressive from stable disease and that RNA splicing dysregulation underlies CLL evolution, which opens new perspectives in terms of biomarkers and therapy.
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Affiliation(s)
- Cristina Bagacean
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Department of Hematology, University Hospital of Brest, Brest, France
| | - Cristina Adela Iuga
- Department of Drug Analysis, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine-MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Anne Bordron
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France
| | - Adrian Tempescul
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Department of Hematology, University Hospital of Brest, Brest, France
| | - Ioana-Ecaterina Pralea
- Department of Proteomics and Metabolomics, MedFuture Research Center for Advanced Medicine-MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | - Melanie Cornen
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France
| | | | | | - Wesley Brooks
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Hussam Saad
- Department of Hematology, University Hospital of Brest, Brest, France
| | | | | | - Mihnea Zdrenghea
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Christian Berthou
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Department of Hematology, University Hospital of Brest, Brest, France
| | - Yves Renaudineau
- Univ Brest, INSERM, UMR1227, B Lymphocytes and Autoimmunity, Brest, France.,Laboratory of Immunology and Immunotherapy, University Hospital of Brest, Brest, France
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4
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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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5
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The Protein Landscape of Chronic Lymphocytic Leukemia (CLL). Blood 2021; 138:2514-2525. [PMID: 34189564 DOI: 10.1182/blood.2020009741] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 06/09/2021] [Indexed: 11/20/2022] Open
Abstract
Many functional consequences of mutations on tumor phenotypes in chronic lymphocytic leukemia (CLL) are unknown. This may be in part due to a scarcity of information on the proteome of CLL. We profiled the proteome of 117 CLL patient samples with data-independent acquisition mass spectrometry (DIA-MS) and integrated the results with genomic, transcriptomic, ex vivo drug response and clinical outcome data. We found trisomy 12, IGHV mutational status, mutated SF3B1, trisomy 19, del(17)(p13), del(11)(q22.3), mutated DDX3X, and MED12 to influence protein expression (FDR < 5%). Trisomy 12 and IGHV status were the major determinants of protein expression variation in CLL as shown by principal component analysis (1055 and 542 differentially expressed proteins, FDR=5%). Gene set enrichment analyses of CLL with trisomy 12 implicated BCR/PI3K/AKT signaling as a tumor driver. These findings were supported by analyses of protein abundance buffering and protein complex formation, which identified limited protein abundance buffering and an upregulated protein complex involved in BCR, AKT, MAPK and PI3K signaling in trisomy 12 CLL. A survey of proteins associated with trisomy 12/IGHV-independent drug response linked STAT2 protein expression with response to kinase inhibitors including BTK and MEK inhibitors. STAT2 was upregulated in U-CLL, trisomy 12 CLL and required for chemokine/cytokine signaling (interferon response). This study highlights the importance of protein abundance data as a non-redundant layer of information in tumor biology, and provides a protein expression reference map for CLL.
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Alsagaby SA, Alhumaydhi FA. Proteomics insights into the pathology and prognosis of chronic lymphocytic leukemia. Saudi Med J 2019; 40:317-327. [PMID: 30957124 PMCID: PMC6506661 DOI: 10.15537/smj.2019.4.23598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable malignant disease of B-lymphocytes characterized by drastically heterogeneous clinical courses. Proteomics is an advanced approach that allows a global profiling of protein expression, providing a valuable chance for the discovery of disease-related proteins. In the last 2 decades, several proteomics studies were conducted on CLL to identify aberrant protein expression underpinning the malignant transformation and progression of the disease. Overall, these studies provided insights into the pathology and prognosis of CLL and reveal protein candidates with the potential to serve as biomarkers and/or therapeutic targets of the tumor. The major findings reported in these studies are discussed here.
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MESH Headings
- Biomarkers, Tumor
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/pathology
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Molecular Targeted Therapy
- Prognosis
- Proteomics/trends
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Affiliation(s)
- Suliman A Alsagaby
- Department of Medical Laboratories Sciences, Faculty of Applied Medical Sciences, Majmaah University, Majmaah, Kingdom of Saudi Arabia. E-mail.
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7
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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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8
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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: 44] [Impact Index Per Article: 7.3] [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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9
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Glazyrin YE, Komarova MA, Bakhtina VI, Silacheva MV, Demko IV, Zamay AS, Zamay TN. A comparative protein profiling of lymphocytes from blood of patients with chronic lymphoid leukemia by high-resolution mass-spectrometry in search of new markers for heterogeneity and disease prognosis. JOURNAL OF ANALYTICAL CHEMISTRY 2017. [DOI: 10.1134/s1061934816130062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Thurgood LA, Chataway TK, Lower KM, Kuss BJ. From genome to proteome: Looking beyond DNA and RNA in chronic lymphocytic leukemia. J Proteomics 2017; 155:73-84. [PMID: 28069558 DOI: 10.1016/j.jprot.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/11/2016] [Accepted: 01/03/2017] [Indexed: 02/07/2023]
Abstract
Chronic lymphocytic leukemia (CLL) remains the most common leukemia in the Western world. Whilst its disease course is extremely heterogeneous (ranging from indolent to aggressive), current methods are unable to accurately predict the clinical journey of each patient. There is clearly a pressing need for both improved prognostication and treatment options for patients with this disease. Whilst molecular studies have analyzed both genetic mutations and gene expression profiles of these malignant B-cells, and as a result have shed light on the pathogenesis of CLL, proteomic studies have been largely overlooked to date. This review summarizes our current knowledge of the proteomics of CLL, and discusses some of the issues in CLL proteomic research, such as reproducibility and data interpretation. In addition, we look ahead to how proteomics may significantly help in the development of a successful treatment for this currently incurable disease.
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Affiliation(s)
- Lauren A Thurgood
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia.
| | - Tim K Chataway
- Department of Physiology, Flinders University, Adelaide, South Australia, Australia
| | - Karen M Lower
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
| | - Bryone J Kuss
- Department of Haematology and Genetic Pathology, Flinders University, Adelaide, South Australia, Australia
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11
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Díez P, Góngora R, Orfao A, Fuentes M. Functional proteomic insights in B-cell chronic lymphocytic leukemia. Expert Rev Proteomics 2016; 14:137-146. [DOI: 10.1080/14789450.2017.1275967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Paula Díez
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafael Góngora
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alberto Orfao
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
- Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
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12
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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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13
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Adamopoulos PG, Kontos CK, Papageorgiou SG, Pappa V, Scorilas A. KLKB1 mRNA overexpression: A novel molecular biomarker for the diagnosis of chronic lymphocytic leukemia. Clin Biochem 2015; 48:849-54. [PMID: 25891023 DOI: 10.1016/j.clinbiochem.2015.04.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES Plasma kallikrein, also known as Fletcher factor or kallikrein B1 (KLKB1), is a serine endopeptidase, like its homologs tissue kallikrein and kallikrein-related peptidases (KLKs). Its physiological role is to catalyze the release of kinins and other vasoactive peptides. Several KLKs have been proposed as putative tumor biomarkers with significant diagnostic and/or prognostic value in human malignancies arising from solid tumors; the most prominent example is the worldwide use of KLK3 (prostate-specific antigen, PSA) in prostate cancer diagnostics. The aim of this study was to analyze KLKB1 mRNA expression in B-cell chronic lymphocytic leukemia (CLL) patients and to examine its diagnostic value as a novel molecular biomarker in CLL. DESIGN AND METHODS Total RNA was isolated from peripheral blood mononuclear cells of sixty-nine patients previously diagnosed with CLL and thirty-one healthy blood donors. After cDNA preparation, a sensitive and cost-effective quantitative real-time PCR (qRT-PCR) methodology was developed and applied for KLKB1 mRNA quantification. Last, we carried out a biostatistical analysis to assess the clinical significance of KLKB1 mRNA expression. RESULTS According to our findings, KLKB1 mRNA expression is significantly higher in CLL patients than in healthy blood donors. Furthermore, KLKB1 mRNA levels are negatively correlated with CD38 expression, an established prognostic biomarker in CLL. Most importantly, KLKB1 mRNA expression possesses important diagnostic value, distinguishing very efficiently CLL patients from non-leukemic population. CONCLUSIONS KLKB1 mRNA expression is a putative molecular biomarker in CLL, meriting investigation in large cohorts of CLL patients and non-leukemic controls.
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Affiliation(s)
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, University of Athens, Athens GR-15701, Greece
| | - Sotirios G Papageorgiou
- Second Department of Internal Medicine, Propaedeutic, University of Athens, University General Hospital "Attikon", Athens GR-12462, Greece
| | - Vassiliki Pappa
- Second Department of Internal Medicine, Propaedeutic, University of Athens, University General Hospital "Attikon", Athens GR-12462, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, University of Athens, Athens GR-15701, Greece.
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14
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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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15
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Alsagaby SA, Khanna S, Hart KW, Pratt G, Fegan C, Pepper C, Brewis IA, Brennan P. Proteomics-Based Strategies To Identify Proteins Relevant to Chronic Lymphocytic Leukemia. J Proteome Res 2014; 13:5051-62. [DOI: 10.1021/pr5002803] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Suliman A. Alsagaby
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
- Department
of Medical Laboratory, College of Science, Majmaah University, King Fahd Street, PO Box 1712, Al-Zulfi, Riyadh Region, 11932, Kingdom of Saudi Arabia
| | - Sanjay Khanna
- TIME
Institute, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14
4XN, United Kingdom
| | - Keith W. Hart
- TIME
Institute, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14
4XN, United Kingdom
| | - Guy Pratt
- CRUK
Institute for Cancer Studies, University of Birmingham, Vincent
Drive, Edgbaston, Birmingham, B15 2TT, United Kingdom
| | - Christopher Fegan
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Christopher Pepper
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
| | - Ian A. Brewis
- TIME
Institute, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14
4XN, United Kingdom
| | - Paul Brennan
- Institute of Cancer & Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, United Kingdom
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16
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Kobeissy FH, Gulbakan B, Alawieh A, Karam P, Zhang Z, Guingab-Cagmat JD, Mondello S, Tan W, Anagli J, Wang K. Post-genomics nanotechnology is gaining momentum: nanoproteomics and applications in life sciences. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:111-31. [PMID: 24410486 DOI: 10.1089/omi.2013.0074] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The post-genomics era has brought about new Omics biotechnologies, such as proteomics and metabolomics, as well as their novel applications to personal genomics and the quantified self. These advances are now also catalyzing other and newer post-genomics innovations, leading to convergences between Omics and nanotechnology. In this work, we systematically contextualize and exemplify an emerging strand of post-genomics life sciences, namely, nanoproteomics and its applications in health and integrative biological systems. Nanotechnology has been utilized as a complementary component to revolutionize proteomics through different kinds of nanotechnology applications, including nanoporous structures, functionalized nanoparticles, quantum dots, and polymeric nanostructures. Those applications, though still in their infancy, have led to several highly sensitive diagnostics and new methods of drug delivery and targeted therapy for clinical use. The present article differs from previous analyses of nanoproteomics in that it offers an in-depth and comparative evaluation of the attendant biotechnology portfolio and their applications as seen through the lens of post-genomics life sciences and biomedicine. These include: (1) immunosensors for inflammatory, pathogenic, and autoimmune markers for infectious and autoimmune diseases, (2) amplified immunoassays for detection of cancer biomarkers, and (3) methods for targeted therapy and automatically adjusted drug delivery such as in experimental stroke and brain injury studies. As nanoproteomics becomes available both to the clinician at the bedside and the citizens who are increasingly interested in access to novel post-genomics diagnostics through initiatives such as the quantified self, we anticipate further breakthroughs in personalized and targeted medicine.
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Affiliation(s)
- Firas H Kobeissy
- 1 Center for Neuroproteomics and Biomarkers Research, Department of Psychiatry, McKnight Brain Institute, University of Florida , Gainesville, Florida
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17
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Bonzon-Kulichenko E, Martínez-Martínez S, Trevisan-Herraz M, Navarro P, Redondo JM, Vázquez J. Quantitative in-depth analysis of the dynamic secretome of activated Jurkat T-cells. J Proteomics 2011; 75:561-71. [DOI: 10.1016/j.jprot.2011.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 07/22/2011] [Accepted: 08/24/2011] [Indexed: 10/17/2022]
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18
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A unique proteomic profile on surface IgM ligation in unmutated chronic lymphocytic leukemia. Blood 2011; 118:e1-15. [PMID: 21602524 DOI: 10.1182/blood-2011-02-335125] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a highly variable clinical course with 2 extreme subsets: indolent, ZAP70(-) and mutated immunoglobulin heavy chain gene (M-CLL); and aggressive, ZAP70(+) and unmutated immunoglobulin heavy chain (UM-CLL). Given the long-term suspicion of antigenic stimulation as a primum movens in the disease, the role of the B-cell receptor has been extensively studied in various experimental settings; albeit scarcely in a comparative dynamic proteomic approach. Here we use a quantitative 2-dimensional fluorescence difference gel electrophoresis technology to compare 48 proteomic profiles of the 2 CLL subsets before and after anti-IgM ligation. Differentially expressed proteins were subsequently identified by mass spectrometry. We show that unstimulated M- and UM-CLL cells display distinct proteomic profiles. Furthermore, anti-IgM stimulation induces a specific proteomic response, more pronounced in the more aggressive CLL. Statistical analyses demonstrate several significant protein variations according to stimulation conditions. Finally, we identify an intermediate form of M-CLL cells, with an indolent profile (ZAP70(-)) but sharing aggressive proteomic profiles alike UM-CLL cells. Collectively, this first quantitative and dynamic proteome analysis of CLL further dissects the complex molecular pathway after B-cell receptor stimulation and depicts distinct proteomic profiles, which could lead to novel molecular stratification of the disease.
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19
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Tseng CW, Yang JC, Chen CN, Huang HC, Chuang KN, Lin CC, Lai HS, Lee PH, Chang KJ, Juan HF. Identification of 14-3-3β in human gastric cancer cells and its potency as a diagnostic and prognostic biomarker. Proteomics 2011; 11:2423-39. [PMID: 21598387 DOI: 10.1002/pmic.201000449] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 03/07/2011] [Accepted: 03/08/2011] [Indexed: 02/06/2023]
Abstract
Gastric cancer is the second most common cause of cancer deaths worldwide and due to its poor prognosis, it is important that specific biomarkers are identified to enable its early detection. Through 2-D gel electrophoresis and MALDI-TOF-TOF-based proteomics approaches, we found that 14-3-3β, which was one of the proteins that were differentially expressed by 5-fluorouracil-treated gastric cancer SC-M1 cells, was upregulated in gastric cancer cells. 14-3-3β levels in tissues and serum were further validated in gastric cancer patients and controls. The results showed that 14-3-3β levels were elevated in tumor tissues (n=40) in comparison to normal tissues (n=40; p<0.01), and serum 14-3-3β levels in cancer patients (n=145) were also significantly higher than those in controls (n=63; p<0.0001). Elevated serum 14-3-3β levels highly correlated with the number of lymph node metastases, tumor size and a reduced survival rate. Moreover, overexpression of 14-3-3β enhanced the growth, invasiveness and migratory activities of tumor cells. Twenty-eight proteins involved in anti-apoptosis and tumor progression were also found to be differentially expressed in 14-3-3β-overexpressing gastric cancer cells. Overall, these results highlight the significance of 14-3-3β in gastric cancer cell progression and suggest that it has the potential to be used as a diagnostic and prognostic biomarker in gastric cancer.
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Affiliation(s)
- Chien-Wei Tseng
- Department of Life Science, Institute of Molecular and Cellular Biology, National Taiwan University, Taipei, Taiwan
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20
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Friedrichs B, Siegel S, Reimer R, Barsoum A, Coggin J, Kabelitz D, Heidorn K, Schulte C, Schmitz N, Zeis M. High expression of the immature laminin receptor protein correlates with mutated IGVH status and predicts a favorable prognosis in chronic lymphocytic leukemia. Leuk Res 2010; 35:721-9. [PMID: 21055809 DOI: 10.1016/j.leukres.2010.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 09/22/2010] [Accepted: 10/04/2010] [Indexed: 11/29/2022]
Abstract
The immature laminin receptor (iLR) is a tumor-associated antigen. We analyzed the expression of iLR on malignant B cells of 134 unselected patient samples with CLL and hypothesized that iLR expression would have prognostic significance due to a differential expression pattern. High ILR expression (cut-off value 30%) was correlated with mutated IGVH status (p<0.0001). Patients with high iLR-expression had a significantly longer time to progression (p=0.039). Combination of CD38, ZAP-70, and iLR by flow cytometry can be used to construct a diagnostic score identifying patients with a median progression free survival of 80 months, if no adverse marker is present.
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Affiliation(s)
- Birte Friedrichs
- Asklepios Clinic St. Georg, Department of Hematology & Stem Cell Transplantation, Hamburg, Germany.
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21
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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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22
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Proteomic analysis of lymphoid and haematopoietic neoplasms: There's more than biomarker discovery. J Proteomics 2010; 73:508-20. [DOI: 10.1016/j.jprot.2009.08.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 08/26/2009] [Accepted: 08/27/2009] [Indexed: 12/29/2022]
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23
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Rees-Unwin KS, Faragher R, Unwin RD, Adams J, Brown PJ, Buckle AM, Pettitt A, Hutchinson CV, Johnson SM, Pulford K, Banham AH, Whetton AD, Lucas G, Mason DY, Burthem J. Ribosome-associated nucleophosmin 1: increased expression and shuttling activity distinguishes prognostic subtypes in chronic lymphocytic leukaemia. Br J Haematol 2009; 148:534-43. [PMID: 19961478 DOI: 10.1111/j.1365-2141.2009.07979.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two distinct groups of chronic lymphocytic leukaemia (CLL) are distinguished by the presence or absence of somatic hypermutation of the immunoglobulin heavy-chain gene. CLL without somatic hypermutation has an adverse outcome, but the precise biological differences that underlie this more aggressive clinical-course are unclear. Using a proteomic approach, we found that the two prognostic forms of CLL were consistently distinguished according to their protein expression pattern. The most important difference observed related to the different expression of nucleophosmin 1 between the two forms of CLL. This different expression was not related to apoptosis, proliferation or gene mutation. However, co-immunoprecipitation experiments identified an association between nucleophosmin 1 and ribosomal proteins. Using immunocytofluorescence, nucleophosmin 1 expression was identified in the nucleoli and nucleoplasm of all cells, but in a proportion of cells, nucleophosmin had been transferred from the nucleoplasm to the cytoplasm. Both the fluorescent intensity, and the frequency of cytoplasmic nucleophosmin 1 expression, was higher in CLL without somatic hypermutation. We propose therefore, that nucleophosmin 1, in association with ribosomal proteins, undergoes nucleo-cytoplasmic shuttling in CLL. This process is most prominent in un-mutated CLL and may signify altered protein biosynthesis.
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Affiliation(s)
- Karen S Rees-Unwin
- School of Cancer & Imaging Sciences, Faculty of Medical & Human Sciences, The University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, UK
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24
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Ajjappala BS, Kim YS, Kim MS, Lee MY, Lee KY, Ki HY, Cha DH, Baek KH. 14-3-3 gamma is stimulated by IL-3 and promotes cell proliferation. THE JOURNAL OF IMMUNOLOGY 2009; 182:1050-60. [PMID: 19124748 DOI: 10.4049/jimmunol.182.2.1050] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
IL-3 plays important roles in the growth and survival of hematopoietic progenitor cells, processes modeled in studies of the IL-3-dependent cell line Ba/F3. To gain insights into molecular mechanisms governing cell fate, we examined the patterns of proteins up-regulated following stimulation of Ba/F3 cells with IL-3. Through two-dimensional electrophoresis and proteomics-based approaches, we identified 11 proteins. Of these, expression of 14-3-3gamma was significantly increased by IL-3 stimulation at both the transcriptional and translational levels. 14-3-3gamma overexpression in Ba/F3 cells abrogated dependence on IL-3 and was associated with activation of PI3K and MAPK signaling cascades, suggesting that the functions of 14-3-3gamma in normal hematopoietic progenitors are to promote survival and growth through the activation of distinct signaling pathways. Additionally, the up-regulation of Bax and Bad was seen with the ablation of 14-3-3gamma, resulting in cell death. These results indicate that deregulated expression of 14-3-3gamma may contribute to malignant transformation, possibly providing a new target for therapeutic intervention in hematopoietic neoplasms.
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Affiliation(s)
- Brijesh S Ajjappala
- Graduate School of Life Science and Biotechnology, Cell and Gene Therapy Research Institute, Pochon CHA University, CHA General Hospital, Seoul, Korea
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25
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Barnidge DR, Jelinek DF, Muddiman DC, Kay NE. Quantitative protein expression analysis of CLL B cells from mutated and unmutated IgV(H) subgroups using acid-cleavable isotope-coded affinity tag reagents. J Proteome Res 2005; 4:1310-7. [PMID: 16083281 PMCID: PMC1403294 DOI: 10.1021/pr050028f] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Relative protein expression levels were compared in leukemic B cells from two patients with chronic lymphocytic leukemia (CLL) having either mutated (M-CLL) or unmutated (UM-CLL) immunoglobulin variable heavy chain genes (IgV(H)). Cells were separated into cytosol and membrane protein fractions then labeled with acid-cleavable ICAT reagents (cICAT). Labeled proteins were digested with trypsin then subjected to SCX and affinity chromatography followed by LC-ESI-MS/MS analysis on a linear ion trap mass spectrometer. A total of 9 proteins from the cytosol fraction and 4 from the membrane fraction showed a 3-fold or greater difference between M-CLL and UM-CLL and a subset of these were examined by Western blot where results concurred with cICAT abundance ratios. The abundance of one of the proteins in particular, the mitochondrial membrane protein cytochrome c oxidase subunit COX G was examined in 6 M-CLL and 6 UM-CLL patients using western blot and results showed significantly greater levels (P < 0.001) in M-CLL patients vs UM-CLL patients. These results demonstrate that stable isotope labeling and mass spectrometry can complement 2D gel electrophoresis and gene microarray technologies for identifying putative and perhaps unique prognostic markers in CLL.
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Affiliation(s)
- David R Barnidge
- Mayo Proteomics Research Center, Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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26
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Thadikkaran L, Siegenthaler MA, Crettaz D, Queloz PA, Schneider P, Tissot JD. Recent advances in blood-related proteomics. Proteomics 2005; 5:3019-34. [PMID: 16041673 DOI: 10.1002/pmic.200402053] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Blood is divided in two compartments, namely, plasma and cells. The latter contain red blood cells, leukocytes, and platelets. From a descriptive medical discipline, hematology has evolved towards a pioneering discipline where molecular biology has permitted the development of prognostic and diagnostic indicators for disease. The recent advance in MS and protein separation now allows similar progress in the analysis of proteins. Proteomics offers great promise for the study of proteins in plasma/serum, indeed a number of proteomics databases for plasma/serum have been established. This is a very complex body fluid containing lipids, carbohydrates, amino acids, vitamins, nucleic acids, hormones, and proteins. About 1500 different proteins have recently been identified, and a number of potential new markers of diseases have been characterized. Here, examples of the enormous promise of plasma/serum proteomic analysis for diagnostic/prognostic markers and information on disease mechanism are given. Within the blood are also a large number of different blood cell types that potentially hold similar information. Proteomics of red blood cells, until now, has not improved our knowledge of these cells, in contrast to the major progresses achieved while studying platelets and leukocytes. In the future, proteomics will change several aspects of hematology.
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Affiliation(s)
- Lynne Thadikkaran
- Service régional vaudois de transfusion sanguine, Rue du Bugnon 27, CH-1005 Lausanne, Switzerland
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27
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Barnidge DR, Tschumper RC, Jelinek DF, Muddiman DC, Kay NE. Protein expression profiling of CLL B cells using replicate off-line strong cation exchange chromatography and LC–MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 819:33-9. [PMID: 15797518 DOI: 10.1016/j.jchromb.2005.01.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Accepted: 01/20/2005] [Indexed: 11/17/2022]
Abstract
In this study we use replicate 2D-LC-MS/MS analyses of crude membranes from B cells derived from a patient with chronic lymphocytic leukemia (CLL) to examine the protein expression profile of CLL B cells. Protein identifications made by replicate 2D-LC-MS/MS analysis of tryptic peptides from detergent solubilized B cell membrane proteins, as well as replicate LC-MS/MS analysis of single off-line strong cation exchange chromatography (SCX) fractions, were analyzed. We show that despite the variance in SCX, capillary LC, and the data-dependent selection of precursor ions, an overlap of 64% between proteins identified in replicate runs was achieved for this system.
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Affiliation(s)
- David R Barnidge
- Mayo Proteomics Research Center, Mayo Clinic College of Medicine, 200 1st Street SW, Rochester, MN 55905, USA.
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Chang J, Van Remmen H, Ward WF, Regnier FE, Richardson A, Cornell J. Processing of Data Generated by 2-Dimensional Gel Electrophoresis for Statistical Analysis: Missing Data, Normalization, and Statistics. J Proteome Res 2004; 3:1210-8. [PMID: 15595730 DOI: 10.1021/pr049886m] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several high-throughput statistical methods were evaluated for processing data generated by two-dimensional polyacrylamide gel electrophoresis, including how to handle missing data, normalization, and statistical analysis of data obtained from 2-D gels. Quantile normalization combined with a nonparametric permutation test based on minimizing false discover rates gave the highest yield of proteins that changed with genotype and detected the anticipated 50% decrease in Mn-superoxide dismutase (MnSOD) protein levels in mitochondrial extracts obtained from MnSOD-deficient mice.
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Affiliation(s)
- Jinsook Chang
- Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78284-7762, USA
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Zent CS, Kay NE. Advances in the understanding of biology and prognosis in chronic lymphocytic leukemia. Curr Oncol Rep 2004; 6:348-54. [PMID: 15291975 DOI: 10.1007/s11912-004-0060-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Chronic lymphocytic leukemia (CLL) has a heterogeneous clinical course and outcome. Recent advances in the diagnosis and molecular characterization of CLL permit improved prediction of disease prognosis, which could result in better management. We review the biology and diagnosis of CLL and the role of analysis of immunoglobulin heavy-chain variable region mutation status, molecular cytogenetics (interphase fluorescence in situ hybridization), and the expression of CD38 and ZAP-70 in the evaluation and management of patients with CLL.
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Affiliation(s)
- Clive S Zent
- Division of Hematology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA.
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Abstract
Abstract
The recent sequencing of a number of genomes has raised the level of opportunities for studies on proteins. This area of research has been described with the all-embracing term, proteomics. In proteomics, the use of mass spectrometric techniques enables genomic databases to be used to establish the identity of proteins with relatively little data, compared to the era before genome sequencing. The use of related analytical techniques also offers the opportunity to gain information on regulation, via posttranslational modification, and potential new diagnostic and prognostic indicators. Relative quantification of proteins and peptides in cellular and extracellular material remains a challenge for proteomics and mass spectrometry. This review presents an analysis of the present and future impact of these proteomic technologies with emphasis on relative quantification for hematologic research giving an appraisal of their potential benefits.
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Affiliation(s)
- Ileana M Cristea
- Department of Biomolecular Sciences, University of Manchester Institute of Science and Technology, Manchester, United Kingdom
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Abstract
Understanding haematological malignancies at the protein level is important as the development of targeted treatments must be based on knowledge regarding the molecular pathogenesis of the tumour, inherited genetic variation and the mode of action of drugs. 'Proteomics' describes the analysis of the entire proteome of a cell or tissue and incorporates multiple technologies including Western blotting, two-dimensional gel electrophoresis, mass spectrometry, and ProteinChip-based technology. Although there are a limited number of studies to date in haematology those performed highlight the potential future impact of these technologies in the discovery of novel markers, proteins associated with drug resistance and the identification of tumour biomarkers which may facilitate the development of a rapid diagnostic test easily applicable in the clinical setting. Rapid large-scale analysis of the proteome in normal pathways and disease offers the opportunity of identification of potential diagnostic/prognostic markers and proteins associated with the malignant phenotype. This review discusses the current situation regarding the use of these technologies and the potential opportunities their future use may offer in the field of haematology.
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Affiliation(s)
- K S Rees-Unwin
- Academic Unit of Haematology and Oncology, University of Leeds, Leeds, UK
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