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Xochelli A, Bikos V, Polychronidou E, Galigalidou C, Agathangelidis A, Charlotte F, Moschonas P, Davis Z, Colombo M, Roumelioti M, Sutton LA, Groenen P, van den Brand M, Boudjoghra M, Algara P, Traverse-Glehen A, Ferrer A, Stalika E, Karypidou M, Kanellis G, Kalpadakis C, Mollejo M, Pangalis G, Vlamos P, Amini RM, Pospisilova S, Gonzalez D, Ponzoni M, Anagnostopoulos A, Giudicelli V, Lefranc MP, Espinet B, Panagiotidis P, Piris MA, Du MQ, Rosenquist R, Papadaki T, Belessi C, Ferrarini M, Oscier D, Tzovaras D, Ghia P, Davi F, Hadzidimitriou A, Stamatopoulos K. Disease-biased and shared characteristics of the immunoglobulin gene repertoires in marginal zone B cell lymphoproliferations. J Pathol 2019; 247:416-421. [PMID: 30484876 DOI: 10.1002/path.5209] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 11/12/2018] [Accepted: 11/21/2018] [Indexed: 01/14/2023]
Abstract
The B cell receptor immunoglobulin (Ig) gene repertoires of marginal zone (MZ) lymphoproliferations were analyzed in order to obtain insight into their ontogenetic relationships. Our cohort included cases with MZ lymphomas (n = 488), i.e. splenic (SMZL), nodal (NMZL) and extranodal (ENMZL), as well as provisional entities (n = 76), according to the WHO classification. The most striking Ig gene repertoire skewing was observed in SMZL. However, restrictions were also identified in all other MZ lymphomas studied, particularly ENMZL, with significantly different Ig gene distributions depending on the primary site of involvement. Cross-entity comparisons of the MZ Ig sequence dataset with a large dataset of Ig sequences (MZ-related or not; n = 65 837) revealed four major clusters of cases sharing homologous ('public') heavy variable complementarity-determining region 3. These clusters included rearrangements from SMZL, ENMZL (gastric, salivary gland, ocular adnexa), chronic lymphocytic leukemia, but also rheumatoid factors and non-malignant splenic MZ cells. In conclusion, different MZ lymphomas display biased immunogenetic signatures indicating distinct antigen exposure histories. The existence of rare public stereotypes raises the intriguing possibility that common, pathogen-triggered, immune-mediated mechanisms may result in diverse B lymphoproliferations due to targeting versatile progenitor B cells and/or operating in particular microenvironments. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Vasilis Bikos
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Eleftheria Polychronidou
- Information Technologies Institute, CERTH, Thessaloniki, Greece
- Department of Informatics, Ionian University, Corfu, Greece
| | | | - Andreas Agathangelidis
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Frédéric Charlotte
- Department of Pathology, Hopital Pitie-Salpetriere and Sorbonne University, Paris, France
| | | | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Monica Colombo
- Molecular Pathology, Ospedale Policlinico SanMartino, Genoa, Italy
| | - Maria Roumelioti
- First Department of Propaedeutic Medicine, University of Athens, Athens, Greece
| | - Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Patricia Groenen
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michiel van den Brand
- Department of Pathology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Myriam Boudjoghra
- Department of Hematology, Hopital Pitie-Salpetriere and Sorbonne University, Paris, France
| | | | | | - Ana Ferrer
- Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | | | - Maria Karypidou
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - George Kanellis
- Hematopathology Department, Evangelismos Hospital, Athens, Greece
| | | | | | | | | | - Rose-Marie Amini
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - David Gonzalez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, UK
| | | | | | - Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics Information System®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UMR CNRS UM, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics Information System®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UMR CNRS UM, Montpellier, France
| | - Blanca Espinet
- Laboratori de Citologia Hematològica i Citogenètica Molecular, Servei de Patologia, Hospital del Mar, Barcelona, Spain
| | | | | | - Ming-Qing Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Manlio Ferrarini
- Direzione Scientifica, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Azienda Ospedaliera Universitaria (AOU) San Martino-IST, Genoa, Italy
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, UK
| | | | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Frederic Davi
- Department of Hematology, Hopital Pitie-Salpetriere and Sorbonne University, Paris, France
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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2
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Panagiotidou E, Kotoulas SC, Kilmpasani M, Pastelli N, Akritidou S, Chatzopoulos E, Bikos V, Bagalas V, Fekete-Passa K, Stanopoulos I, Pataka A. Α 78-year-old female who presents with a non-resolving pneumonia: what is your diagnosis? Breathe (Sheff) 2019; 14:e123-e127. [PMID: 30820252 PMCID: PMC6388653 DOI: 10.1183/20734735.034218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Non-resolving pneumonia with a mass-like radiological appearance raises clinical suspicion of many causes, with malignancy the most prominent. Infectious causes should be investigated thoroughly as they carry a better prognosis. http://ow.ly/QEPL30mLIk4.
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Affiliation(s)
- Evangelia Panagiotidou
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | | | - Maria Kilmpasani
- Laboratory of Pathology, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | - Nikoleta Pastelli
- Laboratory of Pathology, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | - Sofia Akritidou
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | - Evangelos Chatzopoulos
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | - Vasilis Bikos
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | - Vasilios Bagalas
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | - Katalin Fekete-Passa
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece
| | - Ioannis Stanopoulos
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece.,Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athanasia Pataka
- Respiratory Failure Unit, General Hospital of Thessaloniki "G. Papanikolaou", Thessaloniki, Greece.,Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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3
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Lobello C, Bikos V, Janikova A, Pospisilova S. The Role of Oncogenic Tyrosine Kinase NPM-ALK in Genomic Instability. Cancers (Basel) 2018; 10:cancers10030064. [PMID: 29510549 PMCID: PMC5876639 DOI: 10.3390/cancers10030064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 02/20/2018] [Accepted: 02/27/2018] [Indexed: 12/16/2022] Open
Abstract
Genomic stability is crucial for cell life and transmitting genetic material is one of the primary tasks of the cell. The cell needs to be able to recognize any possible error and quickly repair it, and thus, cells have developed several mechanisms to detect DNA damage and promote repair during evolution. The DNA damage response (DDR) and DNA repair pathways ensure the control of possible errors that could impair the duplication of genetic information and introduce variants in the DNA. Endogenous and exogenous factors compromise genomic stability and cause dysregulation in the DDR and DNA repair pathways. Cancer cells often impair these mechanisms to overcome cellular barriers (cellular senescence and/or apoptosis), leading to malignancy. NPM (nucleophosmin)-ALK (anaplastic lymphoma kinase) is an oncogenic tyrosine kinase that is involved in the development of anaplastic large cell lymphoma (ALCL). NPM-ALK is known to be involved in the activation of proliferative and anti-apoptotic signaling pathways. New evidence reveals that NPM-ALK translocation also impairs the ability of cells to maintain the genomic stability through both DDR and DNA repair pathways. This review aims to highlight the role of the oncogenic tyrosine kinase NPM-ALK in the cell, and pointing to new possible therapeutic strategies.
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Affiliation(s)
- Cosimo Lobello
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
| | - Vasilis Bikos
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
| | - Andrea Janikova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, 62500 Brno, Czech Republic.
| | - Sarka Pospisilova
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, 62500 Brno, Czech Republic.
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno, 62500 Brno, Czech Republic.
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4
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Brazdilova K, Plevova K, Skuhrova Francova H, Kockova H, Borsky M, Bikos V, Malcikova J, Oltova A, Kotaskova J, Tichy B, Brychtova Y, Mayer J, Doubek M, Pospisilova S. Multiple productive IGH rearrangements denote oligoclonality even in immunophenotypically monoclonal CLL. Leukemia 2017; 32:234-236. [PMID: 28937682 PMCID: PMC5770588 DOI: 10.1038/leu.2017.274] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- K Brazdilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - K Plevova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - H Skuhrova Francova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - H Kockova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - M Borsky
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - V Bikos
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - J Malcikova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - A Oltova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - J Kotaskova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - B Tichy
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Y Brychtova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - J Mayer
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - M Doubek
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - S Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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5
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Rodríguez-Vicente AE, Bikos V, Hernández-Sánchez M, Malcikova J, Hernández-Rivas JM, Pospisilova S. Next-generation sequencing in chronic lymphocytic leukemia: recent findings and new horizons. Oncotarget 2017; 8:71234-71248. [PMID: 29050359 PMCID: PMC5642634 DOI: 10.18632/oncotarget.19525] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/12/2017] [Indexed: 11/25/2022] Open
Abstract
The rapid progress in next-generation sequencing technologies has significantly contributed to our knowledge of the genetic events associated with the development, progression and treatment resistance of chronic lymphocytic leukemia patients. Together with the discovery of new driver mutations, next-generation sequencing has revealed an immense degree of both intra- and inter-tumor heterogeneity and enabled us to describe marked clonal evolution. Advances in immunogenetics may be implemented to detect minimal residual disease more sensitively and to track clonal B cell populations, their dynamics and molecular characteristics. The interpretation of these aspects is indispensable to thoroughly examine the genetic background of chronic lymphocytic leukemia. We review and discuss the recent results provided by the different next-generation sequencing techniques used in studying the chronic lymphocytic leukemia genome, as well as future perspectives in the methodologies and applications.
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Affiliation(s)
- Ana E Rodríguez-Vicente
- Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, United Kingdom.,IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Vasilis Bikos
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - María Hernández-Sánchez
- IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Hospital Universitario de Salamanca, Salamanca, Spain
| | - Jitka Malcikova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Medical Faculty MU and University Hospital, Brno, Czech Republic
| | - Jesús-María Hernández-Rivas
- IBSAL, IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca, CSIC, Hospital Universitario de Salamanca, Salamanca, Spain.,Hematology Department, Hospital Universitario, Salamanca, Spain.,Department of Medicine, Universidad de Salamanca, Salamanca, Spain
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Medical Faculty MU and University Hospital, Brno, Czech Republic
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6
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Vardi A, Vlachonikola E, Karypidou M, Stalika E, Bikos V, Gemenetzi K, Maramis C, Siorenta A, Anagnostopoulos A, Pospisilova S, Maglaveras N, Chouvarda I, Stamatopoulos K, Hadzidimitriou A. Restrictions in the T-cell repertoire of chronic lymphocytic leukemia: high-throughput immunoprofiling supports selection by shared antigenic elements. Leukemia 2016; 31:1555-1561. [PMID: 27904140 DOI: 10.1038/leu.2016.362] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 10/23/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022]
Abstract
Immunoglobulin (IG) gene repertoire restrictions strongly support antigen selection in the pathogenesis of chronic lymphocytic leukemia (CLL). Given the emerging multifarious interactions between CLL and bystander T cells, we sought to determine whether antigen(s) are also selecting T cells in CLL. We performed a large-scale, next-generation sequencing (NGS) study of the T-cell repertoire, focusing on major stereotyped subsets representing CLL subgroups with undisputed antigenic drive, but also included patients carrying non-subset IG rearrangements to seek for T-cell immunogenetic signatures ubiquitous in CLL. Considering the inherent limitations of NGS, we deployed bioinformatics algorithms for qualitative curation of T-cell receptor rearrangements, and included multiple types of controls. Overall, we document the clonal architecture of the T-cell repertoire in CLL. These T-cell clones persist and further expand overtime, and can be shared by different patients, most especially patients belonging to the same stereotyped subset. Notably, these shared clonotypes appear to be disease-specific, as they are found in neither public databases nor healthy controls. Altogether, these findings indicate that antigen drive likely underlies T-cell expansions in CLL and may be acting in a CLL subset-specific context. Whether these are the same antigens interacting with the malignant clone or tumor-derived antigens remains to be elucidated.
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Affiliation(s)
- A Vardi
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece.,Medical School, University of Crete, Heraklion, Greece
| | - E Vlachonikola
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - M Karypidou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - E Stalika
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - V Bikos
- CEITEC, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - K Gemenetzi
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - C Maramis
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Laboratory of Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - A Siorenta
- Immunology and National Tissue Typing Center, General Hospital of Athens 'G. Gennimatas', Athens, Thessaloniki, Greece
| | - A Anagnostopoulos
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - S Pospisilova
- CEITEC, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - N Maglaveras
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Laboratory of Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - I Chouvarda
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Laboratory of Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - K Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - A Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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7
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Turchaninova MA, Davydov A, Britanova OV, Shugay M, Bikos V, Egorov ES, Kirgizova VI, Merzlyak EM, Staroverov DB, Bolotin DA, Mamedov IZ, Izraelson M, Logacheva MD, Kladova O, Plevova K, Pospisilova S, Chudakov DM. High-quality full-length immunoglobulin profiling with unique molecular barcoding. Nat Protoc 2016; 11:1599-616. [DOI: 10.1038/nprot.2016.093] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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8
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Bikos V, Karypidou M, Stalika E, Baliakas P, Xochelli A, Sutton LA, Papadopoulos G, Agathangelidis A, Papadopoulou E, Davis Z, Algara P, Kanellis G, Traverse-Glehen A, Mollejo M, Anagnostopoulos A, Ponzoni M, Gonzalez D, Pospisilova S, Matutes E, Piris MA, Papadaki T, Ghia P, Rosenquist R, Oscier D, Darzentas N, Tzovaras D, Belessi C, Hadzidimitriou A, Stamatopoulos K. An Immunogenetic Signature of Ongoing Antigen Interactions in Splenic Marginal Zone Lymphoma Expressing IGHV1-2*04 Receptors. Clin Cancer Res 2015; 22:2032-40. [PMID: 26647217 DOI: 10.1158/1078-0432.ccr-15-1170] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 11/19/2015] [Indexed: 11/16/2022]
Abstract
PURPOSE Prompted by the extensive biases in the immunoglobulin (IG) gene repertoire of splenic marginal-zone lymphoma (SMZL), supporting antigen selection in SMZL ontogeny, we sought to investigate whether antigen involvement is also relevant post-transformation. EXPERIMENTAL DESIGN We conducted a large-scale subcloning study of the IG rearrangements of 40 SMZL cases aimed at assessing intraclonal diversification (ID) due to ongoing somatic hypermutation (SHM). RESULTS ID was identified in 17 of 21 (81%) rearrangements using the immunoglobulin heavy variable (IGHV)1-2*04 gene versus 8 of 19 (40%) rearrangements utilizing other IGHV genes (P= 0.001). ID was also evident in most analyzed IG light chain gene rearrangements, albeit was more limited compared with IG heavy chains. Identical sequence changes were shared by subclones from different patients utilizing the IGHV1-2*04 gene, confirming restricted ongoing SHM profiles. Non-IGHV1-2*04 cases displayed both a lower number of ongoing SHMs and a lack of shared mutations (per group of cases utilizing the same IGHV gene). CONCLUSIONS These findings support ongoing antigen involvement in a sizable portion of SMZL and further argue that IGHV1-2*04 SMZL may represent a distinct molecular subtype of the disease.
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Affiliation(s)
- Vasilis Bikos
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece. Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Maria Karypidou
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece. Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | | | - Panagiotis Baliakas
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Andreas Agathangelidis
- Division of Experimental Oncology and Department of Onco-Hematology, Università Vita-Salute San Raffaele and Istituto Scientifico San Raffaele, Milan, Italy
| | | | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Patricia Algara
- Department of Pathology, Hospital Virgen de la Salud, Toledo, Spain
| | - George Kanellis
- Hematopathology Department, Evangelismos Hospital, Athens, Greece
| | | | - Manuela Mollejo
- Department of Pathology, Hospital Virgen de la Salud, Toledo, Spain
| | | | | | - David Gonzalez
- Section of Haemato-Oncology, Institute of Cancer Research, London, United Kingdom
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Estella Matutes
- Section of Haemato-Oncology, Institute of Cancer Research, London, United Kingdom
| | - Miguel Angel Piris
- Hospital Universitario Marques de Valdecilla, Santander, Cantabria, Spain
| | | | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, Università Vita-Salute San Raffaele and Istituto Scientifico San Raffaele, Milan, Italy
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | | | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kostas Stamatopoulos
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece. Institute of Applied Biosciences, CERTH, Thessaloniki, Greece. Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Bystry V, Agathangelidis A, Bikos V, Sutton LA, Baliakas P, Hadzidimitriou A, Stamatopoulos K, Darzentas N. ARResT/AssignSubsets: a novel application for robust subclassification of chronic lymphocytic leukemia based on B cell receptor IG stereotypy. Bioinformatics 2015; 31:3844-6. [PMID: 26249808 DOI: 10.1093/bioinformatics/btv456] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/30/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION An ever-increasing body of evidence supports the importance of B cell receptor immunoglobulin (BcR IG) sequence restriction, alias stereotypy, in chronic lymphocytic leukemia (CLL). This phenomenon accounts for ∼30% of studied cases, one in eight of which belong to major subsets, and extends beyond restricted sequence patterns to shared biologic and clinical characteristics and, generally, outcome. Thus, the robust assignment of new cases to major CLL subsets is a critical, and yet unmet, requirement. RESULTS We introduce a novel application, ARResT/AssignSubsets, which enables the robust assignment of BcR IG sequences from CLL patients to major stereotyped subsets. ARResT/AssignSubsets uniquely combines expert immunogenetic sequence annotation from IMGT/V-QUEST with curation to safeguard quality, statistical modeling of sequence features from more than 7500 CLL patients, and results from multiple perspectives to allow for both objective and subjective assessment. We validated our approach on the learning set, and evaluated its real-world applicability on a new representative dataset comprising 459 sequences from a single institution. AVAILABILITY AND IMPLEMENTATION ARResT/AssignSubsets is freely available on the web at http://bat.infspire.org/arrest/assignsubsets/ CONTACT nikos.darzentas@gmail.com. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Vojtech Bystry
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Andreas Agathangelidis
- Division of Molecular Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute and Università Vita-Salute San Raffaele, Milan, Italy
| | - Vasilis Bikos
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lesley Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden and
| | - Nikos Darzentas
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Abstract
Splenic marginal-zone lymphoma (SMZL) is a rare tumor that has recently emerged as a prototype for how the interplay between genetics and environment shapes the natural history of lymphomas. Indeed, the recent identification of molecular immunogenetic subgroups within SMZL may prove to be relevant not only for the sub-classification of the disease but also for improved understanding of the underlying biology. In contrast to other B-cell lymphomas, SMZL lacks a characteristic genetic lesion, although the majority of cases harbor genomic aberrations, as recently revealed by high-throughput studies that identified recurrent genetic aberrations, several in pathways related to marginal-zone differentiation and B-cell signaling. Here we provide an overview of recent research into the molecular and cellular biology of SMZL and related disorders, with special emphasis on immunogenetics and genomic aberrations, and discuss the value of molecular and cellular markers for the diagnosis and differential diagnosis of these entities.
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Affiliation(s)
- Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life laboratory, Uppsala University , Uppsala , Sweden
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Navarro A, Clot G, Royo C, Jares P, Hadzidimitriou A, Agathangelidis A, Bikos V, Darzentas N, Papadaki T, Salaverria I, Pinyol M, Puig X, Palomero J, Vegliante MC, Amador V, Martinez-Trillos A, Stefancikova L, Wiestner A, Wilson W, Pott C, Calasanz MJ, Trim N, Erber W, Sander B, Ott G, Rosenwald A, Colomer D, Giné E, Siebert R, Lopez-Guillermo A, Stamatopoulos K, Beà S, Campo E. Molecular subsets of mantle cell lymphoma defined by the IGHV mutational status and SOX11 expression have distinct biologic and clinical features. Cancer Res 2012; 72:5307-16. [PMID: 22915760 DOI: 10.1158/0008-5472.can-12-1615] [Citation(s) in RCA: 197] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Mantle cell lymphoma (MCL) is a heterogeneous disease with most patients following an aggressive clinical course, whereas others having an indolent behavior. We conducted an integrative and multidisciplinary analysis of 177 MCL to determine whether the immunogenetic features of the clonotypic B-cell receptors (BcR) may identify different subsets of tumors. Truly unmutated (100% identity) IGHV genes were found in 24% cases, 40% were minimally/borderline mutated (99.9%-97%), 19% significantly mutated (96.9%-95%), and 17% hypermutated (<95%). Tumors with high or low mutational load used different IGHV genes, and their gene expression profiles were also different for several gene pathways. A gene set enrichment analysis showed that MCL with high and low IGHV mutations were enriched in memory and naive B-cell signatures, respectively. Furthermore, the highly mutated tumors had less genomic complexity, were preferentially SOX11-negative, and showed more frequent nonnodal disease. The best cut-off of germline identity of IGHV genes to predict survival was 97%. Patients with high and low mutational load had significant different outcome with 5-year overall survival (OS) of 59% and 40%, respectively (P = 0.004). Nodal presentation and SOX11 expression also predicted for poor OS. In a multivariate analysis, IGHV gene status and SOX11 expression were independent risk factors. In conclusion, these observations suggest the idea that MCL with mutated IGHV, SOX11-negativity, and nonnodal presentation correspond to a subtype of the disease with more indolent behavior.
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Affiliation(s)
- Alba Navarro
- Pathology and Hematology Departments, Hospital Clínic, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Spain
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12
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Bikos V, Stalika E, Baliakas P, Darzentas N, Davis Z, Traverse-Glehen A, Dagklis A, Kanellis G, Anagnostopoulos A, Tsaftaris A, Ponzoni M, Berger F, Felman P, Ghia P, Papadaki T, Oscier D, Belessi C, Stamatopoulos K. Selection of antigen receptors in splenic marginal-zone lymphoma: further support from the analysis of the immunoglobulin light-chain gene repertoire. Leukemia 2012; 26:2567-9. [PMID: 22858907 DOI: 10.1038/leu.2012.207] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Bikos V, Darzentas N, Hadzidimitriou A, Davis Z, Hockley S, Traverse-Glehen A, Algara P, Santoro A, Gonzalez D, Mollejo M, Dagklis A, Gangemi F, Bosler DS, Bourikas G, Anagnostopoulos A, Tsaftaris A, Iannitto E, Ponzoni M, Felman P, Berger F, Belessi C, Ghia P, Papadaki T, Dogan A, Degano M, Matutes E, Piris MA, Oscier D, Stamatopoulos K. Over 30% of patients with splenic marginal zone lymphoma express the same immunoglobulin heavy variable gene: ontogenetic implications. Leukemia 2012; 26:1638-46. [PMID: 22222599 DOI: 10.1038/leu.2012.3] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We performed an immunogenetic analysis of 345 IGHV-IGHD-IGHJ rearrangements from 337 cases with primary splenic small B-cell lymphomas of marginal-zone origin. Three immunoglobulin (IG) heavy variable (IGHV) genes accounted for 45.8% of the cases (IGHV1-2, 24.9%; IGHV4-34, 12.8%; IGHV3-23, 8.1%). Particularly for the IGHV1-2 gene, strong biases were evident regarding utilization of different alleles, with 79/86 rearrangements (92%) using allele (*)04. Among cases more stringently classified as splenic marginal-zone lymphoma (SMZL) thanks to the availability of splenic histopathological specimens, the frequency of IGHV1-2(*)04 peaked at 31%. The IGHV1-2(*)04 rearrangements carried significantly longer complementarity-determining region-3 (CDR3) than all other cases and showed biased IGHD gene usage, leading to CDR3s with common motifs. The great majority of analyzed rearrangements (299/345, 86.7%) carried IGHV genes with some impact of somatic hypermutation, from minimal to pronounced. Noticeably, 75/79 (95%) IGHV1-2(*)04 rearrangements were mutated; however, they mostly (56/75 cases; 74.6%) carried few mutations (97-99.9% germline identity) of conservative nature and restricted distribution. These distinctive features of the IG receptors indicate selection by (super)antigenic element(s) in the pathogenesis of SMZL. Furthermore, they raise the possibility that certain SMZL subtypes could derive from progenitor populations adapted to particular antigenic challenges through selection of VH domain specificities, in particular the IGHV1-2(*)04 allele.
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Affiliation(s)
- V Bikos
- Democritus University of Thrace, Alexandroupolis, Greece
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14
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Kostareli E, Hadzidimitriou A, Stavroyianni N, Darzentas N, Athanasiadou A, Gounari M, Bikos V, Agathagelidis A, Touloumenidou T, Zorbas I, Kouvatsi A, Laoutaris N, Fassas A, Anagnostopoulos A, Belessi C, Stamatopoulos K. Molecular evidence for EBV and CMV persistence in a subset of patients with chronic lymphocytic leukemia expressing stereotyped IGHV4-34 B-cell receptors. Leukemia 2009; 23:919-24. [PMID: 19148139 DOI: 10.1038/leu.2008.379] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The chronic lymphocytic leukemia (CLL) immunoglobulin repertoire is uniquely characterized by the presence of stereotyped B-cell receptors (BCRs). A major BCR stereotype in CLL is shared by immunoglobulin G-switched cases utilizing the immunoglobulin heavy-chain variable 4-34 (IGHV4-34) gene. Increased titers of IGHV4-34 antibodies are detected in selective clinical conditions, including infection by B-cell lymphotropic viruses, particularly Epstein-Barr virus (EBV) and cytomegalovirus (CMV). In this context, we sought evidence for persistent activation by EBV and CMV in CLL cases expressing the IGHV4-34 gene. The study group included 93 CLL cases with an intentional bias for the IGHV4-34 gene. On the basis of real-time PCR results for CMV/EBV DNA, cases were assigned to three groups: (1) double-negative (59/93); (2) single-positive (CMV- or EBV-positive; 25/93); (3) double-positive (9/93). The double-negative group was characterized by heterogeneous IGHV gene repertoire. In contrast, a bias for the IGHV4-34 gene was observed in the single-positive group (9/25 cases; 36%). Remarkably, all nine double-positive cases utilized the IGHV4-34 gene; seven of nine cases expressed the major BCR stereotype as described above. In conclusion, our findings indicate that the interactions of CLL progenitor cells expressing distinctive IGHV4-34 BCRs with viral antigens/superantigens might facilitate clonal expansion and, eventually, leukemic transformation. The exact type, timing and location of these interactions remain to be determined.
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Affiliation(s)
- E Kostareli
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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15
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Smilevska T, Tsakou E, Hadzidimitriou A, Bikos V, Stavroyianni N, Laoutaris N, Fassas A, Alphanagnostopoulos A, Papadaki T, Belessi C, Stamatopoulos K. Immunoglobulin kappa gene repertoire and somatic hypermutation patterns in follicular lymphoma. Blood Cells Mol Dis 2008; 41:215-8. [PMID: 18640859 DOI: 10.1016/j.bcmd.2008.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Accepted: 06/11/2008] [Indexed: 12/30/2022]
Abstract
Immunoglobulin kappa gene usage and somatic mutation patterns were studied in a series of 47 IGKV-J rearrangements amplified in 42 follicular lymphoma (FL) cases. The IGKV1-39/1D-39 gene predominated and was significantly over-represented compared to normal cells, autoreactive cells or other B cell lymphomas. The impact of somatic hypermutation varied significantly; nevertheless, mutation distribution patterns indicated pressure for preservation of the B cell receptor. In conclusion, the present series demonstrates biased usage of IGKV genes in FL and alludes to the important role of immunoglobulin kappa light chains in antigen selection of the clonogenic B cells in FL.
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Affiliation(s)
- Tatjana Smilevska
- Hematology Department and Hematopoietic Cell Transplantation Unit, G. Papanicolaou Hospital, 57010 Asvestohori, Thessaloniki, Greece
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