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Galigalidou C, Zaragoza-Infante L, Chatzidimitriou A, Stamatopoulos K, Psomopoulos F, Agathangelidis A. Purpose-Built Immunoinformatics for BcR IG/TR Repertoire Data Analysis. Methods Mol Biol 2022; 2453:585-603. [PMID: 35622343 DOI: 10.1007/978-1-0716-2115-8_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The study of antigen receptor gene repertoires using next-generation sequencing (NGS) technologies has disclosed an unprecedented depth of complexity, requiring novel computational and analytical solutions. Several bioinformatics workflows have been developed to this end, including the T-cell receptor/immunoglobulin profiler (TRIP), a web application implemented in R shiny, specifically designed for the purposes of comprehensive repertoire analysis, which is the focus of this chapter. TRIP has the potential to perform robust immunoprofiling analysis through the extraction and processing of the IMGT/HighV-Quest output, via a series of functions, ensuring the analysis of high-quality, biologically relevant data through a multilevel process of data filtering. Subsequently, it provides in-depth analysis of antigen receptor gene rearrangements, including (a) clonality assessment; (b) extraction of variable (V), diversity (D), and joining (J) gene repertoires; (c) CDR3 characterization at both the nucleotide and amino acid level; and (d) somatic hypermutation analysis, in the case of immunoglobulin gene rearrangements. Relevant to mention, TRIP enables a high level of customization through the integration of various options in key aspects of the analysis, such as clonotype definition and computation, hence allowing for flexibility without compromising on accuracy.
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Affiliation(s)
- Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Biology and Genetics (MBG), Democritus University of Thrace, Alexandroupolis, Greece
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,First Department of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden.
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
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2
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Galigalidou C, Zaragoza-Infante L, Iatrou A, Chatzidimitriou A, Stamatopoulos K, Agathangelidis A. Understanding Monoclonal B Cell Lymphocytosis: An Interplay of Genetic and Microenvironmental Factors. Front Oncol 2021; 11:769612. [PMID: 34858849 PMCID: PMC8631769 DOI: 10.3389/fonc.2021.769612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 09/02/2021] [Accepted: 10/26/2021] [Indexed: 11/13/2022] Open
Abstract
The term monoclonal B-cell lymphocytosis (MBL) describes the presence of a clonal B cell population with a count of less than 5 × 109/L and no symptoms or signs of disease. Based on the B cell count, MBL is further classified into 2 distinct subtypes: 'low-count' and 'high-count' MBL. High-count MBL shares a series of biological and clinical features with chronic lymphocytic leukemia (CLL), at least of the indolent type, and evolves to CLL requiring treatment at a rate of 1-2% per year, whereas 'low-count' MBL seems to be distinct, likely representing an immunological rather than a pre-malignant condition. That notwithstanding, both subtypes of MBL can carry 'CLL-specific' genomic aberrations such as cytogenetic abnormalities and gene mutations, yet to a much lesser extent compared to CLL. These findings suggest that such aberrations are mostly relevant for disease progression rather than disease onset, indirectly pointing to microenvironmental drive as a key contributor to the emergence of MBL. Understanding microenvironmental interactions is therefore anticipated to elucidate MBL ontogeny and, most importantly, the relationship between MBL and CLL.
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Affiliation(s)
- Chrysi Galigalidou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Laura Zaragoza-Infante
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Hematology Department, University General Hospital of Thessaloniki AHEPA, Thessaloniki, Greece
| | - Anastasia Iatrou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Agathangelidis
- Institute of Applied Biosciences (INAB), Centre for Research and Technology Hellas (CERTH), Thessaloniki, Greece.,Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
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3
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Agathangelidis A, Galigalidou C, Scarfò L, Moysiadis T, Rovida A, Gounari M, Psomopoulos F, Ranghetti P, Galanis A, Davi F, Stamatopoulos K, Chatzidimitriou A, Ghia P. Infrequent "chronic lymphocytic leukemia-specific" immunoglobulin stereotypes in aged individuals with or without low-count monoclonal B-cell lymphocytosis. Haematologica 2021; 106:1178-1181. [PMID: 32586905 PMCID: PMC8018099 DOI: 10.3324/haematol.2020.247908] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Indexed: 12/12/2022] Open
Affiliation(s)
- Andreas Agathangelidis
- Division of Experimental Oncology, Università Vita-Salute, Ospedale San Raffaele, Milan, Italy
| | - Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Lydia Scarfò
- Division of Experimental Oncology, Università Vita-Salute, Ospedale San Raffaele, Milan, Italy
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Alessandra Rovida
- Division of Experimental Oncology, Università Vita-Salute, Ospedale San Raffaele, Milan, Italy
| | - Maria Gounari
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Pamela Ranghetti
- Division of Experimental Oncology, Università Vita-Salute, Ospedale San Raffaele, Milan, Italy
| | - Alex Galanis
- Dept. of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Frederic Davi
- Biological Hematology, Hopital Pitié-Salpetriere, Sorbonne Université, Paris, France
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Paolo Ghia
- Division of Experimental Oncology, Università Vita-Salute, Ospedale San Raffaele, Milan, Italy
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4
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Agathangelidis A, Galigalidou C, Scarfò L, Moysiadis T, Rovida A, Vlachonikola E, Sofou E, Psomopoulos F, Vardi A, Ranghetti P, Siorenta A, Galanis A, Stamatopoulos K, Chatzidimitriou A, Ghia P. High-throughput analysis of the T cell receptor gene repertoire in low-count monoclonal B cell lymphocytosis reveals a distinct profile from chronic lymphocytic leukemia. Haematologica 2020; 105:e515. [PMID: 33054095 PMCID: PMC7556667 DOI: 10.3324/haematol.2019.221275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Andreas Agathangelidis
- Strategic Research Program on CLL and B-cell neoplasia Unit, Div. of Experimental Oncology, Milan
| | - Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Lydia Scarfò
- Strategic Research Program on CLL and B-cell neoplasia Unit, Div. of Experimental Oncology, Milan
| | - Theodoros Moysiadis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Alessandra Rovida
- Strategic Research Program on CLL and B-cell neoplasia Unit, Div. of Experimental Oncology, Milan
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Electra Sofou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Anna Vardi
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Pamela Ranghetti
- Strategic Research Program on CLL and B-cell neoplasia Unit, Div. of Experimental Oncology, Milan
| | - Alexandra Siorenta
- Immunology and National Tissue Typing Center, General Hospital of Athens 'G. Gennimatas', Athens
| | - Alex Galanis
- Department of Molecular Biology and Genetics (MBG), Democritus University of Thrace, Alexandroupolis
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Paolo Ghia
- Strategic Research Program on CLL and B-cell neoplasia Unit, Div. of Experimental Oncology, Milan
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5
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Kotouza MT, Gemenetzi K, Galigalidou C, Vlachonikola E, Pechlivanis N, Agathangelidis A, Sandaltzopoulos R, Mitkas PA, Stamatopoulos K, Chatzidimitriou A, Psomopoulos FE. TRIP - T cell receptor/immunoglobulin profiler. BMC Bioinformatics 2020; 21:422. [PMID: 32993478 PMCID: PMC7525938 DOI: 10.1186/s12859-020-03669-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 03/03/2020] [Accepted: 07/20/2020] [Indexed: 11/16/2022] Open
Abstract
Background Antigen receptors are characterized by an extreme diversity of specificities, which poses major computational and analytical challenges, particularly in the era of high-throughput immunoprofiling by next generation sequencing (NGS). The T cell Receptor/Immunoglobulin Profiler (TRIP) tool offers the opportunity for an in-depth analysis based on the processing of the output files of the IMGT/HighV-Quest tool, a standard in NGS immunoprofiling, through a number of interoperable modules. These provide detailed information about antigen receptor gene rearrangements, including variable (V), diversity (D) and joining (J) gene usage, CDR3 amino acid and nucleotide composition and clonality of both T cell receptors (TR) and B cell receptor immunoglobulins (BcR IG), and characteristics of the somatic hypermutation within the BcR IG genes. TRIP is a web application implemented in R shiny. Results Two sets of experiments have been performed in order to evaluate the efficiency and performance of the TRIP tool. The first used a number of synthetic datasets, ranging from 250k to 1M sequences, and established the linear response time of the tool (about 6 h for 1M sequences processed through the entire BcR IG data pipeline). The reproducibility of the tool was tested comparing the results produced by the main TRIP workflow with the results from a previous pipeline used on the Galaxy platform. As expected, no significant differences were noted between the two tools; although the preselection process seems to be stricter within the TRIP pipeline, about 0.1% more rearrangements were filtered out, with no impact on the final results. Conclusions TRIP is a software framework that provides analytical services on antigen receptor gene sequence data. It is accurate and contains functions for data wrangling, cleaning, analysis and visualization, enabling the user to build a pipeline tailored to their needs. TRIP is publicly available at https://bio.tools/TRIP_-_T-cell_Receptor_Immunoglobulin_Profiler.
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Affiliation(s)
- Maria Th Kotouza
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Katerina Gemenetzi
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Raphael Sandaltzopoulos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, 68100, Greece
| | - Pericles A Mitkas
- Department of Electrical and Computer Engineering, Aristotle University of Thessaloniki, Thessaloniki, 54124, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece
| | - Fotis E Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, 57001, Greece. .,Dept of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden.
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6
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Vardi A, Vlachonikola E, Papazoglou D, Psomopoulos F, Kotta K, Ioannou N, Galigalidou C, Gemenetzi K, Pasentsis K, Kotouza M, Koravou E, Scarfó L, Iskas M, Stavroyianni N, Ghia P, Anagnostopoulos A, Kouvatsi A, Ramsay AG, Stamatopoulos K, Chatzidimitriou A. T-Cell Dynamics in Chronic Lymphocytic Leukemia under Different Treatment Modalities. Clin Cancer Res 2020; 26:4958-4969. [PMID: 32616500 DOI: 10.1158/1078-0432.ccr-19-3827] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/01/2020] [Accepted: 06/25/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Using next-generation sequencing (NGS), we recently documented T-cell oligoclonality in treatment-naïve chronic lymphocytic leukemia (CLL), with evidence indicating T-cell selection by restricted antigens. EXPERIMENTAL DESIGN Here, we sought to comprehensively assess T-cell repertoire changes during treatment in relation to (i) treatment type [fludarabine-cyclophosphamide-rituximab (FCR) versus ibrutinib (IB) versus rituximab-idelalisib (R-ID)], and (ii) clinical response, by combining NGS immunoprofiling, flow cytometry, and functional bioassays. RESULTS T-cell clonality significantly increased at (i) 3 months in the FCR and R-ID treatment groups, and (ii) over deepening clinical response in the R-ID group, with a similar trend detected in the IB group. Notably, in constrast to FCR that induced T-cell repertoire reconstitution, B-cell receptor signaling inhibitors (BcRi) preserved pretreatment clones. Extensive comparisons both within CLL as well as against T-cell receptor sequence databases showed little similarity with other entities, but instead revealed major clonotypes shared exclusively by patients with CLL, alluding to selection by conserved CLL-associated antigens. We then evaluated the functional effect of treatments on T cells and found that (i) R-ID upregulated the expression of activation markers in effector memory T cells, and (ii) both BcRi improved antitumor T-cell immune synapse formation, in marked contrast to FCR. CONCLUSIONS Taken together, our NGS immunoprofiling data suggest that BcRi retain T-cell clones that may have developed against CLL-associated antigens. Phenotypic and immune synapse bioassays support a concurrent restoration of functionality, mostly evident for R-ID, arguably contributing to clinical response.
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Affiliation(s)
- Anna Vardi
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Elisavet Vlachonikola
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Despoina Papazoglou
- Lymphoma Immunology Group, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kostantia Kotta
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Nikolaos Ioannou
- Lymphoma Immunology Group, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Chrysi Galigalidou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Democritus University of Thrace, Department of Molecular Biology and Genetics, Alexandroupolis, Greece
| | - Katerina Gemenetzi
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Democritus University of Thrace, Department of Molecular Biology and Genetics, Alexandroupolis, Greece
| | | | - Maria Kotouza
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Evdoxia Koravou
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Lydia Scarfó
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | - Michail Iskas
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Paolo Ghia
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Anastasia Kouvatsi
- Faculty of Sciences, Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Alan G Ramsay
- Lymphoma Immunology Group, School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences & Medicine, King's College London, London, United Kingdom
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anastasia Chatzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece. .,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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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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8
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Gemenetzi K, Galigalidou C, Vlachonikola E, Stalika E, Xochelli A, Baliakas P, Karypidou M, Touloumenidou T, Minga E, Douka V, Iskas M, Athanasiadou A, Makris A, Stavroyianni N, Anagnostopoulos A, Hadzidimitriou A, Stamatopoulos K. Tp53 gene p72R polymorphism in chronic lymphocytic leukemia: incidence and clinical significance amongst cases with unmutated immunoglobulin receptors. Leuk Lymphoma 2016; 58:726-728. [PMID: 27686405 DOI: 10.1080/10428194.2016.1211276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Katerina Gemenetzi
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece
| | - Chrysi Galigalidou
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece
| | - Elisavet Vlachonikola
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece
| | - Evangelia Stalika
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece.,b Hematology Department and HCT Unit , G. Papanicolaou Hospital , Thessaloniki , Greece
| | - Aliki Xochelli
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece.,b Hematology Department and HCT Unit , G. Papanicolaou Hospital , Thessaloniki , Greece
| | - Panagiotis Baliakas
- c Department of Immunology, Genetics and Pathology, Science for Life Laboratory , Uppsala University , Uppsala , Sweden
| | - Maria Karypidou
- b Hematology Department and HCT Unit , G. Papanicolaou Hospital , Thessaloniki , Greece
| | - Tasoula Touloumenidou
- b Hematology Department and HCT Unit , G. Papanicolaou Hospital , Thessaloniki , Greece
| | - Evangelia Minga
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece
| | - Vasiliki Douka
- b Hematology Department and HCT Unit , G. Papanicolaou Hospital , Thessaloniki , Greece
| | - Michalis Iskas
- b Hematology Department and HCT Unit , G. Papanicolaou Hospital , Thessaloniki , Greece
| | | | - Antonios Makris
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece
| | - Niki Stavroyianni
- b Hematology Department and HCT Unit , G. Papanicolaou Hospital , Thessaloniki , Greece
| | | | - Anastasia Hadzidimitriou
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece.,c Department of Immunology, Genetics and Pathology, Science for Life Laboratory , Uppsala University , Uppsala , Sweden
| | - Kostas Stamatopoulos
- a Institute of Applied Biosciences, Center of Research and Technology Hellas , Thessaloniki , Greece.,c Department of Immunology, Genetics and Pathology, Science for Life Laboratory , Uppsala University , Uppsala , Sweden
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Ntoufa S, Papakonstantinou N, Apollonio B, Gounari M, Galigalidou C, Fonte E, Anagnostopoulos A, Belessi C, Muzio M, Ghia P, Stamatopoulos K. B Cell Anergy Modulated by TLR1/2 and the miR-17∼92 Cluster Underlies the Indolent Clinical Course of Chronic Lymphocytic Leukemia Stereotyped Subset #4. J Immunol 2016; 196:4410-7. [PMID: 27059597 DOI: 10.4049/jimmunol.1502297] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/15/2016] [Indexed: 01/09/2023]
Abstract
Chronic lymphocytic leukemia (CLL) patients assigned to stereotyped subset #4 (mutated IGHV4-34/IGKV2-30 BCR Ig) display a particularly indolent disease course. Immunogenetic studies of the clonotypic BCR Ig of CLL subset #4 suggested a resemblance with B cells rendered anergic through chronic autoantigenic stimulation. In this article, we provide experimental evidence that subset #4 CLL cells show low IgG levels, constitutive ERK1/2 activation, and fail to either release intracellular Ca(2+) or activate MAPK signaling after BCR cross-linking, thus displaying a signature of B cell anergy at both biochemical and functional levels. Interestingly, TLR1/2 triggering restored BCR functionality, likely breaching the anergic state, and this was accompanied by induction of the miR-17∼92 cluster, whose members target critical BCR-associated molecules, including MAPKs. In conclusion, we demonstrate BCR anergy in CLL subset #4 and implicate TLR signaling and the miR-17∼92 cluster in the regulation of the anergic state. This detailed signaling profiling of subset #4 has implications for advanced understanding of the complex regulation of intracellular signaling pathways in CLL, currently a major therapeutic target of the disease.
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Affiliation(s)
- Stavroula Ntoufa
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki 57001, Greece; Hematology Department and Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki 57010, Greece
| | - Nikos Papakonstantinou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki 57001, Greece; Hematology Department and Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki 57010, Greece
| | - Benedetta Apollonio
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Maria Gounari
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Chrysi Galigalidou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki 57001, Greece
| | - Eleonora Fonte
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Achilles Anagnostopoulos
- Hematology Department and Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki 57010, Greece
| | - Chrysoula Belessi
- Hematology Department, Nikea General Hospital, Pireaus 18454, Greece
| | - Marta Muzio
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Paolo Ghia
- Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Lymphoma Unit, Department of Onco-Hematology, Università Vita-Salute San Raffaele, Milan 20132, Italy; and
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki 57001, Greece; Hematology Department and Hematopoietic Cell Transplantation Unit, George Papanikolaou Hospital, Thessaloniki 57010, Greece; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala 75105, Sweden
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