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Liang Y, Chen X, Zhang X, Guo C, Zhang Y. Virus-driven dysregulation of the BCR pathway: a potential mechanism for the high prevalence of HIV related B-cell lymphoma. Ann Hematol 2024:10.1007/s00277-024-05959-7. [PMID: 39196379 DOI: 10.1007/s00277-024-05959-7] [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: 02/23/2024] [Accepted: 08/19/2024] [Indexed: 08/29/2024]
Abstract
In people living with HIV (PLWH), the susceptibility to malignancies is notably augmented, with lymphoma emerging as a predominant malignancy. Even in the antiretroviral therapy (ART) era, aggressive B-cell lymphoma stands out as a paramount concern. Yet, the pathogenesis of HIV related lymphoma (HRL) largely remains an enigma. Recent insights underscore the pivotal role of the dysregulated B cell receptor (BCR) signaling cascade, evidencing its oncogenic potential across a spectrum of lymphomas. Intricate interplays between HIV and BCR structural-functional integrity have been identified in PLWH. In this review, we elucidated the mechanism by which the BCR signaling pathway is involved in HRL, mainly including the following aspects: HIV can reshape BCR structure by modulating of activation-induced cytidine deaminase (AID) and recombination-activating gene (RAG) dynamics; HIV can act as a chronic antigen to activate the BCR signaling pathway, such as upregulating PI3K and MAPK signaling pathway and reducing the expression of CD300a; HIV co-infection with other oncogenic viruses may also influence tumor formation mediated by the BCR signaling pathway. This review aims to elucidate the intricate regulation of the BCR signaling pathway by HIV in B cell lymphoma, providing a novel perspective on the pathogenesis of lymphoma in HIV-affected environments.
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Affiliation(s)
- Ying Liang
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Beijing Institute of Hepatology, Capital Medical University, Beijing, 100069, China
| | - Xue Chen
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Beijing Institute of Hepatology, Capital Medical University, Beijing, 100069, China
| | - Xiuqun Zhang
- Department of Hematology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Caiping Guo
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research Center for Infectious Diseases, Beijing Youan Hospital, Beijing Institute of Hepatology, Capital Medical University, Beijing, 100069, China.
| | - Yulin Zhang
- Department of Respiratory and Critical Care Medicine, Beijing Youan Hospital, Capital Medical University, Beijing100069, China.
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2
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Leeman-Neill RJ, Bhagat G, Basu U. AID in non-Hodgkin B-cell lymphomas: The consequences of on- and off-target activity. Adv Immunol 2024; 161:127-164. [PMID: 38763700 DOI: 10.1016/bs.ai.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Activation induced cytidine deaminase (AID) is a key element of the adaptive immune system, required for immunoglobulin isotype switching and affinity maturation of B-cells as they undergo the germinal center (GC) reaction in peripheral lymphoid tissue. The inherent DNA damaging activity of this enzyme can also have off-target effects in B-cells, producing lymphomagenic chromosomal translocations that are characteristic features of various classes of non-Hodgkin B-cell lymphoma (B-NHL), and generating oncogenic mutations, so-called aberrant somatic hypermutation (aSHM). Additionally, AID has been found to affect gene expression through demethylation as well as altered interactions between gene regulatory elements. These changes have been most thoroughly studied in B-NHL arising from GC B-cells. Here, we describe the most common classes of GC-derived B-NHL and explore the consequences of on- and off-target AID activity in B and plasma cell neoplasms. The relationships between AID expression, including effects of infection and other exposures/agents, mutagenic activity and lymphoma biology are also discussed.
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Affiliation(s)
- Rebecca J Leeman-Neill
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States; Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.
| | - Govind Bhagat
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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Jeusset L, Abdollahi N, Verny T, Armand M, De Septenville A, Davi F, Bernardes JS. ViCloD, an interactive web tool for visualizing B cell repertoires and analyzing intraclonal diversities: application to human B-cell tumors. NAR Genom Bioinform 2023; 5:lqad064. [PMID: 37388820 PMCID: PMC10304752 DOI: 10.1093/nargab/lqad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 05/25/2023] [Accepted: 06/26/2023] [Indexed: 07/01/2023] Open
Abstract
High throughput sequencing of adaptive immune receptor repertoire (AIRR-seq) has provided numerous human immunoglobulin (IG) sequences allowing specific B cell receptor (BCR) studies such as the antigen-driven evolution of antibodies (soluble forms of the membrane-bound IG part of the BCR). AIRR-seq data allows researchers to examine intraclonal differences caused primarily by somatic hypermutations in IG genes and affinity maturation. Exploring this essential adaptive immunity process could help elucidate the generation of antibodies with high affinity or broadly neutralizing activities. Retracing their evolutionary history could also clarify how vaccines or pathogen exposition drive the humoral immune response, and unravel the clonal architecture of B cell tumors. Computational methods are necessary for large-scale analysis of AIRR-seq properties. However, there is no efficient and interactive tool for analyzing intraclonal diversity, permitting users to explore adaptive immune receptor repertoires in biological and clinical applications. Here we present ViCloD, a web server for large-scale visual analysis of repertoire clonality and intraclonal diversity. ViCloD uses preprocessed data in the format defined by the Adaptive Immune Receptor Repertoire (AIRR) Community. Then, it performs clonal grouping and evolutionary analyses, producing a collection of useful plots for clonal lineage inspection. The web server presents diverse functionalities, including repertoire navigation, clonal abundance analysis, and intraclonal evolutionary tree reconstruction. Users can download the analyzed data in different table formats and save the generated plots as images. ViCloD is a simple, versatile, and user-friendly tool that can help researchers and clinicians to analyze B cell intraclonal diversity. Moreover, its pipeline is optimized to process hundreds of thousands of sequences within a few minutes, allowing an efficient investigation of large and complex repertoires.
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Affiliation(s)
- Lucile Jeusset
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | - Nika Abdollahi
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- IMGT, the international ImMunoGeneTics Information System, CNRS, Institute of Human Genetics, Montpellier University, France
| | - Thibaud Verny
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
- Ecole des Mines ParisTech, Paris, France
| | - Marine Armand
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | | | - Frédéric Davi
- Sorbonne Université, AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Paris, France
| | - Juliana Silva Bernardes
- Sorbonne Université, CNRS, UMR 7238, Laboratoire de Biologie Computationnelle et Quantitative, Paris, France
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Zhao Y, Siddiqi I, Wildes TJ, McCracken J, Deak K, Rehder C, Wang E. Chronic Lymphocytic Leukemia With Two B-Cell Populations of Discordant Light Chain Restrictions in Individual Patients. Am J Clin Pathol 2023; 159:337-351. [PMID: 36749322 DOI: 10.1093/ajcp/aqac165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/01/2022] [Indexed: 02/08/2023] Open
Abstract
OBJECTIVES To evaluate clinicopathologic characteristics of biclonal chronic lymphocytic leukemia (CLL). METHODS Retrospectively analyze clinical data and pathologic features. RESULTS Ten cases were identified in which flow cytometry demonstrated an abnormal B-cell population with a CLL-like immunophenotype but showed no definitive light chain restriction. All had cytogenetic abnormalities detected, including seven with two CLL-related abnormalities. Four of these showed features suggestive of clonal evolution, all having del(13q) as a "stem-line" abnormality and three showing del(11q) as a "side-line" abnormality. Five (50%) cases demonstrated deleterious NOTCH1 mutations, in contrast to 11.8% in a control group of monoclonal CLL (P < .05). Of the 10 patients, 5 received treatment, with good/partial response in three cases and therapeutic resistance in one case. The median treatment-free survival was estimated at 68 months. CONCLUSIONS Despite a polytypic pattern of light chain expression, the neoplastic nature of biclonal CLL is suggested by a characteristic CLL phenotype and can be confirmed by cytogenetic and genomic analyses. The two clones with discordant light chain isotypes may share a "stem-line" cytogenetic abnormality, suggesting possible clonal evolution. Biclonal CLL is associated with NOTCH1 mutations, which may occur in a small subclone and gradually evolve in clonal size. Genomic analysis on light chain-sorted and/or chronologically collected samples may provide insight into clonal evolution in CLL.
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Affiliation(s)
- Yue Zhao
- Department of Pathology, The First Hospital and College of Basic Medical Sciences, China Medical University, Shenyang, China.,Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Imran Siddiqi
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tyler J Wildes
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Jenna McCracken
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Kristen Deak
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Catherine Rehder
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Endi Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
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5
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Primary vitreoretinal lymphomas display a remarkably restricted immunoglobulin gene repertoire. Blood Adv 2021; 4:1357-1366. [PMID: 32267931 DOI: 10.1182/bloodadvances.2019000980] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 01/17/2020] [Indexed: 12/17/2022] Open
Abstract
Primary vitreoretinal lymphoma (PVRL) is a high-grade lymphoma affecting the vitreous and/or the retina. The vast majority of cases are histopathologically classified as diffuse large B-cell lymphoma (DLBCL) and considered a subtype of primary central nervous system lymphoma (PCNSL). To obtain more insight into the ontogenetic relationship between PVRL and PCNSL, we adopted an immunogenetic perspective and explored the respective immunoglobulin gene repertoire profiles from 55 PVRL cases and 48 PCNSL cases. In addition, considering that both entities are predominantly related to activated B-cell (ABC) DLBCL, we compared their repertoire with that of publicly available 262 immunoglobulin heavy variable domain gene rearrangement sequences from systemic ABC-type DLBCLs. PVRL displayed a strikingly biased repertoire, with the IGHV4-34 gene being used in 63.6% of cases, which was significantly higher than in PCNSL (34.7%) or in DLBCL (30.2%). Further repertoire bias was evident by (1) restricted associations of IGHV4-34 expressing heavy chains, with κ light chains utilizing the IGKV3-20/IGKJ1 gene pair, including 5 cases with quasi-identical sequences, and (2) the presence of a subset of stereotyped IGHV3-7 rearrangements. All PVRL IGHV sequences were highly mutated, with evidence of antigen selection and ongoing mutations. Finally, half of PVRL and PCNSL cases carried the MYD88 L265P mutation, which was present in all 4 PVRL cases with stereotyped IGHV3-7 rearrangements. In conclusion, the massive bias in the immunoglobulin gene repertoire of PVRL delineates it from PCNSL and points to antigen selection as a major driving force in their development.
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Montesinos-Rongen M, Terrao M, May C, Marcus K, Blümcke I, Hellmich M, Küppers R, Brunn A, Deckert M. The process of somatic hypermutation increases polyreactivity for central nervous system antigens in primary central nervous system lymphoma. Haematologica 2021; 106:708-717. [PMID: 32193251 PMCID: PMC7927892 DOI: 10.3324/haematol.2019.242701] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Indexed: 02/06/2023] Open
Abstract
The immunoglobulin (Ig) heavy and light chain variable gene mutational pattern of the B-cell receptor (BCR) in primary central nervous system lymphoma (PCNSL) cells suggests antigenic selection to drive pathogenesis and confinement to the central nervous system (CNS). This hypothesis is supported by the observation that the tumor B-cell receptor (tBCR) of PCNSL is polyreactive and may be stimulated by CNS proteins. To obtain further insight into the role of the germinal center (GC) reaction on BCR reactivity, we constructed recombinant antibodies (recAb) with Ig heavy and light chain sequences of the corresponding naïve BCR (nBCR) by reverting tBCR somatic mutations in ten PCNSL. Analysis of nBCR-derived recAb reactivity by a protein microarray and immunoprecipitation demonstrated auto- and polyreactivity in all cases. Self- /polyreactivity was not lost during the GC reaction; surprisingly, tBCR significantly increased self-/polyreactivity. In addition to proteins recognized by both the nBCR and tBCR, tBCR gained self-/polyreactivity particularly for proteins expressed in the CNS including proteins of oligodendrocytes/ myelin, the S100 protein family, and splicing factors. Thus, in PCNSL pathogenesis, a faulty GC reaction may increase self-/polyreactivity, hereby facilitating BCR signaling via multiple CNS antigens, and may ultimately foster tumor cell survival in the CNS.
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Affiliation(s)
- Manuel Montesinos-Rongen
- Institute of Neuropathology, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Monica Terrao
- Institute of Neuropathology, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Caroline May
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Katrin Marcus
- Medizinisches Proteom-Center, Ruhr-University Bochum, Bochum, Germany
| | - Ingmar Blümcke
- Department of Neuropathology, University Hospital Erlangen, Erlangen, Germany
| | - Martin Hellmich
- Institute of Medical Statistics and Computational Biology, University Hospital of Cologne, Cologne
| | - Ralf Küppers
- Institute of Cell Biology (Cancer Research), University of Duisburg-Essen, Medical School, Essen
| | - Anna Brunn
- Institute of Neuropathology, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Martina Deckert
- Institute of Neuropathology, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
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7
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Review: Precision medicine and driver mutations: Computational methods, functional assays and conformational principles for interpreting cancer drivers. PLoS Comput Biol 2019; 15:e1006658. [PMID: 30921324 PMCID: PMC6438456 DOI: 10.1371/journal.pcbi.1006658] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
At the root of the so-called precision medicine or precision oncology, which is our focus here, is the hypothesis that cancer treatment would be considerably better if therapies were guided by a tumor’s genomic alterations. This hypothesis has sparked major initiatives focusing on whole-genome and/or exome sequencing, creation of large databases, and developing tools for their statistical analyses—all aspiring to identify actionable alterations, and thus molecular targets, in a patient. At the center of the massive amount of collected sequence data is their interpretations that largely rest on statistical analysis and phenotypic observations. Statistics is vital, because it guides identification of cancer-driving alterations. However, statistics of mutations do not identify a change in protein conformation; therefore, it may not define sufficiently accurate actionable mutations, neglecting those that are rare. Among the many thematic overviews of precision oncology, this review innovates by further comprehensively including precision pharmacology, and within this framework, articulating its protein structural landscape and consequences to cellular signaling pathways. It provides the underlying physicochemical basis, thereby also opening the door to a broader community.
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Wang X, Hao GL, Wang BY, Gao CC, Wang YX, Li LS, Xu JD. Function and dysfunction of plasma cells in intestine. Cell Biosci 2019; 9:26. [PMID: 30911371 PMCID: PMC6417281 DOI: 10.1186/s13578-019-0288-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/01/2019] [Indexed: 12/23/2022] Open
Abstract
As the main player in humoral immunity, antibodies play indispensable roles in the body's immune system. Plasma cells (PCs), as antibody factories, are important contributors to humoral immunity. PCs, recognized by their unique marker CD138, are always discovered in the medullary cords of spleen and lymph nodes and in bone marrow and mucosal lymphoid tissue. This article will review the origin and differentiation of PCs, characteristics of short- and long-lived PCs, and the secretion of antibodies, such as IgA, IgM, and IgG. PCs play a crucial role in the maintenance of intestinal homeostasis using immunomodulation though complex mechanisms. Clearly, PCs play functional roles in maintaining intestinal health, but more details are needed to fully understand all the other effects of intestinal PCs.
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Affiliation(s)
- Xue Wang
- School of Basic Medical Sciences, Xuanwu Hospital, Beijing Capital Medical University, Beijing, 100069 China
| | - Gui-liang Hao
- School of Basic Medical Sciences, Xuanwu Hospital, Beijing Capital Medical University, Beijing, 100069 China
| | - Bo-ya Wang
- Peking University Health Science Center, Beijing, 100081 China
| | - Chen-chen Gao
- Department of Physiology and Pathophysiology, School of Basic Medical Science, Capital Medical University, No. 10, Xitoutiao, Youanmenwai, Fengtai District, Beijing, 100069 China
| | - Yue-xiu Wang
- Department of Teaching Office, International School, Capital Medical University, Beijing, 100069 China
| | - Li-sheng Li
- Function Platform Center, School of Basic Medical Science, Capital Medical University, Beijing, 100069 China
| | - Jing-dong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Science, Capital Medical University, No. 10, Xitoutiao, Youanmenwai, Fengtai District, Beijing, 100069 China
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Agathangelidis A, Psomopoulos F, Stamatopoulos K. Stereotyped B Cell Receptor Immunoglobulins in B Cell Lymphomas. Methods Mol Biol 2019; 1956:139-155. [PMID: 30779034 DOI: 10.1007/978-1-4939-9151-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Comprehensive analysis of the clonotypic B cell receptor immunoglobulin (BcR IG) gene rearrangement sequences in patients with mature B cell neoplasms has led to the identification of significant repertoire restrictions, culminating in the discovery of subsets of patients expressing highly similar, stereotyped BcR IG. This finding strongly supports selection by common epitopes or classes of structurally similar epitopes in the ontogeny of these tumors. BcR IG stereotypy was initially described in chronic lymphocytic leukemia (CLL), where the stereotyped fraction of the disease accounts for a remarkable one-third of patients. However, subsequent studies showed that stereotyped BcR IG are also present in other neoplasms of mature B cells, including mantle cell lymphoma (MCL) and splenic marginal zone lymphoma (SMZL). Subsequent cross-entity comparisons led to the conclusion that stereotyped IG are mostly "disease-specific," implicating distinct immunopathogenetic processes. Interestingly, mounting evidence suggests that a molecular subclassification of lymphomas based on BcR IG stereotypy is biologically and clinically relevant. Indeed, particularly in CLL, patients assigned to the same subset due to expressing a particular stereotyped BcR IG display remarkably consistent biological background and clinical course, at least for major and well-studied subsets. Thus, the robust assignment to stereotyped subsets may assist in the identification of mechanisms underlying disease onset and progression, while also refining risk stratification. In this book chapter, we provide an overview of the recent BcR IG stereotypy studies in mature B cell malignancies and outline previous and current methodological approaches used for the identification of stereotyped IG.
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Affiliation(s)
- Andreas Agathangelidis
- 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
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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10
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Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia. BMC Bioinformatics 2018; 19:414. [PMID: 30453883 PMCID: PMC6245605 DOI: 10.1186/s12859-018-2381-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Although the etiology of chronic lymphocytic leukemia (CLL), the most common type of adult leukemia, is still unclear, strong evidence implicates antigen involvement in disease ontogeny and evolution. Primary and 3D structure analysis has been utilised in order to discover indications of antigenic pressure. The latter has been mostly based on the 3D models of the clonotypic B cell receptor immunoglobulin (BcR IG) amino acid sequences. Therefore, their accuracy is directly dependent on the quality of the model construction algorithms and the specific methods used to compare the ensuing models. Thus far, reliable and robust methods that can group the IG 3D models based on their structural characteristics are missing. Results Here we propose a novel method for clustering a set of proteins based on their 3D structure focusing on 3D structures of BcR IG from a large series of patients with CLL. The method combines techniques from the areas of bioinformatics, 3D object recognition and machine learning. The clustering procedure is based on the extraction of 3D descriptors, encoding various properties of the local and global geometrical structure of the proteins. The descriptors are extracted from aligned pairs of proteins. A combination of individual 3D descriptors is also used as an additional method. The comparison of the automatically generated clusters to manual annotation by experts shows an increased accuracy when using the 3D descriptors compared to plain bioinformatics-based comparison. The accuracy is increased even more when using the combination of 3D descriptors. Conclusions The experimental results verify that the use of 3D descriptors commonly used for 3D object recognition can be effectively applied to distinguishing structural differences of proteins. The proposed approach can be applied to provide hints for the existence of structural groups in a large set of unannotated BcR IG protein files in both CLL and, by logical extension, other contexts where it is relevant to characterize BcR IG structural similarity. The method does not present any limitations in application and can be extended to other types of proteins.
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11
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Rosati E, Baldoni S, De Falco F, Del Papa B, Dorillo E, Rompietti C, Albi E, Falzetti F, Di Ianni M, Sportoletti P. NOTCH1 Aberrations in Chronic Lymphocytic Leukemia. Front Oncol 2018; 8:229. [PMID: 29998084 PMCID: PMC6030253 DOI: 10.3389/fonc.2018.00229] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/05/2018] [Indexed: 01/13/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is an incurable B-cell neoplasm characterized by highly variable clinical outcomes. In recent years, genomic and molecular studies revealed a remarkable heterogeneity in CLL, which mirrored the clinical diversity of this disease. These studies profoundly enhanced our understanding of leukemia cell biology and led to the identification of new biomarkers with potential prognostic and therapeutic significance. Accumulating evidence indicates a key role of deregulated NOTCH1 signaling and NOTCH1 mutations in CLL. This review highlights recent discoveries that improve our understanding of the pathophysiological NOTCH1 signaling in CLL and the clinical impact of NOTCH1 mutations in retrospective and prospective trials. In addition, we discuss the rationale for a therapeutic strategy aiming at inhibiting NOTCH1 signaling in CLL, along with an overview on the currently available NOTCH1-directed approaches.
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Affiliation(s)
- Emanuela Rosati
- Department of Experimental Medicine, Biosciences and Medical Embryology Section, University of Perugia, Perugia, Italy
| | - Stefano Baldoni
- Department of Life, Hematology Section, Health and Environmental Sciences, University of L'Aquila, Perugia, Italy
| | - Filomena De Falco
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Beatrice Del Papa
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Erica Dorillo
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Chiara Rompietti
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Elisa Albi
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Franca Falzetti
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
| | - Mauro Di Ianni
- Department of Medicine and Aging Sciences, University of Chieti Pescara, Chieti, Italy.,Department of Hematology, Transfusion Medicine and Biotechnologies, Ospedale Civile, Pescara, Italy
| | - Paolo Sportoletti
- Institute of Hematology-Centro di Ricerche Emato-Oncologiche (CREO), University of Perugia, Perugia, Italy
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12
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Rosenquist R, Beà S, Du MQ, Nadel B, Pan-Hammarström Q. Genetic landscape and deregulated pathways in B-cell lymphoid malignancies. J Intern Med 2017. [PMID: 28631441 DOI: 10.1111/joim.12633] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With the introduction of next-generation sequencing, the genetic landscape of the complex group of B-cell lymphoid malignancies has rapidly been unravelled in recent years. This has provided important information about recurrent genetic events and identified key pathways deregulated in each lymphoma subtype. In parallel, there has been intense search and development of novel types of targeted therapy that 'hit' central mechanisms in lymphoma pathobiology, such as BTK, PI3K or BCL2 inhibitors. In this review, we will outline the current view of the genetic landscape of selected entities: follicular lymphoma, diffuse large B-cell lymphoma, mantle cell lymphoma, chronic lymphocytic leukaemia and marginal zone lymphoma. We will detail recurrent alterations affecting important signalling pathways, that is the B-cell receptor/NF-κB pathway, NOTCH signalling, JAK-STAT signalling, p53/DNA damage response, apoptosis and cell cycle regulation, as well as other perhaps unexpected cellular processes, such as immune regulation, cell migration, epigenetic regulation and RNA processing. Whilst many of these pathways/processes are commonly altered in different lymphoid tumors, albeit at varying frequencies, others are preferentially targeted in selected B-cell malignancies. Some of these genetic lesions are either involved in disease ontogeny or linked to the evolution of each disease and/or specific clinicobiological features, and some of them have been demonstrated to have prognostic and even predictive impact. Future work is especially needed to understand the therapy-resistant disease, particularly in patients treated with targeted therapy, and to identify novel targets and therapeutic strategies in order to realize true precision medicine in this clinically heterogeneous patient group.
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Affiliation(s)
- R Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - S Beà
- Institut d'Investigacions Biomediques August Pi i Sunyer (IDIBAPS), CIBER de Cáncer, Barcelona, Spain
| | - M-Q Du
- Division of Cellular and Molecular Pathology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - B Nadel
- CNRS, INSERM, CIML, Aix Marseille University, Marseille, France
| | - Q Pan-Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
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13
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Ghia P, Nadel B, Sander B, Stamatopoulos K, Stevenson FK. Early stages in the ontogeny of small B-cell lymphomas: genetics and microenvironment. J Intern Med 2017; 282:395-414. [PMID: 28393412 DOI: 10.1111/joim.12608] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this review, we focus on the mechanisms underlying lymphomagenesis in chronic lymphocytic leukaemia, follicular lymphoma, mantle cell lymphoma and splenic marginal zone lymphoma. The cells of origin of these small B-cell lymphomas are distinct, as are the characteristic chromosomal lesions and clinical courses. One shared feature is retention of expression of surface immunoglobulin. Analysis of this critical receptor reveals the point of differentiation reached by the cell of origin. Additionally, the sequence patterns of the immunoglobulin-variable domains can indicate a role for stimulants of the B-cell receptor before, during and after malignant transformation. The pathways driven via the B-cell receptor are now being targeted by specific kinase inhibitors with exciting clinical effects. To consider routes to pathogenesis, potentially offering earlier intervention, or to identify causative factors, genetic tools are being used to track pretransformation events and the early phases in lymphomagenesis. These methods are revealing that chromosomal changes are only one of the many steps involved, and that the influence of surrounding cells, probably multiple and variable according to tissue location, is required, both to establish tumours and to maintain growth and survival. Similarly, the influence of the tumour microenvironment may protect malignant cells from eradication by treatment, and the resulting minimal residual disease will eventually give rise to relapse. The common and different features of the four lymphomas will be summarized to show how normal B lymphocytes can be subverted to generate tumours, how these tumours evolve and how their weaknesses can be attacked by targeted therapies.
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Affiliation(s)
- P Ghia
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - B Nadel
- Aix-Marseille Université, CNRS, INSERM, CIML, Marseille, France
| | - B Sander
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - K 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
| | - F K Stevenson
- Cancer Research UK Centre, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton, UK
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van den Brand M, Scheijen B, Hess CJ, van Krieken JHJ, Groenen PJTA. Pathways towards indolent B-cell lymphoma - Etiology and therapeutic strategies. Blood Rev 2017; 31:426-435. [PMID: 28802906 DOI: 10.1016/j.blre.2017.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 05/07/2017] [Accepted: 08/04/2017] [Indexed: 02/06/2023]
Abstract
Although patients with indolent B-cell lymphomas have a relatively good survival rate, conventional chemotherapy is not curative. Disease courses are typically characterized by multiple relapses and progressively shorter response duration with subsequent lines of therapy. There has been an explosion of innovative targeted agents in the past years. This review discusses current knowledge on the etiology of indolent B-cell lymphomas with respect to the role of micro-organisms, auto-immune diseases, and deregulated pathways caused by mutations. In particular, knowledge on the mutational landscape of indolent B-cell lymphomas has strongly increased in recent years and harbors great promise for more accurate decision making in the current wide range of therapeutic options. Despite this promise, only in chronic lymphocytic leukemia the detection of TP53 mutations and/or del17p currently have a direct effect on treatment decisions. Nevertheless, it is expected that in the near future the role of genetic testing will increase for prediction of response to targeted treatment as well as for more accurate prediction of prognosis in indolent B-cell lymphomas.
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MESH Headings
- Animals
- DNA Damage
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/microbiology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Lymphoma, B-Cell/etiology
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/microbiology
- Lymphoma, B-Cell/therapy
- Lymphoma, B-Cell, Marginal Zone/etiology
- Lymphoma, B-Cell, Marginal Zone/genetics
- Lymphoma, B-Cell, Marginal Zone/microbiology
- Lymphoma, B-Cell, Marginal Zone/therapy
- Lymphoma, Follicular/etiology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/microbiology
- Lymphoma, Follicular/therapy
- Molecular Targeted Therapy/methods
- Mutation
- Signal Transduction
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Affiliation(s)
- Michiel van den Brand
- Department of Pathology, Radboud university medical center, Geert Grooteplein Zuid 10, 6525GA Nijmegen, The Netherlands; Pathology-DNA, location Rijnstate, Wagnerlaan 55, 6815AD Arnhem, The Netherlands.
| | - Blanca Scheijen
- Department of Pathology, Radboud university medical center, Geert Grooteplein Zuid 10, 6525GA Nijmegen, The Netherlands.
| | - Corine J Hess
- Department of Hematology, Radboud university medical center, Geert Grooteplein Zuid 10, 6525GA Nijmegen, The Netherlands.
| | - J Han Jm van Krieken
- Department of Pathology, Radboud university medical center, Geert Grooteplein Zuid 10, 6525GA Nijmegen, The Netherlands.
| | - Patricia J T A Groenen
- Department of Pathology, Radboud university medical center, Geert Grooteplein Zuid 10, 6525GA Nijmegen, The Netherlands.
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15
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Pham-Ledard A, Prochazkova-Carlotti M, Deveza M, Laforet MP, Beylot-Barry M, Vergier B, Parrens M, Feuillard J, Merlio JP, Gachard N. Molecular analysis of immunoglobulin variable genes supports a germinal center experienced normal counterpart in primary cutaneous diffuse large B-cell lymphoma, leg-type. J Dermatol Sci 2017; 88:238-246. [PMID: 28838616 DOI: 10.1016/j.jdermsci.2017.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 05/09/2017] [Accepted: 07/13/2017] [Indexed: 10/19/2022]
Abstract
BACKGROUND Immunophenotype of primary cutaneous diffuse large B-cell lymphoma, leg-type (PCLBCL-LT) suggests a germinal center-experienced B lymphocyte (BCL2+ MUM1+ BCL6+/-). OBJECTIVES As maturation history of B-cell is "imprinted" during B-cell development on the immunoglobulin gene sequence, we studied the structure and sequence of the variable part of the genes (IGHV, IGLV, IGKV), immunoglobulin surface expression and features of class switching in order to determine the PCLBCL-LT cell of origin. METHODS Clonality analysis with BIOMED2 protocol and VH leader primers was done on DNA extracted from frozen skin biopsies on retrospective samples from 14 patients. The clonal DNA IGHV sequence of the tumor was aligned and compared with the closest germline sequence and homology percentage was calculated. Superantigen binding sites were studied. Features of selection pressure were evaluated with the multinomial Lossos model. RESULTS A functional monoclonal sequence was observed in 14 cases as determined for IGHV (10), IGLV (2) or IGKV (3). IGV mutation rates were high (>5%) in all cases but one (median:15.5%), with superantigen binding sites conservation. Features of selection pressure were identified in 11/12 interpretable cases, more frequently negative (75%) than positive (25%). Intraclonal variation was detected in 3 of 8 tumor specimens with a low rate of mutations. Surface immunoglobulin was an IgM in 12/12 cases. FISH analysis of IGHM locus, deleted during class switching, showed heterozygous IGHM gene deletion in half of cases. The genomic PCR analysis confirmed the deletions within the switch μ region. IGV sequences were highly mutated but functional, with negative features of selection pressure suggesting one or more germinal center passage(s) with somatic hypermutation, but superantigen (SpA) binding sites conservation. Genetic features of class switch were observed, but on the non functional allele and co-existing with primary isotype IgM expression. CONCLUSION These data suggest that cell-of origin is germinal center experienced and superantigen driven selected B-cell, in a stage between germinal center B-cell and plasma cell.
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Affiliation(s)
- Anne Pham-Ledard
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Dermatology Department, CHU Bordeaux,1 avenue Jean Burguet, 33000 Bordeaux, France.
| | - Martina Prochazkova-Carlotti
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Mélanie Deveza
- UMR CNRS 7276, Univ. Limoges,2 avenue Martin Luther King, 87042 Limoges, France
| | | | - Marie Beylot-Barry
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Dermatology Department, CHU Bordeaux,1 avenue Jean Burguet, 33000 Bordeaux, France
| | - Béatrice Vergier
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Pathology Department, CHU Bordeaux,Avenue de Magellan, 33604 Pessac, France
| | - Marie Parrens
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Pathology Department, CHU Bordeaux,Avenue de Magellan, 33604 Pessac, France
| | - Jean Feuillard
- UMR CNRS 7276, Univ. Limoges,2 avenue Martin Luther King, 87042 Limoges, France
| | - Jean-Philippe Merlio
- INSERM U1053, Team 3 Oncogenesis of Cutaneous Lymphomas, Univ. Bordeaux, 146 rue Léo Saignat, 33076 Bordeaux, France; Tumor Bank and Tumor Biology Laboratory,Avenue de Magellan, CHU Bordeaux, 33604 Pessac, France
| | - Nathalie Gachard
- UMR CNRS 7276, Univ. Limoges,2 avenue Martin Luther King, 87042 Limoges, France
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16
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Xochelli A, Baliakas P, Kavakiotis I, Agathangelidis A, Sutton LA, Minga E, Ntoufa S, Tausch E, Yan XJ, Shanafelt T, Plevova K, Boudjogra M, Rossi D, Davis Z, Navarro A, Sandberg Y, Vojdeman FJ, Scarfo L, Stavroyianni N, Sudarikov A, Veronese S, Tzenou T, Karan-Djurasevic T, Catherwood M, Kienle D, Chatzouli M, Facco M, Bahlo J, Pott C, Pedersen LB, Mansouri L, Smedby KE, Chu CC, Giudicelli V, Lefranc MP, Panagiotidis P, Juliusson G, Anagnostopoulos A, Vlahavas I, Antic D, Trentin L, Montillo M, Niemann C, Döhner H, Langerak AW, Pospisilova S, Hallek M, Campo E, Chiorazzi N, Maglaveras N, Oscier D, Gaidano G, Jelinek DF, Stilgenbauer S, Chouvarda I, Darzentas N, Belessi C, Davi F, Hadzidimitriou A, Rosenquist R, Ghia P, Stamatopoulos K. Chronic Lymphocytic Leukemia with Mutated IGHV4-34 Receptors: Shared and Distinct Immunogenetic Features and Clinical Outcomes. Clin Cancer Res 2017; 23:5292-5301. [PMID: 28536306 DOI: 10.1158/1078-0432.ccr-16-3100] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 04/11/2017] [Accepted: 05/18/2017] [Indexed: 11/16/2022]
Abstract
Purpose: We sought to investigate whether B cell receptor immunoglobulin (BcR IG) stereotypy is associated with particular clinicobiological features among chronic lymphocytic leukemia (CLL) patients expressing mutated BcR IG (M-CLL) encoded by the IGHV4-34 gene, and also ascertain whether these associations could refine prognostication.Experimental Design: In a series of 19,907 CLL cases with available immunogenetic information, we identified 339 IGHV4-34-expressing cases assigned to one of the four largest stereotyped M-CLL subsets, namely subsets #4, #16, #29 and #201, and investigated in detail their clinicobiological characteristics and disease outcomes.Results: We identified shared and subset-specific patterns of somatic hypermutation (SHM) among patients assigned to these subsets. The greatest similarity was observed between subsets #4 and #16, both including IgG-switched cases (IgG-CLL). In contrast, the least similarity was detected between subsets #16 and #201, the latter concerning IgM/D-expressing CLL. Significant differences between subsets also involved disease stage at diagnosis and the presence of specific genomic aberrations. IgG subsets #4 and #16 emerged as particularly indolent with a significantly (P < 0.05) longer time-to-first-treatment (TTFT; median TTFT: not yet reached) compared with the IgM/D subsets #29 and #201 (median TTFT: 11 and 12 years, respectively).Conclusions: Our findings support the notion that BcR IG stereotypy further refines prognostication in CLL, superseding the immunogenetic distinction based solely on SHM load. In addition, the observed distinct genetic aberration landscapes and clinical heterogeneity suggest that not all M-CLL cases are equal, prompting further research into the underlying biological background with the ultimate aim of tailored patient management. Clin Cancer Res; 23(17); 5292-301. ©2017 AACR.
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Affiliation(s)
- Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ioannis Kavakiotis
- Department of informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Agathangelidis
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eva Minga
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | | | - Eugen Tausch
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Xiao-Jie Yan
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York
| | - Tait Shanafelt
- Department of Hematology, Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Myriam Boudjogra
- Department of Hematology, Hopital Pitie-Salpetriere and University Pierre et Marie Curie, Paris, France
| | - Davide Rossi
- Division of Haematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Alba Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Yorick Sandberg
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | | | - Lydia Scarfo
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | | | - Silvio Veronese
- Molecular Pathology Unit and Haematology Department, Niguarda Cancer Center, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Tatiana Tzenou
- First Department of Propaedeutic Medicine, University of Athens, Athens, Greece
| | - Teodora Karan-Djurasevic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Mark Catherwood
- Department of Haemato-Oncology, Belfast City Hospital, Belfast, United Kingdom
| | - Dirk Kienle
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Maria Chatzouli
- Hematology Department, Nikea General Hospital, Piraeus, Greece
| | - Monica Facco
- Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padova, Italy
| | - Jasmin Bahlo
- Department I of Internal Medicine and Center of Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | - Christiane Pott
- Second Medical Department, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Karin E Smedby
- Department of Medicine Solna, Clinical Epidemiology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Charles C Chu
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York
| | - Véronique Giudicelli
- IMGT®, the international ImMunoGeneTics information system®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier, France
| | - Marie-Paule Lefranc
- IMGT®, the international ImMunoGeneTics information system®, Université de Montpellier, LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier, France
| | | | - Gunnar Juliusson
- Lund University and Hospital Department of Hematology, Lund Stem Cell Center, Lund, Sweden
| | | | - Ioannis Vlahavas
- Department of informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Darko Antic
- Clinic for Hematology, Clinical Center, Belgrade, Serbia.,Medical faculty, University of Belgrade, Belgrade, Serbia
| | - Livio Trentin
- Department of Medicine, Hematology and Clinical Immunology Branch, Padua University School of Medicine, Padova, Italy
| | - Marco Montillo
- Molecular Pathology Unit and Haematology Department, Niguarda Cancer Center, Niguarda Ca' Granda Hospital, Milan, Italy
| | - Carsten Niemann
- Department of Hematology, Rigshospitalet, Copenhagen, Denmark
| | - Hartmut Döhner
- Department of Internal Medicine III, Ulm University, Ulm, Germany
| | - Anton W Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Hallek
- Department I of Internal Medicine and Center of Integrated Oncology, University Hospital Cologne, Cologne, Germany
| | - Elias Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Nicholas Chiorazzi
- Feinstein Institute for Medical Research, Northwell Health, Manhasset, New York
| | - Nikos Maglaveras
- Laboratory of Medical Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth, United Kingdom
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - Diane F Jelinek
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, United States
| | | | - Ioanna Chouvarda
- Laboratory of Medical Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- Department of Hematology, Hopital Pitie-Salpetriere and University Pierre et Marie Curie, Paris, France
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece. .,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Paolo Ghia
- Division of Experimental Oncology and Department of Onco-Hematology, IRCCS San Raffaele Scientific Institute, Milan, Italy.,Università Vita-Salute San Raffaele and IRCCS Istituto Scientifico San Raffaele, Milan, Italy
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
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17
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Yuan C, Chu CC, Yan XJ, Bagnara D, Chiorazzi N, MacCarthy T. The Number of Overlapping AID Hotspots in Germline IGHV Genes Is Inversely Correlated with Mutation Frequency in Chronic Lymphocytic Leukemia. PLoS One 2017; 12:e0167602. [PMID: 28125682 PMCID: PMC5268644 DOI: 10.1371/journal.pone.0167602] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/16/2016] [Indexed: 02/07/2023] Open
Abstract
The targeting of mutations by Activation-Induced Deaminase (AID) is a key step in generating antibody diversity at the Immunoglobulin (Ig) loci but is also implicated in B-cell malignancies such as chronic lymphocytic leukemia (CLL). AID has previously been shown to preferentially deaminate WRC (W = A/T, R = A/G) hotspots. WGCW sites, which contain an overlapping WRC hotspot on both DNA strands, mutate at much higher frequency than single hotspots. Human Ig heavy chain (IGHV) genes differ in terms of WGCW numbers, ranging from 4 for IGHV3-48*03 to as many as 12 in IGHV1-69*01. An absence of V-region mutations in CLL patients ("IGHV unmutated", or U-CLL) is associated with a poorer prognosis compared to "IGHV mutated" (M-CLL) patients. The reasons for this difference are still unclear, but it has been noted that particular IGHV genes associate with U-CLL vs M-CLL. For example, patients with IGHV1-69 clones tend to be U-CLL with a poor prognosis, whereas patients with IGHV3-30 tend to be M-CLL and have a better prognosis. Another distinctive feature of CLL is that ~30% of (mostly poor prognosis) patients can be classified into "stereotyped" subsets, each defined by HCDR3 similarity, suggesting selection, possibly for a self-antigen. We analyzed >1000 IGHV genes from CLL patients and found a highly significant statistical relationship between the number of WGCW hotspots in the germline V-region and the observed mutation frequency in patients. However, paradoxically, this correlation was inverse, with V-regions with more WGCW hotspots being less likely to be mutated, i.e., more likely to be U-CLL. The number of WGCW hotspots in particular, are more strongly correlated with mutation frequency than either non-overlapping (WRC) hotspots or more general models of mutability derived from somatic hypermutation data. Furthermore, this correlation is not observed in sequences from the B cell repertoires of normal individuals and those with autoimmune diseases.
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Affiliation(s)
- Chaohui Yuan
- Department of Applied Mathematics and Statistics, Stony Brook University, NY, United States of America
| | - Charles C Chu
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America.,Departments of Medicine and Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY, United States of America
| | - Xiao-Jie Yan
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America
| | - Davide Bagnara
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America
| | - Nicholas Chiorazzi
- The Feinstein Institute for Medical Research, Northwell Health, Manhasset, NY, United States of America.,Departments of Medicine and Molecular Medicine, Hofstra Northwell School of Medicine, Hempstead, NY, United States of America
| | - Thomas MacCarthy
- Department of Applied Mathematics and Statistics, Stony Brook University, NY, United States of America
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18
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Antigen receptor stereotypy in chronic lymphocytic leukemia. Leukemia 2016; 31:282-291. [PMID: 27811850 DOI: 10.1038/leu.2016.322] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/30/2016] [Accepted: 10/10/2016] [Indexed: 02/06/2023]
Abstract
The discovery of almost identical or 'stereotyped' B-cell receptor immunoglobulins (BcR IG) among unrelated patients with chronic lymphocytic leukemia (CLL) cemented the idea of antigen selection in disease ontogeny and evolution. The systematic analysis of the stereotypy phenomenon in CLL revealed that around one-third of CLL patients may be grouped into subsets based on shared sequence motifs within the variable heavy complementarity determining region 3. Stereotyped subsets display a strikingly similar biology of the leukemic clones, referring to many different levels, from the immunogenetic and genetic and extending to the epigenetic and functional levels. Even more importantly, the homogeneity of stereotyped subsets has clinical consequences as patients assigned to the same stereotyped subset generally exhibit an overall similar disease course and outcome. In other words, stereotypy-based patient classification of CLL has already provided a more compartmentalized view of this otherwise heterogeneous disease and can assist in refining prognostication models. While this is relevant only for the one-third of cases expressing stereotyped BcR IG; in principle, however, the findings from further analysis of the stereotyped subsets may also contribute towards improved understanding of the remaining non-stereotyped fraction of CLL patients.
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19
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Seifert M, Küppers R. Human memory B cells. Leukemia 2016; 30:2283-2292. [DOI: 10.1038/leu.2016.226] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 06/29/2016] [Accepted: 07/26/2016] [Indexed: 12/20/2022]
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20
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Mansouri L, Papakonstantinou N, Ntoufa S, Stamatopoulos K, Rosenquist R. NF-κB activation in chronic lymphocytic leukemia: A point of convergence of external triggers and intrinsic lesions. Semin Cancer Biol 2016; 39:40-8. [PMID: 27491692 DOI: 10.1016/j.semcancer.2016.07.005] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 07/30/2016] [Indexed: 02/08/2023]
Abstract
The nuclear factor-κB (NF-κB) pathway is constitutively activated in chronic lymphocytic leukemia (CLL) patients, and hence plays a major role in disease development and evolution. In contrast to many other mature B-cell lymphomas, only a few recurrently mutated genes involved in canonical or non-canonical NF-κB activation have been identified in CLL (i.e. BIRC3, MYD88 and NFKBIE mutations) and often at a low frequency. On the other hand, CLL B cells seem 'addicted' to the tumor microenvironment for their survival and proliferation, which is primarily mediated by interaction through a number of cell surface receptors, e.g. the B-cell receptor (BcR), Toll-like receptors and CD40, that in turn activate downstream NF-κB. The importance of cell-extrinsic triggering for CLL pathophysiology was recently also highlighted by the clinical efficacy of novel drugs targeting microenvironmental interactions through the inhibition of BcR signaling. In other words, CLL can be considered a prototype disease for studying the intricate interplay between external triggers and intrinsic aberrations and their combined impact on disease evolution. In this review, we will discuss the current understanding of mechanisms underlying NF-κB deregulation in CLL, including micro-environmental, genetic and epigenetic events, and summarize data generated in murine models resembling human CLL. Finally, we will also discuss different strategies undertaken to intervene with the NF-κB pathway and its upstream mediators.
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Affiliation(s)
- Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Nikos Papakonstantinou
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Stavroula Ntoufa
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Kavakiotis I, Xochelli A, Agathangelidis A, Tsoumakas G, Maglaveras N, Stamatopoulos K, Hadzidimitriou A, Vlahavas I, Chouvarda I. Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia. BMC Bioinformatics 2016; 17 Suppl 5:173. [PMID: 27295298 PMCID: PMC4905615 DOI: 10.1186/s12859-016-1044-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023] Open
Abstract
BACKGROUND Somatic Hypermutation (SHM) refers to the introduction of mutations within rearranged V(D)J genes, a process that increases the diversity of Immunoglobulins (IGs). The analysis of SHM has offered critical insight into the physiology and pathology of B cells, leading to strong prognostication markers for clinical outcome in chronic lymphocytic leukaemia (CLL), the most frequent adult B-cell malignancy. In this paper we present a methodology for integrating multiple immunogenetic and clinocobiological data sources in order to extract features and create high quality datasets for SHM analysis in IG receptors of CLL patients. This dataset is used as the basis for a higher level integration procedure, inspired form social choice theory. This is applied in the Towards Analysis, our attempt to investigate the potential ontogenetic transformation of genes belonging to specific stereotyped CLL subsets towards other genes or gene families, through SHM. RESULTS The data integration process, followed by feature extraction, resulted in the generation of a dataset containing information about mutations occurring through SHM. The Towards analysis performed on the integrated dataset applying voting techniques, revealed the distinct behaviour of subset #201 compared to other subsets, as regards SHM related movements among gene clans, both in allele-conserved and non-conserved gene areas. With respect to movement between genes, a high percentage movement towards pseudo genes was found in all CLL subsets. CONCLUSIONS This data integration and feature extraction process can set the basis for exploratory analysis or a fully automated computational data mining approach on many as yet unanswered, clinically relevant biological questions.
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Affiliation(s)
- Ioannis Kavakiotis
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Andreas Agathangelidis
- Division of Molecular Oncology and Department of Onco-Hematology, San Raffaele Scientific Institute, Milan, Italy
| | - Grigorios Tsoumakas
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Nicos Maglaveras
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Lab of Computing and Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ioannis Vlahavas
- Department of Informatics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioanna Chouvarda
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece.,Lab of Computing and Medical Informatics, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
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22
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Amato T, Abate F, Piccaluga P, Iacono M, Fallerini C, Renieri A, De Falco G, Ambrosio MR, Mourmouras V, Ogwang M, Calbi V, Rabadan R, Hummel M, Pileri S, Leoncini L, Bellan C. Clonality Analysis of Immunoglobulin Gene Rearrangement by Next-Generation Sequencing in Endemic Burkitt Lymphoma Suggests Antigen Drive Activation of BCR as Opposed to Sporadic Burkitt Lymphoma. Am J Clin Pathol 2016; 145:116-27. [PMID: 26712879 PMCID: PMC4778259 DOI: 10.1093/ajcp/aqv011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Objectives: Recent studies using next-generation sequencing (NGS) analysis disclosed the importance of the intrinsic activation of the B-cell receptor (BCR) pathway in the pathogenesis of sporadic Burkitt lymphoma (sBL) due to mutations of TCF3/ID3 genes. Since no definitive data are available on the genetic landscape of endemic Burkitt (eBL), we first assessed the mutation frequency of TCF3/ID3 in eBL compared with sBL and subsequently the somatic hypermutation status of the BCR to answer whether an extrinsic activation of BCR signaling could also be demonstrated in Burkitt lymphoma. Methods: We assessed the mutations of TCF3/ID3 by RNAseq and the BCR status by NGS analysis of the immunoglobulin genes (IGs). Results: We detected mutations of TCF3/ID3 in about 30% of the eBL cases. This rate is significantly lower than that detected in sBL (64%). The NGS analysis of IGs revealed intraclonal diversity, suggesting an active targeted somatic hypermutation process in eBL compared with sBL. Conclusions: These findings support the view that the antigenic pressure plays a key role in the pathogenetic pathways of eBL, which may be partially distinct from those driving sBL development.
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Affiliation(s)
- Teresa Amato
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Abate
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY
| | - Pierpaolo Piccaluga
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine (DIMES), S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Michele Iacono
- Roche Tissue Diagnostic & Sequencing, Roche Diagnostic S.P.A. Monza (MB), Italy
| | - Chiara Fallerini
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Alessandra Renieri
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Giulia De Falco
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Vaselious Mourmouras
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | | | - Roul Rabadan
- Department of Biomedical Informatics, Columbia University College of Physicians and Surgeons, New York, NY
| | - Michael Hummel
- Institut Fur Pathologie, Campus Benjamin Franklin, Charitè, Universitatsmedizin, Berlin, Germany
| | - Stefano Pileri
- Hematopathology Section, Department of Experimental, Diagnostic, and Experimental Medicine (DIMES), S. Orsola-Malpighi Hospital, Bologna University School of Medicine, Bologna, Italy
| | - Lorenzo Leoncini
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Cristiana Bellan
- From the Department of Medical Biotechnologies, University of Siena, Siena, Italy
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23
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Sutton LA, Rosenquist R. Deciphering the molecular landscape in chronic lymphocytic leukemia: time frame of disease evolution. Haematologica 2015; 100:7-16. [PMID: 25552678 DOI: 10.3324/haematol.2014.115923] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Dramatic advances in next generation sequencing technologies have provided a novel opportunity to understand the molecular genetics of chronic lymphocytic leukemia through the comprehensive detection of genetic lesions. While progress is being made in elucidating the clinical significance of recurrently mutated genes, layers of complexity have been added to our understanding of chronic lymphocytic leukemia pathogenesis in the guise of the molecular evolution and (sub)clonal architecture of the disease. As we prepare for an era of tailored therapy, we need to appreciate not only the effect mutations have on drug response but also the impact subclones containing specific mutations have at initial presentation, during therapy and upon relapse. Therefore, although the wealth of emerging genetic data has great potential in helping us devise strategies to improve the therapy and prognosis of patients, focused efforts will be required to follow disease evolution, particularly in the context of novel therapies, in order to translate this knowledge into clinical settings.
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Affiliation(s)
- Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
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24
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Sutton LA, Rosenquist R. The complex interplay between cell-intrinsic and cell-extrinsic factors driving the evolution of chronic lymphocytic leukemia. Semin Cancer Biol 2015; 34:22-35. [DOI: 10.1016/j.semcancer.2015.04.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 01/08/2023]
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25
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Rosenquist R. A new piece to the stereotypy "puzzle" in chronic lymphocytic leukemia. Leuk Lymphoma 2015; 56:3008-9. [PMID: 26133940 DOI: 10.3109/10428194.2015.1068312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Richard Rosenquist
- a Department of Immunology , Genetics and Pathology, Science for Life Laboratory, Uppsala University , Uppsala , Sweden
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26
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Montesinos-Rongen M, Purschke FG, Brunn A, May C, Nordhoff E, Marcus K, Deckert M. Primary Central Nervous System (CNS) Lymphoma B Cell Receptors Recognize CNS Proteins. THE JOURNAL OF IMMUNOLOGY 2015; 195:1312-9. [PMID: 26116512 DOI: 10.4049/jimmunol.1402341] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 05/27/2015] [Indexed: 01/09/2023]
Abstract
Primary lymphoma of the CNS (PCNSL) is a diffuse large B cell lymphoma confined to the CNS. To elucidate its peculiar organ tropism, we generated recombinant Abs (recAbs) identical to the BCR of 23 PCNSLs from immunocompetent patients. Although none of the recAbs showed self-reactivity upon testing with common autoantigens, they recognized 1547 proteins present on a large-scale protein microarray, indicating polyreactivity. Interestingly, proteins (GRINL1A, centaurin-α, BAIAP2) recognized by the recAbs are physiologically expressed by CNS neurons. Furthermore, 87% (20/23) of the recAbs, including all Abs derived from IGHV4-34 using PCNSL, recognized galectin-3, which was upregulated on microglia/macrophages, astrocytes, and cerebral endothelial cells upon CNS invasion by PCNSL. Thus, PCNSL Ig may recognize CNS proteins as self-Ags. Their interaction may contribute to BCR signaling with sustained NF-κB activation and, ultimately, may foster tumor cell proliferation and survival. These data may also explain, at least in part, the affinity of PCNSL cells for the CNS.
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Affiliation(s)
| | - Frauke G Purschke
- Institute of Neuropathology, University Hospital of Cologne, D-50925 Cologne, Germany; and
| | - Anna Brunn
- Institute of Neuropathology, University Hospital of Cologne, D-50925 Cologne, Germany; and
| | - Caroline May
- Medical Proteome-Center, Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Eckhard Nordhoff
- Medical Proteome-Center, Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Katrin Marcus
- Medical Proteome-Center, Ruhr-University Bochum, D-44801 Bochum, Germany
| | - Martina Deckert
- Institute of Neuropathology, University Hospital of Cologne, D-50925 Cologne, Germany; and
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27
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Xochelli A, Sutton LA, Agathangelidis A, Stalika E, Karypidou M, Marantidou F, Lopez AN, Papadopoulos G, Supikova J, Groenen P, Boudjogra M, Sundstrom C, Ponzoni M, Francova HS, Anagnostopoulos A, Pospisilova S, Papadaki T, Tzovaras D, Ghia P, Pott C, Davi F, Campo E, Rosenquist R, Hadzidimitriou A, Belessi C, Stamatopoulos K. Molecular evidence for antigen drive in the natural history of mantle cell lymphoma. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1740-8. [PMID: 25843681 DOI: 10.1016/j.ajpath.2015.02.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 01/23/2015] [Accepted: 02/26/2015] [Indexed: 10/24/2022]
Abstract
To further our understanding about antigen involvement in mantle cell lymphoma (MCL), we analyzed the expression levels of activation-induced cytidine deaminase (AID), a key player in B-cell responses to antigen triggering, in 133 MCL cases; assessed the functionality of AID by evaluating in vivo class switch recombination in 52 MCL cases; and sought for indications of ongoing antigen interactions by exploring intraclonal diversification within 14 MCL cases. The AID full-length transcript and the most frequent splice variants (AID-ΔE4a, AID-ΔE) were detected in 128 (96.2%), 96 (72.2%), and 130 cases (97.7%), respectively. Higher AID full-length transcript levels were significantly associated (P < 0.001) with lack of somatic hypermutation within the clonotypic immunoglobulin heavy variable (IGHV) genes. Median AID transcript levels were higher in lymph node material compared to cases in which peripheral blood was analyzed, implying that clonal behavior is influenced by the microenvironment. Switched tumor-derived IGHV-IGHD-IGHJ transcripts were identified in 5 of 52 cases (9.6%), all of which displayed somatic hypermutation and AID-mRNA expression. Finally, although most cases exhibited low levels of intraclonal diversification, analysis of the mutational activity revealed a precise targeting of somatic hypermutation indicative of an active, ongoing interaction with antigen(s). Collectively, these findings strongly allude to antigen involvement in the natural history of MCL, further challenging the notion of antigen naivety.
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Affiliation(s)
- Aliki Xochelli
- Institute of Applied Biosciences, CERTH, Center for Research and Technology Hellas, Thessaloniki, Greece; Hematology Department and HCT Unit, G. Papanicolaou Hospital, 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
- Laboratory of B cell Neoplasia and Lymphoma Unit, Division of Molecular Oncology and Department of Onco-Hematology, Università Vita-Salute San Raffaele, Milan, Italy
| | - Evangelia Stalika
- Institute of Applied Biosciences, CERTH, Center for Research and Technology Hellas, Thessaloniki, Greece; Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | - Maria Karypidou
- Institute of Applied Biosciences, CERTH, Center for Research and Technology Hellas, Thessaloniki, Greece; Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | | | - Alba Navarro Lopez
- Insititut d'investigacions biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Giorgos Papadopoulos
- Information Technologies Institute, CERTH, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Jana Supikova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Patricia Groenen
- Department of Pathology, Radboud University, Nijmegen Medical Centre, Nijmegen, the Netherlands
| | - Myriam Boudjogra
- Biological Hematology Service, Hopital Pitie-Salpetriere, and UPMC Univ Paris 06, UMRS 1138, Paris, France
| | - Christer Sundstrom
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maurilio Ponzoni
- Pathology Unit and Unit of Lymphoid Malignancies, Istituto Scientifico San Raffaele, Milan, Italy
| | - Hana Skuhrova Francova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Dimitris Tzovaras
- Information Technologies Institute, CERTH, Center for Research and Technology Hellas, Thessaloniki, Greece
| | - Paolo Ghia
- Laboratory of B cell Neoplasia and Lymphoma Unit, Division of Molecular Oncology and Department of Onco-Hematology, Università Vita-Salute San Raffaele, Milan, Italy
| | - Christiane Pott
- II. Medizinische Klinik und Poliklinik, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Frederic Davi
- Biological Hematology Service, Hopital Pitie-Salpetriere, and UPMC Univ Paris 06, UMRS 1138, Paris, France
| | - Elias Campo
- Insititut d'investigacions biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anastasia Hadzidimitriou
- Institute of Applied Biosciences, CERTH, Center for Research and Technology Hellas, Thessaloniki, Greece
| | | | - Kostas Stamatopoulos
- Institute of Applied Biosciences, CERTH, Center for Research and Technology Hellas, Thessaloniki, Greece; Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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28
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Immunoglobulin heavy variable (IGHV) genes and alleles: new entities, new names and implications for research and prognostication in chronic lymphocytic leukaemia. Immunogenetics 2014; 67:61-6. [PMID: 25388851 DOI: 10.1007/s00251-014-0812-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 10/27/2014] [Indexed: 10/24/2022]
Abstract
Νext generation sequencing studies in Homo sapiens have identified novel immunoglobulin heavy variable (IGHV) genes and alleles necessitating changes in the international ImMunoGeneTics information system (IMGT) GENE-DB and reference directories of IMGT/V-QUEST. In chronic lymphocytic leukaemia (CLL), the somatic hypermutation (SHM) status of the clonotypic rearranged IGHV gene is strongly associated with patient outcome. Correct determination of this parameter strictly depends on the comparison of the nucleotide sequence of the clonotypic rearranged IGHV gene with that of the closest germline counterpart. Consequently, changes in the reference directories could, in principle, affect the correct interpretation of the IGHV mutational status in CLL. To this end, we analyzed 8066 productive IG heavy chain (IGH) rearrangement sequences from our consortium both before and after the latest update of the IMGT/V-QUEST reference directory. Differences were identified in 405 cases (5 % of the cohort). In 291/405 sequences (71.9 %), changes concerned only the IGHV gene or allele name, whereas a change in the percent germline identity (%GI) was noted in 114/405 (28.1 %) sequences; in 50/114 (43.8 %) sequences, changes in the %GI led to a change in the mutational set. In conclusion, recent changes in the IMGT reference directories affected the interpretation of SHM in a sizeable number of IGH rearrangement sequences from CLL patients. This indicates that both physicians and researchers should consider a re-evaluation of IG sequence data, especially for those IGH rearrangement sequences that, up to date, have a GI close to 98 %, where caution is warranted.
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29
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Nussinov R, Jang H, Tsai CJ. The structural basis for cancer treatment decisions. Oncotarget 2014; 5:7285-302. [PMID: 25277176 PMCID: PMC4202123 DOI: 10.18632/oncotarget.2439] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/03/2014] [Indexed: 12/31/2022] Open
Abstract
Cancer treatment decisions rely on genetics, large data screens and clinical pharmacology. Here we point out that genetic analysis and treatment decisions may overlook critical elements in cancer development, progression and drug resistance. Two critical structural elements are missing in genetics-based decision-making: the mechanisms of oncogenic mutations and the cellular network which is rewired in cancer. These lay the foundation for the structural basis for cancer treatment decisions, which is rooted in the physical principles of the molecular conformational behavior of single molecules and their interactions. Improved tumor mutational analysis platforms and knowledge of the redundant pathways which can take over in cancer, may not only supplement known actionable findings, but forecast possible cancer progression and resistance. Such forward-looking can be powerful, endowing the oncologist with mechanistic insight and cancer prognosis, and consequently more informed treatment options. Examples include redundant pathways taking over after inhibition of EGFR constitutive activation, mutations in PIK3CA p110α and p85, and the non-hotspot AKT1 mutants conferring constitutive membrane localization.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
- Sackler Inst. of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, U.S.A
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30
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Baliakas P, Strefford JC, Bikos V, Parry M, Stamatopoulos K, Oscier D. Splenic marginal-zone lymphoma: ontogeny and genetics. Leuk Lymphoma 2014; 56:301-10. [PMID: 24798744 DOI: 10.3109/10428194.2014.919636] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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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31
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Thieblemont C, Bertoni F, Copie-Bergman C, Ferreri AJ, Ponzoni M. Chronic inflammation and extra-nodal marginal-zone lymphomas of MALT-type. Semin Cancer Biol 2014; 24:33-42. [DOI: 10.1016/j.semcancer.2013.11.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 11/23/2013] [Accepted: 11/29/2013] [Indexed: 12/26/2022]
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32
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The microenvironment in lymphomas--dissecting the complex crosstalk between tumor cells and 'by-stander' cells. Semin Cancer Biol 2013; 24:1-2. [PMID: 24365642 DOI: 10.1016/j.semcancer.2013.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In lymphomas, it is increasingly apparent that the microenvironment is an essential player not only for lymphoma pathogenesis but also for disease progression and therapy resistance. In recent years, we have begun to understand the complex crosstalk between the neoplastic cells and other immune cells, such as T and NK cells, and stromal cells, as well as the signaling pathways that become aberrantly activated through this dialogue (e.g. B-cell receptor, Toll-like receptor and NF-?B signaling). In this series of reviews, the intricate interplay between lymphoma cells and 'by-stander' cells will be illustrated in representative lymphoma entities, namely Hodgkin lymphomas, follicular lymphomas, marginal-zone lymphomas, chronic lymphocytic leukemia, and T-cell lymphomas, where the crucial role played by the microenvironment has become particularly evident. Furthermore, important clues to the pathobiology of lymphomas have emerged from (i) the recognition of pre-malignant conditions, such as monoclonal B-cell lymphocytosis or in situ lymphomas, (ii) the identification of microbial and/or auto-antigens that are linked to particular entities, as well as (iii) the established increased risk of lymphomas in certain autoimmune/inflammatory conditions, all critical aspects that will be further elaborated in this thematic issue. Our increasing knowledge of these interactions and associations has finally allowed us to design targeted or immune-mediated strategies to interfere with the lymphoma microenvironment, thereby opening promising therapeutic avenues on the road to cure for these yet incurable diseases.
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33
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Baecklund E, Smedby KE, Sutton LA, Askling J, Rosenquist R. Lymphoma development in patients with autoimmune and inflammatory disorders--what are the driving forces? Semin Cancer Biol 2013; 24:61-70. [PMID: 24333759 DOI: 10.1016/j.semcancer.2013.12.001] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 12/03/2013] [Indexed: 12/27/2022]
Abstract
For decades, it has been known that patients with certain autoimmune and inflammatory disorders, such as rheumatoid arthritis (RA) and primary Sjögren's syndrome (pSS), have an increased risk of developing malignant lymphoma. Although the clinico-biological reasons for this association remain largely unknown, our knowledge has improved and new insights have been obtained. First, the direct link between autoimmunity and lymphomagenesis has been strengthened by large epidemiological studies showing a consistent risk increase of lymphoma associated with certain autoimmune/inflammatory conditions in independent cohorts from different countries. Second, a number of local and systemic disease-related risk factors in these diseases have been repeatedly linked to lymphoma development, with the prime examples being disease severity and the degree of inflammatory activity. Considering the key role of B- and T-cell activation in the pathogenesis of both autoimmunity and lymphoma, it is perhaps not surprising that longstanding chronic inflammation and/or antigen stimulation have emerged as major predisposing factors of lymphoma in patients with active autoimmune disease. Finally, increasing evidence suggests that lymphomas associated with autoimmunity constitute a different spectrum of entities compared to lymphomas arising in patients without any known autoimmune or inflammatory conditions, pointing to a different pathobiology. In this review, we summarize the recent literature that supports a direct or indirect link between immune-mediated disease and lymphoma and describe the characteristics of lymphomas developing in the different diseases. We also discuss molecular, genetic and microenvironmental factors that may come into play in the pathobiology of these disorders.
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Affiliation(s)
- Eva Baecklund
- Unit of Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden.
| | - Karin E Smedby
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Johan Askling
- Clinical Epidemiology Unit, Department of Medicine Solna, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden; Rheumatology Unit, Department of Medicine Solna, Karolinska Institutet at Karolinska University Hospital, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Abstract
Lymphomas are a very heterogeneous group of tumors of mature lymphoid cells with quite different morphology, genetics and clinical characteristics, which is also reflected in the numerous entities and sub-entities defined in the most recent WHO classification. Today, it is well-established that lymphomas can evolve due to both 'cell-intrinsic' factors (e.g. acquired genomic aberrations) and 'cell-extrinsic' factors (e.g. microenvironmental stimuli), although for most lymphoma subtypes the precise implicated mechanisms remain to be elucidated. In this thematic issue, a series of reviews have been collected focusing on key evidence for (i) direct or indirect links between antigens and lymphoma development; and, (ii) activated signaling pathways that play an essential role in tumor evolution and progression. Finally, strategies for the management of lymphomas developing due to viral and bacterial infection as well as novel promising therapies designed to hit specific cellular pathways (e.g. B-cell receptor inhibitors) will be summarized and discussed. Altogether, this issue will give the reader important insights into the current knowledge of the diverse mechanisms that come into play during lymphoma development as well as clues to future directions within this broad and intense research field.
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