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Navrkalova V, Plevova K, Radova L, Porc J, Pal K, Malcikova J, Pavlova S, Doubek M, Panovska A, Kotaskova J, Pospisilova S. Integrative NGS testing reveals clonal dynamics of adverse genomic defects contributing to a natural progression in treatment-naïve CLL patients. Br J Haematol 2024; 204:240-249. [PMID: 38062779 DOI: 10.1111/bjh.19191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 01/11/2024]
Abstract
Large-scale next-generation sequencing (NGS) studies revealed extensive genetic heterogeneity, driving a highly variable clinical course of chronic lymphocytic leukaemia (CLL). The evolution of subclonal populations contributes to diverse therapy responses and disease refractoriness. Besides, the dynamics and impact of subpopulations before therapy initiation are not well understood. We examined changes in genomic defects in serial samples of 100 untreated CLL patients, spanning from indolent to aggressive disease. A comprehensive NGS panel LYNX, which provides targeted mutational analysis and genome-wide chromosomal defect assessment, was employed. We observed dynamic changes in the composition and/or proportion of genomic aberrations in most patients (62%). Clonal evolution of gene variants prevailed over the chromosomal alterations. Unsupervised clustering based on aberration dynamics revealed four groups of patients with different clinical behaviour. An adverse cluster was associated with fast progression and early therapy need, characterized by the expansion of TP53 defects, ATM mutations, and 18p- alongside dynamic SF3B1 mutations. Our results show that clonal evolution is active even without therapy pressure and that repeated genetic testing can be clinically relevant during long-term patient monitoring. Moreover, integrative NGS testing contributes to the consolidated evaluation of results and accurate assessment of individual patient prognosis.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Lenka Radova
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jakub Porc
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jitka Malcikova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Center of Molecular Medicine, CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
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2
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Yin H, Wang J, Tan Y, Jiang M, Zhang H, Meng G. Transcription factor abnormalities in B-ALL leukemogenesis and treatment. Trends Cancer 2023; 9:855-870. [PMID: 37407363 DOI: 10.1016/j.trecan.2023.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023]
Abstract
The biological regulation of transcription factors (TFs) and repressor proteins is an important mechanism for maintaining cell homeostasis. In B cell acute lymphoblastic leukemia (B-ALL) TF abnormalities occur at high frequency and are often recognized as the major driving factor in carcinogenesis. We provide an in-depth review of molecular mechanisms of six major TF rearrangements in B-ALL, including DUX4-rearranged (DUX4-R), MEF2D-R, ZNF384-R, ETV6-RUNX1 and TCF3-PBX1 fusions, and KMT2A-R. In addition, the therapeutic options and prognoses for patients who harbor these TF abnormalities are discussed. This review aims to provide an up-to-date panoramic view of how TF-based oncogenic fusions might drive carcinogenesis and impact on potential therapeutic exploration of B-ALL treatments.
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Affiliation(s)
- Hongxin Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Junfei Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Yangxia Tan
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Minghao Jiang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Hao Zhang
- Institute for Translational Brain Research, Ministry of Education (MOE) Frontiers Center for Brain Science, Fudan University, 200032 Shanghai, China.
| | - Guoyu Meng
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine, Rui-Jin Hospital, School of Medicine and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200025, China.
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3
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Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders. Blood Adv 2021; 5:3188-3198. [PMID: 34424321 DOI: 10.1182/bloodadvances.2020004056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/16/2021] [Indexed: 11/20/2022] Open
Abstract
Current diagnostic standards for lymphoproliferative disorders include multiple tests for detection of clonal immunoglobulin (IG) and/or T-cell receptor (TCR) rearrangements, translocations, copy-number alterations (CNAs), and somatic mutations. The EuroClonality-NGS DNA Capture (EuroClonality-NDC) assay was designed as an integrated tool to characterize these alterations by capturing IGH switch regions along with variable, diversity, and joining genes of all IG and TCR loci in addition to clinically relevant genes for CNA and mutation analysis. Diagnostic performance against standard-of-care clinical testing was assessed in a cohort of 280 B- and T-cell malignancies from 10 European laboratories, including 88 formalin-fixed paraffin-embedded samples and 21 reactive lesions. DNA samples were subjected to the EuroClonality-NDC protocol in 7 EuroClonality-NGS laboratories and analyzed using a bespoke bioinformatic pipeline. The EuroClonality-NDC assay detected B-cell clonality in 191 (97%) of 197 B-cell malignancies and T-cell clonality in 71 (97%) of 73 T-cell malignancies. Limit of detection (LOD) for IG/TCR rearrangements was established at 5% using cell line blends. Chromosomal translocations were detected in 145 (95%) of 152 cases known to be positive. CNAs were validated for immunogenetic and oncogenetic regions, highlighting their novel role in confirming clonality in somatically hypermutated cases. Single-nucleotide variant LOD was determined as 4% allele frequency, and an orthogonal validation using 32 samples resulted in 98% concordance. The EuroClonality-NDC assay is a robust tool providing a single end-to-end workflow for simultaneous detection of B- and T-cell clonality, translocations, CNAs, and sequence variants.
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4
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Aslan B, Kismali G, Chen LS, Iles LR, Mahendra M, Peoples M, Gagea M, Fowlkes NW, Zheng X, Wang J, Vellano CP, Marszalek JR, Bertilaccio MTS, Gandhi V. Development and characterization of prototypes for in vitro and in vivo mouse models of ibrutinib-resistant CLL. Blood Adv 2021; 5:3134-3146. [PMID: 34424317 PMCID: PMC8405195 DOI: 10.1182/bloodadvances.2020003821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 04/26/2021] [Indexed: 01/16/2023] Open
Abstract
Although ibrutinib improves the overall survival of patients with chronic lymphocytic leukemia (CLL), some patients still develop resistance, most commonly through point mutations affecting cysteine residue 481 (C481) in Bruton's tyrosine kinase (BTKC481S and BTKC481R). To enhance our understanding of the biological impact of these mutations, we established cell lines that overexpress wild-type or mutant BTK in in vitro and in vivo models that mimic ibrutinib-sensitive and -resistant CLL. MEC-1 cell lines stably overexpressing wild-type or mutant BTK were generated. All cell lines coexpressed GFP, were CD19+ and CD23+, and overexpressed BTK. Overexpression of wild-type or mutant BTK resulted in increased signaling, as evidenced by the induction of p-BTK, p-PLCγ2, and p-extracellular signal-related kinase (ERK) levels, the latter further augmented upon IgM stimulation. In all cell lines, cell cycle profiles and levels of BTK expression were similar, but the RNA sequencing and reverse-phase protein array results revealed that the molecular transcript and protein profiles were distinct. To mimic aggressive CLL, we created xenograft mouse models by transplanting the generated cell lines into Rag2-/-γc-/- mice. Spleens, livers, bone marrow, and peripheral blood were collected. All mice developed CLL-like disease with systemic involvement (engraftment efficiency, 100%). We observed splenomegaly, accumulation of leukemic cells in the spleen and liver, and macroscopically evident necrosis. CD19+ cells accumulated in the spleen, bone marrow, and peripheral blood. The overall survival duration was slightly lower in mice expressing mutant BTK. Our cell lines and murine models mimicking ibrutinib-resistant CLL will serve as powerful tools to test reversible BTK inhibitors and novel, non-BTK-targeted therapeutics.
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Affiliation(s)
| | | | | | | | | | | | - Mihai Gagea
- Department of Veterinary Medicine and Surgery
| | | | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, and
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, and
| | | | | | | | - Varsha Gandhi
- Department of Experimental Therapeutics
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
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5
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Nelde A, Maringer Y, Bilich T, Salih HR, Roerden M, Heitmann JS, Marcu A, Bauer J, Neidert MC, Denzlinger C, Illerhaus G, Aulitzky WE, Rammensee HG, Walz JS. Immunopeptidomics-Guided Warehouse Design for Peptide-Based Immunotherapy in Chronic Lymphocytic Leukemia. Front Immunol 2021; 12:705974. [PMID: 34305947 PMCID: PMC8297687 DOI: 10.3389/fimmu.2021.705974] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/24/2021] [Indexed: 12/30/2022] Open
Abstract
Antigen-specific immunotherapies, in particular peptide vaccines, depend on the recognition of naturally presented antigens derived from mutated and unmutated gene products on human leukocyte antigens, and represent a promising low-side-effect concept for cancer treatment. So far, the broad application of peptide vaccines in cancer patients is hampered by challenges of time- and cost-intensive personalized vaccine design, and the lack of neoepitopes from tumor-specific mutations, especially in low-mutational burden malignancies. In this study, we developed an immunopeptidome-guided workflow for the design of tumor-associated off-the-shelf peptide warehouses for broadly applicable personalized therapeutics. Comparative mass spectrometry-based immunopeptidome analyses of primary chronic lymphocytic leukemia (CLL) samples, as representative example of low-mutational burden tumor entities, and a dataset of benign tissue samples enabled the identification of high-frequent non-mutated CLL-associated antigens. These antigens were further shown to be recognized by pre-existing and de novo induced T cells in CLL patients and healthy volunteers, and were evaluated as pre-manufactured warehouse for the construction of personalized multi-peptide vaccines in a first clinical trial for CLL (NCT04688385). This workflow for the design of peptide warehouses is easily transferable to other tumor entities and can provide the foundation for the development of broad personalized T cell-based immunotherapy approaches.
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Affiliation(s)
- Annika Nelde
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Yacine Maringer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Tatjana Bilich
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Helmut R Salih
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Malte Roerden
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen, Tübingen, Germany
| | - Jonas S Heitmann
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany
| | - Ana Marcu
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Jens Bauer
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Marian C Neidert
- Department of Neurosurgery, Cantonal Hospital St. Gallen, St. Gallen, Switzerland
| | | | - Gerald Illerhaus
- Clinic for Hematology and Oncology, Klinikum Stuttgart, Stuttgart, Germany
| | - Walter Erich Aulitzky
- Department of Hematology, Oncology and Palliative Medicine, Robert-Bosch-Krankenhaus Stuttgart, Stuttgart, Germany
| | - Hans-Georg Rammensee
- Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), partner site Tübingen, Tübingen, Germany
| | - Juliane S Walz
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK), Department of Internal Medicine, University Hospital Tübingen, Tübingen, Germany.,Department of Immunology, Institute for Cell Biology, University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology and Robert Bosch Center for Tumor Diseases (RBCT), Stuttgart, Germany
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6
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Navrkalova V, Plevova K, Hynst J, Pal K, Mareckova A, Reigl T, Jelinkova H, Vrzalova Z, Stranska K, Pavlova S, Panovska A, Janikova A, Doubek M, Kotaskova J, Pospisilova S. LYmphoid NeXt-Generation Sequencing (LYNX) Panel: A Comprehensive Capture-Based Sequencing Tool for the Analysis of Prognostic and Predictive Markers in Lymphoid Malignancies. J Mol Diagn 2021; 23:959-974. [PMID: 34082072 DOI: 10.1016/j.jmoldx.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023] Open
Abstract
B-cell neoplasms represent a clinically heterogeneous group of hematologic malignancies with considerably diverse genomic architecture recently endorsed by next-generation sequencing (NGS) studies. Because multiple genetic defects have a potential or confirmed clinical impact, a tendency toward more comprehensive testing of diagnostic, prognostic, and predictive markers is desired. This study introduces the design, validation, and implementation of an integrative, custom-designed, capture-based NGS panel titled LYmphoid NeXt-generation sequencing (LYNX) for the analysis of standard and novel molecular markers in the most common lymphoid neoplasms (chronic lymphocytic leukemia, acute lymphoblastic leukemia, diffuse large B-cell lymphoma, follicular lymphoma, and mantle cell lymphoma). A single LYNX test provides the following: i) accurate detection of mutations in all coding exons and splice sites of 70 lymphoma-related genes with a sensitivity of 5% variant allele frequency, ii) reliable identification of large genome-wide (≥6 Mb) and recurrent chromosomal aberrations (≥300 kb) in at least 20% of the clonal cell fraction, iii) the assessment of immunoglobulin and T-cell receptor gene rearrangements, and iv) lymphoma-specific translocation detection. Dedicated bioinformatic pipelines were designed to detect all markers mentioned above. The LYNX panel represents a comprehensive, up-to-date tool suitable for routine testing of lymphoid neoplasms with research and clinical applicability. It allows a wide adoption of capture-based targeted NGS in clinical practice and personalized management of patients with lymphoproliferative diseases.
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Affiliation(s)
- Veronika Navrkalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jakub Hynst
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karol Pal
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Department of Internal Medicine II - Hematology and Oncology, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Andrea Mareckova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Tomas Reigl
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Jelinkova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Zuzana Vrzalova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Andrea Janikova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Michael Doubek
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Jana Kotaskova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, Masaryk University and University Hospital Brno, Brno, Czech Republic; Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic.
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7
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Jiménez I, Tazón-Vega B, Abrisqueta P, Nieto JC, Bobillo S, Palacio-García C, Carabia J, Valdés-Mas R, Munuera M, Puigdefàbregas L, Parra G, Esteve-Codina A, Franco-Jarava C, Iacoboni G, Terol MJ, García-Marco JA, Crespo M, Bosch F. Immunological and genetic kinetics from diagnosis to clinical progression in chronic lymphocytic leukemia. Biomark Res 2021; 9:37. [PMID: 34016160 PMCID: PMC8138982 DOI: 10.1186/s40364-021-00290-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 04/26/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Mechanisms driving the progression of chronic lymphocytic leukemia (CLL) from its early stages are not fully understood. The acquisition of molecular changes at the time of progression has been observed in a small fraction of patients, suggesting that CLL progression is not mainly driven by dynamic clonal evolution. In order to shed light on mechanisms that lead to CLL progression, we investigated longitudinal changes in both the genetic and immunological scenarios. METHODS We performed genetic and immunological longitudinal analysis using paired primary samples from untreated CLL patients that underwent clinical progression (sampling at diagnosis and progression) and from patients with stable disease (sampling at diagnosis and at long-term asymptomatic follow-up). RESULTS Molecular analysis showed limited and non-recurrent molecular changes at progression, indicating that clonal evolution is not the main driver of clinical progression. Our analysis of the immune kinetics found an increasingly dysfunctional CD8+ T cell compartment in progressing patients that was not observed in those patients that remained asymptomatic. Specifically, terminally exhausted effector CD8+ T cells (T-betdim/-EomeshiPD1hi) accumulated, while the the co-expression of inhibitory receptors (PD1, CD244 and CD160) increased, along with an altered gene expression profile in T cells only in those patients that progressed. In addition, malignant cells from patients at clinical progression showed enhanced capacity to induce exhaustion-related markers in CD8+ T cells ex vivo mainly through a mechanism dependent on soluble factors including IL-10. CONCLUSIONS Altogether, we demonstrate that the interaction with the immune microenvironment plays a key role in clinical progression in CLL, thereby providing a rationale for the use of early immunotherapeutic intervention.
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Affiliation(s)
- Isabel Jiménez
- Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, C/Natzaret 115-117, 08035, Barcelona, Spain.,Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Bárbara Tazón-Vega
- Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Servei d'Hematologia, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Pau Abrisqueta
- Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Servei d'Hematologia, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Juan C Nieto
- Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, C/Natzaret 115-117, 08035, Barcelona, Spain.,Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Sabela Bobillo
- Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Servei d'Hematologia, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Carles Palacio-García
- Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Servei d'Hematologia, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Júlia Carabia
- Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, C/Natzaret 115-117, 08035, Barcelona, Spain.,Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | - Magdalena Munuera
- Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, C/Natzaret 115-117, 08035, Barcelona, Spain.,Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Lluís Puigdefàbregas
- Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, C/Natzaret 115-117, 08035, Barcelona, Spain.,Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Genís Parra
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, 08002, Barcelona, Spain
| | - Anna Esteve-Codina
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08003, Barcelona, Spain.,Universitat Pompeu Fabra, 08002, Barcelona, Spain
| | - Clara Franco-Jarava
- Servei d'Immunologia, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - Gloria Iacoboni
- Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Servei d'Hematologia, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
| | - María José Terol
- Department of Hematology, Clínic University Hospital, INCLIVA Biomedical Research Institute, 46010, Valencia, Spain
| | | | - Marta Crespo
- Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, C/Natzaret 115-117, 08035, Barcelona, Spain.,Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Francesc Bosch
- Department de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Servei d'Hematologia, Vall d'Hebron Hospital Universitari, Experimental Hematology, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain.
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8
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Pérez-Carretero C, González-Gascón-y-Marín I, Rodríguez-Vicente AE, Quijada-Álamo M, Hernández-Rivas JÁ, Hernández-Sánchez M, Hernández-Rivas JM. The Evolving Landscape of Chronic Lymphocytic Leukemia on Diagnosis, Prognosis and Treatment. Diagnostics (Basel) 2021; 11:diagnostics11050853. [PMID: 34068813 PMCID: PMC8151186 DOI: 10.3390/diagnostics11050853] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 04/25/2021] [Accepted: 05/05/2021] [Indexed: 12/22/2022] Open
Abstract
The knowledge of chronic lymphocytic leukemia (CLL) has progressively deepened during the last forty years. Research activities and clinical studies have been remarkably fruitful in novel findings elucidating multiple aspects of the pathogenesis of the disease, improving CLL diagnosis, prognosis and treatment. Whereas the diagnostic criteria for CLL have not substantially changed over time, prognostication has experienced an expansion with the identification of new biological and genetic biomarkers. Thanks to next-generation sequencing (NGS), an unprecedented number of gene mutations were identified with potential prognostic and predictive value in the 2010s, although significant work on their validation is still required before they can be used in a routine clinical setting. In terms of treatment, there has been an impressive explosion of new approaches based on targeted therapies for CLL patients during the last decade. In this current chemotherapy-free era, BCR and BCL2 inhibitors have changed the management of CLL patients and clearly improved their prognosis and quality of life. In this review, we provide an overview of these novel advances, as well as point out questions that should be further addressed to continue improving the outcomes of patients.
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Affiliation(s)
- Claudia Pérez-Carretero
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
| | | | - Ana E. Rodríguez-Vicente
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - Miguel Quijada-Álamo
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
| | - José-Ángel Hernández-Rivas
- Department of Hematology, Infanta Leonor University Hospital, 28031 Madrid, Spain; (I.G.-G.-y-M.); (J.-Á.H.-R.)
- Department of Medicine, Complutense University, 28040 Madrid, Spain
| | - María Hernández-Sánchez
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
- Correspondence: (M.H.-S.); (J.M.H.-R.); Tel.: +34-923-294-812 (M.H.-S. & J.M.H.-R.)
| | - Jesús María Hernández-Rivas
- Cancer Research Center (IBMCC) CSIC-University of Salamanca, 37007 Salamanca, Spain; (C.P.-C.); (A.E.R.-V.); (M.Q.-Á.)
- Instituto de Investigación Biomédica (IBSAL), 37007 Salamanca, Spain
- Department of Hematology, University Hospital of Salamanca, 37007 Salamanca, Spain
- Department of Medicine, University of Salamanca, 37008 Salamanca, Spain
- Correspondence: (M.H.-S.); (J.M.H.-R.); Tel.: +34-923-294-812 (M.H.-S. & J.M.H.-R.)
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9
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Clonal dynamics in chronic lymphocytic leukemia. Blood Adv 2020; 3:3759-3769. [PMID: 31770443 DOI: 10.1182/bloodadvances.2019000367] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/20/2019] [Indexed: 12/28/2022] Open
Abstract
Chronic lymphocytic leukemia has a highly variable disease course across patients, thought to be driven by the vast inter- and intrapatient molecular heterogeneity described in several large-scale DNA-sequencing studies conducted over the past decade. Although the last 5 years have seen a dramatic shift in the therapeutic landscape for chronic lymphocytic leukemia, including the regulatory approval of several potent targeted agents (ie, idelalisib, ibrutinib, venetoclax), the vast majority of patients still inevitably experience disease recurrence or persistence. Recent genome-wide sequencing approaches have helped to identify subclonal populations within tumors that demonstrate a broad spectrum of somatic mutations, diverse levels of response to therapy, patterns of repopulation, and growth kinetics. Understanding the impact of genetic, epigenetic, and transcriptomic features on clonal growth dynamics and drug response will be an important step toward the selection and timing of therapy.
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10
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Gutierrez C, Wu CJ. Clonal dynamics in chronic lymphocytic leukemia. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2019; 2019:466-475. [PMID: 31808879 PMCID: PMC6913465 DOI: 10.1182/hematology.2019000367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Chronic lymphocytic leukemia has a highly variable disease course across patients, thought to be driven by the vast inter- and intrapatient molecular heterogeneity described in several large-scale DNA-sequencing studies conducted over the past decade. Although the last 5 years have seen a dramatic shift in the therapeutic landscape for chronic lymphocytic leukemia, including the regulatory approval of several potent targeted agents (ie, idelalisib, ibrutinib, venetoclax), the vast majority of patients still inevitably experience disease recurrence or persistence. Recent genome-wide sequencing approaches have helped to identify subclonal populations within tumors that demonstrate a broad spectrum of somatic mutations, diverse levels of response to therapy, patterns of repopulation, and growth kinetics. Understanding the impact of genetic, epigenetic, and transcriptomic features on clonal growth dynamics and drug response will be an important step toward the selection and timing of therapy.
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MESH Headings
- Adenine/analogs & derivatives
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Epigenesis, Genetic
- Gene Expression Regulation, Leukemic
- Genome-Wide Association Study
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Male
- Middle Aged
- Mutation
- Piperidines
- Purines/therapeutic use
- Pyrazoles/therapeutic use
- Pyrimidines/therapeutic use
- Quinazolinones/therapeutic use
- Sulfonamides/therapeutic use
- Transcriptome
- Whole Genome Sequencing
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Affiliation(s)
- Catherine Gutierrez
- Harvard Medical School, Boston, MA; and Dana-Farber Cancer Institute, Boston, MA
| | - Catherine J Wu
- Harvard Medical School, Boston, MA; and Dana-Farber Cancer Institute, Boston, MA
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11
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Ramassone A, D'Argenio A, Veronese A, Basti A, Soliman SHA, Volinia S, Bassi C, Pagotto S, Ferracin M, Lupini L, Saccenti E, Balatti V, Pepe F, Rassenti LZ, Innocenti I, Autore F, Marzetti L, Mariani-Costantini R, Kipps TJ, Negrini M, Laurenti L, Visone R. Genetic dynamics in untreated CLL patients with either stable or progressive disease: a longitudinal study. J Hematol Oncol 2019; 12:114. [PMID: 31744508 PMCID: PMC6862808 DOI: 10.1186/s13045-019-0802-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 01/30/2023] Open
Abstract
Clonal evolution of chronic lymphocytic leukemia (CLL) often follows chemotherapy and is associated with adverse outcome, but also occurs in untreated patients, in which case its predictive role is debated. We investigated whether the selection and expansion of CLL clone(s) precede an aggressive disease shift. We found that clonal evolution occurs in all CLL patients, irrespective of the clinical outcome, but is faster during disease progression. In particular, changes in the frequency of nucleotide variants (NVs) in specific CLL-related genes may represent an indicator of poor clinical outcome.
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Affiliation(s)
- Alice Ramassone
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Andrea D'Argenio
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Angelo Veronese
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Alessio Basti
- Department of Neuroscience, Imaging and Clinical Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Institute for Advanced Biomedical Technologies (ITAB), University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Shimaa Hassan AbdelAziz Soliman
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Department of Medicine and Aging Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Cristian Bassi
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Sara Pagotto
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Department of Medical, Oral and Biotechnological Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Laura Lupini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Elena Saccenti
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Veronica Balatti
- Department of Cancer Biology and Genetics and Comprehensive Cancer Center at the Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Felice Pepe
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Department of Medical, Oral and Biotechnological Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Laura Z Rassenti
- Department of Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.,Chronic Lymphocytic Leukemia Research Consortium, San Diego, CA, USA
| | - Idanna Innocenti
- Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy
| | - Francesco Autore
- Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy
| | - Laura Marzetti
- Department of Neuroscience, Imaging and Clinical Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Institute for Advanced Biomedical Technologies (ITAB), University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Renato Mariani-Costantini
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy.,Department of Medical, Oral and Biotechnological Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy
| | - Thomas J Kipps
- Department of Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.,Chronic Lymphocytic Leukemia Research Consortium, San Diego, CA, USA
| | - Massimo Negrini
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Luca Laurenti
- Fondazione Policlinico Universitario A Gemelli IRCCS, Rome, Italy
| | - Rosa Visone
- Unit of General Pathology, Center for Advanced Studies and Technology (CAST), University G. d'Annunzio Chieti-Pescara, Chieti, Italy. .,Department of Medical, Oral and Biotechnological Sciences, University G. d'Annunzio Chieti-Pescara, Chieti, Italy.
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