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Hoffmann J, Eminovic S, Wilhelm C, Krause SW, Neubauer A, Thrun MC, Ultsch A, Brendel C. Prediction of Clinical Outcomes with Explainable Artificial Intelligence in Patients with Chronic Lymphocytic Leukemia. Curr Oncol 2023; 30:1903-1915. [PMID: 36826109 PMCID: PMC9955184 DOI: 10.3390/curroncol30020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 01/29/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND The International Prognostic Index (IPI) is applied to predict the outcome of chronic lymphocytic leukemia (CLL) with five prognostic factors, including genetic analysis. We investigated whether multiparameter flow cytometry (MPFC) data of CLL samples could predict the outcome by methods of explainable artificial intelligence (XAI). Further, XAI should explain the results based on distinctive cell populations in MPFC dot plots. METHODS We analyzed MPFC data from the peripheral blood of 157 patients with CLL. The ALPODS XAI algorithm was used to identify cell populations that were predictive of inferior outcomes (death, failure of first-line treatment). The diagnostic ability of each XAI population was evaluated with receiver operating characteristic (ROC) curves. RESULTS ALPODS defined 17 populations with higher ability than the CLL-IPI to classify clinical outcomes (ROC: area under curve (AUC) 0.95 vs. 0.78). The best single classifier was an XAI population consisting of CD4+ T cells (AUC 0.78; 95% CI 0.70-0.86; p < 0.0001). Patients with low CD4+ T cells had an inferior outcome. The addition of the CD4+ T-cell population enhanced the predictive ability of the CLL-IPI (AUC 0.83; 95% CI 0.77-0.90; p < 0.0001). CONCLUSIONS The ALPODS XAI algorithm detected highly predictive cell populations in CLL that may be able to refine conventional prognostic scores such as IPI.
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Affiliation(s)
- Joerg Hoffmann
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, University Hospital Giessen and Marburg, Baldingerstrasse, 35043 Marburg, Germany
- Correspondence:
| | - Semil Eminovic
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, University Hospital Giessen and Marburg, Baldingerstrasse, 35043 Marburg, Germany
| | - Christian Wilhelm
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, University Hospital Giessen and Marburg, Baldingerstrasse, 35043 Marburg, Germany
| | - Stefan W. Krause
- Department of Medicine 5, Universitätsklinikum Erlangen, Maximiliansplatz 2, 91054 Erlangen, Germany
| | - Andreas Neubauer
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, University Hospital Giessen and Marburg, Baldingerstrasse, 35043 Marburg, Germany
| | - Michael C. Thrun
- Databionics, Mathematics and Computer Science, Philipps University Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Alfred Ultsch
- Databionics, Mathematics and Computer Science, Philipps University Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Cornelia Brendel
- Department of Hematology, Oncology and Immunology, Philipps University Marburg, University Hospital Giessen and Marburg, Baldingerstrasse, 35043 Marburg, Germany
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Mascheroni P, Savvopoulos S, Alfonso JCL, Meyer-Hermann M, Hatzikirou H. Improving personalized tumor growth predictions using a Bayesian combination of mechanistic modeling and machine learning. COMMUNICATIONS MEDICINE 2021; 1:19. [PMID: 35602187 PMCID: PMC9053281 DOI: 10.1038/s43856-021-00020-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/08/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In clinical practice, a plethora of medical examinations are conducted to assess the state of a patient's pathology producing a variety of clinical data. However, investigation of these data faces two major challenges. Firstly, we lack the knowledge of the mechanisms involved in regulating these data variables, and secondly, data collection is sparse in time since it relies on patient's clinical presentation. The former limits the predictive accuracy of clinical outcomes for any mechanistic model. The latter restrains any machine learning algorithm to accurately infer the corresponding disease dynamics. METHODS Here, we propose a novel method, based on the Bayesian coupling of mathematical modeling and machine learning, aiming at improving individualized predictions by addressing the aforementioned challenges. RESULTS We evaluate the proposed method on a synthetic dataset for brain tumor growth and analyze its performance in predicting two relevant clinical outputs. The method results in improved predictions in almost all simulated patients, especially for those with a late clinical presentation (>95% patients show improvements compared to standard mathematical modeling). In addition, we test the methodology in two additional settings dealing with real patient cohorts. In both cases, namely cancer growth in chronic lymphocytic leukemia and ovarian cancer, predictions show excellent agreement with reported clinical outcomes (around 60% reduction of mean squared error). CONCLUSIONS We show that the combination of machine learning and mathematical modeling approaches can lead to accurate predictions of clinical outputs in the context of data sparsity and limited knowledge of disease mechanisms.
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Affiliation(s)
- Pietro Mascheroni
- Braunschweig Integrated Centre of Systems Biology and Helmholtz Centre for Infectious Research, Braunschweig, Germany
| | - Symeon Savvopoulos
- grid.5596.f0000 0001 0668 7884KU Leuven, Department of Chemical Engineering, Leuven, Belgium
| | - Juan Carlos López Alfonso
- Braunschweig Integrated Centre of Systems Biology and Helmholtz Centre for Infectious Research, Braunschweig, Germany
| | - Michael Meyer-Hermann
- Braunschweig Integrated Centre of Systems Biology and Helmholtz Centre for Infectious Research, Braunschweig, Germany ,Centre for Individualized Infection Medicine, Hannover, Germany ,grid.6738.a0000 0001 1090 0254Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Haralampos Hatzikirou
- grid.440568.b0000 0004 1762 9729Mathematics Department, Khalifa University, Abu Dhabi, UAE ,grid.4488.00000 0001 2111 7257Centre for Information Services and High Performance Computing, TU Dresden, Dresden, Germany
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3
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Oppezzo P, Navarrete M, Chiorazzi N. AID in Chronic Lymphocytic Leukemia: Induction and Action During Disease Progression. Front Oncol 2021; 11:634383. [PMID: 34041018 PMCID: PMC8141630 DOI: 10.3389/fonc.2021.634383] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 12/12/2022] Open
Abstract
The enzyme activation-induced cytidine deaminase (AID) initiates somatic hypermutation (SHM) and class switch recombination (CSR) of immunoglobulin (Ig) genes, critical actions for an effective adaptive immune response. However, in addition to the benefits generated by its physiological roles, AID is an etiological factor for the development of human and murine leukemias and lymphomas. This review highlights the pathological role of AID and the consequences of its actions on the development, progression, and therapeutic refractoriness of chronic lymphocytic leukemia (CLL) as a model disease for mature lymphoid malignancies. First, we summarize pertinent aspects of the expression and function of AID in normal B lymphocytes. Then, we assess putative causes for AID expression in leukemic cells emphasizing the role of an activated microenvironment. Thirdly, we discuss the role of AID in lymphomagenesis, in light of recent data obtained by NGS analyses on the genomic landscape of leukemia and lymphomas, concentrating on the frequency of AID signatures in these cancers and correlating previously described tumor-gene drivers with the presence of AID off-target mutations. Finally, we discuss how these changes could affect tumor suppressor and proto-oncogene targets and how they could be associated with disease progression. Collectively, we hope that these sections will help to better understand the complex paradox between the physiological role of AID in adaptive immunity and its potential causative activity in B-cell malignancies.
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Affiliation(s)
- Pablo Oppezzo
- Research Laboratory on Chronic Lymphocytic Leukemia, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | | | - Nicholas Chiorazzi
- The Karches Center for Oncology Research, The Feinstein Institutes for Medical Research, New York, NY, United States
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Hamid AB, Petreaca RC. Secondary Resistant Mutations to Small Molecule Inhibitors in Cancer Cells. Cancers (Basel) 2020; 12:cancers12040927. [PMID: 32283832 PMCID: PMC7226513 DOI: 10.3390/cancers12040927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 04/05/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Secondary resistant mutations in cancer cells arise in response to certain small molecule inhibitors. These mutations inevitably cause recurrence and often progression to a more aggressive form. Resistant mutations may manifest in various forms. For example, some mutations decrease or abrogate the affinity of the drug for the protein. Others restore the function of the enzyme even in the presence of the inhibitor. In some cases, resistance is acquired through activation of a parallel pathway which bypasses the function of the drug targeted pathway. The Catalogue of Somatic Mutations in Cancer (COSMIC) produced a compendium of resistant mutations to small molecule inhibitors reported in the literature. Here, we build on these data and provide a comprehensive review of resistant mutations in cancers. We also discuss mechanistic parallels of resistance.
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5
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Mouse acute leukemia develops independent of self-renewal and differentiation potentials in hematopoietic stem and progenitor cells. Blood Adv 2020; 3:419-431. [PMID: 30733302 DOI: 10.1182/bloodadvances.2018022400] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/03/2019] [Indexed: 12/17/2022] Open
Abstract
The cell of origin, defined as the normal cell in which the transformation event first occurs, is poorly identified in leukemia, despite its importance in understanding of leukemogenesis and improving leukemia therapy. Although hematopoietic stem cells (HSCs) and hematopoietic progenitor cells (HPCs) were used for leukemia models, whether their self-renewal and differentiation potentials influence the initiation and development of leukemia is largely unknown. In this study, the self-renewal and differentiation potentials in 2 distinct types of HSCs (HSC1 [CD150+CD41-CD34-Lineage-Sca-1+c-Kit+ cells] and HSC2 [CD150-CD41-CD34-Lineage-Sca-1+c-Kit+ cells]) and 3 distinct types of HPCs (HPC1 [CD150+CD41+CD34-Lineage-Sca-1+c-Kit+ cells], HPC2 [CD150+CD41+CD34+Lineage-Sca-1+c-Kit+ cells], and HPC3 [CD150-CD41-CD34+Lineage-Sca-1+c-Kit+ cells]) were isolated from adult mouse bone marrow, and examined by competitive repopulation assay. Then, cells from each population were retrovirally transduced to initiate MLL-AF9 acute myelogenous leukemia (AML) and the intracellular domain of NOTCH-1 T-cell acute lymphoblastic leukemia (T-ALL). AML and T-ALL similarly developed from all HSC and HPC populations, suggesting multiple cellular origins of leukemia. New leukemic stem cells (LSCs) were also identified in these AML and T-ALL models. Notably, switching between immunophenotypical immature and mature LSCs was observed, suggesting that heterogeneous LSCs play a role in the expansion and maintenance of leukemia. Based on this mouse model study, we propose that acute leukemia arises from multiple cells of origin independent of the self-renewal and differentiation potentials in hematopoietic stem and progenitor cells and is amplified by LSC switchover.
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6
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Stankovic T. Fine tuning of p53 functions between normal and leukemic cells: a new strategy for the treatment of chronic lymphocytic leukemia. Haematologica 2019; 104:2332-2334. [PMID: 31787615 DOI: 10.3324/haematol.2019.230896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
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7
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Vatanmakanian M, Tavallaie M, Ghadami S. Imatinib independent aberrant methylation of NOV/CCN3 in chronic myelogenous leukemia patients: a mechanism upstream of BCR-ABL1 function? Cell Commun Signal 2019; 17:38. [PMID: 31014357 PMCID: PMC6480731 DOI: 10.1186/s12964-019-0350-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/03/2019] [Indexed: 12/18/2022] Open
Abstract
Background The NOV gene product, CCN3, has been reported in a diverse range of tumors to serve as a negative growth regulator, while acting as a tumor suppressor in Chronic Myelogenous Leukemia (CML). However, the precise mechanism of its silencing in CML is poorly understood. In the current study, we aimed to query if the gene regulation of CCN3 is mediated by the promoter methylation in the patients with CML. In addition, to clarify whether the epigenetic silencing is affected by BCR-ABL1 inhibition, we assessed the methylation status in the patients at different time intervals following the tyrosine kinase inhibition using imatinib therapy, as the first-line treatment for this type of leukemia. Methods To address this issue, we applied bisulfite-sequencing technique as a high-resolution method to study the regulatory segment of the CCN3 gene. The results were analyzed in newly diagnosed CML patients as well as following imatinib therapy. We also evaluated the correlation of CCN3 promoter methylation with BCR-ABL1 levels. Results Our findings revealed that the methylation occurs frequently in the promoter region of CML patients showing a significant increase of the methylated percentage at the CpG sites compared to normal individuals. Interestingly, this hypermethylation was indicated to be independent of BCR-ABL1 titers in both groups, which might suggest a mechanism beyond the BCR-ABL1 function. Conclusion Despite suggesting that the CCN3 hypermethylation acts as a molecular mechanism independent of BCR-ABL1 function in CML patients, this scenario requires further validation by complementary experiments. In the case of acting upstream of BCR-ABL1 signaling, the methylation marker can provide early detection and a novel platform for targeted epigenetic modifiers for efficient treatment in imatinib resistant patients.
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Affiliation(s)
- Mousa Vatanmakanian
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran
| | - Mahmood Tavallaie
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran
| | - Shirin Ghadami
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Mollasadra Ave., Vanak Square, Tehran, Iran.
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Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia. Blood 2018; 132:2375-2388. [PMID: 30181176 DOI: 10.1182/blood-2017-09-804401] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 08/24/2018] [Indexed: 12/17/2022] Open
Abstract
Genomic studies have recently identified RPS15 as a new driver gene in aggressive and chemorefractory cases of chronic lymphocytic leukemia (CLL). RPS15 encodes a ribosomal protein whose conserved C-terminal domain extends into the decoding center of the ribosome. We demonstrate that mutations in highly conserved residues of this domain affect protein stability, by increasing its ubiquitin-mediated degradation, and cell-proliferation rates. On the other hand, we show that mutated RPS15 can be loaded into the ribosomes, directly impacting on global protein synthesis and/or translational fidelity in a mutation-specific manner. Quantitative mass spectrometry analyses suggest that RPS15 variants may induce additional alterations in the translational machinery, as well as a metabolic shift at the proteome level in HEK293T and MEC-1 cells. These results indicate that CLL-related RPS15 mutations might act following patterns known for other ribosomal diseases, likely switching from a hypo- to a hyperproliferative phenotype driven by mutated ribosomes. In this scenario, loss of translational fidelity causing altered cell proteostasis can be proposed as a new molecular mechanism involved in CLL pathobiology.
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9
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Chronic lymphocytic leukemia and mantle cell lymphoma: crossroads of genetic and microenvironment interactions. Blood 2018; 131:2283-2296. [PMID: 29666114 DOI: 10.1182/blood-2017-10-764373] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/03/2018] [Indexed: 02/07/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) are 2 well-defined entities that diverge in their basic pathogenic mechanisms and clinical evolution but they share epidemiological characteristics, cells of origin, molecular alterations, and clinical features that differ from other lymphoid neoplasms. CLL and MCL are classically considered indolent and aggressive neoplasms, respectively. However, the clinical evolution of both tumors is very heterogeneous, with subsets of patients having stable disease for a long time whereas others require immediate intervention. Both CLL and MCL include 2 major molecular subtypes that seem to derive from antigen-experienced CD5+ B cells that retain a naive or memory-like epigenetic signature and carry a variable load of immunoglobulin heavy-chain variable region somatic mutations from truly unmutated to highly mutated, respectively. These 2 subtypes of tumors differ in their molecular pathways, genomic alterations, and clinical behavior, being more aggressive in naive-like than memory-like-derived tumors in both CLL and MCL. The pathogenesis of the 2 entities integrates the relevant influence of B-cell receptor signaling, tumor cell microenvironment interactions, genomic alterations, and epigenome modifications that configure the evolution of the tumors and offer new possibilities for therapeutic intervention. This review will focus on the similarities and differences of these 2 tumors based on recent studies that are enhancing the understanding of their pathogenesis and creating solid bases for new management strategies.
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10
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Hallek M, Shanafelt TD, Eichhorst B. Chronic lymphocytic leukaemia. Lancet 2018; 391:1524-1537. [PMID: 29477250 DOI: 10.1016/s0140-6736(18)30422-7] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 10/30/2017] [Accepted: 11/13/2017] [Indexed: 12/15/2022]
Abstract
Important advances in understanding the pathogenesis of chronic lymphocytic leukaemia in the past two decades have led to the development of new prognostic tools and novel targeted therapies that have improved clinical outcome. Chronic lymphocytic leukaemia is the most common type of leukaemia in developed countries, and the median age at diagnosis is 72 years. The criteria for initiating treatment rely on the Rai and Binet staging systems and on the presence of disease-related symptoms. For many patients with chronic lymphocytic leukaemia, treatment with chemotherapy and anti-CD20 monoclonal antibodies is the standard of care. The impressive efficacy of kinase inhibitors ibrutinib and idelalisib and the BCL-2 antagonist venetoclax have changed the standard of care in specific subsets of patients. In this Seminar, we review the recent progress in the management of chronic lymphocytic leukaemia and highlight new questions surrounding the optimal disease management.
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MESH Headings
- Adenine/analogs & derivatives
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Bridged Bicyclo Compounds, Heterocyclic/therapeutic use
- Diagnosis, Differential
- Genetic Predisposition to Disease
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/etiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Mutation
- Piperidines
- Prognosis
- Purines/therapeutic use
- Pyrazoles/therapeutic use
- Pyrimidines/therapeutic use
- Quinazolinones/therapeutic use
- Recurrence
- Risk Factors
- Sulfonamides/therapeutic use
- Survival Analysis
- Treatment Outcome
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Affiliation(s)
- Michael Hallek
- Department of Internal Medicine, Center of Integrated Oncology Köln Bonn, University Hospital of Cologne, Cologne, Germany.
| | | | - Barbara Eichhorst
- Department of Internal Medicine, Center of Integrated Oncology Köln Bonn, University Hospital of Cologne, Cologne, Germany
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Fischer K, Hallek M. Optimizing frontline therapy of CLL based on clinical and biological factors. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2017; 2017:338-345. [PMID: 29222276 PMCID: PMC6142543 DOI: 10.1182/asheducation-2017.1.338] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The heterogeneity of the clinical course of chronic lymphocytic leukemia (CLL) ranges from an indolent course, where patients do not require therapy for many years, to a very aggressive disease, where treatment is required soon after diagnosis and relapses may occur early. The improved tools for prognostication allow predicting the outcome of patients with increasing reliability. Some markers also allow selecting more specific therapies with improved activity in the presence of certain genetic or clinical features of CLL. Of these markers, TP53 dysfunction, age, the presence of comorbidities and the immunoglobulin heavy-chain variable region gene mutational status, or serum markers such as β2-microglobulin have shown independent prognostic value in multiple prospective trials. During the last 10 years, multiple novel agents have become available. The advent of oral kinase inhibitors or Bcl-2 antagonists has provided highly effective options with acceptable toxicity. This manuscript summarizes the current evidence of the available treatment options and proposes an integrated algorithm for the frontline therapy of CLL.
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MESH Headings
- Administration, Oral
- Age Factors
- Algorithms
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Humans
- Immunoglobulin Heavy Chains/genetics
- Immunoglobulin Heavy Chains/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Mutation
- Protein Kinase Inhibitors/therapeutic use
- Proto-Oncogene Proteins c-bcl-2/genetics
- Proto-Oncogene Proteins c-bcl-2/metabolism
- Tumor Suppressor Protein p53/genetics
- Tumor Suppressor Protein p53/metabolism
- beta 2-Microglobulin/genetics
- beta 2-Microglobulin/metabolism
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Affiliation(s)
- Kirsten Fischer
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Cologne, Germany; and
| | - Michael Hallek
- Department I of Internal Medicine, Center of Integrated Oncology Cologne Bonn, University of Cologne, Cologne, Germany; and
- CECAD–Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, Cologne, Germany
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12
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Ferrando AA, López-Otín C. Clonal evolution in leukemia. Nat Med 2017; 23:1135-1145. [PMID: 28985206 DOI: 10.1038/nm.4410] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/26/2017] [Indexed: 02/06/2023]
Abstract
Human leukemias are liquid malignancies characterized by diffuse infiltration of the bone marrow by transformed hematopoietic progenitors. The accessibility of tumor cells obtained from peripheral blood or through bone marrow aspirates, together with recent advances in cancer genomics and single-cell molecular analysis, have facilitated the study of clonal populations and their genetic and epigenetic evolution over time with unprecedented detail. The results of these analyses challenge the classic view of leukemia as a clonal homogeneous diffuse tumor and introduce a more complex and dynamic scenario. In this review, we present current concepts on the role of clonal evolution in lymphoid and myeloid leukemia as a driver of tumor initiation, disease progression and relapse. We also discuss the implications of these concepts in our understanding of the evolutionary mechanisms involved in leukemia transformation and therapy resistance.
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Affiliation(s)
- Adolfo A Ferrando
- Department of Pediatrics, Columbia University, New York, New York, USA
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Spain
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13
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Eichhorst B, Hallek M. Prognostication of chronic lymphocytic leukemia in the era of new agents. HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2016; 2016:149-155. [PMID: 27913474 PMCID: PMC6142472 DOI: 10.1182/asheducation-2016.1.149] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The prognosis of chronic lymphocytic leukemia (CLL) is very heterogeneous. Therefore, a plethora of prognostic factors has been identified to allow a better prediction of the individual prognosis of a given patient. The clinical staging systems by Rai and Binet have been the backbone of clinical management for several decades. The advent of genetic and biochemical markers, as well as next-generation sequencing has provided several markers that can predict the prognosis of patients with CLL. Using this knowledge, several scores have been created to improve predicting overall survival and/or treatment-free survival. These prognostic scores were developed in the era of chemotherpay/chemoimmunotherapy. Therefore, they now need to be tested with novel agents. However, despite tremendously improved therapeutic options, CLL patients with TP53 dysfunction or a complex karyotype remain at very high risk and seem to have a shorter (treatment-free) survival. The recently published international prognostic index (CLL IPI) incorporates most of these factors and provides a tool to analyze outcome in the modern era of targeted therapies.
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MESH Headings
- Biomarkers, Tumor/genetics
- Disease-Free Survival
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Survival Rate
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Barbara Eichhorst
- Department I for Internal Medicine and Centre of Integrated Oncology, and
| | - Michael Hallek
- Department I for Internal Medicine and Centre of Integrated Oncology, and
- CECAD—Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases, University of Cologne, Cologne, Germany
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Identifying High-Risk Chronic Lymphocytic Leukemia: A Pathogenesis-Oriented Appraisal of Prognostic and Predictive Factors in Patients Treated with Chemotherapy with or without Immunotherapy. Mediterr J Hematol Infect Dis 2016; 8:e2016047. [PMID: 27872727 PMCID: PMC5111525 DOI: 10.4084/mjhid.2016.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 09/16/2016] [Indexed: 11/21/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) displays an extremely variable clinical behaviour. Accurate prognostication and prediction of response to treatment are important in an era of effective first-line regimens and novel molecules for high risk patients. Because a plethora of prognostic biomarkers were identified, but few of them were validated by multivariable analysis in comprehensive prospective studies, we applied in this survey stringent criteria to select papers from the literature in order to identify the most reproducible prognostic/predictive markers. Each biomarker was analysed in terms of reproducibility across the different studies with respect to its impact on time to first treatment (TTFT), progression free survival (PFS), overall survival (OS) and response to treatment. We were able to identify the following biomarkers as the most reliable in guiding risk stratification in the daily clinical practice: 17p-/TP53 mutations, IGHV unmutated configuration, short telomeres and 11q-. However, the method for measuring telomere length was not validated yet and 11q- was predictive of inferior OS only in those patients who did not receive FCR-like combinations. Stage and lymphocytosis were predictive of shorter TTFT and age, high serum thymidine kinase levels and poor performance status were predictive of shorter OS. Using our criteria no parameter was found to independently predict for inferior response to treatment.
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15
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Genetic evolution in chronic lymphocytic leukaemia. Best Pract Res Clin Haematol 2016; 29:67-78. [PMID: 27742073 DOI: 10.1016/j.beha.2016.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 06/30/2016] [Accepted: 08/04/2016] [Indexed: 11/21/2022]
Abstract
Next-generation sequencing provides a comprehensive understanding of the genomic, epigenomic and transcriptomic underpinnings of chronic lymphocytic leukaemia. Recent studies have uncovered new drivers, including mutations in non-coding regions, and signalling pathways whose role in cancer was previously unknown or poorly understood. Moreover, massive scale epigenomics and transcriptomics have supplied the foundations for the cellular origin of the disease. Some drivers could be targeted pharmacologically, and the ability to detect mutations present in minority subclones might even allow treatment before clonal selection occurs, thus preventing disease refractoriness. As our understanding broadens and ongoing technological innovation propels new achievements, we will certainly learn how to apply it in our daily practice.
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Present and future of personalized medicine in CLL. Best Pract Res Clin Haematol 2016; 29:100-110. [PMID: 27742064 DOI: 10.1016/j.beha.2016.08.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 07/19/2016] [Accepted: 08/04/2016] [Indexed: 12/27/2022]
Abstract
Medicine has been 'personalized' (i.e. centred in persons) since its foundation. Recently, however, the term 'personalized medicine' (or, better, 'precision medicine') has been introduced to define 'a form of medicine that uses information about a person's genes, proteins, and environment to prevent, diagnose, and treat disease'. This concept has gained momentum thanks to next-generation-sequencing (NGS) techniques that allow identification of molecular characteristics unique to the patient and to the tumour. It is hoped that NGS will not only contribute to a better understanding of chronic lymphocytic leukaemia (CLL), but will identify disease subsets that could benefit from specific treatment interventions. Recent advances in diagnosis (e.g. high-resolution immunophenotyping, markers of genetic abnormalities), prognosis (e.g. biomarkers), response predictors [e.g. del(17p)/TP53 mutations even at subclonal level], treatment (e.g. BCR signalling inhibitors, BCL2 antagonists, CAR-T cells) and methods to evaluate minimal residual disease constitute good examples of tools facilitating 'personalized' management of patients with CLL.
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Freund P, Porpaczy EA, Le T, Gruber M, Pausz C, Staber P, Jäger U, Vanura K. Cannabinoid Receptors Are Overexpressed in CLL but of Limited Potential for Therapeutic Exploitation. PLoS One 2016; 11:e0156693. [PMID: 27248492 PMCID: PMC4889125 DOI: 10.1371/journal.pone.0156693] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 05/18/2016] [Indexed: 12/16/2022] Open
Abstract
The cannabinoid receptors 1 and 2 (CNR1&2) are overexpressed in a variety of malignant diseases and cannabinoids can have noteworthy impact on tumor cell viability and tumor growth. Patients diagnosed with chronic lymphocytic leukemia (CLL) present with very heterogeneous disease characteristics translating into highly differential risk properties. To meet the urgent need for refinement in risk stratification at diagnosis and the search for novel therapies we studied CNR expression and response to cannabinoid treatment in CLL. Expression levels of CNR1&2 were determined in 107 CLL patients by real-time PCR and analyzed with regard to prognostic markers and survival. Cell viability of primary CLL cells was determined in suspension and co-culture after incubation in increasing cannabinoid concentrations under normal and reduced serum conditions and in combination with fludarabine. Impact of cannabinoids on migration of CLL cells towards CXCL12 was determined in transwell plates. We found CNR1&2 to be overexpressed in CLL compared to healthy B-cells. Discriminating between high and low expressing subgroups, only high CNR1 expression was associated with two established high risk markers and conferred significantly shorter overall and treatment free survival. Viability of CLL primary cells was reduced in a dose dependent fashion upon incubation with cannabinoids, however, healthy cells were similarly affected. Under serum reduced conditions, no significant differences were observed within suspension and co-culture, respectively, however, the feeder layer contributed significantly to the survival of CLL cells compared to suspension culture conditions. No significant differences were observed when treating CLL cells with cannabinoids in combination with fludarabine. Interestingly, biologic activity of cannabinoids was independent of both CNR1&2 expression. Finally, we did not observe an inhibition of CXCL12-induced migration by cannabinoids. In contrast to other tumor entities, our data suggest a limited usability of cannabinoids for CLL therapy. Nonetheless, we could define CNR1 mRNA expression as novel prognostic marker.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Coculture Techniques
- Female
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Male
- Middle Aged
- Prognosis
- RNA, Messenger/genetics
- Receptors, Cannabinoid/genetics
- Receptors, Cannabinoid/metabolism
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Affiliation(s)
- Patricia Freund
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Edit A. Porpaczy
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Trang Le
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Michaela Gruber
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Clemens Pausz
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Philipp Staber
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Ulrich Jäger
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
| | - Katrina Vanura
- Division of Hematology and Hemostaseology, Department of Medicine I, Medical University of Vienna, Vienna, Austria
- * E-mail:
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Rai KR, Jain P. Chronic lymphocytic leukemia (CLL)-Then and now. Am J Hematol 2016; 91:330-40. [PMID: 26690614 DOI: 10.1002/ajh.24282] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 12/15/2015] [Indexed: 12/27/2022]
Abstract
The field of chronic lymphocytic leukemia (CLL) has witnessed considerable change since the time clinical staging was introduced in clinical practice in 1975. Over the years, the prognostication in CLL has expanded with the addition in late 90s of mutational status of variable region of immunoglobulin heavy chain (IGHV), and chromosomal analyses using fluorescent in situ hybridization (FISH). More recently, stereotypy of BCR (B cell receptor) and whole exome sequencing (WES) based discovery of specific mutations such as NOTCH1, TP53, SF3B1, XPO-1, BIRC3, ATM, and RPS15 further refined the current prognostication system in CLL. In therapy, the field of CLL has seen major changes from oral chlorambucil and steroids prior to 1980s, to chemo-immunotherapy (CIT) with fludarabine, cyclophosphamide, rituximab (FCR) to the orally administered targeted therapeutic agents inhibiting kinases in the B cell receptor (BCR) signaling pathway such as Ibrutinib (BTK inhibitor) and Idelalisib (p110 PI3Kδ inhibitor) and novel anti-CD20 mAb's (monoclonal antibodies) such as obinutuzumab. This progress is continuing and other targeted therapeutics such as Bcl2 antagonists (Venetoclax or ABT-199) and finally chimeric antigen receptor against T cells (CART) are in the process of being developed. This review is an attempt to summarize the major benchmarks in the prognostication and in the therapy of CLL. The topic allocated to us by Dr Ayalew Tefferi and Dr Carlo Brugnara is very appropriate to reminisce what our understanding of chronic lymphocytic leukemia (CLL) was in 1976 and how rapidly have the advances occurring in this field affected the patients with CLL.
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Affiliation(s)
- Kanti R. Rai
- Division of Hematology-Oncology, NSLIJ-Hofstra School of Medicine, Long Island Jewish Medical Center; CLL Research and Treatment Program; New Hyde Park New York
| | - Preetesh Jain
- Department of Internal Medicine; University of Texas Medical School at Houston; Texas
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Savvopoulos S, Misener R, Panoskaltsis N, Pistikopoulos EN, Mantalaris A. A Personalized Framework for Dynamic Modeling of Disease Trajectories in Chronic Lymphocytic Leukemia. IEEE Trans Biomed Eng 2016; 63:2396-2404. [PMID: 26929022 DOI: 10.1109/tbme.2016.2533658] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is the most common peripheral blood and bone marrow cancer in the developed world. This manuscript proposes mathematical model equations representing the disease dynamics of B-cell CLL. We interconnect delay differential cell cycle models in each of the tumor-involved disease centers using physiologically relevant cell migration. We further introduce five hypothetical case studies representing CLL heterogeneity commonly seen in clinical practice and demonstrate how the proposed CLL model framework may capture disease pathophysiology across patient types. We conclude by exploring the capacity of the proposed temporally- and spatially distributed model to capture the heterogeneity of CLL disease progression. By using global sensitivity analysis, the critical parameters influencing disease trajectory over space and time are: 1) the initial number of CLL cells in peripheral blood, the number of involved lymph nodes, the presence and degree of splenomegaly; 2) the migratory fraction of nonproliferating as well as proliferating CLL cells from bone marrow into blood and of proliferating CLL cells from blood into lymph nodes; and 3) the parameters inducing nonproliferative cells to proliferate. The proposed model offers a practical platform that may be explored in future personalized patient protocols once validated.
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Clinical impact of clonal and subclonal TP53, SF3B1, BIRC3, NOTCH1, and ATM mutations in chronic lymphocytic leukemia. Blood 2016; 127:2122-30. [PMID: 26837699 DOI: 10.1182/blood-2015-07-659144] [Citation(s) in RCA: 235] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 01/29/2016] [Indexed: 12/30/2022] Open
Abstract
Genomic studies have revealed the complex clonal heterogeneity of chronic lymphocytic leukemia (CLL). The acquisition and selection of genomic aberrations may be critical to understanding the progression of this disease. In this study, we have extensively characterized the mutational status of TP53, SF3B1, BIRC3, NOTCH1, and ATM in 406 untreated CLL cases by ultra-deep next-generation sequencing, which detected subclonal mutations down to 0.3% allele frequency. Clonal dynamics were examined in longitudinal samples of 48 CLL patients. We identified a high proportion of subclonal mutations, isolated or associated with clonal aberrations. TP53 mutations were present in 10.6% of patients (6.4% clonal, 4.2% subclonal), ATM mutations in 11.1% (7.8% clonal, 1.3% subclonal, 2% germ line mutations considered pathogenic), SF3B1 mutations in 12.6% (7.4% clonal, 5.2% subclonal), NOTCH1 mutations in 21.8% (14.2% clonal, 7.6% subclonal), and BIRC3 mutations in 4.2% (2% clonal, 2.2% subclonal). ATM mutations, clonal SF3B1, and both clonal and subclonal NOTCH1 mutations predicted for shorter time to first treatment irrespective of the immunoglobulin heavy-chain variable-region gene (IGHV) mutational status. Clonal and subclonal TP53 and clonal NOTCH1 mutations predicted for shorter overall survival together with the IGHV mutational status. Clonal evolution in longitudinal samples mainly occurred in cases with mutations in the initial samples and was observed not only after chemotherapy but also in untreated patients. These findings suggest that the characterization of the subclonal architecture and its dynamics in the evolution of the disease may be relevant for the management of CLL patients.
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Cramer P, Hallek M, Eichhorst B. State-of-the-Art Treatment and Novel Agents in Chronic Lymphocytic Leukemia. Oncol Res Treat 2016; 39:25-32. [DOI: 10.1159/000443903] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/12/2016] [Indexed: 11/19/2022]
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Valdés-Mas R, Gutiérrez-Abril J, Puente XS, López-Otín C. Chronic lymphocytic leukemia: looking into the dark side of the genome. Cell Death Differ 2016; 23:7-9. [PMID: 26611460 PMCID: PMC4815973 DOI: 10.1038/cdd.2015.155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- R Valdés-Mas
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - J Gutiérrez-Abril
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - X S Puente
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
| | - C López-Otín
- Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, Oviedo, Spain
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Del Giudice I, Marinelli M, Wang J, Bonina S, Messina M, Chiaretti S, Ilari C, Cafforio L, Raponi S, Mauro FR, Di Maio V, De Propris MS, Nanni M, Ciardullo C, Rossi D, Gaidano G, Guarini A, Rabadan R, Foà R. Inter- and intra-patient clonal and subclonal heterogeneity of chronic lymphocytic leukaemia: evidences from circulating and lymph nodal compartments. Br J Haematol 2015; 172:371-383. [PMID: 26597680 DOI: 10.1111/bjh.13859] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/22/2015] [Indexed: 02/02/2023]
Abstract
Whole exome sequencing and copy number aberration (CNA) analysis were performed on cells taken from peripheral blood (PB) and lymph nodes (LN) of patients with chronic lymphocytic leukaemia (CLL). Of 64 non-silent somatic mutations, 54 (84·4%) were clonal in both compartments, 3 (4·7%) were PB-specific and 7 (10·9%) were LN-specific. Most of the LN- or PB-specific mutations were subclonal in the other corresponding compartment (variant frequency 0·5-5·3%). Of 41 CNAs, 27 (65·8%) were shared by both compartments and 7 (17·1%) were LN- or PB-specific. Overall, 6 of 9 cases (66·7%) showed genomic differences between the compartments. At subsequent relapse, Case 10, with 6 LN-specific lesions, and Case 100, with 6 LN-specific and 8 PB-specific lesions, showed, in the PB, the clonal expansion of LN-derived lesions with an adverse impact: SF3B1 mutation, BIRC3 deletion, del8(p23·3-p11·1), del9(p24·3-p13·1) and gain 2(p25·3-p14). CLL shows an intra-patient clonal heterogeneity according to the disease compartment, with both LN and PB-specific mutations/CNAs. The LN microenvironment might contribute to the clonal selection of unfavourable lesions, as LN-derived mutations/CNAs can appear in the PB at relapse.
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Affiliation(s)
- Ilaria Del Giudice
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Marilisa Marinelli
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Jiguang Wang
- Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, US
| | - Silvia Bonina
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Monica Messina
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Sabina Chiaretti
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Caterina Ilari
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Luciana Cafforio
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Sara Raponi
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Francesca Romana Mauro
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Valeria Di Maio
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Maria Stefania De Propris
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Mauro Nanni
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Carmela Ciardullo
- Division of Haematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Davide Rossi
- Division of Haematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Gianluca Gaidano
- Division of Haematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Anna Guarini
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
| | - Raul Rabadan
- Department of Biomedical Informatics, Center for Computational Biology and Bioinformatics, Columbia University, New York, US
| | - Robin Foà
- Division of Haematology, Department of Cellular Biotechnologies and Haematology, Sapienza University, Rome, Italy
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24
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Mutations driving CLL and their evolution in progression and relapse. Nature 2015; 526:525-30. [PMID: 26466571 PMCID: PMC4815041 DOI: 10.1038/nature15395] [Citation(s) in RCA: 766] [Impact Index Per Article: 85.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 08/11/2015] [Indexed: 01/05/2023]
Abstract
Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. We identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized cancer drivers (RPS15, IKZF3) and collectively identify RNA processing and export, MYC activity and MAPK signaling as central pathways involved in CLL. Clonality analysis of this large dataset further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing datasets of clinically informative samples enable the discovery of novel cancer genes and the network of relationships between the driver events and their impact on disease relapse and clinical outcome.
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25
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Rodríguez D, Bretones G, Arango JR, Valdespino V, Campo E, Quesada V, López-Otín C. Molecular pathogenesis of CLL and its evolution. Int J Hematol 2015; 101:219-28. [PMID: 25630433 DOI: 10.1007/s12185-015-1733-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 01/14/2015] [Indexed: 12/11/2022]
Abstract
In spite of being the most prevalent adult leukemia in Western countries, the molecular mechanisms driving the establishment and progression of chronic lymphocytic leukemia (CLL) remain largely unknown. In recent years, the use of next-generation sequencing techniques has uncovered new and, in some cases, unexpected driver genes with prognostic and therapeutic value. The mutational landscape of CLL is characterized by high-genetic and epigenetic heterogeneity, low mutation recurrence and a long tail of cases with undefined driver genes. On the other hand, the use of deep sequencing has also revealed high intra-tumor heterogeneity and provided a detailed picture of clonal evolution processes. This phenomenon, in which aberrant DNA methylation can also participate, appears to be tightly associated to poor outcomes and chemo-refractoriness, thus providing a new subject for therapeutic intervention. Hence, and having in mind the limitations derived from the CLL complexity thus described, the application of massively parallel sequencing studies has unveiled a wealth of information that is expected to substantially improve patient staging schemes and CLL clinical management.
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Affiliation(s)
- David Rodríguez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología-IUOPA, Universidad de Oviedo, 33006, Oviedo, Spain
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26
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Abstract
Over the past few years, massively parallel sequencing technologies have revealed with high resolution the tremendous genetic and epigenetic heterogeneity in chronic lymphocytic leukemia (CLL). We have learned how the molecular architecture differs not only between affected individuals but also within samples and over time. These insights have catalyzed our understanding of the pathobiology of CLL and point to critical signaling pathways in the development and progression of the disease. Several key driver alterations have been identified, which serve to refine prognostic schemata but also to inspire the development of new therapeutic strategies. Ongoing advances in technology promise to further elucidate the molecular basis of CLL, and this knowledge is anticipated to aid us in understanding and addressing the clinical challenge presented by the vast variability in the clinical course of patients with CLL.
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MESH Headings
- Chromosome Aberrations
- Epigenomics
- Genetic Heterogeneity
- Genome/genetics
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Receptors, Antigen, B-Cell/genetics
- Receptors, Antigen, B-Cell/metabolism
- Signal Transduction/genetics
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Affiliation(s)
- Michaela Gruber
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Broad Institute, Cambridge, MA; Department of Internal Medicine I, Division of Haematology and Haemostaseology, Medical University of Vienna, Vienna, Austria
| | - Catherine J Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; Broad Institute, Cambridge, MA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
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Villamor N, López-Guillermo A, López-Otín C, Campo E. Next-generation sequencing in chronic lymphocytic leukemia. Semin Hematol 2014; 50:286-95. [PMID: 24246696 DOI: 10.1053/j.seminhematol.2013.09.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The use of next-generation sequencing (NGS) has expanded our knowledge of the genomic alterations in chronic lymphocytic leukemia (CLL) and provides new tools for analyzing leukemic clonal architecture. Recent studies have demonstrated substantial differences in genomic alterations between mutated and unmutated IGHV subgroups, which reflect distinct molecular pathways and mutagenic mechanisms in the pathogenesis of the disease. The mutational profile of CLL can be characterized by a relatively low number of somatic mutations per case, few recurrent mutations at moderate frequency (5%-15%) and a long tail of recurrent lower frequency somatic mutations. Functional and clinical studies of novel mutations have uncovered new mechanisms involved in the pathogenesis of the disease, revealing new insights into CLL molecular evolution that could ultimately translate into improvements in the management of patients. The clonal architecture of CLL shows striking heterogeneity between patients, which could have important clinical implications. In summary, NGS studies of CLL are expanding our fundamental knowledge on the molecular mechanisms involved in the pathogenesis of the disease and offering new perspectives for the clinical management of the patients.
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Affiliation(s)
- Neus Villamor
- Unitat d'Hematopatologia, Servei d'Anatomia Patològica, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain.
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28
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Abstract
PURPOSE OF REVIEW Next-generation sequencing of whole genomes, exomes and DNA methylomes in chronic lymphocytic leukemia (CLL) has provided the first comprehensive view of somatic mutations and methylation changes in this disease. This review summarizes the recent findings in this field and their impact on our current understanding of this neoplasm. RECENT FINDINGS Genomic studies have revealed a remarkable molecular heterogeneity of the disease, with only few genes mutated in up to 10-15% of the patients and a relatively large number of genes recurrently mutated at low frequency. The mutated genes tend to cluster in different pathways that include NOTCH1 signaling, RNA splicing, processing and transport machinery, innate inflammatory response, and DNA damage and cell cycle control, among others. NOTCH1 and SF3B1 mutations are emerging as new drivers of aggressive forms of the disease. Genome-wide methylation studies have shown that CLL transformation is associated with a massive hypomethylation phenomenon frequently affecting the enhancer regions. This epigenetic reprogramming maintains an imprint of the putative cell of origin from naïve and memory B-cells. SUMMARY Genomic and epigenomic studies of CLL are reshaping our understanding of the disease and provide new perspective for a more individualized diagnosis and new potential therapeutic targets.
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29
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Landscape of somatic mutations and clonal evolution in mantle cell lymphoma. Proc Natl Acad Sci U S A 2013; 110:18250-5. [PMID: 24145436 DOI: 10.1073/pnas.1314608110] [Citation(s) in RCA: 397] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an aggressive tumor, but a subset of patients may follow an indolent clinical course. To understand the mechanisms underlying this biological heterogeneity, we performed whole-genome and/or whole-exome sequencing on 29 MCL cases and their respective matched normal DNA, as well as 6 MCL cell lines. Recurrently mutated genes were investigated by targeted sequencing in an independent cohort of 172 MCL patients. We identified 25 significantly mutated genes, including known drivers such as ataxia-telangectasia mutated (ATM), cyclin D1 (CCND1), and the tumor suppressor TP53; mutated genes encoding the anti-apoptotic protein BIRC3 and Toll-like receptor 2 (TLR2); and the chromatin modifiers WHSC1, MLL2, and MEF2B. We also found NOTCH2 mutations as an alternative phenomenon to NOTCH1 mutations in aggressive tumors with a dismal prognosis. Analysis of two simultaneous or subsequent MCL samples by whole-genome/whole-exome (n = 8) or targeted (n = 19) sequencing revealed subclonal heterogeneity at diagnosis in samples from different topographic sites and modulation of the initial mutational profile at the progression of the disease. Some mutations were predominantly clonal or subclonal, indicating an early or late event in tumor evolution, respectively. Our study identifies molecular mechanisms contributing to MCL pathogenesis and offers potential targets for therapeutic intervention.
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30
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Landau DA, Carter SL, Getz G, Wu CJ. Clonal evolution in hematological malignancies and therapeutic implications. Leukemia 2013; 28:34-43. [PMID: 23979521 DOI: 10.1038/leu.2013.248] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 07/22/2013] [Accepted: 08/14/2013] [Indexed: 12/19/2022]
Abstract
The ability of cancer to evolve and adapt is a principal challenge to therapy in general and to the paradigm of targeted therapy in particular. This ability is fueled by the co-existence of multiple, genetically heterogeneous subpopulations within the cancer cell population. Increasing evidence has supported the idea that these subpopulations are selected in a Darwinian fashion, by which the genetic landscape of the tumor is continuously reshaped. Massively parallel sequencing has enabled a recent surge in our ability to study this process, adding to previous efforts using cytogenetic methods and targeted sequencing. Altogether, these studies reveal the complex evolutionary trajectories occurring across individual hematological malignancies. They also suggest that while clonal evolution may contribute to resistance to therapy, treatment may also hasten the evolutionary process. New insights into this process challenge us to understand the impact of treatment on clonal evolution and inspire the development of novel prognostic and therapeutic strategies.
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Affiliation(s)
- D A Landau
- 1] Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA [2] Broad Institute, Cambridge, MA, USA [3] Department of Hematology, Yale Cancer Center, New Haven, CT, USA [4] Université Paris Diderot, Paris, France
| | | | - G Getz
- 1] Broad Institute, Cambridge, MA, USA [2] Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA, USA
| | - C J Wu
- 1] Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA [2] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA [3] Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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Soldini D, Campo E. Genetic sequencing studies in Burkitt's lymphoma: what can we learn about tumorigenesis? Expert Rev Hematol 2013; 6:219-21. [PMID: 23782073 DOI: 10.1586/ehm.13.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Quesada V, Ramsay AJ, Rodríguez D, Puente XS, Campo E, López-Otín C. The genomic landscape of chronic lymphocytic leukemia: clinical implications. BMC Med 2013; 11:124. [PMID: 23656622 PMCID: PMC3655884 DOI: 10.1186/1741-7015-11-124] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/12/2013] [Indexed: 01/06/2023] Open
Abstract
A precise understanding of the genomic and epigenomic features of chronic lymphocytic leukemia (CLL) may benefit the study of the disease's staging and treatment. While recent reports have shed some light on these aspects, several challenges need to be addressed before translating this research into clinical practice. Thus, even the best candidate driver genes display low mutational rates compared to other tumors. This means that a large percentage of cases do not display clear tumor-driving point mutations, or show candidate driving point mutations with no obvious biochemical relationship to the more frequently mutated genes. This genomic landscape probably reflects either an unknown underlying biochemical mechanism playing a key role in CLL or multiple biochemical pathways independently driving the development of this tumor. The elucidation of either scenario will have important consequences on the clinical management of CLL. Herein, we review the recent advances in the definition of the genomic landscape of CLL and the ongoing research to characterize the underlying biochemical events that drive this disease.
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Affiliation(s)
- Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Universidad de Oviedo - IUOPA, Oviedo, Spain.
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Bassaganyas L, Beà S, Escaramís G, Tornador C, Salaverria I, Zapata L, Drechsel O, Ferreira PG, Rodriguez-Santiago B, Tubio JMC, Navarro A, Martín-García D, López C, Martínez-Trillos A, López-Guillermo A, Gut M, Ossowski S, López-Otín C, Campo E, Estivill X. Sporadic and reversible chromothripsis in chronic lymphocytic leukemia revealed by longitudinal genomic analysis. Leukemia 2013; 27:2376-9. [PMID: 23612016 PMCID: PMC3865532 DOI: 10.1038/leu.2013.127] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- L Bassaganyas
- 1] Center for Genomic Regulation (CRG), Barcelona, Spain [2] Pompeu Fabra University (UPF) Barcelona, Spain [3] Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain [4] Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
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Rodríguez D, Ramsay AJ, Quesada V, Garabaya C, Campo E, Freije JMP, López-Otín C. Functional analysis of sucrase–isomaltase mutations from chronic lymphocytic leukemia patients. Hum Mol Genet 2013; 22:2273-82. [DOI: 10.1093/hmg/ddt078] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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