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Gybeľ T, Čada Š, Klementová D, Schwalm MP, Berger BT, Šebesta M, Knapp S, Bryja V. Splice variants of CK1α and CK1α-like: Comparative analysis of subcellular localization, kinase activity and function in the Wnt signaling pathway. J Biol Chem 2024:107407. [PMID: 38796065 DOI: 10.1016/j.jbc.2024.107407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/28/2024] Open
Abstract
Members of the casein kinase 1 (CK1) family are important regulators of multiple signaling pathways. CK1α is a well-known negative regulator of the Wnt/β-catenin pathway, which promotes the degradation of β-catenin via its phosphorylation of Ser45. In contrast, the closest paralog of CK1α, CK1α-like, is a poorly characterized kinase of unknown function. In this study we show that the deletion of CK1α, but not CK1α-like, resulted in a strong activation of the Wnt/β-catenin pathway. Wnt-3a treatment further enhanced the activation, which suggests there are at least two modes, a CK1α-dependent and Wnt-dependent, of β-catenin regulation. Rescue experiments showed that only 2 out of 10 naturally occurring splice CK1α/α-like variants were able to rescue the augmented Wnt/β-catenin signaling caused by CK1α-deficiency in cells. Importantly, the ability to phosphorylate β-catenin on Ser45 in the in vitro kinase assay was required but not sufficient for such rescue. Our compound CK1α and GSK3α/β knock out models suggest that the additional non-redundant function of CK1α in the Wnt pathway beyond Ser45-β-catenin phosphorylation includes Axin phosphorylation. Finally, we established NanoBRET assays for the three most common CK1α splice variants as well as CK1α-like. Target engagement data revealed comparable potency of known CK1α inhibitors for all CK1α variants but not for CK1α-like. In summary, our work brings important novel insights into the biology of CK1α, including evidence for the lack of redundancy with other CK1 kinases in the negative regulation of the Wnt/β-catenin pathway at the level of β-catenin and Axin.
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Affiliation(s)
- Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Štěpán Čada
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Darja Klementová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic; CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Benedict-Tilman Berger
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, Frankfurt am Main, Germany
| | - Marek Šebesta
- CEITEC-Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 9, Frankfurt am Main, Germany; Structural Genomics Consortium, Johann Wolfgang Goethe-University, Max-von-Laue-Strasse 15, Frankfurt am Main, Germany; German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DKTK site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic; Department of Cytokinetics, Institute of Biophysics of the Czech Academy of Sciences, 612 65 Brno, Czech Republic.
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2
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Kurucova T, Reblova K, Janovska P, Porc JP, Navrkalova V, Pavlova S, Malcikova J, Plevova K, Tichy B, Doubek M, Bryja V, Kotaskova J, Pospisilova S. Unveiling the dynamics and molecular landscape of a rare chronic lymphocytic leukemia subpopulation driving refractoriness: insights from single-cell RNA sequencing. Mol Oncol 2024. [PMID: 38770541 DOI: 10.1002/1878-0261.13663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/28/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
Early identification of resistant cancer cells is currently a major challenge, as their expansion leads to refractoriness. To capture the dynamics of these cells, we made a comprehensive analysis of disease progression and treatment response in a chronic lymphocytic leukemia (CLL) patient using a combination of single-cell and bulk genomic methods. At diagnosis, the patient presented with unfavorable genetic markers, including notch receptor 1 (NOTCH1) mutation and loss(11q). The initial and subsequent treatment lines did not lead to a durable response and the patient developed refractory disease. Refractory CLL cells featured substantial dysregulation in B-cell phenotypic markers such as human leukocyte antigen (HLA) genes, immunoglobulin (IG) genes, CD19 molecule (CD19), membrane spanning 4-domains A1 (MS4A1; previously known as CD20), CD79a molecule (CD79A) and paired box 5 (PAX5), indicating B-cell de-differentiation and disease transformation. We described the clonal evolution and characterized in detail two cell populations that emerged during the refractory disease phase, differing in the presence of high genomic complexity. In addition, we successfully tracked the cells with high genomic complexity back to the time before treatment, where they formed a rare subpopulation. We have confirmed that single-cell RNA sequencing enables the characterization of refractory cells and the monitoring of their development over time.
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Affiliation(s)
- Terezia Kurucova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kamila Reblova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Pavlina Janovska
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jakub Pawel Porc
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Veronika Navrkalova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Sarka Pavlova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Jitka Malcikova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Boris Tichy
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Michael Doubek
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Vitezslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jana Kotaskova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Center of Molecular Medicine, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
- Institute of Medical Genetics and Genomics, Faculty of Medicine, Masaryk University and University Hospital Brno, Czech Republic
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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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4
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Dubaic M, Peskova L, Hampl M, Weissova K, Celiker C, Shylo NA, Hruba E, Kavkova M, Zikmund T, Weatherbee SD, Kaiser J, Barta T, Buchtova M. Role of ciliopathy protein TMEM107 in eye development: insights from a mouse model and retinal organoid. Life Sci Alliance 2023; 6:e202302073. [PMID: 37863656 PMCID: PMC10589122 DOI: 10.26508/lsa.202302073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023] Open
Abstract
Primary cilia are cellular surface projections enriched in receptors and signaling molecules, acting as signaling hubs that respond to stimuli. Malfunctions in primary cilia have been linked to human diseases, including retinopathies and ocular defects. Here, we focus on TMEM107, a protein localized to the transition zone of primary cilia. TMEM107 mutations were found in patients with Joubert and Meckel-Gruber syndromes. A mouse model lacking Tmem107 exhibited eye defects such as anophthalmia and microphthalmia, affecting retina differentiation. Tmem107 expression during prenatal mouse development correlated with phenotype occurrence, with enhanced expression in differentiating retina and optic stalk. TMEM107 deficiency in retinal organoids resulted in the loss of primary cilia, down-regulation of retina-specific genes, and cyst formation. Knocking out TMEM107 in human ARPE-19 cells prevented primary cilia formation and impaired response to Smoothened agonist treatment because of ectopic activation of the SHH pathway. Our data suggest TMEM107 plays a crucial role in early vertebrate eye development and ciliogenesis in the differentiating retina.
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Affiliation(s)
- Marija Dubaic
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucie Peskova
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Hampl
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kamila Weissova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Canan Celiker
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Natalia A Shylo
- Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Eva Hruba
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Michaela Kavkova
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomas Zikmund
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Scott D Weatherbee
- Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
- Biology Department, Fairfield University, Fairfield, CT, USA
| | - Jozef Kaiser
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomas Barta
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marcela Buchtova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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5
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Bennett R, Anderson MA, Seymour JF. Unresolved questions in selection of therapies for treatment-naïve chronic lymphocytic leukemia. J Hematol Oncol 2023; 16:72. [PMID: 37422670 PMCID: PMC10329329 DOI: 10.1186/s13045-023-01469-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/19/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND The treatment landscape for chronic lymphocytic leukemia (CLL) continues to undergo considerable evolution. Optimal selection of initial therapy from multiple effective options provides a major challenge for clinicians, who need to consider both disease and patient factors in conjunction with a view to sequencing available therapies in event of disease relapse. REVIEW We explore the most topical clinically relevant unresolved questions through discussion of important available pertinent literature and propose expert opinion based on these data. (1) Shrinking role of chemoimmunotherapy (CIT); while novel therapies are generally superior, we highlight the utility of FCR for IGHV-mutated CLL. (2) Choosing between inhibitors of Bruton's tyrosine kinase (BTKi); while efficacy between agents is likely similar there are important differences in toxicity profiles, including the incidence of cardiac arrhythmia and hypertension. (3) BTKi with or without anti-CD20 monoclonal antibodies (mAb); while obinutuzumab-acalabrutinib (AO) may confer superior progression-free survival to acalabrutinib (Acala), this is not true of rituximab (Ritux) to ibrutinib (Ib)-we highlight that potential for increased side effects should be carefully considered. (4) Continuous BTKi versus time-limited venetoclax-obinutuzumab (VenO); we propose that venetoclax (Ven)-based therapy is generally preferable to BTKi with exception of TP53 aberrant disease. (5) BTKi-Ven versus VenO as preferred time-limited therapy; we discuss comparable efficacies and the concerns about simultaneous 1L exposure to both BTKi and Ven drug classes. (6) Utility of triplet therapy (BTKi-Ven-antiCD20 mAb) versus VenO; similar rates of complete response are observed yet with greater potential for adverse events. (7) Optimal therapy for TP53 aberrant CLL; while limited data are available, there are likely effective novel therapy combinations for TP53 aberrant disease including BTKi, BTKi-Ven ± antiCD20 mAb. CONCLUSION Frontline therapy for CLL should be selected based on efficacy considering the patient specific biologic profile of their disease and potential toxicities, considering patient comorbidities and preferences. With the present paradigm of sequencing effective agents, 1L combinations of novel therapies should be used with caution in view of potential adverse events and theoretical resistance mechanism concerns in the absence of compelling randomized data to support augmented efficacy.
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Affiliation(s)
- Rory Bennett
- Department of Clinical Haematology, Royal Melbourne Hospital and Peter MacCallum Cancer Centre, 305 Grattan St, Parkville, Melbourne, VIC, 3000, Australia
| | - Mary Ann Anderson
- Department of Clinical Haematology, Royal Melbourne Hospital and Peter MacCallum Cancer Centre, 305 Grattan St, Parkville, Melbourne, VIC, 3000, Australia
- Division of Blood Cells and Blood Cancer, The Walter and Eliza Hall Institute, 1G, Royal Parade, Parkville, Melbourne, VIC, 3052, Australia
- University of Melbourne, Grattan St, Parkville, Melbourne, VIC, 3010, Australia
| | - John F Seymour
- Department of Clinical Haematology, Royal Melbourne Hospital and Peter MacCallum Cancer Centre, 305 Grattan St, Parkville, Melbourne, VIC, 3000, Australia.
- University of Melbourne, Grattan St, Parkville, Melbourne, VIC, 3010, Australia.
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Marks JA, Wang X, Fenu EM, Bagg A, Lai C. TP53 in AML and MDS: The new (old) kid on the block. Blood Rev 2023; 60:101055. [PMID: 36841672 DOI: 10.1016/j.blre.2023.101055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
MDS and AML are clonal hematopoietic stem cell disorders of increasing incidence, having a variable prognosis based, among others, on co-occurring molecular abnormalities. TP53 mutations are frequently detected in these myeloid neoplasms and portend a poor prognosis with known therapeutic resistance. This article provides a timely review of the complexity of TP53 alterations, providing updates in diagnosis and prognosis based on new 2022 International Consensus Classification (ICC) and World Health Organization (WHO) guidelines. The article addresses optimal testing strategies and reviews current and arising therapeutic approaches. While the treatment landscape for this molecular subgroup is under active development, further exploration is needed to optimize the care of this group of patients with unmet needs.
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Affiliation(s)
- Jennifer A Marks
- Department of Medicine, Division of Hematology and Oncology, Georgetown University, 3800 Reservoir Road NW, Washington, D.C. 20007, USA.
| | - Xin Wang
- Department of Medicine, Division of Hematology and Oncology, Georgetown University, 3800 Reservoir Road NW, Washington, D.C. 20007, USA; Department of Medicine, Division of Hematology-Oncology, University of Pennsylvania, 12 South Pavilion, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
| | - Elena M Fenu
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA.
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Division of Hematopathology, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA.
| | - Catherine Lai
- Department of Medicine, Division of Hematology-Oncology, University of Pennsylvania, 12 South Pavilion, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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Mollstedt J, Mansouri L, Rosenquist R. Precision diagnostics in chronic lymphocytic leukemia: Past, present and future. Front Oncol 2023; 13:1146486. [PMID: 37035166 PMCID: PMC10080996 DOI: 10.3389/fonc.2023.1146486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/10/2023] [Indexed: 04/11/2023] Open
Abstract
Genetic diagnostics of hematological malignancies has evolved dramatically over the years, from chromosomal banding analysis to next-generation sequencing, with a corresponding increased capacity to detect clinically relevant prognostic and predictive biomarkers. In diagnostics of patients with chronic lymphocytic leukemia (CLL), we currently apply fluorescence in situ hybridization (FISH)-based analysis to detect recurrent chromosomal aberrations (del(11q), del(13q), del(17p) and trisomy 12) as well as targeted sequencing (IGHV and TP53 mutational status) for risk-stratifying purposes. These analyses are performed before start of any line of treatment and assist in clinical decision-making including selection of targeted therapy (BTK and BCL2 inhibitors). Here, we present the current view on the genomic landscape of CLL, including an update on recent advances with potential for clinical translation. We discuss different state-of-the-art technologies that are applied to enable precision diagnostics in CLL and highlight important genomic markers with current prognostic and/or predictive impact as well as those of prospective clinical relevance. In the coming years, it will be important to develop more comprehensive genomic analyses that can capture all types of relevant genetic aberrations, but also to develop highly sensitive assays to detect minor mutations that affect therapy response or confer resistance to targeted therapies. Finally, we will bring up the potential of new technologies and multi-omics analysis to further subclassify the disease and facilitate implementation of precision medicine approaches in this still incurable disease.
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Affiliation(s)
- John Mollstedt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Larry Mansouri
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- *Correspondence: Richard Rosenquist,
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8
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Mancikova V, Pesova M, Pavlova S, Helma R, Zavacka K, Hejret V, Taus P, Hynst J, Plevova K, Malcikova J, Pospisilova S. Distinct p53 phosphorylation patterns in chronic lymphocytic leukemia patients are reflected in the activation of circumjacent pathways upon DNA damage. Mol Oncol 2022; 17:82-97. [PMID: 36334078 PMCID: PMC9812841 DOI: 10.1002/1878-0261.13337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 09/21/2022] [Accepted: 11/04/2022] [Indexed: 11/06/2022] Open
Abstract
TP53 gene abnormalities represent the most important biomarker in chronic lymphocytic leukemia (CLL). Altered protein modifications could also influence p53 function, even in the wild-type protein. We assessed the impact of p53 protein phosphorylations on p53 functions as an alternative inactivation mechanism. We studied p53 phospho-profiles induced by DNA-damaging agents (fludarabine, doxorubicin) in 71 TP53-intact primary CLL samples. Doxorubicin induced two distinct phospho-profiles: profile I (heavily phosphorylated) and profile II (hypophosphorylated). Profile II samples were less capable of activating p53 target genes upon doxorubicin exposure, resembling TP53-mutant samples at the transcriptomic level, whereas standard p53 signaling was triggered in profile I. ATM locus defects were more common in profile II. The samples also differed in the basal activity of the hypoxia pathway: the highest level was detected in TP53-mutant samples, followed by profile II and profile I. Our study suggests that wild-type TP53 CLL cells with less phosphorylated p53 show TP53-mutant-like behavior after DNA damage. p53 hypophosphorylation and the related lower ability to respond to DNA damage are linked to ATM locus defects and the higher basal activity of the hypoxia pathway.
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Affiliation(s)
- Veronika Mancikova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Michaela Pesova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Sarka Pavlova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Robert Helma
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Kristyna Zavacka
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Vaclav Hejret
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Petr Taus
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Jakub Hynst
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic
| | - Karla Plevova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic,Institute of Medical Genetics and Genomics, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Jitka Malcikova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic,Department of Internal Medicine – Hematology and Oncology, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic,Institute of Medical Genetics and Genomics, Faculty of MedicineMasaryk University and University Hospital BrnoCzech Republic
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9
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De Luca G, Cerruti G, Lastraioli S, Conte R, Ibatici A, Di Felice N, Morabito F, Monti P, Fronza G, Matis S, Colombo M, Fabris S, Ciarrocchi A, Neri A, Menichini P, Ferrarini M, Nozza P, Fais F, Cutrona G, Dono M. The spectrum of subclonal TP53 mutations in chronic lymphocytic leukemia: A next generation sequencing retrospective study. Hematol Oncol 2022; 40:962-975. [PMID: 35961859 PMCID: PMC10086786 DOI: 10.1002/hon.3063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 12/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a hematological disorder with complex clinical and biological behavior. TP53 mutational status and cytogenetic assessment of the deletion of the corresponding locus (17p13.1) are considered the most relevant biomarkers associated with pharmaco-predictive response, chemo-refractoriness, and worse prognosis in CLL patients. The implementation of Next Generation Sequencing (NGS) methodologies in the clinical laboratory allows for comprehensively analyzing the TP53 gene and detecting mutations with allele frequencies ≤10%, that is, "subclonal mutations". We retrospectively studied TP53 gene mutational status by NGS in 220 samples from 171 CLL patients. TP53 mutations were found in 60/220 (27.3%) samples and 47/171 (27.5%) patients. Interestingly, subclonal mutations could be detected in 31/60 samples (51.7%) corresponding to 25 patients (25/47, 53.2%). We identified 44 distinct subclonal TP53 mutations clustered in the central DNA-binding domain of p53 protein (exons 5-8, codons 133-286). Missense mutations were predominant (>80%), whereas indels, nonsense, and splice site variants were less represented. All subclonal TP53 variants but one [p.(Pro191fs)] were already described in NCI and/or Seshat databases as "damaging" and/or "probably damaging" mutations (38/44, 86% and 6/44, 14%, respectively). Longitudinal samples were available for 37 patients. Almost half of them displayed at least one TP53 mutant subclone, which could be alone (4/16, 25%) or concomitant with other TP53 mutant clonal ones (12/16, 75%); different patterns of mutational dynamics overtimes were documented. In conclusion, utilization of NGS in our "real-life" cohort of CLL patients demonstrated an elevated frequency of subclonal TP53 mutations. This finding indicates the need for precisely identifying these mutations during disease since the clones carrying them may become predominant and be responsible for therapy failures.
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Affiliation(s)
- Giuseppa De Luca
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Giannamaria Cerruti
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Sonia Lastraioli
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Romana Conte
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Adalberto Ibatici
- Hematology Unit and Bone Marrow Transplantation, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Nikki Di Felice
- Hematology Unit and Bone Marrow Transplantation, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Fortunato Morabito
- Biotechnology Research Unit, Aprigliano, A.O./ASP of Cosenza, Cosenza, Italy.,Department of Hematology and Bone Marrow Transplant Unit, Augusta Victoria Hospital, East Jerusalem, Israel
| | - Paola Monti
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Gilberto Fronza
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Serena Matis
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Monica Colombo
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Sonia Fabris
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Antonino Neri
- Scientific Directorate, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy
| | - Paola Menichini
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Manlio Ferrarini
- Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Paolo Nozza
- Department of Pathology, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Franco Fais
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Department of Experimental Medicine, University of Genoa, Genoa, Italy
| | - Giovanna Cutrona
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Mariella Dono
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
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10
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Sladeček S, Radaszkiewicz KA, Bőhmová M, Gybeľ T, Radaszkiewicz TW, Pacherník J. Dual specificity phosphatase 7 drives the formation of cardiac mesoderm in mouse embryonic stem cells. PLoS One 2022; 17:e0275860. [PMID: 36227898 PMCID: PMC9560500 DOI: 10.1371/journal.pone.0275860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022] Open
Abstract
Dual specificity phosphatase 7 (DUSP7) is a protein belonging to a broad group of phosphatases that can dephosphorylate phosphoserine/phosphothreonine as well as phosphotyrosine residues within the same substrate. DUSP7 has been linked to the negative regulation of mitogen activated protein kinases (MAPK), and in particular to the regulation of extracellular signal-regulated kinases 1 and 2 (ERK1/2). MAPKs play an important role in embryonic development, where their duration, magnitude, and spatiotemporal activity must be strictly controlled by other proteins, among others by DUSPs. In this study, we focused on the effect of DUSP7 depletion on the in vitro differentiation of mouse embryonic stem (ES) cells. We showed that even though DUSP7 knock-out ES cells do retain some of their basic characteristics, when it comes to differentiation, they preferentially differentiate towards neural cells, while the formation of early cardiac mesoderm is repressed. Therefore, our data indicate that DUSP7 is necessary for the correct formation of neuroectoderm and cardiac mesoderm during the in vitro differentiation of ES cells.
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Affiliation(s)
- Stanislava Sladeček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Martina Bőhmová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Jiří Pacherník
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail:
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11
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Five Percent Variant Allele Frequency Is a Reliable Reporting Threshold for TP53 Variants Detected by Next Generation Sequencing in Chronic Lymphocytic Leukemia in the Clinical Setting. Hemasphere 2022; 6:e761. [PMID: 35935605 PMCID: PMC9348859 DOI: 10.1097/hs9.0000000000000761] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022] Open
Abstract
The clinical significance of small TP53 clones detected with next generation sequencing (NGS) in chronic lymphocytic leukemia is an issue of active debate. According to the official guidelines, treatment decisions should be guided only by variants with variant allele frequency (VAF) ≥10%. We present data on 325 consecutive patients with chronic lymphocytic leukemia analyzed with NGS. In total 47 pathogenic/likely pathogenic (P/LP), TP53 variants were detected in 26 patients (8%). Eleven of these (23%) were in the 5% to 10% VAF range and reported according to our institutional policy. All TP53 variants in the 5% to 10% VAF range were confirmed (100% concordance) with a second NGS panel. Our results where further validated with the performance of Sanger sequencing and digital droplet PCR (ddPCR). In 12 patients with available fluorescence in situ hybridization data and TP53 mutations within 5% to 10% VAF, deletion of chromosome 17p (del(17p)) was detectable in only 1 patient. We propose a robust diagnostic algorithm, which allows the safe detection and reporting of TP53 variants with VAF down to 5% in the clinical setting. Our study provides evidence that NGS is equally potent to detect variants with VAF 5% to 10% compared to those with VAF 10% to 15%, highlighting the urgent need for harmonization of NGS methodologies across diagnostic laboratories.
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12
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Soussi T, Baliakas P. Landscape of TP53 Alterations in Chronic Lymphocytic Leukemia via Data Mining Mutation Databases. Front Oncol 2022; 12:808886. [PMID: 35251978 PMCID: PMC8890000 DOI: 10.3389/fonc.2022.808886] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/20/2022] [Indexed: 11/16/2022] Open
Abstract
Locus-specific databases are invaluable tools for both basic and clinical research. The extensive information they contain is gathered from the literature and manually curated by experts. Cancer genome sequencing projects generate an immense amount of data, which are stored directly in large repositories (cancer genome databases). The presence of a TP53 defect (17p deletion and/or TP53 mutations) is an independent prognostic factor in chronic lymphocytic leukemia (CLL) and TP53 status analysis has been adopted in routine clinical practice. For that reason, TP53 mutation databases have become essential for the validation of the plethora of TP53 variants detected in tumor samples. TP53 profiles in CLL are characterized by a great number of subclonal TP53 mutations with low variant allelic frequencies and the presence of multiple minor subclones harboring different TP53 mutations. In this review, we describe the various characteristics of the multiple levels of heterogeneity of TP53 variants in CLL through the analysis of TP53 mutation databases and the utility of their diagnosis in the clinic.
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Affiliation(s)
- Thierry Soussi
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Sorbonne Université, UPMC Univ Paris 06, Paris, France
| | - Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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13
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Olbertova H, Plevova K, Pavlova S, Malcikova J, Kotaskova J, Stranska K, Spunarova M, Trbusek M, Navrkalova V, Dvorackova B, Tom N, Pal K, Jarosova M, Brychtova Y, Panovska A, Doubek M, Pospisilova S. Evolution of TP53 abnormalities during CLL disease course is associated with telomere length changes. BMC Cancer 2022; 22:137. [PMID: 35114947 PMCID: PMC8812042 DOI: 10.1186/s12885-022-09221-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 01/19/2022] [Indexed: 11/10/2022] Open
Abstract
Background Telomeres are protective structures at chromosome ends which shorten gradually with increasing age. In chronic lymphocytic leukemia (CLL), short telomeres have been associated with unfavorable disease outcome, but the link between clonal evolution and telomere shortening remains unresolved. Methods We investigated relative telomere length (RTL) in a well-characterized cohort of 198 CLL patients by qPCR and focused in detail on a subgroup 26 patients who underwent clonal evolution of TP53 mutations (evolTP53). In the evolTP53 subgroup we explored factors influencing clonal evolution and corresponding changes in telomere length through measurements of telomerase expression, lymphocyte doubling time, and BCR signaling activity. Results At baseline, RTL of the evolTP53 patients was scattered across the entire RTL spectrum observed in our CLL cohort. RTL changed in the follow-up samples of 16/26 (62%) evolTP53 cases, inclining to reach intermediate RTL values, i.e., longer telomeres shortened compared to baseline while shorter ones prolonged. For the first time we show that TP53 clonal shifts are linked to RTL change, including unexpected RTL prolongation. We further investigated parameters associated with RTL changes. Unstable telomeres were significantly more frequent among younger patients (P = 0.032). Shorter telomeres were associated with decreased activity of the B-cell receptor signaling components p-ERK1/2, p-ZAP-70/SYK, and p-NFκB (P = 0.04, P = 0.01, and P = 0.02, respectively). Conclusions Our study revealed that changes of telomere length reflect evolution in leukemic subclone proportion, and are associated with specific clinico-biological features of the explored cohort. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09221-z.
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Affiliation(s)
- Helena Olbertova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Sarka Pavlova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jitka Malcikova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jana Kotaskova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Kamila Stranska
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michaela Spunarova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martin Trbusek
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Veronika Navrkalova
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Barbara Dvorackova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Nikola Tom
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Karol Pal
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic
| | - Marie Jarosova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Medical Genetics and Genomics Faculty of Medicine, Masaryk University and University Hospital Brno, Brno, Czech Republic
| | - Yvona Brychtova
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michael Doubek
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic.,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, 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
- Central European Institute of Technology, Masaryk University, 625 00, Brno, Czech Republic. .,Department of Internal Medicine Hematology and Oncology, University Hospital Brno and Faculty of Medicine, 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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14
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Kwok M, Wu CJ. Clonal Evolution of High-Risk Chronic Lymphocytic Leukemia: A Contemporary Perspective. Front Oncol 2021; 11:790004. [PMID: 34976831 PMCID: PMC8716560 DOI: 10.3389/fonc.2021.790004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Clonal evolution represents the natural process through which cancer cells continuously search for phenotypic advantages that enable them to develop and expand within microenvironmental constraints. In chronic lymphocytic leukemia (CLL), clonal evolution underpins leukemic progression and therapeutic resistance, with differences in clonal evolutionary dynamics accounting for its characteristically diverse clinical course. The past few years have witnessed profound changes in our understanding of CLL clonal evolution, facilitated by a maturing definition of high-risk CLL and an increasing sophistication of next-generation sequencing technology. In this review, we offer a modern perspective on clonal evolution of high-risk CLL, highlighting recent discoveries, paradigm shifts and unresolved questions. We appraise recent advances in our understanding of the molecular basis of CLL clonal evolution, focusing on the genetic and non-genetic sources of intratumoral heterogeneity, as well as tumor-immune dynamics. We review the technological innovations, particularly in single-cell technology, which have fostered these advances and represent essential tools for future discoveries. In addition, we discuss clonal evolution within several contexts of particular relevance to contemporary clinical practice, including the settings of therapeutic resistance to CLL targeted therapy and immunotherapy, as well as Richter transformation of CLL to high-grade lymphoma.
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Affiliation(s)
- Marwan Kwok
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Catherine J. Wu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA, United States
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15
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Zavacka K, Plevova K. Chromothripsis in Chronic Lymphocytic Leukemia: A Driving Force of Genome Instability. Front Oncol 2021; 11:771664. [PMID: 34900721 PMCID: PMC8661134 DOI: 10.3389/fonc.2021.771664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/01/2021] [Indexed: 11/22/2022] Open
Abstract
Chromothripsis represents a mechanism of massive chromosome shattering and reassembly leading to the formation of derivative chromosomes with abnormal functions and expression. It has been observed in many cancer types, importantly, including chronic lymphocytic leukemia (CLL). Due to the associated chromosomal rearrangements, it has a significant impact on the pathophysiology of the disease. Recent studies have suggested that chromothripsis may be more common than initially inferred, especially in CLL cases with adverse clinical outcome. Here, we review the main features of chromothripsis, the challenges of its assessment, and the potential benefit of its detection. We summarize recent findings of chromothripsis occurrence across hematological malignancies and address its causes and consequences in the context of CLL clinical features, as well as chromothripsis-related molecular abnormalities described in published CLL studies. Furthermore, we discuss the use of the current knowledge about genome functions associated with chromothripsis in the optimization of treatment strategies in CLL.
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Affiliation(s)
- Kristyna Zavacka
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno & Faculty of Medicine, Masaryk University, Brno, Czechia.,Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno & Faculty of Medicine, Masaryk University, Brno, Czechia.,Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czechia.,Institute of Medical Genetics and Genomics, University Hospital Brno & Masaryk University, Brno, Czechia
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16
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Radaszkiewicz T, Nosková M, Gömöryová K, Vondálová Blanářová O, Radaszkiewicz KA, Picková M, Víchová R, Gybeľ T, Kaiser K, Demková L, Kučerová L, Bárta T, Potěšil D, Zdráhal Z, Souček K, Bryja V. RNF43 inhibits WNT5A-driven signaling and suppresses melanoma invasion and resistance to the targeted therapy. eLife 2021; 10:65759. [PMID: 34702444 PMCID: PMC8550759 DOI: 10.7554/elife.65759] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/28/2021] [Indexed: 12/30/2022] Open
Abstract
RNF43 is an E3 ubiquitin ligase and known negative regulator of WNT/β-catenin signaling. We demonstrate that RNF43 is also a regulator of noncanonical WNT5A-induced signaling in human cells. Analysis of the RNF43 interactome using BioID and immunoprecipitation showed that RNF43 can interact with the core receptor complex components dedicated to the noncanonical Wnt pathway such as ROR1, ROR2, VANGL1, and VANGL2. RNF43 triggers VANGL2 ubiquitination and proteasomal degradation and clathrin-dependent internalization of ROR1 receptor and inhibits ROR2 activation. These activities of RNF43 are physiologically relevant and block pro-metastatic WNT5A signaling in melanoma. RNF43 inhibits responses to WNT5A, which results in the suppression of invasive properties of melanoma cells. Furthermore, RNF43 prevented WNT5A-assisted development of resistance to BRAF V600E and MEK inhibitors. Next, RNF43 acted as melanoma suppressor and improved response to targeted therapies in vivo. In line with these findings, RNF43 expression decreases during melanoma progression and RNF43-low patients have a worse prognosis. We conclude that RNF43 is a newly discovered negative regulator of WNT5A-mediated biological responses that desensitizes cells to WNT5A.
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Affiliation(s)
- Tomasz Radaszkiewicz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Nosková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristína Gömöryová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Olga Vondálová Blanářová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Markéta Picková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,International Clinical Research Center FNUSA-ICRC, Brno, Czech Republic
| | - Ráchel Víchová
- Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karol Kaiser
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucia Demková
- Laboratory of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Kučerová
- Laboratory of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tomáš Bárta
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karel Souček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,International Clinical Research Center FNUSA-ICRC, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
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17
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Cafforio L, Raponi S, Cappelli LV, Ilari C, Soscia R, De Propris MS, Mariglia P, Rigolin GM, Bardi A, Peragine N, Piciocchi A, Arena V, Mauro FR, Cuneo A, Guarini A, Foa R, Del Giudice I. Treatment with ibrutinib does not induce a TP53 clonal evolution in chronic lymphocytic leukemia. Haematologica 2021; 107:334-337. [PMID: 34647439 PMCID: PMC8719070 DOI: 10.3324/haematol.2020.263715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 11/09/2022] Open
Abstract
Not available.
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Affiliation(s)
- Luciana Cafforio
- Hematology, Department of Translational and Precision Medicine, Sapienza University
| | - Sara Raponi
- Hematology, Department of Translational and Precision Medicine, Sapienza University
| | | | - Caterina Ilari
- Hematology, Department of Translational and Precision Medicine, Sapienza University
| | - Roberta Soscia
- Hematology, Department of Translational and Precision Medicine, Sapienza University
| | | | - Paola Mariglia
- Hematology, Department of Translational and Precision Medicine, Sapienza University
| | - Gian Matteo Rigolin
- Hematology Section, Department of Medical Science, Azienda Ospedaliero-Universitaria Arcispedale S. Anna, University of Ferrara
| | - Antonella Bardi
- Hematology Section, Department of Medical Science, Azienda Ospedaliero-Universitaria Arcispedale S. Anna, University of Ferrara
| | - Nadia Peragine
- Hematology, Department of Translational and Precision Medicine, Sapienza University
| | | | | | | | - Antonio Cuneo
- Hematology Section, Department of Medical Science, Azienda Ospedaliero-Universitaria Arcispedale S. Anna, University of Ferrara
| | - Anna Guarini
- Department of Molecular Medicine, Sapienza University, Rome
| | - Robin Foa
- Hematology, Department of Translational and Precision Medicine, Sapienza University
| | - Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University.
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18
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Kwok M, Agathanggelou A, Davies N, Stankovic T. Targeting the p53 Pathway in CLL: State of the Art and Future Perspectives. Cancers (Basel) 2021; 13:4681. [PMID: 34572908 PMCID: PMC8468925 DOI: 10.3390/cancers13184681] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/16/2021] [Accepted: 09/16/2021] [Indexed: 12/20/2022] Open
Abstract
The p53 pathway is a desirable therapeutic target, owing to its critical role in the maintenance of genome integrity. This is exemplified in chronic lymphocytic leukemia (CLL), one of the most common adult hematologic malignancies, in which functional loss of p53 arising from genomic aberrations are frequently associated with clonal evolution, disease progression, and therapeutic resistance, even in the contemporary era of CLL targeted therapy and immunotherapy. Targeting the 'undruggable' p53 pathway therefore arguably represents the holy grail of cancer research. In recent years, several strategies have been proposed to exploit p53 pathway defects for cancer treatment. Such strategies include upregulating wild-type p53, restoring tumor suppressive function in mutant p53, inducing synthetic lethality by targeting collateral genome maintenance pathways, and harnessing the immunogenicity of p53 pathway aberrations. In this review, we will examine the biological and clinical implications of p53 pathway defects, as well as our progress towards development of therapeutic approaches targeting the p53 pathway, specifically within the context of CLL. We will appraise the opportunities and pitfalls associated with these therapeutic strategies, and evaluate their place amongst the array of new biological therapies for CLL.
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Affiliation(s)
- Marwan Kwok
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
- Centre for Clinical Haematology, Queen Elizabeth Hospital Birmingham, Birmingham B15 2SY, UK
| | - Angelo Agathanggelou
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
| | - Nicholas Davies
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
| | - Tatjana Stankovic
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2SY, UK; (A.A.); (N.D.)
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19
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Mancikova V, Peschelova H, Kozlova V, Ledererova A, Ladungova A, Verner J, Loja T, Folber F, Mayer J, Pospisilova S, Smida M. Performance of anti-CD19 chimeric antigen receptor T cells in genetically defined classes of chronic lymphocytic leukemia. J Immunother Cancer 2021; 8:jitc-2019-000471. [PMID: 32217767 PMCID: PMC7206910 DOI: 10.1136/jitc-2019-000471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 01/25/2023] Open
Abstract
Background While achieving prolonged remissions in other B cell-derived malignancies, chimeric antigen receptor (CAR) T cells still underperform when injected into patients with chronic lymphocytic leukemia (CLL). We studied the influence of genetics on CLL response to anti-CD19 CAR T-cell therapy. Methods First, we studied 32 primary CLL samples composed of 26 immunoglobulin heavy-chain gene variable (IGHV)-unmutated (9 ATM-mutated, 8 TP53-mutated, and 9 without mutations in ATM, TP53, NOTCH1 or SF3B1) and 6 IGHV-mutated samples without mutations in the above-mentioned genes. Then, we mimicked the leukemic microenvironment in the primary cells by ‘2S stimulation’ through interleukin-2 and nuclear factor kappa B. Finally, CRISPR/Cas9-generated ATM-knockout and TP53-knockout clones (four and seven, respectively) from CLL-derived cell lines MEC1 and HG3 were used. All these samples were exposed to CAR T cells. In vivo survival study in NSG mice using HG3 wild-type (WT), ATM-knockout or TP53-knockout cells was also performed. Results Primary unstimulated CLL cells were specifically eliminated after >24 hours of coculture with CAR T cells. ‘2S’ stimulated cells showed increased survival when exposed to CAR T cells compared with unstimulated ones, confirming the positive effect of this stimulation on CLL cells’ in vitro fitness. After 96 hours of coculture, there was no difference in survival among the genetic classes. Finally, CAR T cells were specifically activated in vitro in the presence of target knockout cell lines as shown by the production of interferon-γ when compared with control (CTRL) T cells (p=0.0020), but there was no difference in knockout cells’ survival. In vivo, CAR T cells prolonged the survival of mice injected with WT, TP53-knockout and ATM-knockout HG3 tumor cells as compared with CTRL T cells (p=0.0485, 0.0204 and <0.0001, respectively). When compared with ATM-knockout, TP53-knockout disease was associated with an earlier time of onset (p<0.0001), higher tumor burden (p=0.0002) and inefficient T-cell engraftment (p=0.0012). Conclusions While in vitro no differences in survival of CLL cells of various genetic backgrounds were observed, CAR T cells showed a different effectiveness at eradicating tumor cells in vivo depending on the driver mutation. Early disease onset, high-tumor burden and inefficient T-cell engraftment, associated with TP53-knockout tumors in our experimental setting, ultimately led to inferior performance of CAR T cells.
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Affiliation(s)
- Veronika Mancikova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic .,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Helena Peschelova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Veronika Kozlova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Aneta Ledererova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Adriana Ladungova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jan Verner
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Loja
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Frantisek Folber
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiri Mayer
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michal Smida
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic .,Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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20
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Resistance to Bruton's Tyrosine Kinase Inhibitors: The Achilles Heel of Their Success Story in Lymphoid Malignancies. Blood 2021; 138:1099-1109. [PMID: 34320163 DOI: 10.1182/blood.2020006783] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
Bruton's tyrosine kinase inhibitors (BTKi) have significantly changed the treatment landscape for patients with B-cell malignancies including chronic lymphocytic leukemia (CLL), Waldenstrom's macroglobulinemia (WM), mantle cell lymphoma (MCL), and marginal zone lymphoma (MZL). Unfortunately, patients with BTKi resistant disease have shortened survival. Clinical and molecular risk factors, such as number of prior therapies and presence of TP53 mutations, can be used to predict patients at the highest risk of developing BTKi resistance. Many mechanisms of BTKi resistance have been reported with mutations in BTK and phospholipase C g 2 supported with the most data. The introduction of venetoclax has lengthened the survival of patients with BTKi resistant disease. Ongoing clinical trials with promising treatment modalities such as next-generation BTKi and chimeric antigen receptor T-cell therapy have reported promising efficacy in patients with BTKi resistant disease. Continued research focusing on resistance mechanisms and methods of how to circumvent resistance is needed to further prolong the survival of patients with BTKi resistant B-cell malignancies.
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21
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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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22
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Paclíková P, Radaszkiewicz TW, Potěšil D, Harnoš J, Zdráhal Z, Bryja V. Roles of individual human Dishevelled paralogs in the Wnt signalling pathways. Cell Signal 2021; 85:110058. [PMID: 34082011 DOI: 10.1016/j.cellsig.2021.110058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 12/21/2022]
Abstract
Dishevelled (DVL) proteins are key mediators of most Wnt pathways. In all vertebrates, three DVL paralogs are present (DVL1, DVL2 and DVL3) but it is poorly defined to what extent they are functionally redundant. Here, we generated T-REx HEK 293 cells with only one DVL paralog (i.e., DVL1-only, DVL2-only, and DVL3-only) and compared their response to Wnt-3a and Wnt-5a ligands with wild type and DVL triple knockout cells. We show that DVL is essential, in addition to the previously shown Wnt-3a-induced phosphorylation of LRP6 and transcriptional activation of TCF/LEF-dependent reporter, also for Wnt-3a-induced degradation of AXIN1 and Wnt-5a-induced phosphorylation of ROR1. We have quantified the molar ratios of DVL1:DVL2:DVL3 in our model to be approximately 4:80:16. Interestingly, DVL-only cells do not compensate for the lack of other paralogs and are still fully functional in all analyzed readouts with the exception of Wnt-3a-induced transcription assessed by TopFlash assay. In this assay, the DVL1-only cell line was the most potent; on the contrary, the DVL3-only cell line exhibited only the negligible capacity to mediate Wnt signals. Using a novel model system - complementation assays in T-REx HEK 293 with amplified Wnt signal response (RNF43/ZNRF3/DVL1/DVL2/DVL3 penta KO cells) we demonstrate that it is not the total amount of DVL but ratio of individual paralogs what decides the signal strength. In sum, this study contributes to our better understanding of the role of individual human DVL paralogs in the Wnt pathway.
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Affiliation(s)
- Petra Paclíková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jakub Harnoš
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic; Institute of Biophysics, Academy of Sciences of Czech Republic, Brno, Czech Republic.
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23
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Bödör C, Kotmayer L, László T, Takács F, Barna G, Kiss R, Sebestyén E, Nagy T, Hegyi LL, Mikala G, Fekete S, Farkas P, Balogh A, Masszi T, Demeter J, Weisinger J, Alizadeh H, Kajtár B, Kohl Z, Szász R, Gergely L, Gurbity Pálfi T, Sulák A, Kollár B, Egyed M, Plander M, Rejtő L, Szerafin L, Ilonczai P, Tamáska P, Pettendi P, Lévai D, Schneider T, Sebestyén A, Csermely P, Matolcsy A, Mátrai Z, Alpár D. Screening and monitoring of the BTK C481S mutation in a real-world cohort of patients with relapsed/refractory chronic lymphocytic leukaemia during ibrutinib therapy. Br J Haematol 2021; 194:355-364. [PMID: 34019713 DOI: 10.1111/bjh.17502] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/01/2021] [Indexed: 11/28/2022]
Abstract
The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib has revolutionised the therapeutic landscape of chronic lymphocytic leukaemia (CLL). Acquired mutations emerging at position C481 in the BTK tyrosine kinase domain are the predominant genetic alterations associated with secondary ibrutinib resistance. To assess the correlation between disease progression, and the emergence and temporal dynamics of the most common resistance mutation BTKC481S , sensitive (10-4 ) time-resolved screening was performed in 83 relapsed/refractory CLL patients during single-agent ibrutinib treatment. With a median follow-up time of 40 months, BTKC481S was detected in 48·2% (40/83) of the patients, with 80·0% (32/40) of them showing disease progression during the examined period. In these 32 cases, representing 72·7% (32/44) of all patients experiencing relapse, emergence of the BTKC481S mutation preceded the symptoms of clinical relapse with a median of nine months. Subsequent Bcl-2 inhibition therapy applied in 28/32 patients harbouring BTKC481S and progressing on ibrutinib conferred clinical and molecular remission across the patients. Our study demonstrates the clinical value of sensitive BTKC481S monitoring with the largest longitudinally analysed real-world patient cohort reported to date and validates the feasibility of an early prediction of relapse in the majority of ibrutinib-treated relapsed/refractory CLL patients experiencing disease progression.
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Affiliation(s)
- Csaba Bödör
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Lili Kotmayer
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tamás László
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ferenc Takács
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Barna
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Richárd Kiss
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Endre Sebestyén
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tibor Nagy
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Lajos László Hegyi
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Mikala
- South-Pest Central Hospital-National Institute of Hematology and Infectology, Budapest, Hungary
| | - Sándor Fekete
- South-Pest Central Hospital-National Institute of Hematology and Infectology, Budapest, Hungary
| | - Péter Farkas
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Alexandra Balogh
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Tamás Masszi
- Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary
| | - Judit Demeter
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Júlia Weisinger
- Department of Internal Medicine and Oncology, Semmelweis University, Budapest, Hungary
| | - Hussain Alizadeh
- 1st Department of Internal Medicine, Clinical Centre, University of Pécs, Pécs, Hungary
| | - Béla Kajtár
- Department of Pathology, University of Pécs Medical School, Pécs, Hungary
| | - Zoltán Kohl
- 1st Department of Internal Medicine, Clinical Centre, University of Pécs, Pécs, Hungary
| | - Róbert Szász
- Division of Hematology, Department of Internal Medicine, University of Debrecen, Debrecen, Hungary
| | - Lajos Gergely
- Division of Hematology, Department of Internal Medicine, University of Debrecen, Debrecen, Hungary
| | - Timea Gurbity Pálfi
- 2nd Department of Internal Medicine and Cardiology Center, University of Szeged, Szeged, Hungary
| | - Adrienn Sulák
- 2nd Department of Internal Medicine and Cardiology Center, University of Szeged, Szeged, Hungary
| | - Balázs Kollár
- Kaposi Mór University Teaching Hospital of County Somogy, Kaposvár, Hungary
| | - Miklós Egyed
- Kaposi Mór University Teaching Hospital of County Somogy, Kaposvár, Hungary
| | - Márk Plander
- Markusovszky University Teaching Hospital, Szombathely, Hungary
| | - László Rejtő
- Hospitals of County Szabolcs-Szatmár-Bereg and University Teaching Hospital, Nyíregyháza, Hungary
| | - László Szerafin
- Hospitals of County Szabolcs-Szatmár-Bereg and University Teaching Hospital, Nyíregyháza, Hungary
| | - Péter Ilonczai
- Hospitals of County Szabolcs-Szatmár-Bereg and University Teaching Hospital, Nyíregyháza, Hungary.,Markhot Ferenc Teaching Hospital of County Heves, Eger, Hungary
| | - Péter Tamáska
- Borsod-Abaúj-Zemplén County Hospital and University Teaching Hospital, Miskolc, Hungary
| | - Piroska Pettendi
- Hetényi Géza Hospital and Clinic of County Jász-Nagykun-Szolnok, Szolnok, Hungary
| | - Dóra Lévai
- National Institute of Oncology, Budapest, Hungary
| | | | - Anna Sebestyén
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Péter Csermely
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - András Matolcsy
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Karolinska Institute, Solna, Sweden
| | - Zoltán Mátrai
- South-Pest Central Hospital-National Institute of Hematology and Infectology, Budapest, Hungary
| | - Donát Alpár
- HCEMM-SE Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
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24
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Brieghel C, Aarup K, Torp MH, Andersen MA, Yde CW, Tian X, Wiestner A, Ahn IE, Niemann CU. Clinical Outcomes in Patients with Multi-Hit TP53 Chronic Lymphocytic Leukemia Treated with Ibrutinib. Clin Cancer Res 2021; 27:4531-4538. [PMID: 33963002 DOI: 10.1158/1078-0432.ccr-20-4890] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/23/2021] [Accepted: 05/04/2021] [Indexed: 01/21/2023]
Abstract
PURPOSE TP53 aberration (TP53 mutation and/or 17p deletion) is the most important predictive marker in chronic lymphocytic leukemia (CLL). Although each TP53 aberration is considered an equal prognosticator, the prognostic value of carrying isolated (single-hit) or multiple (multi-hit) TP53 aberrations remains unclear, particularly in the context of targeted agents. PATIENTS AND METHODS We performed deep sequencing of TP53 using baseline samples collected from 51 TP53 aberrant patients treated with ibrutinib in a phase II study (NCT01500733). RESULTS We identified TP53 mutations in 43 patients (84%) and del(17p) in 47 (92%); 9 and 42 patients carried single-hit and multi-hit TP53, respectively. The multi-hit TP53 subgroup was enriched with younger patients who had prior treatments and unmutated immunoglobulin heavy-chain variable region gene status. We observed significantly shorter overall survival, progression-free survival (PFS), and time-to-progression (TTP) in patients with multi-hit TP53 compared with those with single-hit TP53. Clinical outcomes were similar in patient subgroups stratified by 2 or >2 TP53 aberrations. In multivariable analyses, multi-hit TP53 CLL was independently associated with inferior PFS and TTP. In sensitivity analyses, excluding mutations below 1% VAF demonstrated similar outcome. Results were validated in an independent population-based cohort of 112 patients with CLL treated with ibrutinib. CONCLUSIONS In this study, single-hit TP53 defines a distinct subgroup of patients with an excellent long-term response to single-agent ibrutinib, whereas multi-hit TP53 is independently associated with shorter PFS. These results warrant further investigations on prognostication and management of multi-hit TP53 CLL.See related commentary by Bomben et al., p. 4462.
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Affiliation(s)
- Christian Brieghel
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Kathrine Aarup
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mathias H Torp
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael A Andersen
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christina W Yde
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Xin Tian
- Office of Biostatistics Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Adrian Wiestner
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Inhye E Ahn
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Carsten U Niemann
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.
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25
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Low-burden TP53 mutations in CLL: Clinical impact and clonal evolution within the context of different treatment options. Blood 2021; 138:2670-2685. [PMID: 33945616 PMCID: PMC8703362 DOI: 10.1182/blood.2020009530] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 04/19/2021] [Indexed: 11/20/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) patients with TP53 mutations experience chemo-refractory disease and are therefore indicated for targeted therapy. However, the significance of low-burden TP53 mutations with <10% variant allele frequency (VAF) remains a matter of debate. Here we describe clonal evolution scenarios of low-burden TP53 mutations and analyzed their clinical impact in a "real-world" CLL cohort. TP53 status was assessed by targeted NGS in 511 patients entering first-line treatment with chemo/immunotherapy and 159 relapsed patients treated with targeted agents. Within the pre-therapy cohort, 16% of patients carried low-burden TP53 mutations (0.1-10% VAF). While their presence did not significantly shorten event-free survival after first-line therapy, it affected overall survival (OS). For a subgroup with TP53 mutations of 1-10% VAF, the impact on OS was only observed in patients with unmutated IGHV that had not received targeted therapy, as patients benefited from switching to targeted agents regardless of initial TP53 mutational status. Analysis of the clonal evolution of low-burden TP53 mutations showed that the highest expansion rates were associated with FCR in both first and second-line treatment (median VAF increase 14.8x and 11.8x, respectively) in contrast to treatment with less intense chemo/immunotherapy regimens (1.6x) and without treatment (0.8x). In the relapsed cohort, 33% of patients carried low-burden TP53 mutations, which did not expand significantly upon targeted treatment (median VAF change 1x). Sporadic cases of TP53-mut clonal shifts were connected with the development of resistance-associated mutations. Altogether, our data support the incorporation of low-burden TP53 variants in clinical decision-making.
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26
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Sutton LA, Ljungström V, Enjuanes A, Cortese D, Skaftason A, Tausch E, Stano Kozubik K, Nadeu F, Armand M, Malcikova J, Pandzic T, Forster J, Davis Z, Oscier D, Rossi D, Ghia P, Strefford JC, Pospisilova S, Stilgenbauer S, Davi F, Campo E, Stamatopoulos K, Rosenquist R, On Behalf Of The European Research Initiative On Cll Eric. Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study. Haematologica 2021; 106:682-691. [PMID: 32273480 PMCID: PMC7927885 DOI: 10.3324/haematol.2019.234716] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Next-generation sequencing (NGS) has transitioned from research to clinical routine, yet the comparability of different technologies for mutation profiling remains an open question. We performed a European multicenter (n=6) evaluation of three amplicon-based NGS assays targeting 11 genes recurrently mutated in chronic lymphocytic leukemia. Each assay was assessed by two centers using 48 pre-characterized chronic lymphocytic leukemia samples; libraries were sequenced on the Illumina MiSeq instrument and bioinformatics analyses were centralized. Across all centers the median percentage of target reads ≥100x ranged from 94.2-99.8%. In order to rule out assay-specific technical variability, we first assessed variant calling at the individual assay level i.e., pairwise analysis of variants detected amongst partner centers. After filtering for variants present in the paired normal sample and removal of PCR/sequencing artefacts, the panels achieved 96.2% (Multiplicom), 97.7% (TruSeq) and 90% (HaloPlex) concordance at a variant allele frequency (VAF) >0.5%. Reproducibility was assessed by looking at the inter-laboratory variation in detecting mutations and 107 of 115 (93% concordance) mutations were detected by all six centers, while the remaining eight variants (7%) were undetected by a single center. Notably, 6 of 8 of these variants concerned minor subclonal mutations (VAF <5%). We sought to investigate low-frequency mutations further by using a high-sensitivity assay containing unique molecular identifiers, which confirmed the presence of several minor subclonal mutations. Thus, while amplicon-based approaches can be adopted for somatic mutation detection with VAF >5%, after rigorous validation, the use of unique molecular identifiers may be necessary to reach a higher sensitivity and ensure consistent and accurate detection of low-frequency variants.
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Affiliation(s)
- Lesley-Ann Sutton
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Viktor Ljungström
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Anna Enjuanes
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Diego Cortese
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Aron Skaftason
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Eugen Tausch
- Department of Internal Medicine III, Ulm University,Ulm, Germany
| | - Katerina Stano Kozubik
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ferran Nadeu
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Marine Armand
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Jikta Malcikova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jade Forster
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zadie Davis
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - David Oscier
- Department of Hematology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Davide Rossi
- Hematology Department, Oncology Institute of Southern Switzerland and Institute of Oncology Research, Bellinzona, Switzerland
| | - Paolo Ghia
- Division of Experimental Oncology, Università Vita-Salute San Raffaele and IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Jonathan C Strefford
- Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Sarka Pospisilova
- Center of Molecular Medicine, CEITEC - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Frederic Davi
- AP-HP, Hopital Pitie-Salpetriere, Department of Hematology, Sorbonne Université, Paris, France
| | - Elias Campo
- Institut d’Investigacions Biomèdiques August Pi iSunyer (IDIBAPS), Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain and Hospital Clínic of Barcelona, Universitat de Barcelona, Barcelona, Spain
| | - Kostas Stamatopoulos
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Institute of Applied Biosciences, Center for Research and Technology, Thessaloniki, Greec
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden,Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Stockholm, Sweden
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Locher M, Jukic E, Bohn JP, Untergasser G, Steurer M, Cramer CA, Schwendinger S, Vogi V, Verdorfer I, Witsch-Baumgartner M, Nachbaur D, Gunsilius E, Wolf D, Zschocke J, Steiner N. Clonal dynamics in a composite chronic lymphocytic leukemia and hairy cell leukemia-variant. Genes Chromosomes Cancer 2020; 60:287-292. [PMID: 33277788 PMCID: PMC7984250 DOI: 10.1002/gcc.22925] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/28/2022] Open
Abstract
Composite lymphoma is the rare simultaneous manifestation of two distinct lymphomas. Chronic lymphocytic leukemia (CLL) has a propensity for occurring in composite lymphomas, a phenomenon that remains to be elucidated. We applied cytogenetics, droplet digital polymerase chain reaction, and massively parallel sequencing to analyze longitudinally a patient with CLL, who 3 years later showed transformation to a hairy cell leukemia-variant (HCL-V). Outgrowth of the IGHV4-34-positive HCL-V clone at the expense of the initially dominant CLL clone with trisomy 12 and MED12 mutation started before CLL-guided treatment and was accompanied by a TP53 mutation, which was already detectable at diagnosis of CLL. Furthermore, deep sequencing of IGH showed a composite lymphoma with presence of both disease components at all analyzed timepoints (down to a minor clone: major clone ratio of ~1:1000). Overall, our analyses showed a disease course that resembled clonal dynamics reported for malignancies with intratumoral heterogeneity and illustrate the utility of deep sequencing of IGH to detect distinct clonal populations at diagnosis, monitor clonal response to therapy, and possibly improve clinical outcomes.
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Affiliation(s)
- Maurus Locher
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Emina Jukic
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Jan-Paul Bohn
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerold Untergasser
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Michael Steurer
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Simon Schwendinger
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Verena Vogi
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Irmgard Verdorfer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | | | - David Nachbaur
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Eberhard Gunsilius
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Wolf
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria.,Medical Clinic III, Oncology, Hematology, Immuno-Oncology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Normann Steiner
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
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28
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Gonzalez-Rodriguez AP, Payer AR, Menendez-Suarez JJ, Sordo-Bahamonde C, Lorenzo-Herrero S, Zanabili J, Fonseca A, Gonzalez-Huerta AJ, Palomo P, Gonzalez S. Driver Mutations and Single Copy Number Abnormalities Identify Binet Stage A Patients with Chronic Lymphocytic Leukemia with Aggressive Progression. J Clin Med 2020; 9:jcm9113695. [PMID: 33213108 PMCID: PMC7698623 DOI: 10.3390/jcm9113695] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/12/2020] [Indexed: 01/24/2023] Open
Abstract
The correlation between progression and the genetic characteristics of Binet stage A patients with chronic lymphocytic leukemia (CLL) detected by whole exome sequencing (WES) was analyzed in 55 patients. The median follow-up for the patients was 102 months. During the follow-up, 24 patients (43%) progressed. Univariate Cox analysis showed that the presence of driver mutations, the accumulation of two or more mutations, the presence of adverse mutations, immunoglobulin heavy chain genes (IGHV) mutation status and unfavorable single copy number abnormalities (SCNAs) were associated with a higher risk of progression. Particularly, the occurrence of an adverse mutation and unfavorable SCNAs increased the risk of progression nine-fold and five-fold, respectively. Nevertheless, only the occurrence of adverse mutations retained statistical significance in the multivariate analysis. All patients carrying an unfavorable mutation progressed with a median progression-free survival (PFS) of 29 months. The accumulation of two or more mutations also increased the risk of progression with a median PFS of 29 months. The median PFS of patients with unfavorable SCNAs was 38 months. Combining mutations and SCNAs, patients may be stratified into three groups with different prognostic outcomes: adverse (17% probability of five-year PFS), protective (86% probability of five-year PFS) and neither (62% probability of five-year PFS, p < 0.001). Overall, the analysis of the mutational status of patients with CLL at an early stage of the disease may allow the identification of patients with a high risk of progression. The feasibility of an early therapeutic intervention in these particular patients requires further investigation.
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Affiliation(s)
- Ana P. Gonzalez-Rodriguez
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain; (A.R.P.); (J.Z.); (A.F.); (A.J.G.-H.); (P.P.)
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain; (C.S.-B.); (S.L.-H.); (S.G.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Correspondence:
| | - Angel R. Payer
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain; (A.R.P.); (J.Z.); (A.F.); (A.J.G.-H.); (P.P.)
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain; (C.S.-B.); (S.L.-H.); (S.G.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
| | - Juan J. Menendez-Suarez
- Departamento de Biología Funcional, Inmunología, Universidad de Oviedo, 33006 Oviedo, Spain;
| | - Christian Sordo-Bahamonde
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain; (C.S.-B.); (S.L.-H.); (S.G.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento de Biología Funcional, Inmunología, Universidad de Oviedo, 33006 Oviedo, Spain;
| | - Seila Lorenzo-Herrero
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain; (C.S.-B.); (S.L.-H.); (S.G.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento de Biología Funcional, Inmunología, Universidad de Oviedo, 33006 Oviedo, Spain;
| | - Joud Zanabili
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain; (A.R.P.); (J.Z.); (A.F.); (A.J.G.-H.); (P.P.)
| | - Ariana Fonseca
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain; (A.R.P.); (J.Z.); (A.F.); (A.J.G.-H.); (P.P.)
| | - Ana Julia Gonzalez-Huerta
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain; (A.R.P.); (J.Z.); (A.F.); (A.J.G.-H.); (P.P.)
| | - Pilar Palomo
- Department of Hematology, Hospital Universitario Central de Asturias (HUCA), 33011 Oviedo, Spain; (A.R.P.); (J.Z.); (A.F.); (A.J.G.-H.); (P.P.)
| | - Segundo Gonzalez
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Spain; (C.S.-B.); (S.L.-H.); (S.G.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento de Biología Funcional, Inmunología, Universidad de Oviedo, 33006 Oviedo, Spain;
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29
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Tausch E, Beck P, Schlenk RF, Jebaraj BM, Dolnik A, Yosifov DY, Hillmen P, Offner F, Janssens A, Babu KG, Grosicki S, Mayer J, Panagiotidis P, McKeown A, Gupta IV, Skorupa A, Pallaud C, Bullinger L, Mertens D, Döhner H, Stilgenbauer S. Prognostic and predictive role of gene mutations in chronic lymphocytic leukemia: results from the pivotal phase III study COMPLEMENT1. Haematologica 2020; 105:2440-2447. [PMID: 33054084 PMCID: PMC7556677 DOI: 10.3324/haematol.2019.229161] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/07/2020] [Indexed: 11/09/2022] Open
Abstract
Next generation sequencing studies in Chronic lymphocytic leukemia (CLL) have revealed novel genetic variants that have been associated with disease characteristics and outcome. The aim of this study was to evaluate the prognostic value of recurrent molecular abnormalities in patients with CLL. Therefore, we assessed their incidences and associations with other clinical and genetic markers in the prospective multicenter COMPLEMENT1 trial (treatment naive patients not eligible for intensive treatment randomized to chlorambucil (CHL) vs. ofatumumab-CHL (O-CHL)). Baseline samples were available from 383 patients (85.6%) representative of the total trial cohort. Mutations were analyzed by amplicon-based targeted next generation sequencing (tNGS). In 52.2% of patients we found at least one mutation and the incidence was highest in NOTCH1 (17.0%), followed by SF3B1 (14.1%), ATM (11.7%), TP53 (10.2%), POT1 (7.0%), RPS15 (4.4%), FBXW7 (3.4%), MYD88 (2.6%) and BIRC3 (2.3%). While most mutations lacked prognostic significance, TP53 (HR2.02,p<0.01), SF3B1 (HR1.66,p=0.01) and NOTCH1 (HR1.39,p=0.03) were associated with inferior PFS in univariate analysis. Multivariate analysis confirmed the independent prognostic role of TP53 for PFS (HR1.71,p=0.04) and OS (HR2.78,p=0.02) and of SF3B1 for PFS only (HR1.52,p=0.02). Notably, NOTCH1 mutation status separates patients with a strong and a weak benefit from ofatumumab addition to CHL (NOTCH1wt:HR0.50,p<0.01, NOTCH1mut:HR0.81,p=0.45). In summary, TP53 and SF3B1 were confirmed as independent prognostic and NOTCH1 as a predictive factor for reduced ofatumumab efficacy in a randomized chemo (immune)therapy CLL trial. These results validate NGS-based mutation analysis in a multicenter trial and provide a basis for expanding molecular testing in the prognostic workup of patients with CLL. ClinicalTrials.gov registration number: NCT00748189.
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MESH Headings
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Mutation
- Phosphoproteins/genetics
- Prognosis
- Prospective Studies
- RNA Splicing Factors/genetics
- Receptor, Notch1/genetics
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Affiliation(s)
- Eugen Tausch
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
| | - Philipp Beck
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
| | - Richard F. Schlenk
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
- NCT-Trial Center, National Center for Tumor Diseases, German Cancer Research Center, Heidelberg, Germany
| | | | - Anna Dolnik
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
- Klinik für Innere Medizin mit Schwerpunkt Hämatologie, Onkologie und Tumorimmunologie, Charité, Berlin
| | - Deyan Y. Yosifov
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Peter Hillmen
- Department of Haematology, St. James's University Hospital, Leeds, UK
| | | | | | | | - Sebastian Grosicki
- Department of Hematology and Cancer Prevention, School of Public Health, Silesian Medical University in Katowice, Katowice, Poland
| | - Jiri Mayer
- Department of Haematology-Oncology, University Hospital Brno, Brno, Czech Republic
| | | | - Astrid McKeown
- Oncology Global Medicines Development, AstraZeneca, Melbourn, UK
| | | | | | | | - Lars Bullinger
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
- Klinik für Innere Medizin mit Schwerpunkt Hämatologie, Onkologie und Tumorimmunologie, Charité, Berlin
| | - Daniel Mertens
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
- Mechanisms of Leukemogenesis, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hartmut Döhner
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
| | - Stephan Stilgenbauer
- Depar tment of Internal Medicine III, Ulm University, Ulm, Germany
- Department for Hematology, Oncology and Rheumatology, Saarland University Medical School, Homburg/Saar, Germany
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30
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Moia R, Patriarca A, Mahmoud AM, Ferri V, Favini C, Rasi S, Deambrogi C, Gaidano G. Assessing prognosis of chronic lymphocytic leukemia using biomarkers and genetics. Expert Opin Orphan Drugs 2020. [DOI: 10.1080/21678707.2020.1804860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Riccardo Moia
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | - Andrea Patriarca
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | - Abdurraouf Mokhtar Mahmoud
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | - Valentina Ferri
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | - Chiara Favini
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | - Silvia Rasi
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | - Clara Deambrogi
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Università del Piemonte Orientale and Azienda Ospedaliero-Universitaria Maggiore della Carità, Novara, Italy
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31
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Morabito F, Gentile M, Monti P, Recchia AG, Menichini P, Skafi M, Atrash M, De Luca G, Bossio S, Al-Janazreh H, Galimberti S, Salah Z, Morabito L, Mujahed A, Hindiyeh M, Dono M, Fais F, Cutrona G, Neri A, Tripepi G, Fronza G, Ferrarini M. TP53 dysfunction in chronic lymphocytic leukemia: clinical relevance in the era of B-cell receptors and BCL-2 inhibitors. Expert Opin Investig Drugs 2020; 29:869-880. [PMID: 32551999 DOI: 10.1080/13543784.2020.1783239] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Patients with TP53 dysfunction, assessed by del(17p) or TP53 mutations, respond poorly to chemo-immunotherapy and fare better with the new therapies (BCR and BCL-2 inhibitors); however, it is unclear whether their response is similar to that of patients without anomalies or whether there is currently an adequate determination of TP53 dysfunction. AREA COVERED A literature search was undertaken on clinical trials and real-world experience data on patients with TP53 dysfunction treated with different protocols. Moreover, data on the TP53 biological function and on the tests currently employed for its assessment were reviewed. EXPERT OPINION Although TP53 dysfunction has less negative influence on the new biological therapies, patients with these alterations, particularly those with biallelic inactivation of TP53, have a worst outcome with these therapies than those without alterations. At present, a determination of TP53, particularly with next generation sequencing (NGS) methodologies, may be sufficient for the identifications of the patients unsuitable for chemo-immunotherapy, although integration with del(17p) would be advisable. For the future, more extensive determinations of the TP53 status, including functional assays, may become part of the current armamentarium for a better patient stratification and treatment with newer protocols.
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Affiliation(s)
- Fortunato Morabito
- Hematology Department and Bone Marrow Transplant Unit, Cancer Care Center, Augusta Victoria Hospital , Jerusalem, Israel.,Biotechnology Research Unit, Aprigliano, AO/ASP , Cosenza, Italy
| | - Massimo Gentile
- Biotechnology Research Unit, Aprigliano, AO/ASP , Cosenza, Italy.,Hematology Unit, Hematology and Oncology Department , Cosenza, Italy
| | - Paola Monti
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino , Genoa, Italy
| | | | - Paola Menichini
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino , Genoa, Italy
| | - Mamdouh Skafi
- Hematology Department and Bone Marrow Transplant Unit, Cancer Care Center, Augusta Victoria Hospital , Jerusalem, Israel
| | - Moien Atrash
- Hematology Department and Bone Marrow Transplant Unit, Cancer Care Center, Augusta Victoria Hospital , Jerusalem, Israel
| | - Giuseppa De Luca
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino , Genoa, Italy
| | - Sabrina Bossio
- Biotechnology Research Unit, Aprigliano, AO/ASP , Cosenza, Italy
| | - Hamdi Al-Janazreh
- Hematology Department and Bone Marrow Transplant Unit, Cancer Care Center, Augusta Victoria Hospital , Jerusalem, Israel
| | | | - Zaidoun Salah
- The Lautenberg Center for General and Tumor Immunology, Department of Immunology and Cancer Research-Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School , Jerusalem, Israel
| | - Lucio Morabito
- Humanitas Clinical and Research Center, IRCCS , Rozzano, Italy
| | - Alham Mujahed
- Laboratory Department, Cancer Care Center, Augusta Victoria Hospital , Jerusalem, Israel
| | - Musa Hindiyeh
- Laboratory Department, Cancer Care Center, Augusta Victoria Hospital , Jerusalem, Israel
| | - Mariella Dono
- Molecular Diagnostic Unit, IRCCS Ospedale Policlinico San Martino , Genoa, Italy
| | - Franco Fais
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino , Genova, Italy.,Department of Experimental Medicine, University of Genoa , Genoa, Italy
| | - Giovanna Cutrona
- Molecular Pathology Unit, IRCCS Ospedale Policlinico San Martino , Genova, Italy
| | - Antonino Neri
- Department of Oncology and Hemato-Oncology, University of Milan , Milan, Italy.,Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico , Milan, Italy
| | | | - Gilberto Fronza
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino , Genoa, Italy
| | - Manlio Ferrarini
- Department of Experimental Medicine, University of Genoa , Genoa, Italy
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Chauffaille MDLLF, Zalcberg I, Barreto WG, Bendit I. Detection of somatic TP53 mutations and 17p deletions in patients with chronic lymphocytic leukemia: a review of the current methods. Hematol Transfus Cell Ther 2020; 42:261-268. [PMID: 32660851 PMCID: PMC7417461 DOI: 10.1016/j.htct.2020.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 05/11/2020] [Accepted: 05/21/2020] [Indexed: 01/09/2023] Open
Abstract
Chronic lymphocytic leukemia is the most common hematologic malignancy among adults in Western countries. Several studies show that somatic mutations in the TP53 gene are present in up to 50% of patients with relapsed or refractory chronic lymphocytic leukemia. This study aims to review and compare the methods used to detect somatic TP53 mutations and/or 17p deletions and analyze their importance in the chronic lymphocytic leukemia diagnosis and follow-up. In chronic lymphocytic leukemia patients with refractory or recurrent disease, the probability of clonal expansion of cells with the TP53 mutation and/or 17p deletion is very high. The studies assessed showed several methodologies able to detect these changes. For the 17p deletion, the chromosome G-banding (karyotype) and interphase fluorescence in situ hybridization are the most sensitive. For somatic mutations involving the TP53 gene, moderate or high-coverage read next-generation sequencing and Sanger sequencing are the most recommended ones. The TP53 gene mutations represent a strong adverse prognostic factor for patient survival and treatment resistance in chronic lymphocytic leukemia. Patients carrying low-proportion TP53 mutation (less than 20–25% of all alleles) remain a challenge to these tests. Thus, for any of the methods employed, it is essential that the laboratory conduct its analytical validation, documenting its accuracy, precision and sensitivity/limit of detection.
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Affiliation(s)
| | - Ilana Zalcberg
- Centro de Transplante de Medula Óssea, Instituto Nacional do Cancer (CEMO-INCA), Rio de Janeiro, RJ, Brazil; GeneOne, DASA, São Paulo, SP, Brazil
| | | | - Israel Bendit
- Laboratório de Biologia do Tumor do Serviço de Hematologia do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (FMUSP), São Paulo, SP, Brazil
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Radaszkiewicz T, Bryja V. Protease associated domain of RNF43 is not necessary for the suppression of Wnt/β-catenin signaling in human cells. Cell Commun Signal 2020; 18:91. [PMID: 32527265 PMCID: PMC7291719 DOI: 10.1186/s12964-020-00559-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/23/2020] [Indexed: 12/19/2022] Open
Abstract
Background RNF43 and its homolog ZNRF3 are transmembrane E3 ubiquitin ligases frequently mutated in many human cancer types. Their main role relays on the inhibition of canonical Wnt signaling by the negative regulation of frizzled receptors and LRP5/6 co-receptors levels at the plasma membrane. Intracellular RING domains of RNF43/ZNRF3 mediate the key enzymatic activity of these proteins, but the function of the extracellular Protease Associated (PA) fold in the inhibition of Wnt/β-catenin pathway is controversial up-to date, apart from the interaction with secreted antagonists R-spondin family proteins shown by the crystallographic studies. Methods In our research we utilised cell-based approaches to study the role of RNF43 lacking PA domain in the canonical Wnt signalling pathway transduction. We developed controlled overexpression (TetON) and CRISPR/Cas9 mediated knock-out models in human cells. Results RNF43ΔPA mutant activity impedes canonical Wnt pathway, as manifested by the reduced phosphorylation of LRP6, DVL2 and DVL3 and by the decreased β-catenin-dependent gene expression. Finally, rescue experiments in the CRISPR/Cas9 derived RNF43/ZNRF3 double knock-out cell lines showed that RNFΔPA overexpression is enough to inhibit activation of LRP6 and β-catenin activity as shown by the Western blot and Top flash dual luciferase assays. Moreover, RNF43 variant without PA domain was not sensitive to the R-spondin1 treatment. Conclusion Taken together, our results help to understand better the mode of RNF43 tumor suppressor action and solve some discrepancies present in the field. Video Abstract
Graphical Abstract ![]()
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Affiliation(s)
- Tomasz Radaszkiewicz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic. .,Department of Cytokinetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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Blakemore SJ, Clifford R, Parker H, Antoniou P, Stec-Dziedzic E, Larrayoz M, Davis Z, Kadalyayil L, Colins A, Robbe P, Vavoulis D, Forster J, Carr L, Morilla R, Else M, Bryant D, McCarthy H, Walewska RJ, Steele AJ, Chan J, Speight G, Stankovic T, Cragg MS, Catovsky D, Oscier DG, Rose-Zerilli MJJ, Schuh A, Strefford JC. Clinical significance of TP53, BIRC3, ATM and MAPK-ERK genes in chronic lymphocytic leukaemia: data from the randomised UK LRF CLL4 trial. Leukemia 2020; 34:1760-1774. [PMID: 32015491 PMCID: PMC7326706 DOI: 10.1038/s41375-020-0723-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/06/2019] [Accepted: 01/22/2020] [Indexed: 12/11/2022]
Abstract
Despite advances in chronic lymphocytic leukaemia (CLL) treatment, globally chemotherapy remains a central treatment modality, with chemotherapy trials representing an invaluable resource to explore disease-related/genetic features contributing to long-term outcomes. In 499 LRF CLL4 cases, a trial with >12 years follow-up, we employed targeted resequencing of 22 genes, identifying 623 mutations. After background mutation rate correction, 11/22 genes were recurrently mutated at frequencies between 3.6% (NFKBIE) and 24% (SF3B1). Mutations beyond Sanger resolution (<12% VAF) were observed in all genes, with KRAS mutations principally composed of these low VAF variants. Firstly, employing orthogonal approaches to confirm <12% VAF TP53 mutations, we assessed the clinical impact of TP53 clonal architecture. Whilst ≥ 12% VAF TP53mut cases were associated with reduced PFS and OS, we could not demonstrate a difference between <12% VAF TP53 mutations and either wild type or ≥12% VAF TP53mut cases. Secondly, we identified biallelic BIRC3 lesions (mutation and deletion) as an independent marker of inferior PFS and OS. Finally, we observed that mutated MAPK-ERK genes were independent markers of poor OS in multivariate survival analysis. In conclusion, our study supports using targeted resequencing of expanded gene panels to elucidate the prognostic impact of gene mutations.
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Affiliation(s)
- Stuart J Blakemore
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Department I of Internal Medicine, Centre of Excellence in Aging Research, University of Cologne, Cologne, Germany
| | - Ruth Clifford
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Helen Parker
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Pavlos Antoniou
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Ewa Stec-Dziedzic
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Marta Larrayoz
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Zadie Davis
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Latha Kadalyayil
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Andrew Colins
- Genetic Epidemiology and Bioinformatics, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Pauline Robbe
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Dimitris Vavoulis
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Jade Forster
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Louise Carr
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Ricardo Morilla
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Monica Else
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Dean Bryant
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Helen McCarthy
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Renata J Walewska
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Andrew J Steele
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Jacqueline Chan
- Oxford Gene Technology, Begbroke Science Park, Begbroke, Oxfordshire, UK
| | - Graham Speight
- Oxford Gene Technology, Begbroke Science Park, Begbroke, Oxfordshire, UK
| | - Tanja Stankovic
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Services, IBR West, University of Birmingham, Birmingham, UK
| | - Mark S Cragg
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,Antibody & Vaccine Group, Centre for Cancer Immunology, Cancer Sciences Unit, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - David G Oscier
- Department of Molecular Pathology, Royal Bournemouth Hospital, Bournemouth, UK
| | - Matthew J J Rose-Zerilli
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Anna Schuh
- Oxford National Institute for Health Research Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, UK
| | - Jonathan C Strefford
- Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.
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Kotrbová A, Ovesná P, Gybel' T, Radaszkiewicz T, Bednaříková M, Hausnerová J, Jandáková E, Minář L, Crha I, Weinberger V, Záveský L, Bryja V, Pospíchalová V. WNT signaling inducing activity in ascites predicts poor outcome in ovarian cancer. Am J Cancer Res 2020; 10:537-552. [PMID: 31903136 PMCID: PMC6929979 DOI: 10.7150/thno.37423] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 10/04/2019] [Indexed: 12/14/2022] Open
Abstract
High grade serous carcinoma of the ovary, fallopian tube, and peritoneum (HGSC) is the deadliest gynecological disease which results in a five-year survival rate of 30% or less. HGSC is characterized by the early and rapid development of metastases accompanied by a high frequency of ascites i.e. the pathological accumulation of fluid in peritoneum. Ascites constitute a complex tumor microenvironment and contribute to disease progression by largely unknown mechanisms. Methods: Malignant ascites obtained from HGSC patients who had undergone cytoreductive surgery were tested for their ability to induce WNT signaling in the Kuramochi cell line, a novel and clinically relevant in vitro model of HGSC. Next, cancer spheroids (the main form of metastatic cancer cells in ascites) were evaluated with respect to WNT signaling. Kuramochi cells were used to determine the role of individual WNT signaling branches in the adoption of metastatic stem cell-like behavior by HGSC cells. Furthermore, we analyzed genomic and transcriptomic data on WNT/Planar Cell Polarity (PCP) components retrieved from public cancer databases and corroborated with primary patient samples and validated antibodies on the protein level. Results: We have shown that ascites are capable of inducing WNT signaling in primary HGSC cells and HGSC cell line, Kuramochi. Importantly, patients whose ascites cannot activate WNT pathway present with less aggressive disease and a considerably better outcome including overall survival (OS). Functionally, the activation of non-canonical WNT/PCP signaling by WNT5A (and not canonical WNT/β-catenin signaling by WNT3A) promoted the metastatic stem-cell (metSC) like behavior (i.e. self-renewal, migration, and invasion) of HGSC cells. The pharmacological inhibition of casein kinase 1 (CK1) as well as genetic ablation (dishevelled 3 knock out) of the pathway blocked the WNT5A-induced effect. Additionally, WNT/PCP pathway components were differentially expressed between healthy and tumor tissue as well as between the primary tumor and metastases. Additionally, ascites which activated WNT/PCP signaling contained the typical WNT/PCP ligand WNT5A and interestingly, patients with high levels of WNT5A protein in their ascites exhibited poor progression-free survival (PFS) and OS in comparison to patients with low or undetectable ascitic WNT5A. Together, our results suggest the existence of a positive feedback loop between tumor cells producing WNT ligands and ascites that distribute WNT activity to cancer cells in the peritoneum, in order to promote their pro-metastatic features and drive HGSC progression. Conclusions: Our results highlight the role of WNT/PCP signaling in ovarian cancerogenesis, indicate a possible therapeutic potential of CK1 inhibitors for HGSC, and strongly suggest that the detection of WNT pathway inducing activity ascites (or WNT5A levels in ascites as a surrogate marker) could be a novel prognostic tool for HGSC patients.
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PRIMA-1 MET cytotoxic effect correlates with p53 protein reduction in TP53-mutated chronic lymphocytic leukemia cells. Leuk Res 2019; 89:106288. [PMID: 31924585 DOI: 10.1016/j.leukres.2019.106288] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/13/2022]
Abstract
TP53 gene defects represent the most unfavorable prognostic factor in chronic lymphocytic leukemia (CLL). Although recently introduced small-molecule B-cell receptor signalling inhibitors have revolutionized CLL treatment, data for ibrutinib still point to impaired prognosis for TP53-affected patients. Among cancer-associated TP53 mutations, missense substitutions predominate and typically result in a high mutated-p53 protein level. Therefore, rescuing the p53 tumor suppressor function through specific small molecules restoring p53 wild-type (wt) conformation represents an attractive therapeutic strategy for cancer patients with TP53 missense mutations. We tested the effect of mutated-p53 reactivating molecule PRIMA-1MET in 62 clinical CLL samples characterized for TP53 mutations and p53 protein level. At the subtle PRIMA-1MET concentrations (1-4 μM), most samples manifested concentration-dependent viability decrease and, conversely, apoptosis induction, with the response being similar in both the TP53-mutated and TP53-wt groups, as well as in the TP53-mutated samples with p53 protein stabilization and without it. PRIMA-1MET was able to reduce mutated p53 protein in a proportion of TP53-mutated CLL samples, and this reduction correlated with a significantly stronger viability decrease and apoptosis induction than samples with stable p53 levels. CLL cells are mostly sensitive to PRIMA-1MET apart from those with stable mutated p53.
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37
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Raponi S, Del Giudice I, Marinelli M, Wang J, Cafforio L, Ilari C, Piciocchi A, Messina M, Bonina S, Tavolaro S, Bordyuh M, Mariglia P, Peragine N, Mauro FR, Chiaretti S, Molica S, Gentile M, Visentin A, Trentin L, Rigolin GM, Cuneo A, Diop F, Rossi D, Gaidano G, Guarini A, Rabadan R, Foà R. Genetic landscape of ultra-stable chronic lymphocytic leukemia patients. Ann Oncol 2019; 29:966-972. [PMID: 29365086 DOI: 10.1093/annonc/mdy021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL) has a heterogeneous clinical course. Beside patients requiring immediate treatment, others show an initial indolent phase followed by progression and others do not progress for decades. The latter two subgroups usually display mutated IGHV genes and a favorable FISH profile. Patients and methods Patients with absence of disease progression for over 10 years (10-34) from diagnosis were defined as ultra-stable CLL (US-CLL). Forty US-CLL underwent extensive characterization including whole exome sequencing (WES), ultra-deep sequencing and copy number aberration (CNA) analysis to define their unexplored genetic landscape. Microarray analysis, comparing US-CLL with non-US-CLL with similar immunogenetic features (mutated IGHV/favorable FISH), was also carried out to recognize US-CLL at diagnosis. Results WES was carried out in 20 US-CLL and 84 non-silent somatic mutations in 78 genes were found. When re-tested in a validation cohort of 20 further US-CLL, no recurrent lesion was identified. No clonal mutations of NOTCH1, BIRC3, SF3B1 and TP53 were found, including ATM and other potential progression driving mutations. CNA analysis identified 31 lesions, none with known poor prognostic impact. No novel recurrent lesion was identified: most cases showed no lesions (38%) or an isolated del(13q) (31%). The expression of 6 genes, selected from a gene expression profile analysis by microarray and quantified by droplet digital PCR on a cohort of 79 CLL (58 US-CLL and 21 non-US-CLL), allowed to build a decision-tree capable of recognizing at diagnosis US-CLL patients. Conclusions The genetic landscape of US-CLL is characterized by the absence of known unfavorable driver mutations/CNA and of novel recurrent genetic lesions. Among CLL patients with favorable immunogenetics, a decision-tree based on the expression of 6 genes may identify at diagnosis patients who are likely to maintain an indolent disease for decades.
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Affiliation(s)
- S Raponi
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - I Del Giudice
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - M Marinelli
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - J Wang
- Division of Life Science and Department of Chemical and Biological Engineering, Hong Kong University of Science and Technology, Hong Kong
| | - L Cafforio
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - C Ilari
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - A Piciocchi
- GIMEMA Data Centre, GIMEMA Foundation, Rome, Italy
| | - M Messina
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Bonina
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Tavolaro
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - M Bordyuh
- Department of Systems Biology, Columbia University, New York, USA; Department of, Biomedical Informatics, Columbia University, New York, USA
| | - P Mariglia
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - N Peragine
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - F R Mauro
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Chiaretti
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy
| | - S Molica
- Department of Hematology-Oncology, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| | - M Gentile
- Hematology Uni, Department of Hemato-Oncology, Ospedale Annunziata, Cosenza, Italy
| | - A Visentin
- Hematology Sectio, Department of Clinical and Experimental Medicine, University of Padova, Padova, Italy
| | - L Trentin
- Hematology Sectio, Department of Clinical and Experimental Medicine, University of Padova, Padova, Italy
| | - G M Rigolin
- Hematology Sectio, Azienda Ospedaliero Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - A Cuneo
- Hematology Sectio, Azienda Ospedaliero Universitaria Arcispedale S. Anna, University of Ferrara, Ferrara, Italy
| | - F Diop
- Division of Hematolog, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - D Rossi
- Department of Hematology, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland; Institute of Oncology Research, Bellinzona, Switzerland
| | - G Gaidano
- Division of Hematolog, Department of Translational Medicine, University of Eastern Piedmont, Novara, Italy
| | - A Guarini
- Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - R Rabadan
- Department of Systems Biology, Columbia University, New York, USA; Department of, Biomedical Informatics, Columbia University, New York, USA
| | - R Foà
- Hematolog, Department of Cellular Biotechnologies and Hematology, Sapienza University, Rome, Italy.
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Garziera M, Cecchin E, Giorda G, Sorio R, Scalone S, De Mattia E, Roncato R, Gagno S, Poletto E, Romanato L, Ecca F, Canzonieri V, Toffoli G. Clonal Evolution of TP53 c.375+1G>A Mutation in Pre- and Post- Neo-Adjuvant Chemotherapy (NACT) Tumor Samples in High-Grade Serous Ovarian Cancer (HGSOC). Cells 2019; 8:cells8101186. [PMID: 31581548 PMCID: PMC6829309 DOI: 10.3390/cells8101186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/22/2019] [Accepted: 09/30/2019] [Indexed: 12/25/2022] Open
Abstract
Carboplatin/paclitaxel is the reference regimen in the treatment of advanced high-grade serous ovarian cancer (HGSOC) in neo-adjuvant chemotherapy (NACT) before interval debulking surgery (IDS). To identify new genetic markers of platinum-resistance, next-generation sequencing (NGS) analysis of 26 cancer-genes was performed on paired matched pre- and post-NACT tumor and blood samples in a patient with stage IV HGSOC treated with NACT-IDS, showing platinum-refractory/resistance and poor prognosis. Only the TP53 c.375+1G>A somatic mutation was identified in both tumor samples. This variant, associated with aberrant splicing, was in trans configuration with the 72Arg allele of the known germline polymorphism TP53 c.215C>G (p. Pro72Arg). In the post-NACT tumor sample we observed the complete expansion of the TP53 c.375+1G>A driver mutant clone with somatic loss of the treatment-sensitive 72Arg allele. NGS results were confirmed with Sanger method and immunostaining for p53, BRCA1, p16, WT1, and Ki-67 markers were evaluated. This study showed that (i) the splice mutation in TP53 was present as an early driver mutation at diagnosis; (ii) the mutational profile was shared in pre- and post-NACT tumor samples; (iii) the complete expansion of a single dominant mutant clone through loss of heterozygosity (LOH) had occurred, suggesting a possible mechanism of platinum-resistance in HGSOC under the pressure of NACT.
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Affiliation(s)
- Marica Garziera
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Erika Cecchin
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Giorgio Giorda
- Gynecological Oncology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Roberto Sorio
- Medical Oncology Unit C, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Simona Scalone
- Medical Oncology Unit C, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Elena De Mattia
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Rossana Roncato
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Sara Gagno
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Elena Poletto
- Medical Oncology, "Santa Maria della Misericordia" University Hospital, ASUIUD, 33100 Udine, Italy.
| | - Loredana Romanato
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Fabrizio Ecca
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
- Department of Medical, Surgical and Health Sciences, University of Trieste, 34127 Trieste, Italy.
| | - Giuseppe Toffoli
- Experimental and Clinical Pharmacology Unit, Centro di Riferimento Oncologico (CRO), IRCCS, 33081 Aviano, Italy.
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Stranska K, Plevova K, Skuhrova Francova H, Skabrahova H, von Jagwitz-Biegnitz M, Radova L, Panovska A, Hrobkova S, Brychtova Y, Urbanova R, Smolej L, Simkovic M, Zuchnicka J, Mohammadova L, Spacek M, Mayer J, Pospisilova S, Doubek M. Profiling of biological and environmental risk factors in immunogenetic subgroups of chronic lymphocytic leukemia - Czech national study. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2019; 164:425-434. [PMID: 31558845 DOI: 10.5507/bp.2019.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 09/04/2019] [Indexed: 11/23/2022] Open
Abstract
AIMS This is a nation-wide survey of chronic lymphocytic leukemia (CLL) patients at six large hematology centers in the Czech Republic. The aim was to identify specific populations, social, and health characteristics of CLL subgroups divided according to the immunogenetic features of their B cell receptors (BCRs) and clonality. PATIENTS AND METHODS Questionnaires directed to specific health, social, and environmental conditions were collected in a cohort of 573 CLL patients. For these patients, immunoglobulin heavy chain gene rearrangements were also analyzed in order to gain information about their clonality, IGHV mutational status, and the presence of stereotyped BCRs. Data extracted from the questionnaires were analyzed statistically in the context of immunogenetic features of the cohort. RESULTS There were no statistically significant differences in the data collected in the survey between patients with mutated and patients with unmutated IGHV. However, patients with oligoclonal CLL reported health conditions such as hypercholesterolemia, hypertension, herpes simplex, tumors, and also, separately, CLL in 1st degree relatives, more often than their monoclonal counterparts. In patients with stereotyped BCRs, we found more frequent alcohol consumption and gastric infections in subset #1 cases and frequent cholecystectomies and familial CLL in subset #2 cases. CONCLUSION To the best of our knowledge, this study is the first to investigate CLL immunogenetic features and clonality in the context of epidemiological data. We reported statistically significant associations suggesting the influence of certain health and social conditions on a number of clonal populations expanding in CLL and also on characteristic BCR features, especially stereotypy.
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Affiliation(s)
- Kamila Stranska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karla Plevova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Hana Skuhrova Francova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Hana Skabrahova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Magdalena von Jagwitz-Biegnitz
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Lenka Radova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Panovska
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Stanislava Hrobkova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Yvona Brychtova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Renata Urbanova
- Department of Hemato-Oncology, Faculty of Medicine and Dentistry, Palacky University Olomouc and University Hospital Olomouc, Czech Republic
| | | | | | - Jana Zuchnicka
- Department of Hematooncology, University Hospital Ostrava, Czech Republic
| | - Lekaa Mohammadova
- Department of Hematology and Oncology, University Hospital Pilsen, Czech Republic
| | | | - Jiri Mayer
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic.,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.,Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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40
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Del Giudice I, Raponi S, Della Starza I, De Propris MS, Cavalli M, De Novi LA, Cappelli LV, Ilari C, Cafforio L, Guarini A, Foà R. Minimal Residual Disease in Chronic Lymphocytic Leukemia: A New Goal? Front Oncol 2019; 9:689. [PMID: 31555576 PMCID: PMC6727319 DOI: 10.3389/fonc.2019.00689] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
In chronic lymphocytic leukemia (CLL), there is a growing interest for minimal residual disease (MRD) monitoring, due to the availability of drug combinations capable of unprecedented complete clinical responses. The standardized and most commonly applied methods to assess MRD in CLL are based on flow cytometry (FCM) and, to a lesser extent, real-time quantitative PCR (RQ-PCR) with allele-specific oligonucleotide (ASO) primers of immunoglobulin heavy chain genes (IgH). Promising results are being obtained using droplet digital PCR (ddPCR) and next generation sequencing (NGS)-based approaches, with some advantages and a potential higher sensitivity compared to the standardized methodologies. Plasma cell-free DNA can also be explored as a more precise measure of residual disease from all different compartments, including the lymph nodes. From a clinical point of view, CLL MRD quantification has proven an independent prognostic marker of progression-free survival (PFS) and overall survival (OS) after chemoimmunotherapy as well as after allogeneic transplantation. In the era of mechanism-driven drugs, the paradigms of CLL treatment are being revolutionized, challenging the use of chemoimmunotherapy even in first-line. The continuous administration of ibrutinib single agent has led to prolonged PFS and OS in relapsed/refractory and treatment naïve CLL, including those with TP53 deletion/mutation or unmutated IGHV genes, though the clinical responses are rarely complete. More recently, chemo-free combinations of venetoclax+rituximab, venetoclax+obinutuzumab or ibrutinib+venetoclax have been shown capable of inducing undetectable MRD in the bone marrow, opening the way to protocols exploring a MRD-based duration of treatment, aiming at disease eradication. Thus, beside a durable disease control desirable particularly for older patients and/or for those with comorbidities, a MRD-negative complete remission is becoming a realistic prospect for CLL patients in an attempt to obtain a long-lasting eradication and possibly cure of the disease. Here we discuss the standardized and innovative technical approaches for MRD detection in CLL, the clinical impact of MRD monitoring in chemoimmunotherapy and chemo-free trials and the future clinical implications of MRD monitoring in CLL patients outside of clinical trials.
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Affiliation(s)
- Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Sara Raponi
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy.,GIMEMA Foundation, Rome, Italy
| | - Maria Stefania De Propris
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Marzia Cavalli
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Lucia Anna De Novi
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Luca Vincenzo Cappelli
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Caterina Ilari
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Luciana Cafforio
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
| | - Anna Guarini
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University of Rome, Rome, Italy
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41
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Gángó A, Alpár D, Galik B, Marosvári D, Kiss R, Fésüs V, Aczél D, Eyüpoglu E, Nagy N, Nagy Á, Krizsán S, Reiniger L, Farkas P, Kozma A, Ádám E, Tasnády S, Réti M, Matolcsy A, Gyenesei A, Mátrai Z, Bödör C. Dissection of subclonal evolution by temporal mutation profiling in chronic lymphocytic leukemia patients treated with ibrutinib. Int J Cancer 2019; 146:85-93. [PMID: 31180577 DOI: 10.1002/ijc.32502] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/17/2019] [Accepted: 05/28/2019] [Indexed: 12/12/2022]
Abstract
The Bruton's tyrosine kinase (BTK) inhibitor ibrutinib is inducing durable responses in chronic lymphocytic leukemia (CLL) patients with refractory/relapsed disease or with TP53 defect, with BTK and phospholipase C gamma 2 (PLCG2) mutations representing the predominant mechanisms conferring secondary ibrutinib resistance. To understand the landscape of genomic changes and the dynamics of subclonal architecture associated with ibrutinib treatment, an ultra-deep next-generation sequencing analysis of 30 recurrently mutated genes was performed on sequential samples of 20 patients, collected before and during single-agent ibrutinib treatment. Mutations in the SF3B1, MGAand BIRC3 genes were enriched during ibrutinib treatment, while aberrations in the BTK, PLCG2, RIPK1, NFKBIE and XPO1 genes were exclusively detected in posttreatment samples. Besides the canonical mutations, four novel BTK mutations and three previously unreported PLCG2 variants were identified. BTK and PLCG2 mutations were backtracked in five patients using digital droplet PCR and were detectable on average 10.5 months before clinical relapse. With a median follow-up time of 36.5 months, 7/9 patients harboring BTK mutations showed disease progression based on clinical and/or laboratory features. In conclusion, subclonal heterogeneity, dynamic clonal selection and various patterns of clonal variegation were identified with novel resistance-associated BTK mutations in individual patients treated with ibrutinib.
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Affiliation(s)
- Ambrus Gángó
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Donát Alpár
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bence Galik
- Bioinformatics Research Group, Bioinformatics and Sequencing Core Facilities, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Department of Clinical Molecular Biology, Medical University of Bialystok, Białystok, Poland
| | - Dóra Marosvári
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Richárd Kiss
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória Fésüs
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Dóra Aczél
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ediz Eyüpoglu
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Noémi Nagy
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ákos Nagy
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Szilvia Krizsán
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Lilla Reiniger
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Péter Farkas
- 3rd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - András Kozma
- Department of Haematology and Stem Cell Transplantation, St. István and St. László Hospital, Budapest, Hungary
| | - Emma Ádám
- Department of Haematology and Stem Cell Transplantation, St. István and St. László Hospital, Budapest, Hungary
| | - Szabolcs Tasnády
- Department of Haematology and Stem Cell Transplantation, St. István and St. László Hospital, Budapest, Hungary
| | - Marienn Réti
- Department of Haematology and Stem Cell Transplantation, St. István and St. László Hospital, Budapest, Hungary
| | - András Matolcsy
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Attila Gyenesei
- Bioinformatics Research Group, Bioinformatics and Sequencing Core Facilities, Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Department of Clinical Molecular Biology, Medical University of Bialystok, Białystok, Poland
| | - Zoltán Mátrai
- Department of Haematology and Stem Cell Transplantation, St. István and St. László Hospital, Budapest, Hungary
| | - Csaba Bödör
- MTA-SE Momentum Molecular Oncohematology Research Group, 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
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42
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Spunarova M, Tom N, Pavlova S, Mraz M, Brychtova Y, Doubek M, Panovska A, Skuhrova Francova H, Brzobohata A, Pospisilova S, Mayer J, Trbusek M. Impact of gene mutations and chromosomal aberrations on progression-free survival in chronic lymphocytic leukemia patients treated with front-line chemoimmunotherapy: Clinical practice experience. Leuk Res 2019; 81:75-81. [DOI: 10.1016/j.leukres.2019.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/16/2019] [Accepted: 04/24/2019] [Indexed: 02/03/2023]
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43
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Lukášová E, Řezáčová M, Bačíková A, Šebejová L, Vávrová J, Kozubek S. Distinct cellular responses to replication stress leading to apoptosis or senescence. FEBS Open Bio 2019; 9:870-890. [PMID: 30982228 PMCID: PMC6487726 DOI: 10.1002/2211-5463.12632] [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: 04/17/2018] [Revised: 01/09/2019] [Accepted: 01/25/2019] [Indexed: 12/12/2022] Open
Abstract
Replication stress (RS) is a major driver of genomic instability and tumorigenesis. Here, we investigated whether RS induced by the nucleotide analog fludarabine and specific kinase inhibitors [e.g. targeting checkpoint kinase 1 (Chk1) or ataxia telangiectasia and Rad3‐related (ATR)] led to apoptosis or senescence in four cancer cell lines differing in TP53 mutation status and expression of lamin A/C (LA/C). RS resulted in uneven chromatin condensation in all cell types, as evidenced by the presence of metaphasic chromosomes with unrepaired DNA damage, as well as detection of less condensed chromatin in the same nucleus, frequent ultrafine anaphase bridges, and micronuclei. We observed that responses to these chromatin changes may be distinct in individual cell types, suggesting that expression of lamin A/C and lamin B1 (LB1) may play an important role in the transition of damaged cells to senescence. MCF7 mammary carcinoma cells harboring wild‐type p53 (WT‐p53) and LA/C responded to RS by transition to senescence with a significant reduction of lamin B receptor and LB1 proteins. In contrast, a lymphoid cancer cell line WSU‐NHL (WT‐p53) lacking LA/C and expressing low levels of LB1 died after several hours, while lines MEC‐1 and SU‐DHL‐4, both with mutated p53, and SU‐DHL‐4 with mutations in LA/C, died at different rates by apoptosis. Our results show that, in addition to being influenced by p53 mutation status, the response to RS (apoptosis or senescence) may also be influenced by lamin A/C and LB1 status.
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Affiliation(s)
- Emilie Lukášová
- Department of Cell Biology and Radiobiology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Martina Řezáčová
- Department of Medical Biochemistry, Faculty of Medicine in Hradec Králové, Charles University in Prague, Hradec Králové, Czech Republic
| | - Alena Bačíková
- Department of Cell Biology and Radiobiology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
| | - Ludmila Šebejová
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Jiřina Vávrová
- Department of Radiobiology, Faculty of Military Health Sciences Hradec Králové, University of Defence Brno, Hradec Králové, Czech Republic
| | - Stanislav Kozubek
- Department of Cell Biology and Radiobiology, Institute of Biophysics, The Czech Academy of Sciences, Brno, Czech Republic
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44
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Prochazka KT, Pregartner G, Rücker FG, Heitzer E, Pabst G, Wölfler A, Zebisch A, Berghold A, Döhner K, Sill H. Clinical implications of subclonal TP53 mutations in acute myeloid leukemia. Haematologica 2019; 104:516-523. [PMID: 30309854 PMCID: PMC6395341 DOI: 10.3324/haematol.2018.205013] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/09/2018] [Indexed: 01/02/2023] Open
Abstract
The role of subclonal TP53 mutations, defined by a variant allele frequency of <20%, has not been addressed in acute myeloid leukemia yet. We, therefore, analyzed their prognostic value in a cohort of 1,537 patients with newly diagnosed disease, prospectively treated within three trials of the "German-Austrian Acute Myeloid Leukemia Study Group". Mutational analysis was performed by targeted deep sequencing and patients with TP53 mutations were categorized by their variant allele frequency into groups with frequencies >40%, 20%-40% and <20%. A total of 108 TP53 mutations were found in 98 patients (6.4%). Among these, 61 patients had variant allele frequencies >40%, 19 had variant allele frequencies between 20%-40% and 18 had frequencies <20%. Compared to specimens with clonal TP53 mutations, those with subclonal ones showed significantly fewer complex karyotypes and chromosomal losses. In either TP53-mutated group, patients experienced significantly fewer complete responses (P<0.001) and had worse overall and event-free survival rates (P<0.0001). In Cox regression analyses adjusting for age, white blood cell count, cytogenetic risk and type of acute myeloid leukemia, the adverse prognostic effect of TP53 mutations remained significant for all TP53-mutated subgroups. These data suggest that subclonal TP53 mutations are a novel prognostic parameter in acute myeloid leukemia and emphasize the usefulness of next-generation sequencing technologies for risk stratification in this disorder. The study was registered at ClinicalTrials.gov with number NCT00146120.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Alleles
- Chromosome Aberrations
- Clonal Evolution/genetics
- Female
- Gene Frequency
- Genes, p53
- Humans
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/therapy
- Male
- Middle Aged
- Mutation
- Prognosis
- Young Adult
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Affiliation(s)
| | - Gudrun Pregartner
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria
| | - Frank G Rücker
- Department of Internal Medicine III, University Hospital of Ulm, Germany
| | - Ellen Heitzer
- Institute of Human Genetics, Medical University of Graz, Austria
| | - Gabriel Pabst
- Division of Hematology, Medical University of Graz, Austria
| | - Albert Wölfler
- Division of Hematology, Medical University of Graz, Austria
| | - Armin Zebisch
- Division of Hematology, Medical University of Graz, Austria
| | - Andrea Berghold
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, Austria
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Germany
| | - Heinz Sill
- Division of Hematology, Medical University of Graz, Austria
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45
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Lu J, Böttcher M, Walther T, Mougiakakos D, Zenz T, Huber W. Energy metabolism is co-determined by genetic variants in chronic lymphocytic leukemia and influences drug sensitivity. Haematologica 2019; 104:1830-1840. [PMID: 30792207 PMCID: PMC6717593 DOI: 10.3324/haematol.2018.203067] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 02/14/2019] [Indexed: 12/14/2022] Open
Abstract
Chronic lymphocytic leukemia cells have an altered energy metabolism compared to normal B cells. While there is a growing understanding of the molecular heterogeneity of the disease, the extent of metabolic heterogeneity and its relation to molecular heterogeneity has not been systematically studied. Here, we assessed 11 bioenergetic features, primarily reflecting cell oxidative phosphorylation and glycolytic activity, in leukemic cells from 140 chronic lymphocytic leukemia patients using metabolic flux analysis. We examined these bioenergetic features for relationships with molecular profiles (including genetic aberrations, transcriptome and methylome profiles) of the tumors, their ex vivo responses to a panel of 63 compounds, and with clinical data. We observed that leukemic cells with mutated immunoglobulin variable heavy-chain show significantly lower glycolytic activity than cells with unmutated immunoglobulin variable heavy-chain. Accordingly, several key glycolytic genes (PFKP, PGAM1 and PGK1) were found to be down-regulated in samples harboring mutated immunoglobulin variable heavy-chain. In addition, 8q24 copy number gains, 8p12 deletions, 13q14 deletions and ATM mutations were identified as determinants of cellular respiration. The metabolic state of leukemic cells was associated with drug sensitivity; in particular, higher glycolytic activity was linked to increased resistance towards several drugs including rotenone, navitoclax, and orlistat. In addition, we found glycolytic capacity and glycolytic reserve to be predictors of overall survival (P<0.05) independently of established genetic predictors. Taken together, our study shows that heterogeneity in the energy metabolism of chronic lymphocytic leukemia cells is influenced by genetic variants and this could be therapeutically exploited in the selection of therapeutic strategies.
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Affiliation(s)
- Junyan Lu
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Martin Böttcher
- Department of Internal Medicine 5, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Tatjana Walther
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany
| | - Dimitrios Mougiakakos
- Department of Internal Medicine 5, Hematology and Oncology, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Thorsten Zenz
- Molecular Therapy in Hematology and Oncology, National Center for Tumor Diseases and German Cancer Research Centre, Heidelberg, Germany .,Department of Medical Oncology and Hematology, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Wolfgang Huber
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
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46
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Yamamoto Y, Uemura M, Fujita M, Maejima K, Koh Y, Matsushita M, Nakano K, Hayashi Y, Wang C, Ishizuya Y, Kinouchi T, Hayashi T, Matsuzaki K, Jingushi K, Kato T, Kawashima A, Ujike T, Nagahara A, Fujita K, Imamura R, Nakagawa H, Nonomura N. Clinical significance of the mutational landscape and fragmentation of circulating tumor DNA in renal cell carcinoma. Cancer Sci 2019; 110:617-628. [PMID: 30536551 PMCID: PMC6361573 DOI: 10.1111/cas.13906] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/03/2018] [Accepted: 12/03/2018] [Indexed: 02/06/2023] Open
Abstract
Reliable biomarkers for renal cell carcinoma (RCC) have yet to be determined. Circulating tumor DNA (ctDNA) is an emerging resource to detect and monitor molecular characteristics of various tumors. The present study aims to clarify the clinical utility of ctDNA for RCC. Fifty-three patients histologically diagnosed with clear cell RCC were enrolled. Targeted sequencing was carried out using plasma cell-free DNA (cfDNA) and tumor DNA. We applied droplet digital PCR (ddPCR) to validate detected mutations. cfDNA fragment size was also evaluated using a microfluidics-based platform and sequencing. Proportion of cfDNA fragments was defined as the ratio of small (50-166 bp) to large (167-250 bp) cfDNA fragments. Association of mutant allele frequency of ctDNA with clinical course was analyzed. Prognostic potential was evaluated using log-rank test. A total of 38 mutations across 16 (30%) patients were identified from cfDNA, including mutations in TP53 (n = 6) and VHL (n = 5), and median mutant allele frequency of ctDNA was 10%. We designed specific ddPCR probes for 11 mutations and detected the same mutations in both cfDNA and tumor DNA. Positive ctDNA was significantly associated with a higher proportion of cfDNA fragments (P = .033), indicating RCC patients with ctDNA had shorter fragment sizes of cfDNA. Interestingly, the changes of mutant allele frequency in ctDNA concurrently correlated with clinical course. Positive ctDNA and fragmentation of cfDNA were significantly associated with poor cancer-specific survival (P < .001, P = .011). In conclusion, our study shows the clinical utility of ctDNA status and cfDNA fragment size as biomarkers for prognosis and disease monitoring in RCC.
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Affiliation(s)
- Yoshiyuki Yamamoto
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Motohide Uemura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan.,Department of Therapeutic Urologic Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Masashi Fujita
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Kazuhiro Maejima
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Yoko Koh
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Makoto Matsushita
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kosuke Nakano
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yujiro Hayashi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Cong Wang
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yu Ishizuya
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Toshiro Kinouchi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takuji Hayashi
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kyosuke Matsuzaki
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kentaro Jingushi
- Department of Therapeutic Urologic Oncology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Taigo Kato
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Atsunari Kawashima
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Takeshi Ujike
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akira Nagahara
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Kazutoshi Fujita
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryoichi Imamura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hidewaki Nakagawa
- Laboratory for Cancer Genomics, RIKEN Center for Integrative Medical Sciences, Tokyo, Japan
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Suita, Japan
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47
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Christopoulos P, Dietz S, Kirchner M, Volckmar AL, Endris V, Neumann O, Ogrodnik S, Heussel CP, Herth FJ, Eichhorn M, Meister M, Budczies J, Allgäuer M, Leichsenring J, Zemojtel T, Bischoff H, Schirmacher P, Thomas M, Sültmann H, Stenzinger A. Detection of TP53 Mutations in Tissue or Liquid Rebiopsies at Progression Identifies ALK+ Lung Cancer Patients with Poor Survival. Cancers (Basel) 2019; 11:cancers11010124. [PMID: 30669647 PMCID: PMC6356563 DOI: 10.3390/cancers11010124] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/17/2022] Open
Abstract
Anaplastic lymphoma kinase (ALK) sequencing can identify resistance mechanisms and guide next-line therapy in ALK+ non-small-cell lung cancer (NSCLC), but the clinical significance of other rebiopsy findings remains unclear. We analysed all stage-IV ALK+ NSCLC patients with longitudinally assessable TP53 status treated in our institutions (n = 62). Patients with TP53 mutations at baseline (TP53mutbas, n = 23) had worse overall survival (OS) than patients with initially wild-type tumours (TP53wtbas, n = 39, 44 vs. 62 months in median, p = 0.018). Within the generally favourable TP53wtbas group, detection of TP53 mutations at progression defined a “converted” subgroup (TP53mutconv, n = 9) with inferior OS, similar to that of TP53mutbas and shorter than that of patients remaining TP53 wild-type (TP53wtprogr, 45 vs. 94 months, p = 0.043). Progression-free survival (PFS) under treatment with tyrosine kinase inhibitors (TKI) for TP53mutconv was comparable to that of TP53mutbas and also shorter than that of TP53wtprogr cases (5 and 8 vs. 13 months, p = 0.0039). Fewer TP53wtprogr than TP53mutbas or TP53mutconv cases presented with metastatic disease at diagnosis (67% vs. 91% or 100%, p < 0.05). Thus, acquisition of TP53 mutations at progression is associated with more aggressive disease, shorter TKI responses and inferior OS in ALK+ NSCLC, comparable to primary TP53 mutated cases.
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Affiliation(s)
- Petros Christopoulos
- Department of Thoracic Oncology, Heidelberg University Hospital, Heidelberg 69126, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
| | - Steffen Dietz
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.
| | - Martina Kirchner
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
| | - Anna-Lena Volckmar
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
| | - Volker Endris
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
| | - Olaf Neumann
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
| | - Simon Ogrodnik
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany.
| | - Claus-Peter Heussel
- Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik at Heidelberg University Hospital, Heidelberg 69126, Germany.
- Department of Diagnostic and Interventional Radiology, Heidelberg University Hospital, Heidelberg 69120, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
| | - Felix J Herth
- Department of Pneumology, Thoraxklinik at Heidelberg University Hospital, Heidelberg 69126, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
| | - Martin Eichhorn
- Department of Surgery, Thoraxklinik at Heidelberg University Hospital, Heidelberg 69126, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
| | - Michael Meister
- Translational Research Unit, Thoraxklinik at Heidelberg University Hospital, Heidelberg 69126, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
| | - Jan Budczies
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.
| | - Michael Allgäuer
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
| | - Jonas Leichsenring
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
| | - Tomasz Zemojtel
- BIH-Genomics Core Unit, Charité-Universitätsmedizin Berlin, Berlin 13125, Germany.
| | - Helge Bischoff
- Department of Thoracic Oncology, Heidelberg University Hospital, Heidelberg 69126, Germany.
| | - Peter Schirmacher
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.
| | - Michael Thomas
- Department of Thoracic Oncology, Heidelberg University Hospital, Heidelberg 69126, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg 69120, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.
| | - Albrecht Stenzinger
- Institute of Pathology, Heidelberg University Hospital, Heidelberg 69120, Germany.
- Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg 69120, Germany.
- German Cancer Consortium (DKTK), Heidelberg 69120, Germany.
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48
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Kimura S, Seki M, Yoshida K, Shiraishi Y, Akiyama M, Koh K, Imamura T, Manabe A, Hayashi Y, Kobayashi M, Oka A, Miyano S, Ogawa S, Takita J. NOTCH1 pathway activating mutations and clonal evolution in pediatric T-cell acute lymphoblastic leukemia. Cancer Sci 2019; 110:784-794. [PMID: 30387229 PMCID: PMC6361559 DOI: 10.1111/cas.13859] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
Molecular mechanisms involved in the relapse of T‐cell acute lymphoblastic leukemia (T‐ALL) are not fully understood, although activating NOTCH1 signaling due to NOTCH1/FBXW7 alterations is a major oncogenic driver. To unravel the relevance of NOTCH1/FBXW7 mutations associated with relapse, we performed whole–exome sequencing in 30 pediatric T‐ALL cases, among which 11 diagnosis‐relapse paired cases were further investigated to track the clonal evolution of relapse using amplicon–based deep sequencing. NOTCH1/FBXW7 alterations were detected in 73.3% (diagnosis) and 72.7% (relapse) of cases. Single nucleotide variations in the heterodimerization domain were the most frequent (40.0%) at diagnosis, whereas proline, glutamic acid, serine, threonine–rich (PEST) domain alterations were the most frequent at relapse (54.5%). Comparison between non–relapsed and relapsed cases at diagnosis showed a predominance of PEST alterations in relapsed cases (P = .045), although we failed to validate this in the TARGET cohort. Based on the clonal analysis of diagnosis‐relapse samples, we identified NOTCH1 “switching” characterized by different NOTCH1 mutations in a major clone between diagnosis and relapse samples in 2 out of 11 diagnosis‐relapse paired cases analyzed. We found another NOTCH1 “switching” case in a previously reported Berlin‐Frankfurt‐Münster cohort (n = 13), indicating NOTCH1 importance in both the development and progression of T‐ALL. Despite the limitations of having a small sample size and a non–minimal residual disease–based protocol, our results suggest that the presence of NOTCH1 mutations might contribute to the disease relapse of T‐ALL.
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Affiliation(s)
- Shunsuke Kimura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Hiroshima University, Hiroshima, Japan
| | - Masafumi Seki
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masaharu Akiyama
- Department of Pediatrics, The Jikei University School of Medicine, Tokyo, Japan
| | - Katsuyoshi Koh
- Department of Hematology/Oncology, Saitama Children's Medical Center, Saitama, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Atsushi Manabe
- Department of Pediatrics, St. Luke's International Hospital, Tokyo, Japan
| | | | - Masao Kobayashi
- Department of Pediatrics, Hiroshima University, Hiroshima, Japan
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Junko Takita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Pediatrics, Kyoto University, Kyoto, Japan
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49
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Pavlova S, Smardova J, Tom N, Trbusek M. Detection and Functional Analysis of TP53 Mutations in CLL. Methods Mol Biol 2019; 1881:63-81. [PMID: 30350198 DOI: 10.1007/978-1-4939-8876-1_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Chronic lymphocytic leukemia (CLL) represents a prototype disease in which TP53 gene defects lead to inferior prognosis. Here, we present two distinct methodologies which can be used to identify TP53 mutations in CLL patients; both protocols are primarily intended for research purposes. The functional analysis of separated alleles in yeast (FASAY) can be flexibly adapted to a variable number of samples and provides an immediate functional readout of identified mutations. Amplicon-based next-generation sequencing then allows for a high throughput and accurately detects subclonal TP53 variants (sensitivity <1% of mutated cells).
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MESH Headings
- Alleles
- DNA Mutational Analysis/instrumentation
- DNA Mutational Analysis/methods
- Genes, Reporter/genetics
- High-Throughput Nucleotide Sequencing/instrumentation
- High-Throughput Nucleotide Sequencing/methods
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/blood
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Mutation
- Neoplastic Cells, Circulating/pathology
- Saccharomyces cerevisiae/genetics
- Transfection/instrumentation
- Transfection/methods
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Sarka Pavlova
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jana Smardova
- Department of Pathology, University Hospital Brno, Brno, Czech Republic
| | - Nikola Tom
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Martin Trbusek
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno, Brno, Czech Republic.
- Faculty of Medicine, Masaryk University, Brno, Czech Republic.
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50
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The planar cell polarity protein VANG-1/Vangl negatively regulates Wnt/β-catenin signaling through a Dvl dependent mechanism. PLoS Genet 2018; 14:e1007840. [PMID: 30532125 PMCID: PMC6307821 DOI: 10.1371/journal.pgen.1007840] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 12/27/2018] [Accepted: 11/19/2018] [Indexed: 11/19/2022] Open
Abstract
Van Gogh-like (Vangl) and Prickle (Pk) are core components of the non-canonical Wnt planar cell polarity pathway that controls epithelial polarity and cell migration. Studies in vertebrate model systems have suggested that Vangl and Pk may also inhibit signaling through the canonical Wnt/β-catenin pathway, but the functional significance of this potential cross-talk is unclear. In the nematode C. elegans, the Q neuroblasts and their descendants migrate in opposite directions along the anteroposterior body axis. The direction of these migrations is specified by Wnt signaling, with activation of canonical Wnt signaling driving posterior migration, and non-canonical Wnt signaling anterior migration. Here, we show that the Vangl ortholog VANG-1 influences the Wnt signaling response of the Q neuroblasts by negatively regulating canonical Wnt signaling. This inhibitory activity depends on a carboxy-terminal PDZ binding motif in VANG-1 and the Dishevelled ortholog MIG-5, but is independent of the Pk ortholog PRKL-1. Moreover, using Vangl1 and Vangl2 double mutant cells, we show that a similar mechanism acts in mammalian cells. We conclude that cross-talk between VANG-1/Vangl and the canonical Wnt pathway is an evolutionarily conserved mechanism that ensures robust specification of Wnt signaling responses. Wnt proteins are signaling molecules with a wide range of functions in embryonic development and the maintenance of adult tissues. Wnt proteins can trigger several different signaling pathways that are grouped in β-catenin dependent (canonical) and independent (non-canonical) signaling mechanisms. Here, we have investigated cross-talk between these different Wnt signaling pathways. We show that VANG-1/Vangl, a component of the non-canonical planar cell polarity pathway, negatively regulates canonical Wnt signaling. We propose that this cross-talk mechanism ensures that Wnt stimulated cells always activate the proper downstream signaling response.
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