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Oder B, Chatzidimitriou A, Langerak AW, Rosenquist R, Österholm C. Recent revelations and future directions using single-cell technologies in chronic lymphocytic leukemia. Front Oncol 2023; 13:1143811. [PMID: 37091144 PMCID: PMC10117666 DOI: 10.3389/fonc.2023.1143811] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically and biologically heterogeneous disease with varying outcomes. In the last decade, the application of next-generation sequencing technologies has allowed extensive mapping of disease-specific genomic, epigenomic, immunogenetic, and transcriptomic signatures linked to CLL pathogenesis. These technologies have improved our understanding of the impact of tumor heterogeneity and evolution on disease outcome, although they have mostly been performed on bulk preparations of nucleic acids. As a further development, new technologies have emerged in recent years that allow high-resolution mapping at the single-cell level. These include single-cell RNA sequencing for assessment of the transcriptome, both of leukemic and non-malignant cells in the tumor microenvironment; immunogenetic profiling of B and T cell receptor rearrangements; single-cell sequencing methods for investigation of methylation and chromatin accessibility across the genome; and targeted single-cell DNA sequencing for analysis of copy-number alterations and single nucleotide variants. In addition, concomitant profiling of cellular subpopulations, based on protein expression, can also be obtained by various antibody-based approaches. In this review, we discuss different single-cell sequencing technologies and how they have been applied so far to study CLL onset and progression, also in response to treatment. This latter aspect is particularly relevant considering that we are moving away from chemoimmunotherapy to targeted therapies, with a potentially distinct impact on clonal dynamics. We also discuss new possibilities, such as integrative multi-omics analysis, as well as inherent limitations of the different single-cell technologies, from sample preparation to data interpretation using available bioinformatic pipelines. Finally, we discuss future directions in this rapidly evolving field.
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Affiliation(s)
- Blaž Oder
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Anastasia Chatzidimitriou
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Anton W. Langerak
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Cecilia Österholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
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Gordeeva V, Sharova E, Arapidi G. Progress in Methods for Copy Number Variation Profiling. Int J Mol Sci 2022; 23:ijms23042143. [PMID: 35216262 PMCID: PMC8879278 DOI: 10.3390/ijms23042143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/09/2022] [Accepted: 02/11/2022] [Indexed: 02/04/2023] Open
Abstract
Copy number variations (CNVs) are the predominant class of structural genomic variations involved in the processes of evolutionary adaptation, genomic disorders, and disease progression. Compared with single-nucleotide variants, there have been challenges associated with the detection of CNVs owing to their diverse sizes. However, the field has seen significant progress in the past 20–30 years. This has been made possible due to the rapid development of molecular diagnostic methods which ensure a more detailed view of the genome structure, further complemented by recent advances in computational methods. Here, we review the major approaches that have been used to routinely detect CNVs, ranging from cytogenetics to the latest sequencing technologies, and then cover their specific features.
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Affiliation(s)
- Veronika Gordeeva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Correspondence:
| | - Elena Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
| | - Georgij Arapidi
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia; (E.S.); (G.A.)
- Moscow Institute of Physics and Technology, National Research University, Moscow Oblast, 141701 Moscow, Russia
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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3
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Tang Z, Kanagal-Shamanna R, Tang G, Patel K, Medeiros LJ, Toruner GA. Analytical and clinical performance of chromosomal microarrays compared with FISH panel and conventional karyotyping in patients with chronic lymphocytic leukemia. Leuk Res 2021; 108:106616. [PMID: 34022744 DOI: 10.1016/j.leukres.2021.106616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/26/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022]
Abstract
In this single center retrospective analysis on 102 CLL patients, we assessed analytical and clinical performance of CMA against a targeted FISH panel (ATM, TP53, CEP12, D13S319 and LAMP1 loci) and karyotyping. CMA yielded additional information compared to karyotype in 39 cases (38 %). On the other hand, while CMA detected aberrations were also detected by FISH in all 31 cases (30 %), aberrations with low clonal size (<30 %) detected by FISH were missed by CMA. When evaluated with National Cancer Center Network (NCCN) guidelines, the capture rate of prognostic relevant cytogenetic information for FISH only, FISH + Chromosomes and FISH + CMA analyses were 95, 96 and 100 % respectively. With Cancer Cytogenomics Consortium (CGC) Criteria, these figures for FISH only, FISH + Chromosomes and FISH + CMA were 88 %, 92 and 100 % respectively. In conclusion, CMA provides additional analytical information to FISH and karyotyping, but this information has a clinical utility only in a small number of patients. Limit of detection (LOD) issues preclude replacement of FISH by CMA, but CMA may be a viable alternative to karyotyping. Further research is warranted.
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Affiliation(s)
- Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Keyur Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, United States.
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4
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The future of laboratory testing in chronic lymphocytic leukaemia. Pathology 2021; 53:377-384. [PMID: 33678426 DOI: 10.1016/j.pathol.2021.01.006] [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: 11/06/2020] [Revised: 01/31/2021] [Accepted: 01/31/2021] [Indexed: 01/24/2023]
Abstract
Chronic lymphocytic leukaemia (CLL) is a malignant lymphoproliferative disorder characterised by the accumulation of dysfunctional B-lymphocytes in the blood and lymphoid tissues. It is a clonally complex disease with a high degree of both intra-tumoural and inter-patient heterogeneity. This variability leads to a wide range of clinical outcomes and highlights the critical need for accurate prognostic tests in CLL. With the advent of a range of new targeted agents for CLL in recent years, there is also a clinical need for improved predictive tests to therapy. This review of laboratory testing in CLL focuses on emerging technologies for prognostication including single nucleotide polymorphism microarray for karyotypic analysis, targeted next generation sequencing analysis of the immunoglobulin heavy chain variable region gene as well as genes recurrently mutated in the disease such as TP53, and detection of minimal residual disease.
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Jondreville L, Krzisch D, Chapiro E, Nguyen‐Khac F. The complex karyotype and chronic lymphocytic leukemia: prognostic value and diagnostic recommendations. Am J Hematol 2020; 95:1361-1367. [PMID: 32777106 DOI: 10.1002/ajh.25956] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/31/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal abnormalities are frequently observed in patients with chronic lymphocytic leukemia (CLL) and have prognostic value. Deletions of the short arm of chromosome 17 (and/or mutations TP53) predict resistance to chemoimmunotherapy and shorter progression-free survival after targeted therapies. Although the complex karyotype (CK) is strongly predictive of a poor prognosis in hematologic malignancies such acute myeloid leukemia or myelodysplastic syndrome, its value in CLL is subject to debate. Here, we review the literature on the CK in CLL and examine its prognostic value with different treatments. We also propose a standardized method for defining a CK in all types of hematopoietic neoplasm.
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Affiliation(s)
- Ludovic Jondreville
- INSERM, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team Centre de Recherche des Cordeliers Paris France
| | - Daphné Krzisch
- INSERM, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team Centre de Recherche des Cordeliers Paris France
| | - Elise Chapiro
- INSERM, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team Centre de Recherche des Cordeliers Paris France
- Service dʼHématologie Biologique Sorbonne Université, Hôpital Pitié‐Salpêtrière, APHP Paris France
| | - Florence Nguyen‐Khac
- INSERM, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team Centre de Recherche des Cordeliers Paris France
- Service dʼHématologie Biologique Sorbonne Université, Hôpital Pitié‐Salpêtrière, APHP Paris France
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6
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SOHO State of the Art Updates and Next Questions: Clonal Evolution in Chronic Lymphocytic Leukemia. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2020; 20:779-784. [PMID: 33039357 DOI: 10.1016/j.clml.2020.08.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 12/27/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is an indolent disease with a long-lasting clinical course, with indication for treatment only when symptomatic. Its clinical heterogeneity is widely reported, with some patients requiring treatment soon after diagnosis because of development of cytopenia or bulky lymphadenopathy, and others showing a stable or a slowly progressive disease not requiring treatment for decades. Longitudinal sampling of peripheral blood, with accessible tumor cells and circulating tumor DNA, enabled the analysis of disease growing dynamics and the characterization of clonal evolution. Here we describe the main known features of CLL genomics and its shaping upon treatment, which can lead to progression, treatment refractoriness, or transformation into an aggressive lymphoma.
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Crassini K, Stevenson WS, Mulligan SP, Best OG. Molecular pathogenesis of chronic lymphocytic leukaemia. Br J Haematol 2019; 186:668-684. [DOI: 10.1111/bjh.16102] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Kyle Crassini
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
| | - William S. Stevenson
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
| | - Stephen P. Mulligan
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
- School of Life and Environmental Science University of Sydney Sydney NSW Australia
| | - O. Giles Best
- Northern Blood Research Centre Kolling Institute of Medical Research SydneyNSWAustralia
- School of Life and Environmental Science University of Sydney Sydney NSW Australia
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8
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Chen C, Heng EYH, Lim AST, Lau LC, Lim TH, Wong GC, Tien SL. Chromosomal microarray analysis is superior in identifying cryptic aberrations in patients with acute lymphoblastic leukemia at diagnosis/relapse as a single assay. Int J Lab Hematol 2019; 41:561-571. [PMID: 31112375 DOI: 10.1111/ijlh.13052] [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: 03/10/2019] [Revised: 04/23/2019] [Accepted: 04/27/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Conventional cytogenetics (CC) is important in diagnosis, therapy, monitoring of post-transplant bone marrow, and prognosis assessment of acute lymphoblastic leukemia (ALL). However, due to the nature of ALL, CC often encounters difficulties of complex karyotype, poor chromosome morphology, low mitotic index, or normal cells dividing only. In contrast, chromosomal microarray analysis (CMA) showed a specificity >99% and a sensitivity of 100% in chronic lymphocytic leukemia (CLL) patients. Here, we report our experience with CMA on adult ALL patients. METHODS Thirty-three bone marrow/blood samples from ALL patients (aged 18-79 years, median 44) at diagnosis/relapse, analyzed by CC and/or fluorescence in situ hybridization (FISH), were recruited. Chromosomal microarray analysis results were compared with CC. Fluorescence in situ hybridization analysis, if available, was applied when there was a discrepancy. RESULTS Copy-neutral loss-of-heterozygosity (CN-LOH) was found in 8 cases (24.2%). Only CN-LOH at 9p was recurrent (3 cases, 9.1%). Copy number alterations (CNAs) were detected in 6 of 9 cases (66.7%) with normal karyotypes, in 3 of 5 cases (60.0%) with sole "balanced" translocations, and in 18 of 19 cases (94.7%) with complex karyotypes. Common CNAs involved CDKN2A/2B (30.3%), IKZF1 (27.3%), PAX5 (9.1%), RB1 (9.1%), BTG1 (6.7%), and ETV6 (6.7%), which regulate cell cycle, B lymphopoiesis, or act as tumor suppressors in ALL. Copy number alteration detection rate by CMA was 81.8% (27 of 33 cases) as compared to 57.6% (19 of 33 cases) by CC. CONCLUSION Incorporation of CMA as a routine clinical test at the time of diagnosis/relapse, in conjunction with CC and/or FISH, is highly recommended.
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Affiliation(s)
- Chuanfei Chen
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Evelyn Yee Hsieh Heng
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Alvin Soon Tiong Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Lai Ching Lau
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Tse Hui Lim
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore
| | - Gee Chuan Wong
- Department of Haematology, Singapore General Hospital, Singapore, Singapore
| | - Sim Leng Tien
- Cytogenetics Laboratory, Department of Molecular Pathology, Division of Pathology, Singapore General Hospital, Singapore, Singapore.,Department of Haematology, Singapore General Hospital, Singapore, Singapore
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9
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Kostopoulou F, Gabillaud C, Chapiro E, Grange B, Tran J, Bouzy S, Degaud M, Ghamlouch H, Le Garff-Tavernier M, Maloum K, Choquet S, Leblond V, Gabarre J, Lavaud A, Morel V, Roos-Weil D, Uzunov M, Guieze R, Bernard OA, Susin SA, Tournilhac O, Nguyen-Khac F. Gain of the short arm of chromosome 2 (2p gain) has a significant role in drug-resistant chronic lymphocytic leukemia. Cancer Med 2019; 8:3131-3141. [PMID: 31066214 PMCID: PMC6558483 DOI: 10.1002/cam4.2123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 02/07/2019] [Accepted: 03/12/2019] [Indexed: 12/27/2022] Open
Abstract
The different types of drug resistance encountered in chronic lymphocytic leukemia (CLL) cannot be fully accounted for by the 17p deletion (and/or TP53 mutation), a complex karyotype (CK), immunoglobulin heavy‐chain variable region genes (IGHV) status and gene mutations. Hence, we sought to assess the associations between recurrent genomic abnormalities in CLL and the disease's development and outcome. To this end, we analyzed 64 samples from patients with CLL and gain of the short arm of chromosome 2 (2p+), which is frequent in late‐stage and relapsed/refractory CLL. We found that fludarabine/cyclophosphamide/rituximab (a common first‐line treatment in CLL) is not effective in removing the 2p+ clone ‐ even in samples lacking a CK, the 17p deletion or unmutated IGHV. Our results suggest strongly that patients with CLL should be screened for 2p+ (using karyotyping and fluorescence in situ hybridization) before a treatment option is chosen. Longer follow‐up is now required to evaluate bendamustine‐rituximab, ibrutinib, and idelalisib‐rituximab treatments.
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Affiliation(s)
- Fotini Kostopoulou
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France.,Molecular Diagnostics Laboratory, KARYO Ltd, Thessaloniki, Greece
| | - Clementine Gabillaud
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Elise Chapiro
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France.,INSERM U1138, Centre de Recherche des Cordeliers, Sorbonne Université, Paris, France
| | - Beatrice Grange
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Julie Tran
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Simon Bouzy
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Michael Degaud
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Hussein Ghamlouch
- Gustave Roussy, INSERM U1170, Université Paris-Saclay, Villejuif, France
| | - Magali Le Garff-Tavernier
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France.,INSERM U1138, Centre de Recherche des Cordeliers, Sorbonne Université, Paris, France
| | - Karim Maloum
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Sylvain Choquet
- Service d'Hématologie Clinique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Veronique Leblond
- Service d'Hématologie Clinique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Jean Gabarre
- Service d'Hématologie Clinique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Anne Lavaud
- Service d'Hématologie Clinique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Veronique Morel
- Service d'Hématologie Clinique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Damien Roos-Weil
- Service d'Hématologie Clinique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Madalina Uzunov
- Service d'Hématologie Clinique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Romain Guieze
- Service d'Hématologie Clinique et de Thérapie Cellulaire, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Olivier A Bernard
- Gustave Roussy, INSERM U1170, Université Paris-Saclay, Villejuif, France
| | - Santos A Susin
- INSERM U1138, Centre de Recherche des Cordeliers, Sorbonne Université, Paris, France
| | - Olivier Tournilhac
- Service d'Hématologie Clinique et de Thérapie Cellulaire, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Florence Nguyen-Khac
- Service d'Hématologie Biologique, Sorbonne Université, Hôpital Pitié-Salpêtrière, APHP, Paris, France.,INSERM U1138, Centre de Recherche des Cordeliers, Sorbonne Université, Paris, France
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Hüllein J, Słabicki M, Rosolowski M, Jethwa A, Habringer S, Tomska K, Kurilov R, Lu J, Scheinost S, Wagener R, Huang Z, Lukas M, Yavorska O, Helfrich H, Scholtysik R, Bonneau K, Tedesco D, Küppers R, Klapper W, Pott C, Stilgenbauer S, Burkhardt B, Löffler M, Trümper LH, Hummel M, Brors B, Zapatka M, Siebert R, Kreuz M, Keller U, Huber W, Zenz T. MDM4 Is Targeted by 1q Gain and Drives Disease in Burkitt Lymphoma. Cancer Res 2019; 79:3125-3138. [DOI: 10.1158/0008-5472.can-18-3438] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/11/2019] [Accepted: 04/15/2019] [Indexed: 11/16/2022]
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11
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Chin-Yee B, Sadikovic B, Chin-Yee IH. Genomic data in prognostic models-what is lost in translation? The case of deletion 17p and mutant TP53 in chronic lymphocytic leukaemia. Br J Haematol 2019; 188:652-660. [PMID: 30836431 DOI: 10.1111/bjh.15827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Genomic technologies are revolutionizing the practice of haematology-oncology, leading to improved disease detection, more accurate prognostication and targeted treatment decisions. These advances, however, have also introduced new clinical challenges, which include problems of prognostic underdetermination and its attendant risks of over- and undertreatment. Genomic data is generated from different technologies, from cytogenetics to next-generation sequencing, which are often interpreted interchangeably and in a binary fashion-as the presence or absence of a given chromosomal deletion or mutation-an oversimplification which may lead to mistaken prognosis. We discuss the clinical use of one such prognostic marker, represented by sequence and copy number alterations in TP53, located on chromosome 17p. Mutations in TP53 are strongly linked to poor prognosis in a variety of haematological malignancies, including chronic lymphocytic leukaemia (CLL). We review studies in CLL which utilize the 17p deletion or TP53 mutations for prognostic stratification with specific focus on the technologies used for detection, the thresholds established for clinical significance, and the clinical contexts in which these alterations are identified. The case of CLL illustrates issues arising from simplistic, binary interpretation of genetic testing and highlights the need to apply a critical lens when incorporating genomics into prognostic models.
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Affiliation(s)
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Ian H Chin-Yee
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, Canada.,Department of Medicine, Division of Hematology, Western University, London, ON, Canada
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12
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Assessing copy number aberrations and copy-neutral loss-of-heterozygosity across the genome as best practice: An evidence-based review from the Cancer Genomics Consortium (CGC) working group for chronic lymphocytic leukemia. Cancer Genet 2018; 228-229:236-250. [DOI: 10.1016/j.cancergen.2018.07.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/29/2018] [Accepted: 07/01/2018] [Indexed: 01/18/2023]
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13
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Campo E, Cymbalista F, Ghia P, Jäger U, Pospisilova S, Rosenquist R, Schuh A, Stilgenbauer S. TP53 aberrations in chronic lymphocytic leukemia: an overview of the clinical implications of improved diagnostics. Haematologica 2018; 103:1956-1968. [PMID: 30442727 PMCID: PMC6269313 DOI: 10.3324/haematol.2018.187583] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 10/26/2018] [Indexed: 12/19/2022] Open
Abstract
Chronic lymphocytic leukemia is associated with a highly heterogeneous disease course in terms of clinical outcomes and responses to chemoimmunotherapy. This heterogeneity is partly due to genetic aberrations identified in chronic lymphocytic leukemia cells such as mutations of TP53 and/or deletions in chromosome 17p [del(17p)], resulting in loss of one TP53 allele. These aberrations are associated with markedly decreased survival and predict impaired response to chemoimmunotherapy thus being among the strongest predictive markers guiding treatment decisions in chronic lymphocytic leukemia. Clinical trials demonstrate the importance of accurately testing for TP53 aberrations [both del(17p) and TP53 mutations] before each line of treatment to allow for appropriate treatment decisions that can optimize patients' outcomes. The current report reviews the diagnostic methods to detect TP53 disruption better, the role of TP53 aberrations in treatment decisions and current therapies available for patients with chronic lymphocytic leukemia carrying these abnormalities. The standardization in sequencing technologies for accurate identification of TP53 mutations and the importance of continued evaluation of TP53 aberrations throughout initial and subsequent lines of therapy remain unmet clinical needs as new therapeutic alternatives become available.
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Affiliation(s)
- Elias Campo
- Hospital Clinic of Barcelona, University of Barcelona, Institute of Biomedical Research August Pi i Sunyer (IDIBAPS), Barcelona, and CIBERONC, Spain
| | - Florence Cymbalista
- Hôpital Avicenne, AP-HP, UMR INSERMU978/Paris 13 University, Bobigny, France
| | - Paolo Ghia
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | | | - Sarka Pospisilova
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | | | - Stephan Stilgenbauer
- Internal Medicine III, Ulm University, Germany and Innere Medizin I, Universitätsklinikum des Saarlandes, Homburg, Germany
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Roos-Weil D, Nguyen-Khac F, Chevret S, Touzeau C, Roux C, Lejeune J, Cosson A, Mathis S, Feugier P, Leprêtre S, Béné MC, Baron M, Raynaud S, Struski S, Eclache V, Sutton L, Lesty C, Merle-Béral H, Cymbalista F, Ysebaert L, Davi F, Leblond V. Mutational and cytogenetic analyses of 188 CLL patients with trisomy 12: A retrospective study from the French Innovative Leukemia Organization (FILO) working group. Genes Chromosomes Cancer 2018; 57:533-540. [PMID: 30203893 DOI: 10.1002/gcc.22650] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/09/2018] [Accepted: 06/09/2018] [Indexed: 12/28/2022] Open
Abstract
Trisomy 12 (tri12) is the second most frequent chromosomal aberration (15%-20%) in chronic lymphocytic leukemia (CLL). Tri12 confers an intermediate prognosis but is a heterogeneous entity. We examined whether additional mutational or chromosomal alterations might impact tri12 patient outcomes. This retrospective study, carried out by the French Innovative Leukemia Organization, included 188 tri12 patients with comprehensive information on immunoglobulin heavy chain (IGHV) gene status, karyotypic/FISH abnormalities, and NOTCH1, TP53, SF3B1, and MYD88 mutations. The main cytogenetic abnormalities associated with tri12 were del(13q) (25%), additional trisomies (14%) (including tri19 (10%) and tri18 (4%)), 14q32 translocations (10%), del(17p) (6.5%), del(14q) (4%), and del(11q) (4%). Unmutated (UM) IGHV, NOTCH1, and TP53, mutations were identified in respectively 66%, 25%, and 8.5% of cases. Multivariate analyses showed that additional trisomies (HR = 0.43, 95% CI = 0.23-0.78, P = .01) were associated with a significantly longer time to first treatment in Binet stage A patients and with a lower risk of relapse (HR = 0.37, 95% CI = 0.15-0.9, P = .03) in the overall tri12 population. Binet stage B/C, TP53 disruption, and UM IGHV status were associated with a shorter time to next treatment, while Binet stage B/C (HR = 4, 95% CI = 1.6-4.9, P = .002) and TP53 disruption (HR = 5, 95% CI = 1.94-12.66, P = .001) conferred shorter overall survival in multivariate comparisons. These data indicate that additional cytogenetic and mutational abnormalities, and particularly additional trisomies, IGHV status, and TP53 disruption, influence tri12 patient outcomes and could improve risk stratification in this population.
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Affiliation(s)
- Damien Roos-Weil
- Sorbonne Universités, UPMC Univ Paris 06, AP-HP, GRC-11, Groupe de recherche clinique sur les hémopathies lymphoïdes (GRECHY), Hôpital Pitié-Salpétrière, APHP, Paris, France
| | - Florence Nguyen-Khac
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, APHP, Paris, France.,Centre de Recherche des Cordeliers, INSERM UMRS 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Paris, France
| | - Sylvie Chevret
- Département de Biostatistique et Informatique Médicale (DBIM), Hôpital Saint Louis, APHP, Paris, France
| | | | - Clémence Roux
- Laboratoire d'Hématologie, Hôpital Pasteur, CHU de Nice, Nice, France
| | - Julie Lejeune
- Département de Biostatistique et Informatique Médicale (DBIM), Hôpital Saint Louis, APHP, Paris, France
| | - Adrien Cosson
- Centre de Recherche des Cordeliers, INSERM UMRS 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Paris, France
| | - Stéphanie Mathis
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Pierre Feugier
- Service d'Hématologie, Hôpitaux de Brabois, Vandoeuvre Les Nancy, France
| | | | | | - Marine Baron
- Sorbonne Universités, UPMC Univ Paris 06, AP-HP, GRC-11, Groupe de recherche clinique sur les hémopathies lymphoïdes (GRECHY), Hôpital Pitié-Salpétrière, APHP, Paris, France
| | | | - Stéphanie Struski
- Département d'Hématologie, CHU de Toulouse, Université de Toulouse, Centre de Recherche sur le Cancer de Toulouse (CRCT), Toulouse, France
| | - Virginie Eclache
- Laboratoire d'Hématologie, Hôpital Avicenne, AP-HP, Bobigny, France
| | - Laurent Sutton
- Service d'Hématologie, Centre Hospitalier Victor Dupouy, Argenteuil, France
| | - Claude Lesty
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Hélène Merle-Béral
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Florence Cymbalista
- Service d'Hématologie Biologique, GHUPSSD, AP-HP, U978 INSERM, Université Paris 13, Sorbonne Paris Cité, Labex Inflamex, Bobigny, France
| | | | - Frédéric Davi
- Service d'Hématologie Biologique, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Véronique Leblond
- Sorbonne Universités, UPMC Univ Paris 06, AP-HP, GRC-11, Groupe de recherche clinique sur les hémopathies lymphoïdes (GRECHY), Hôpital Pitié-Salpétrière, APHP, Paris, France
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15
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Zhou W, Goldin L, Wang M, McMaster ML, Jones K, Burdett L, Chanock SJ, Yeager M, Dean M, Caporaso N. Combined somatic mutation and copy number analysis in the survival of familial CLL. Br J Haematol 2018; 181:604-613. [PMID: 29687880 PMCID: PMC6010231 DOI: 10.1111/bjh.15239] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/16/2018] [Indexed: 02/06/2023]
Abstract
Recurrent large-scale somatic copy number alterations (SCNAs), and somatic point mutations can be analysed to stratify patients with chronic lymphocytic leukaemia (CLL) into distinct prognostic groups. To investigate the relationship between SCNAs and somatic mutations, we performed whole-exome sequencing and single nucleotide polymorphism microarray analyses on 98 CLL patients from 40 families with a high burden of CLL. Overall, 69 somatic mutations in 29 CLL driver genes were detected among 45 subjects (46%), with the most frequently mutated genes being TP53 (8·2%), NOTCH1 (8·2%) and ATM (5·1%). Additionally, 142 SCNAs from 54 subjects (57%) were detected, including losses of chromosome 13q14 (28·9%), 11q (5·6%), 17p (2·1%), and gain of chromosome 12 (4·2%). We found that patients having both an adverse point mutation in a CLL driver gene and an unfavourable SCNA tended to have poorer survival (Hazard ratio [HR] = 3·17, 95% confidence interval [CI] = 0·97-10·35; P = 0·056) than patients having either a point mutation (HR = 1·34, 95%CI = 0·66-2·71; P = 0·42) or SCNAs (HR = 2·65, 95%CI = 0·77-9·13; P = 0·12). TP53 mutation carriers were associated with the poorest overall survival (HR = 4·39, 95%CI = 1·28-15·04; P = 0·018). Our study suggests that combining SCNA and mutational data could contribute to predicting outcome in familial CLL.
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Affiliation(s)
- Weiyin Zhou
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Lynn Goldin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Mary L. McMaster
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Laurie Burdett
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, Maryland, 21702, USA
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
| | - Neil Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, Maryland, 20892, USA
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16
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Chari R, Lockwood WW, Lam WL. Computational Methods for the Analysis of Array Comparative Genomic Hybridization. Cancer Inform 2017. [DOI: 10.1177/117693510600200007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Array comparative genomic hybridization (array CGH) is a technique for assaying the copy number status of cancer genomes. The widespread use of this technology has lead to a rapid accumulation of high throughput data, which in turn has prompted the development of computational strategies for the analysis of array CGH data. Here we explain the principles behind array image processing, data visualization and genomic profile analysis, review currently available software packages, and raise considerations for future software development.
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Affiliation(s)
- Raj Chari
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - William W. Lockwood
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
- These authors contributed equally to this work
| | - Wan L. Lam
- Cancer Genetics and Developmental Biology, British Columbia Cancer Research Centre, Vancouver BC, Canada V5Z 1L3
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17
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Cosson A, Chapiro E, Bougacha N, Lambert J, Herbi L, Cung HA, Algrin C, Keren B, Damm F, Gabillaud C, Brunelle-Navas MN, Davi F, Merle-Béral H, Le Garff-Tavernier M, Roos-Weil D, Choquet S, Uzunov M, Morel V, Leblond V, Maloum K, Lepretre S, Feugier P, Lesty C, Lejeune J, Sutton L, Landesman Y, Susin SA, Nguyen-Khac F. Gain in the short arm of chromosome 2 (2p+) induces gene overexpression and drug resistance in chronic lymphocytic leukemia: analysis of the central role of XPO1. Leukemia 2017; 31:1625-1629. [PMID: 28344316 DOI: 10.1038/leu.2017.100] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
MESH Headings
- Apoptosis
- Chromosomes, Human, Pair 2
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Gene Expression Regulation, Leukemic
- Humans
- Hydrazines/pharmacology
- Hydrazines/therapeutic use
- Karyopherins/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Receptors, Cytoplasmic and Nuclear/genetics
- Triazoles/pharmacology
- Triazoles/therapeutic use
- Exportin 1 Protein
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Affiliation(s)
- A Cosson
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - E Chapiro
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - N Bougacha
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - J Lambert
- Service de Biostatistique et Informatique Médicale, Hôpital Saint Louis, Paris, France
| | - L Herbi
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - H-A Cung
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - C Algrin
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - B Keren
- Département de génétique, GH Pitié-Salpêtrière, Paris, France
| | - F Damm
- INSERM U1170, Institut Gustave Roussy, Villejuif, France
| | - C Gabillaud
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - M-N Brunelle-Navas
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - F Davi
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - H Merle-Béral
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - M Le Garff-Tavernier
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - D Roos-Weil
- INSERM U1170, Institut Gustave Roussy, Villejuif, France
| | - S Choquet
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - M Uzunov
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - V Morel
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - V Leblond
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - K Maloum
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - S Lepretre
- Département d'Hématologie, Hôpital Becquerel, Rouen, France
| | - P Feugier
- Pôle d'Hématologie, Hôpital Brabois, Vandoeuvre-les-Nancy, France
| | - C Lesty
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
| | - J Lejeune
- Service de Biostatistique et Informatique Médicale, Hôpital Saint Louis, Paris, France
| | - L Sutton
- Service d'Hématologie Clinique, Hôpital d'Argenteuil, Argenteuil, France
| | | | - S A Susin
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
| | - F Nguyen-Khac
- INSERM UMR_S 1138, Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, Centre de Recherche des Cordeliers, Paris, France
- Sorbonne Universités, UPMC Univ Paris 06, UMR_S 1138, Centre de Recherche des Cordeliers, Paris, France
- Service d'Hématologie Biologique, GH Pitié-Salpêtrière, Paris, France
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18
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The MYCN Protein in Health and Disease. Genes (Basel) 2017; 8:genes8040113. [PMID: 28358317 PMCID: PMC5406860 DOI: 10.3390/genes8040113] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 12/22/2022] Open
Abstract
MYCN is a member of the MYC family of proto-oncogenes. It encodes a transcription factor, MYCN, involved in the control of fundamental processes during embryonal development. The MYCN protein is situated downstream of several signaling pathways promoting cell growth, proliferation and metabolism of progenitor cells in different developing organs and tissues. Conversely, deregulated MYCN signaling supports the development of several different tumors, mainly with a childhood onset, including neuroblastoma, medulloblastoma, rhabdomyosarcoma and Wilms’ tumor, but it is also associated with some cancers occurring during adulthood such as prostate and lung cancer. In neuroblastoma, MYCN-amplification is the most consistent genetic aberration associated with poor prognosis and treatment failure. Targeting MYCN has been proposed as a therapeutic strategy for the treatment of these tumors and great efforts have allowed the development of direct and indirect MYCN inhibitors with potential clinical use.
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19
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The mutational signature of chronic lymphocytic leukemia. Biochem J 2016; 473:3725-3740. [DOI: 10.1042/bcj20160256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/23/2016] [Indexed: 01/14/2023]
Abstract
Advances in next-generation sequencing technologies continue to unravel the cancer genome, identifying key biological pathways important for disease pathogenesis and clinically relevant genetic lesions. These studies have provided unprecedented resolution of the cancer genome, facilitating significant advances in the ability to detect many cancers, and predict patients who will develop an aggressive disease or respond poorly to treatment. The mature B-cell neoplasm chronic lymphocytic leukaemia remains at the forefront of these genomic analyses, largely due its protracted natural history and the accessibility to suitable material for study. We now possess a comprehensive view of the genomic copy number mutational landscape of the disease, as well as a detail description of clonal evolution, and the molecular mechanisms that drive the acquisition of genomic lesions and more broadly, genomic complexity. Here, recent genomic insights with associated biological and clinical implications will be reviewed.
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20
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Vermeesch JR, Melotte C, Froyen G, Van Vooren S, Dutta B, Maas N, Vermeulen S, Menten B, Speleman F, De Moor B, Van Hummelen P, Marynen P, Fryns JP, Devriendt K. Molecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis. J Histochem Cytochem 2016; 53:413-22. [PMID: 15750031 DOI: 10.1369/jhc.4a6436.2005] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Array CGH (comparative genomic hybridization) enables the identification of chromosomal copy number changes. The availability of clone sets covering the human genome opens the possibility for the widespread use of array CGH for both research and diagnostic purposes. In this manuscript we report on the parameters that were critical for successful implementation of the technology, assess quality criteria, and discuss the potential benefits and pitfalls of the technology for improved pre- and postnatal constitutional genetic diagnosis. We propose to name the genome-wide array CGH “molecular karyotyping,” in analogy with conventional karyotyping that uses staining methods to visualize chromosomes.
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21
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Schoumans J, Suela J, Hastings R, Muehlematter D, Rack K, van den Berg E, Berna Beverloo H, Stevens-Kroef M. Guidelines for genomic array analysis in acquired haematological neoplastic disorders. Genes Chromosomes Cancer 2016; 55:480-91. [PMID: 26774012 DOI: 10.1002/gcc.22350] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Revised: 01/09/2016] [Accepted: 01/09/2016] [Indexed: 12/19/2022] Open
Abstract
Genetic profiling is important for disease evaluation and prediction of prognosis or responsiveness to therapy in neoplasia. Microarray technologies, including array comparative genomic hybridization and single-nucleotide polymorphism-detecting arrays, have in recent years been introduced into the diagnostic setting for specific types of haematological malignancies and solid tumours. It can be used as a complementary test or depending on the neoplasia investigated, also as a standalone test. However, comprehensive and readable presentation of frequently identified complex genomic profiles remains challenging. To assist diagnostic laboratories, standardization and minimum criteria for clinical interpretation and reporting of acquired genomic abnormalities detected through arrays in neoplastic disorders are presented.
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Affiliation(s)
- Jacqueline Schoumans
- Unité De Génétique Du Cancer, Service De Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, CH-1011, Switzerland
| | - Javier Suela
- Cytogenomics Laboratory, NIMGenetics, Madrid, Spain
| | - Ros Hastings
- Cytogenetic External Quality Assessment, Women's Centre, John Radcliffe Hospital, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Dominique Muehlematter
- Unité De Génétique Du Cancer, Service De Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne, CH-1011, Switzerland
| | - Katrina Rack
- Institut De Pathologie Et De Génétique, Gosselies, Belgium
- West Midland Regional Genetic Laboratory, Birmingham Womens Hospital, Birmingham, UK
| | - Eva van den Berg
- Dept Genet, University Groningen, University Medical Centre Groningen, Groningen, the Netherlands
| | - H Berna Beverloo
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - Marian Stevens-Kroef
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
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22
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Roos-Weil D, Nguyen-Khac F, Bernard OA. Chronic lymphocytic leukemia: Time to go past genomics? Am J Hematol 2016; 91:518-28. [PMID: 26800490 DOI: 10.1002/ajh.24301] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 12/20/2022]
Abstract
Recent advances in massively parallel sequencing technologies have provided a detailed picture of the mutational landscape in CLL and underscored the vast degree of interpatient and intratumor heterogeneities. These studies have led to the characterization of novel putative driver genes and recurrently affected biological pathways, and to the modeling of CLL clonal evolution. We herein review selected aspects including recent advances in the biology of CLL and present cellular and biological processes involved in the development of CLL and potentially other mature B-cell lymphoproliferative neoplasms.
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Affiliation(s)
- Damien Roos-Weil
- Institut National De La Santé Et De La Recherche Médicale (INSERM) U1170; Villejuif France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay; France
- Equipe Labellisée Ligue Nationale Contre Le Cancer
| | - Florence Nguyen-Khac
- INSERM U1138; Paris France
- Université Pierre Et Marie Curie-Paris 6; France
- Service D'hématologie Biologique, Hôpital Pitié-Salpêtrière, APHP; Paris France
| | - Olivier A. Bernard
- Institut National De La Santé Et De La Recherche Médicale (INSERM) U1170; Villejuif France
- Gustave Roussy, Villejuif, France
- Université Paris Saclay; France
- Equipe Labellisée Ligue Nationale Contre Le Cancer
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23
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Baliakas P, Puiggros A, Xochelli A, Sutton LA, Nguyen-Khac F, Gardiner A, Plevova K, Minga E, Hadzidimitriou A, Walewska R, McCarthy H, Ortega M, Collado R, González T, Granada I, Luño E, Kotašková J, Moysiadis T, Davis Z, Stavroyianni N, Anagnostopoulos A, Strefford JC, Pospisilova S, Davi F, Athanasiadou A, Rosenquist R, Oscier D, Espinet B, Stamatopoulos K. Additional trisomies amongst patients with chronic lymphocytic leukemia carrying trisomy 12: the accompanying chromosome makes a difference. Haematologica 2016; 101:e299-302. [PMID: 27102498 DOI: 10.3324/haematol.2015.140202] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Anna Puiggros
- Laboratori de Citogenètica Molecular Servei de Patologia Hospital del Mar, Barcelona, Spain Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Aliki Xochelli
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | - Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - Florence Nguyen-Khac
- AP-HP, Pitie-Salpetriere Hospital, Department of Hematology, and UPMC Univ Paris 06, UMRS 1138, France
| | - Anne Gardiner
- Department of Haematology, Royal Bournemouth Hospital, UK
| | - Karla Plevova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Czech Republic
| | - Eva Minga
- Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
| | | | | | - Helen McCarthy
- Department of Haematology, Royal Bournemouth Hospital, UK
| | | | - Rosa Collado
- Consorcio Hospital General Universitario de Valencia, Spain
| | - Teresa González
- Fundación Pública Galega de Medicina Xenómica, Santiago de Compostela, Spain
| | - Isabel Granada
- Institut de Recerca Contra la Leucèmia Josep Carreras (IJC), ICO-Hospital GeransTrias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Elisa Luño
- Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Jana Kotašková
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Czech Republic
| | | | - Zadie Davis
- Department of Haematology, Royal Bournemouth Hospital, UK
| | - Niki Stavroyianni
- Hematology Department and HCT Unit, G. Papanicolaou Hospital, Thessaloniki, Greece
| | | | | | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University and University Hospital Brno, Czech Republic
| | - Frederic Davi
- AP-HP, Pitie-Salpetriere Hospital, Department of Hematology, and UPMC Univ Paris 06, UMRS 1138, France
| | | | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, UK
| | - Blanca Espinet
- Laboratori de Citogenètica Molecular Servei de Patologia Hospital del Mar, Barcelona, Spain Grup de Recerca Translacional en Neoplàsies Hematològiques, Cancer Research Program, IMIM-Hospital del Mar, Barcelona, Spain
| | - Kostas Stamatopoulos
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Sweden Institute of Applied Biosciences, CERTH, Thessaloniki, Greece
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Salaverria I, Martín‐Garcia D, López C, Clot G, García‐Aragonés M, Navarro A, Delgado J, Baumann T, Pinyol M, Martin‐Guerrero I, Carrió A, Costa D, Queirós AC, Jayne S, Aymerich M, Villamor N, Colomer D, González M, López‐Guillermo A, Campo E, Dyer MJS, Siebert R, Armengol L, Beà S. Detection of chromothripsis-like patterns with a custom array platform for chronic lymphocytic leukemia. Genes Chromosomes Cancer 2015; 54:668-80. [PMID: 26305789 PMCID: PMC4832286 DOI: 10.1002/gcc.22277] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/04/2015] [Accepted: 06/04/2015] [Indexed: 02/04/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a common disease with highly variable clinical course. Several recurrent chromosomal alterations are associated with prognosis and may guide risk-adapted therapy. We have developed a targeted genome-wide array to provide a robust tool for ascertaining abnormalities in CLL and to overcome limitations of the 4-marker fluorescence in situ hybridization (FISH). DNA from 180 CLL patients were hybridized to the qChip®Hemo array with a high density of probes covering commonly altered loci in CLL (11q22-q23, 13q14, and 17p13), nine focal regions (2p15-p16.1, 2p24.3, 2q13, 2q36.3-q37.1, 3p21.31, 8q24.21, 9p21.3, 10q24.32, and 18q21.32-q21.33) and two larger regions (6q14.1-q22.31 and 7q31.33-q33). Overall, 86% of the cases presented copy number alterations (CNA) by array. There was a high concordance of array findings with FISH (84% sensitivity, 100% specificity); all discrepancies corresponded to subclonal alterations detected only by FISH. A chromothripsis-like pattern was detected in eight cases. Three showed concomitant shattered 5p with gain of TERT along with isochromosome 17q. Presence of 11q loss was associated with shorter time to first treatment (P = 0.003), whereas 17p loss, increased genomic complexity, and chromothripsis were associated with shorter overall survival (P < 0.001, P = 0.001, and P = 0.02, respectively). In conclusion, we have validated a targeted array for the diagnosis of CLL that accurately detects, in a single experiment, all relevant CNAs, genomic complexity, chromothripsis, copy number neutral loss of heterozygosity, and CNAs not covered by the FISH panel. This test may be used as a practical tool to stratify CLL patients for routine diagnostics or clinical trials.
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Affiliation(s)
- Itziar Salaverria
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - David Martín‐Garcia
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Cristina López
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
- Institute of Human Genetics, University Hospital Schleswig‐Holstein, Campus Kiel/Christian‐Albrechts UniversityKielGermany
| | - Guillem Clot
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Manel García‐Aragonés
- R&D, Department, Quantitative Genomic Medicine Laboratories (qGenomics)BarcelonaSpain
| | - Alba Navarro
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Julio Delgado
- Department of HematologyHospital Clínic, IDIBAPSBarcelonaSpain
| | - Tycho Baumann
- Department of HematologyHospital Clínic, IDIBAPSBarcelonaSpain
| | - Magda Pinyol
- Genomics UnitInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Idoia Martin‐Guerrero
- Institute of Human Genetics, University Hospital Schleswig‐Holstein, Campus Kiel/Christian‐Albrechts UniversityKielGermany
- Department of Genetics, Physical Anthropology and Animal PhysiologyUniversity of the Basque CountryLeioaSpain
| | - Ana Carrió
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Dolors Costa
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Ana C. Queirós
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, Department of Biochemistry, University of LeicesterLeicesterUK
| | - Marta Aymerich
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Neus Villamor
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Dolors Colomer
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Marcos González
- Department of HematologyHospital Clínico‐IBSAL, Cancer Institute of Salamanca‐IBMCC (USAL‐CSIC)SalamancaSpain
| | | | - Elías Campo
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
| | - Martin J. S. Dyer
- Ernest and Helen Scott Haematological Research Institute, Department of Biochemistry, University of LeicesterLeicesterUK
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig‐Holstein, Campus Kiel/Christian‐Albrechts UniversityKielGermany
| | - Lluís Armengol
- R&D, Department, Quantitative Genomic Medicine Laboratories (qGenomics)BarcelonaSpain
| | - Sílvia Beà
- Hematopathology Unit, Hospital Clínic Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)BarcelonaSpain
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25
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Sutton LA, Rosenquist R. The complex interplay between cell-intrinsic and cell-extrinsic factors driving the evolution of chronic lymphocytic leukemia. Semin Cancer Biol 2015; 34:22-35. [DOI: 10.1016/j.semcancer.2015.04.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/24/2015] [Accepted: 04/27/2015] [Indexed: 01/08/2023]
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26
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Strefford JC. The genomic landscape of chronic lymphocytic leukaemia: biological and clinical implications. Br J Haematol 2014; 169:14-31. [PMID: 25496136 DOI: 10.1111/bjh.13254] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic lymphocytic leukaemia (CLL) remains at the forefront of the genetic analysis of human tumours, principally due its prevalence, protracted natural history and accessibility to suitable material for analysis. With the application of high-throughput genetic technologies, we have an unbridled view of the architecture of the CLL genome, including a comprehensive description of the copy number and mutational landscape of the disease, a detailed picture of clonal evolution during pathogenesis, and the molecular mechanisms that drive genomic instability and therapeutic resistance. This work has nuanced the prognostic importance of established copy number alterations, and identified novel prognostically relevant gene mutations that function within biological pathways that are attractive treatment targets. Herein, an overview of recent genomic discoveries will be reviewed, with associated biological and clinical implications, and a view into how clinical implementation may be facilitated.
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Affiliation(s)
- Jonathan C Strefford
- Cancer Genomics, Academic Unit of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
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27
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Sutton LA, Rosenquist R. Clonal evolution in chronic lymphocytic leukemia: impact of subclonality on disease progression. Expert Rev Hematol 2014; 8:71-8. [PMID: 25345442 DOI: 10.1586/17474086.2015.972930] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In recent years, next-generation sequencing has unraveled the molecular landscape in chronic lymphocytic leukemia with the discovery of a number of recurrently mutated genes. Mutations in several of these genes, such as NOTCH1, SF3B1 and BIRC3, are linked to a more aggressive disease with early disease progression, short time-to-first-treatment and even chemorefractoriness. Although in its infancy, we have also begun to understand the complex dynamics of subclonal diversity and its impact on disease outcome. From pioneering studies, we know that certain genetic events are found in the majority of chronic lymphocytic leukemia cells and are considered as 'clonal driver mutations' (e.g., +12, 13q-), whereas others, present only in a fraction of the tumor, are deemed to be 'subclonal driver mutations' for example, TP53 and SF3B1. Over the coming years, we need to gain a deeper insight into the dynamics of this subclonal architecture to understand how, at an individual level, chronic lymphocytic leukemia patients should be followed, which will be particularly relevant as novel targeted therapies begin to emerge.
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Affiliation(s)
- Lesley-Ann Sutton
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751-85, Uppsala, Sweden
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28
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Genetic abnormalities in chronic lymphocytic leukemia: where we are and where we go. BIOMED RESEARCH INTERNATIONAL 2014; 2014:435983. [PMID: 24967369 PMCID: PMC4054680 DOI: 10.1155/2014/435983] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/22/2014] [Indexed: 12/17/2022]
Abstract
Chromosomal abnormalities in chronic lymphocytic leukemia (CLL) are detected in up to 80% of patients. Among them, deletions of 11q, 13q, 17p, and trisomy 12 have a known prognostic value and play an important role in CLL pathogenesis and evolution, determining patients outcome and therapeutic strategies. Standard methods used to identify these genomic aberrations include both conventional G-banding cytogenetics (CGC) and fluorescence in situ hybridization (FISH). Although FISH analyses have been implemented as the gold standard, CGC allows the identification of chromosomal translocations and complex karyotypes, the latest associated with poor outcome. Genomic arrays have a higher resolution that allows the detection of cryptic abnormalities, although these have not been fully implemented in routine laboratories. In the last years, next generation sequencing (NGS) methods have identified a wide range of gene mutations (e.g., TP53, NOTCH1, SF3B1, and BIRC3) which have improved our knowledge about CLL development, allowing us to refine both the prognostic subgroups and better therapeutic strategies. Clonal evolution has also recently arisen as a key point in CLL, integrating cytogenetic alterations and mutations in a dynamic model that improve our understanding about its clinical course and relapse.
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29
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Arefi M, Robledo C, Peñarrubia MJ, García de Coca A, Cordero M, Hernández-Rivas JM, García JL. Genomic analysis of clonal eosinophils by CGH arrays reveals new genetic regions involved in chronic eosinophilia. Eur J Haematol 2014; 93:422-8. [PMID: 24813417 DOI: 10.1111/ejh.12379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2014] [Indexed: 12/22/2022]
Abstract
To assess the presence of genetic imbalances in patients with myeloproliferative neoplasms (MPNs), 38 patients with chronic eosinophilia were studied by array comparative genomic hybridization (aCGH): seven had chronic myelogenous leukaemia (CML), BCR-ABL1 positive, nine patients had myeloproliferative neoplasia Ph- (MPN-Ph-), three had a myeloid neoplasm associated with a PDGFRA rearrangement, and the remaining two cases were Lymphoproliferative T neoplasms associated with eosinophilia. In addition, 17 patients had a secondary eosinophilia and were used as controls. Eosinophilic enrichment was carried out in all cases. Genomic imbalances were found in 76% of all MPN patients. Losses on 20q were the most frequent genetic abnormality in MPNs (32%), affected the three types of MPN studied. This study also found losses at 11q13.3 in 26% of patients with MPN-Ph- and in 19p13.11 in two of the three patients with an MPN associated with a PDGFRA rearrangement. In addition, 29% of patients with CML had losses on 8q24. In summary, aCGH revealed clonality in eosinophils in most MPNs, suggesting that it could be a useful technique for defining clonality in these diseases. The presence of genetic losses in new regions could provide new insights into the knowledge of these MPN associated with eosinophilia.
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Affiliation(s)
- Maryam Arefi
- Department of Hematology, Hospital Clínico Universitario, Valladolid, Spain
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30
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Urbankova H, Papajik T, Plachy R, Holzerova M, Balcarkova J, Divoka M, Prochazka V, Pikalova Z, Indrak K, Jarosova M. Array-based karyotyping in chronic lymphocytic leukemia (CLL) detects new unbalanced abnormalities that escape conventional cytogenetics and CLL FISH panel. Biomed Pap Med Fac Univ Palacky Olomouc Czech Repub 2014; 158:56-64. [DOI: 10.5507/bp.2012.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/27/2012] [Indexed: 02/07/2023] Open
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31
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Rose-Zerilli MJJ, Forster J, Parker H, Parker A, Rodríguez AE, Chaplin T, Gardiner A, Steele AJ, Collins A, Young BD, Skowronska A, Catovsky D, Stankovic T, Oscier DG, Strefford JC. ATM mutation rather than BIRC3 deletion and/or mutation predicts reduced survival in 11q-deleted chronic lymphocytic leukemia: data from the UK LRF CLL4 trial. Haematologica 2014; 99:736-42. [PMID: 24584352 DOI: 10.3324/haematol.2013.098574] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
ATM mutation and BIRC3 deletion and/or mutation have independently been shown to have prognostic significance in chronic lymphocytic leukemia. However, the relative clinical importance of these abnormalities in patients with a deletion of 11q encompassing the ATM gene has not been established. We screened a cohort of 166 patients enriched for 11q-deletions for ATM mutations and BIRC3 deletion and mutation and determined the overall and progression-free survival among the 133 of these cases treated within the UK LRF CLL4 trial. SNP6.0 profiling demonstrated that BIRC3 deletion occurred in 83% of 11q-deleted cases and always co-existed with ATM deletion. For the first time we have demonstrated that 40% of BIRC3-deleted cases have concomitant deletion and mutation of ATM. While BIRC3 mutations were rare, they exclusively occurred with BIRC3 deletion and a wild-type residual ATM allele. In 11q-deleted cases, we confirmed that ATM mutation was associated with a reduced overall and progression-free survival comparable to that seen with TP53 abnormalities, whereas BIRC3 deletion and/or mutation had no impact on overall and progression-free survival. In conclusion, in 11q-deleted patients treated with first-line chemotherapy, ATM mutation rather than BIRC3 deletion and/or mutation identifies a subgroup with a poorer outcome.
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32
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Pei J, Robu V, Feder M, Cheung M, Neumann-Domer E, Talarchek J, Dulaimi E, Millenson MM, Testa JR. Copy neutral loss of heterozygosity in 20q in chronic lymphocytic leukemia/small lymphocytic lymphoma. Cancer Genet 2014; 207:98-102. [PMID: 24704113 DOI: 10.1016/j.cancergen.2014.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 02/10/2014] [Accepted: 02/10/2014] [Indexed: 01/26/2023]
Abstract
Single nucleotide polymorphism (SNP)-based chromosome microarray analysis was used to uncover copy neutral loss of heterozygosity (LOH) in the long arm of chromosome 20 in blood or bone marrow specimens from three patients with chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL). All three patients presented with lymph node enlargement. Whereas one of the patients has had a complicated clinical course, the other two have a more indolent disease. Sequence analysis of the tumor suppressor gene ASXL1, which is located in 20q and is commonly mutated in malignant myeloid diseases and occasionally in CLL/SLL specimens, revealed no mutations in our three patients with copy neutral LOH in 20q. The possible contribution of other imprinted microRNAs and antisense genes residing in 20q to the pathogenesis of a subset of CLL/SLL patients is discussed. These findings illustrate the value of SNP arrays for the detection of novel recurrent genomic alterations that may contribute to CLL/SLL onset or progression.
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Affiliation(s)
- Jianming Pei
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA; Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Valentin Robu
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Madelyn Feder
- Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Mitchell Cheung
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Erin Neumann-Domer
- Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Essel Dulaimi
- Department of Pathology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael M Millenson
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Joseph R Testa
- Cancer Biology Program, Fox Chase Cancer Center, Philadelphia, PA, USA; Clinical Cytogenomics Laboratory, Fox Chase Cancer Center, Philadelphia, PA, USA.
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33
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Konialis C, Savola S, Karapanou S, Markaki A, Karabela M, Polychronopoulou S, Ampatzidou M, Voulgarelis M, Viniou NA, Variami E, Koumarianou A, Zoi K, Hagnefelt B, Schouten JP, Pangalos C. Routine application of a novel MLPA-based first-line screening test uncovers clinically relevant copy number aberrations in haematological malignancies undetectable by conventional cytogenetics. Hematology 2013; 19:217-24. [DOI: 10.1179/1607845413y.0000000112] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
| | | | | | | | | | - Sophia Polychronopoulou
- Department of Paediatric Haematology-Oncology‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | - Maria Ampatzidou
- Department of Paediatric Haematology-Oncology‘Aghia Sophia’ Children's Hospital, Athens, Greece
| | - Michael Voulgarelis
- Pathophysiology DepartmentSchool of Medicine, University of Athens, Athens, Greece
| | - Nora-Athina Viniou
- 1st Pathology ClinicUniversity of Athens, Laiko Hospital, Athens, Greece
| | - Eleni Variami
- 1st Pathology ClinicUniversity of Athens, Laiko Hospital, Athens, Greece
| | | | - Katerina Zoi
- Haematology Research LaboratoryBiomedical Research Foundation, Academy of Athens, Athens, Greece
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34
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Sanjmyatav J, Hauke S, Gajda M, Hartmann A, Moch H, Meyer B, Pryalukhin A, Grimm MO, Junker K. Establishment of a Multicolour Fluorescence In Situ Hybridisation-based Assay for Subtyping of Renal Cell Tumours. Eur Urol 2013; 64:689-91. [DOI: 10.1016/j.eururo.2013.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 06/06/2013] [Indexed: 11/28/2022]
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Improgo MR, Brown JR. Genomic approaches to chronic lymphocytic leukemia. Hematol Oncol Clin North Am 2013; 27:157-71. [PMID: 23561468 DOI: 10.1016/j.hoc.2013.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
This article discusses recent advances in genomic approaches used to understand chronic lymphocytic leukemia. Tools for analyzing DNA-level lesions are described, data obtained from these various platforms summarized, and the clinical relevance of these findings discussed.
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Affiliation(s)
- Ma Reina Improgo
- Department of Medical Oncology, Dana-Farber Cancer Institute, CLL Center, Harvard Medical School, Boston, MA 02215, USA
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36
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Jimenez-Zepeda VH, Chng WJ, Schop RF, Braggio E, Leis JF, Kay N, Fonseca R. Recurrent Chromosome Abnormalities Define Nonoverlapping Unique Subgroups of Tumors in Patients With Chronic Lymphocytic Leukemia and Known Karyotypic Abnormalities. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2013; 13:467-76. [DOI: 10.1016/j.clml.2013.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/02/2013] [Accepted: 05/02/2013] [Indexed: 11/16/2022]
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37
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Combined patterns of IGHV repertoire and cytogenetic/molecular alterations in monoclonal B lymphocytosis versus chronic lymphocytic leukemia. PLoS One 2013; 8:e67751. [PMID: 23844084 PMCID: PMC3701012 DOI: 10.1371/journal.pone.0067751] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/21/2013] [Indexed: 11/21/2022] Open
Abstract
Background Chronic lymphocytic leukemia (CLL)-like monoclonal B lymphocytosis (MBL) with (MBLhi) or without (MBLlo) absolute B-lymphocytosis precedes most CLL cases,the specific determinants for malignant progression remaining unknown. Methodology/Principal Findings For this purpose, simultaneous iFISH and molecular analysis of well-established cytogenetic alterations of chromosomes 11, 12, 13, 14 and 17 together with the pattern of rearrangement of the IGHV genes were performed in CLL-like cells from MBL and CLL cases. Our results based on 78 CLL-like MBL and 117 CLL clones from 166 subjects living in the same geographical area, show the existence of three major groups of clones with distinct but partially overlapping patterns of IGHV gene usage, IGHV mutational status and cytogenetic alterations. These included a group enriched in MBLlo clones expressing specific IGHV subgroups (e.g. VH3-23) with no or isolated good-prognosis cytogenetic alterations, a second group which mainly consisted of clinical MBLhi and advanced stage CLL with a skewed but different CLL-associated IGHV gene repertoire (e.g. VH1-69), frequently associated with complex karyotypes and poor-prognosis cytogenetic alterations, and a third group of clones with intermediate features, with prevalence of mutated IGHV genes, and higher numbers of del(13q)+ clonal B-cells. Conclusions/Significance These findings suggest that the specific IGHV repertoire and IGHV mutational status of CLL-like B-cell clones may modulate the type of cytogenetic alterations acquired, their rate of acquisition and/or potentially also their clinical consequences. Further long-term follow-up studies investigating the IGHV gene repertoire of MBLlo clones in distinct geographic areas and microenvironments are required to confirm our findings and shed light on the potential role of some antigen-binding BCR specificities contributing to clonal evolution.
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38
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Landau DA, Wu CJ. Chronic lymphocytic leukemia: molecular heterogeneity revealed by high-throughput genomics. Genome Med 2013; 5:47. [PMID: 23731665 PMCID: PMC3706960 DOI: 10.1186/gm451] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Chronic lymphocytic leukemia (CLL) has been consistently at the forefront of genetic research owing to its prevalence and the accessibility of sample material. Recently, genome-wide technologies have been intensively applied to CLL genetics, with remarkable progress. Single nucleotide polymorphism arrays have identified recurring chromosomal aberrations, thereby focusing functional studies on discrete genomic lesions and leading to the first implication of somatic microRNA disruption in cancer. Next-generation sequencing (NGS) has further transformed our understanding of CLL by identifying novel recurrently mutated putative drivers, including the unexpected discovery of somatic mutations affecting spliceosome function. NGS has further enabled in-depth examination of the transcriptional and epigenetic changes in CLL that accompany genetic lesions, and has shed light on how different driver events appear at different stages of disease progression and clonally evolve with relapsed disease. In addition to providing important insights into disease biology, these discoveries have significant translational potential. They enhance prognosis by highlighting specific lesions associated with poor clinical outcomes (for example, driver events such as mutations in the splicing factor subunit gene SF3B1) or with increased clonal heterogeneity (for example, the presence of subclonal driver mutations). Here, we review new genomic discoveries in CLL and discuss their possible implications in the era of precision medicine.
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Affiliation(s)
- Dan A Landau
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA ; Broad Institute, Cambridge, MA 02142, USA ; Department of Hematology, Yale Cancer Center, New Haven, CT 06510, USA ; Université Paris Diderot, Paris 75013, France
| | - Catherine J Wu
- Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA ; Division of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA ; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
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39
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Rosenquist R, Cortese D, Bhoi S, Mansouri L, Gunnarsson R. Prognostic markers and their clinical applicability in chronic lymphocytic leukemia: where do we stand? Leuk Lymphoma 2013; 54:2351-64. [PMID: 23480493 DOI: 10.3109/10428194.2013.783913] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is a clinically and biologically heterogeneous disease where the majority of patients have an indolent disease course, while others may experience a far more aggressive disease, treatment failure and poor overall survival. During the last two decades, there has been an intense search to find novel biomarkers that can predict prognosis as well as guide treatment decisions. Two of the most reliable molecular prognostic markers, both of which are offered in routine diagnostics, are the immunoglobulin heavy chain variable (IGHV) gene mutational status and fluorescence in situ hybridization (FISH) detection of prognostically relevant genomic aberrations (e.g. 11q-, 13q-, +12 and 17p-). In addition to these markers, a myriad of additional biomarkers have been postulated as potential prognosticators in CLL, on the protein (e.g. CD38, ZAP70, TCL1), the RNA (e.g. LPL, CLLU1, micro-RNAs) and the genomic (e.g. TP53, NOTCH1, SF3B1 and BIRC3 mutations) level. Efforts are now being made to test these novel markers in larger patient cohorts as well as in prospective trials, with the ultimate goal to combine the "best" markers in a "CLL prognostic index" applicable for the individual patient. Although it is clear that these studies have significantly improved our knowledge regarding both prognostication and the biology of the disease, there is still an immediate need for recognizing biomarkers that can predict therapy response, and efforts should now focus on addressing this pertinent issue. In the present article, we review the extensive literature in the field of prognostic markers in CLL, focus on the most clinically relevant markers and discuss future directions regarding biomarkers in CLL.
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Affiliation(s)
- Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Uppsala University , Uppsala , Sweden
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40
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Rodríguez-Vicente AE, Díaz MG, Hernández-Rivas JM. Chronic lymphocytic leukemia: a clinical and molecular heterogenous disease. Cancer Genet 2013; 206:49-62. [DOI: 10.1016/j.cancergen.2013.01.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/21/2013] [Accepted: 01/24/2013] [Indexed: 12/11/2022]
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Gunnarsson R, Mansouri L, Rosenquist R. Exploring the genetic landscape in chronic lymphocytic leukemia using high-resolution technologies. Leuk Lymphoma 2013; 54:1583-90. [PMID: 23167608 DOI: 10.3109/10428194.2012.751530] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract During recent years, microarray-based technologies and next-generation sequencing (NGS) have been applied in chronic lymphocytic leukemia (CLL) in order to identify novel genomic aberrations that may contribute to the pathogenesis of the disease. Even though high-resolution microarray studies have confirmed the importance of the known recurrent aberrations, i.e. del(11q), trisomy 12, del(13q) and del(17p), and have more precisely delineated the genomic borders of these aberrations, only a few novel aberrations, found at a low frequency, have been detected with these techniques. In contrast to this, the application of NGS technology of the coding genome (exome sequencing) or the entire genome (whole-genome sequencing) has unveiled a number of novel recurrent mutations in e.g. the NOTCH1, SF3B1 and BIRC3 genes. Importantly, mutations in these latter genes were reported to be associated with a particularly poor outcome, similar to TP53 aberrations, and may play key roles in tumor development, treatment resistance and prognosis. In this review, we not only summarize the latest achievements using array-based or NGS technologies, but also point to new directions for research aiming to unravel the complex genetic "map" in CLL and its prognostic subsets.
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Affiliation(s)
- Rebeqa Gunnarsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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42
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Park S, Moon HS, Lee DS, Kim HC, Chun H. High-throughput on-chip leukemia diagnosis. Int J Lab Hematol 2013; 35:480-90. [PMID: 23414350 DOI: 10.1111/ijlh.12054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 12/18/2012] [Indexed: 01/04/2023]
Abstract
Advances in lab-on-a-chip technologies enabled programmable, reconfigurable, and scalable manipulation of a variety of laboratory procedures. Samples, reagents, and fluids can be precisely controlled; buffer temperature, pH, and concentration control systems as well as a variety of detection systems can be integrated on a small chip. These advantages have attracted attention in various fields of clinical application including leukemia diagnosis and research. A lot of research on lab-on-a-chip based diagnosis has been reported and the field is rapidly expanding. This review describes recent developments of lab-on-a-chip technologies as solutions to challenges for high-throughput leukemia diagnosis.
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Affiliation(s)
- S Park
- Interdisciplinary Program, Bioengineering Major, Graduate School, Seoul National University, Seoul, Korea
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43
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Mian M, Rinaldi A, Mensah AA, Rossi D, Ladetto M, Forconi F, Marasca R, Uhr M, Stussi G, Kwee I, Cavalli F, Gaidano G, Zucca E, Bertoni F. Large genomic aberrations detected by SNP array are independent prognosticators of a shorter time to first treatment in chronic lymphocytic leukemia patients with normal FISH. Ann Oncol 2013; 24:1378-84. [PMID: 23372049 DOI: 10.1093/annonc/mds646] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Genomic complexity can predict the clinical course of patients affected by chronic lymphocytic leukemia (CLL) with a normal FISH. However, large studies are still lacking. Here, we analyzed a large series of CLL patients and also carried out the so far largest comparison of FISH versus single-nucleotide polymorphism (SNP) array in this disease. PATIENTS AND METHODS SNP-array data were derived from a previously reported dataset. RESULTS Seventy-seven of 329 CLL patients (23%) presented with a normal FISH. At least one large (>5 Mb) genomic aberration was detected by SNP array in 17 of 77 patients (22%); this finding significantly affected TTT. There was no correlation with the presence of TP53 mutations. In multivariate analysis, including age, Binet stage, IGHV genes mutational status and large genomic lesion, the latter three factors emerged as independent prognosticators. The concordance between FISH and SNP array varied between 84 and 97%, depending on the specific genomic locus investigated. CONCLUSIONS SNP array detected additional large genomic aberrations not covered by the standard FISH panel predicting the outcome of CLL patients.
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Affiliation(s)
- M Mian
- Lymphoma and Genomics Research Program, IOR Institute of Oncology Research, Bellinzona, Switzerland
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44
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Véronèse L, Tournilhac O, Combes P, Prie N, Pierre-Eymard E, Guièze R, Veyrat-Masson R, Bay JO, Vago P, Tchirkov A. Contribution of MLPA to routine diagnostic testing of recurrent genomic aberrations in chronic lymphocytic leukemia. Cancer Genet 2013; 206:19-25. [PMID: 23313109 DOI: 10.1016/j.cancergen.2012.12.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/03/2012] [Accepted: 12/03/2012] [Indexed: 02/03/2023]
Abstract
To better define the place of multiplex ligation-dependent probe amplification (MLPA) in routine cytogenetic diagnosis in chronic lymphocytic leukemia (CLL), we compared MLPA and fluorescence in situ hybridization (iFISH) data obtained in 77 CLL patients. Although MLPA detected most recurrent copy number genomic aberrations (90.9%), false-negative results were found in cases with small-size abnormal clones and false-positive MLPA findings resulting from point mutations (TP53) or an apparent lack of probe specificity (chromosome 19) were observed. Thus, MLPA may be a useful complementary but not alternative approach for iFISH testing of genomic aberration in CLL.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Chromosome Aberrations/statistics & numerical data
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 12/genetics
- Chromosomes, Human, Pair 13/genetics
- Chromosomes, Human, Pair 17/genetics
- Diagnostic Tests, Routine/methods
- Female
- Gene Frequency
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/epidemiology
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Male
- Middle Aged
- Multiplex Polymerase Chain Reaction/methods
- Prognosis
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Affiliation(s)
- Lauren Véronèse
- Clermont-Ferrand University Hospital, Department of Medical Cytogenetics, 63003 Clermont-Ferrand, France
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45
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Fabris S, Mosca L, Cutrona G, Lionetti M, Agnelli L, Ciceri G, Barbieri M, Maura F, Matis S, Colombo M, Gentile M, Recchia AG, Anna Pesce E, Di Raimondo F, Musolino C, Gobbi M, Di Renzo N, Mauro FR, Brugiatelli M, Ilariucci F, Lipari MG, Angrilli F, Consoli U, Fragasso A, Molica S, Festini G, Vincelli I, Cortelezzi A, Federico M, Morabito F, Ferrarini M, Neri A. Chromosome 2p gain in monoclonal B-cell lymphocytosis and in early stage chronic lymphocytic leukemia. Am J Hematol 2013; 88:24-31. [PMID: 23044996 DOI: 10.1002/ajh.23340] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/03/2012] [Accepted: 09/05/2012] [Indexed: 12/17/2022]
Abstract
Recent studies have described chromosome 2p gain as a recurrent lesion in chronic lymphocytic leukemia (CLL). We investigated the 2p gain and its relationship with common prognostic biomarkers in a prospective series of 69 clinical monoclonal B-cell lymphocytosis (cMBL) and 218 early stage (Binet A) CLL patients. The 2p gain was detected by FISH in 17 patients (6%, 16 CLL, and 1 cMBL) and further characterized by single nucleotide polymorphism-array. Overall, unfavorable cytogenetic deletions, i.e., del(11)(q23) and del(17)(p13) (P = 0.002), were significantly more frequent in 2p gain cases, as well as unmutated status of IGHV (P < 1 × 10(-4) ) and CD38 (P < 1 × 10(-4) ) and ZAP-70 positive expression (P = 0.003). Furthermore, 2p gain patients had significantly higher utilization of stereotyped B-cell receptors compared with 2p negative patients (P = 0.009), and the incidence of stereotyped subset #1 in 2p gain patients was significantly higher than that found in the remaining CLLs (P = 0.031). Transcriptional profiling analysis identified several genes significantly upregulated in 2p gain CLLs, most of which mapped to 2p. Among these, NCOA1 and ROCK2 are known for their involvement in tumor progression in several human cancers, whereas among those located in different chromosomes, CAV1 at 7q31.1 has been recently identified to play a critical role in CLL progression. Thus, 2p gain can be present since the early stages of the disease, particularly in those cases characterized by other poor prognosis markers. The finding of genes upregulated in the cells with 2p gain provides new insights to define the pathogenic role of this lesion.
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MESH Headings
- Adult
- Aged
- Biomarkers, Tumor/biosynthesis
- Biomarkers, Tumor/genetics
- Chromosomes, Human, Pair 2/genetics
- Chromosomes, Human, Pair 2/metabolism
- Chromosomes, Human, Pair 7/genetics
- Chromosomes, Human, Pair 7/metabolism
- Female
- Gene Expression Regulation, Leukemic
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Lymphocytosis/diagnosis
- Lymphocytosis/genetics
- Lymphocytosis/metabolism
- Male
- Middle Aged
- Neoplasm Proteins/biosynthesis
- Neoplasm Proteins/genetics
- Neoplasm Staging
- Prognosis
- Prospective Studies
- Up-Regulation/genetics
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Affiliation(s)
- Sonia Fabris
- Dipartimento di Scienze Cliniche e di Comunità, Università degli Studi di Milano e Ematologia 1 CTMO, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Italy
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Abstract
Abstract
Several prognostic markers based on genetic, phenotypic, and molecular characteristics of chronic lymphocytic leukemia (CLL) B cells have emerged in the past decade. The clinical utility of these newer prognostic indicators, alone or in combination with each other and other clinical predictive systems, is still being determined. This chapter attempts to define biologic and molecular underpinnings of 3 sets of prognostic indicators in CLL: genetic abnormalities quantified by FISH and/or defined by exploratory sensitive molecular techniques, expression of specific proteins in or on CLL cells (ie, CD38, CD49d, and ZAP-70), and the IGHV mutation status of a CLL clone. Although not demonstrated conclusively, each probably reflects the biologic properties of the leukemic cells of individual CLL patients. This reflection may be direct, indicating a specific property of the CLL cell itself, or indirect, representing how the CLL cell interacts with the host's microenvironment. The new tyrosine kinase inhibitors that are currently in clinical trials support this interpretation. These and other biology-based indicators of patient clinical course and outcome can be used as starting points from which to understand and treat CLL.
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47
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High-resolution genomic profiling of chronic lymphocytic leukemia reveals new recurrent genomic alterations. Blood 2012; 120:4783-94. [DOI: 10.1182/blood-2012-04-423517] [Citation(s) in RCA: 159] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Abstract
To identify genomic alterations in chronic lymphocytic leukemia (CLL), we performed single-nucleotide polymorphism–array analysis using Affymetrix Version 6.0 on 353 samples from untreated patients entered in the CLL8 treatment trial. Based on paired-sample analysis (n = 144), a mean of 1.8 copy number alterations per patient were identified; approximately 60% of patients carried no copy number alterations other than those detected by fluorescence in situ hybridization analysis. Copy-neutral loss-of-heterozygosity was detected in 6% of CLL patients and was found most frequently on 13q, 17p, and 11q. Minimally deleted regions were refined on 13q14 (deleted in 61% of patients) to the DLEU1 and DLEU2 genes, on 11q22.3 (27% of patients) to ATM, on 2p16.1-2p15 (gained in 7% of patients) to a 1.9-Mb fragment containing 9 genes, and on 8q24.21 (5% of patients) to a segment 486 kb proximal to the MYC locus. 13q deletions exhibited proximal and distal breakpoint cluster regions. Among the most common novel lesions were deletions at 15q15.1 (4% of patients), with the smallest deletion (70.48 kb) found in the MGA locus. Sequence analysis of MGA in 59 samples revealed a truncating mutation in one CLL patient lacking a 15q deletion. MNT at 17p13.3, which in addition to MGA and MYC encodes for the network of MAX-interacting proteins, was also deleted recurrently.
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48
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Puiggros A, Puigdecanet E, Salido M, Ferrer A, Abella E, Gimeno E, Nonell L, Herranz MJ, Galván AB, Rodríguez-Rivera M, Melero C, Pairet S, Bellosillo B, Serrano S, Florensa L, Solé F, Espinet B. Genomic arrays in chronic lymphocytic leukemia routine clinical practice: are we ready to substitute conventional cytogenetics and fluorescence in situ hybridization techniques? Leuk Lymphoma 2012; 54:986-95. [PMID: 22994157 DOI: 10.3109/10428194.2012.731598] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Chronic lymphocytic leukemia (CLL) is characterized by a highly variable clinical course. Del(11q) and del(17p), routinely studied by conventional G-banding cytogenetics (CGC) and fluorescence in situ hybridization (FISH), have been related to progression and shorter overall survival. Recently, array-based karyotyping has gained acceptance as a high-resolution new tool for detecting genomic imbalances. The aim of the present study was to compare genomic arrays with CGC and FISH to ascertain whether the current techniques could be substituted in routine procedures. We analyzed 70 patients with CLL using the Cytogenetics Whole-Genome 2.7M Array and CytoScan HD Array (Affymetrix), CGC and FISH with the classical CLL panel. Whereas 31.4% and 68.6% of patients presented abnormalities when studied by CGC and FISH, respectively, these rates increased when arrays were also analyzed (78.6% and 80%). Although abnormality detection is higher when arrays are applied, one case with del(11q) and three with del(17p) were missed by genomic arrays due to their limited sensitivity. We consider that the complete substitution of CGC and FISH by genomic arrays in routine laboratories could negatively affect the management of some patients harboring 11q or 17p deletions. In conclusion, genomic arrays are valid to detect known and novel genomic imbalances in CLL, but should be maintained as a complementary tool to the current techniques.
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Affiliation(s)
- Anna Puiggros
- Programa de Recerca en Càncer, Grup de Recerca Translacional en Neoplàsies Hematològiques (GRETNHE), IMIM-Hospital del Mar, Barcelona, Spain
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49
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Clinical Application of Array-Based Comparative Genomic Hybridization for the Identification of Prognostically Important Genetic Alterations in Chronic Lymphocytic Leukemia. Mol Diagn Ther 2012; 12:271-80. [DOI: 10.1007/bf03256292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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50
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Rodríguez AE, Robledo C, García JL, González M, Gutiérrez NC, Hernández JA, Sandoval V, García de Coca A, Recio I, Risueño A, Martín-Núñez G, García E, Fisac R, Conde J, de Las Rivas J, Hernández JM. Identification of a novel recurrent gain on 20q13 in chronic lymphocytic leukemia by array CGH and gene expression profiling. Ann Oncol 2012; 23:2138-2146. [PMID: 22228453 DOI: 10.1093/annonc/mdr579] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND The presence of genetic changes is a hallmark of chronic lymphocytic leukemia (CLL). The most common cytogenetic abnormalities with independent prognostic significance in CLL are 13q14, ATM and TP53 deletions and trisomy 12. However, CLL displays a great genetic and biological heterogeneity. The aim of this study was to analyze the genomic imbalances in CLL cytogenetic subsets from both genomic and gene expression perspectives to identify new recurrent alterations. PATIENTS AND METHODS The genomic imbalances and expression levels of 67 patients were analyzed. The novel recurrent abnormalities detected with bacterial artificial chromosome array were confirmed by FISH and oligonucleotide microarrays. In all cases, gene expression profiling was assessed. RESULTS Copy number alterations were identified in 75% of cases. Overall, the results confirmed FISH studies for the regions frequently involved in CLL and also defined a new recurrent gain on chromosome 20q13.12, in 19% (13/67) of the CLL patients. Oligonucleotide expression correlated with the regions of loss or gain of genomic material, suggesting that the changes in gene expression are related to alterations in copy number. CONCLUSION Our study demonstrates the presence of a recurrent gain in 20q13.12 associated with overexpression of the genes located in this region, in CLL cytogenetic subgroups.
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Affiliation(s)
- A E Rodríguez
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - C Robledo
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - J L García
- Instituto de Estudios de Ciencias de la Salud de Castilla y León (IECSCYL)-HUSAL, Castill y León
| | - M González
- Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca
| | - N C Gutiérrez
- Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca
| | - J A Hernández
- Department of Hematology, Hospital Infanta Leonor, Madrid
| | - V Sandoval
- Department of Hematology, Hospital Virgen Blanca, León
| | - A García de Coca
- Department of Hematology, Hospital Clínico Universitario, Valladolid
| | - I Recio
- Department of Hematology, Hospital Nuestra Señora de Sonsoles, Ávila
| | - A Risueño
- Bioinformatics and Functional Genomics, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - G Martín-Núñez
- Department of Hematology, Hospital Virgen del Puerto, Plasencia
| | - E García
- Genomics and Proteomics Unit, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - R Fisac
- Department of Hematology, Hospital General de Segovia, Segovia
| | - J Conde
- Department of Hematology, Hospital del Río Hortega, Valladolid, Spain
| | - J de Las Rivas
- Bioinformatics and Functional Genomics, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca
| | - J M Hernández
- IBMCC, Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca; Department of Hematology, Hospital Clínico Universitario de Salamanca, Salamanca.
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