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Nadeu F, Clot G, Delgado J, Martín-García D, Baumann T, Salaverria I, Beà S, Pinyol M, Jares P, Navarro A, Suárez-Cisneros H, Aymerich M, Rozman M, Villamor N, Colomer D, González M, Alcoceba M, Terol MJ, Navarro B, Colado E, Payer ÁR, Puente XS, López-Otín C, López-Guillermo A, Enjuanes A, Campo E. Clinical impact of the subclonal architecture and mutational complexity in chronic lymphocytic leukemia. Leukemia 2018; 32:645-653. [PMID: 28924241 PMCID: PMC5843898 DOI: 10.1038/leu.2017.291] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/07/2017] [Accepted: 09/05/2017] [Indexed: 12/11/2022]
Abstract
Genome studies of chronic lymphocytic leukemia (CLL) have revealed the remarkable subclonal heterogeneity of the tumors, but the clinical implications of this phenomenon are not well known. We assessed the mutational status of 28 CLL driver genes by deep-targeted next-generation sequencing and copy number alterations (CNA) in 406 previously untreated patients and 48 sequential samples. We detected small subclonal mutations (0.6-25% of cells) in nearly all genes (26/28), and they were the sole alteration in 22% of the mutated cases. CNA tended to be acquired early in the evolution of the disease and remained stable, whereas the mutational heterogeneity increased in a subset of tumors. The prognostic impact of different genes was related to the size of the mutated clone. Combining mutations and CNA, we observed that the accumulation of driver alterations (mutational complexity) gradually shortened the time to first treatment independently of the clonal architecture, IGHV status and Binet stage. Conversely, the overall survival was associated with the increasing subclonal diversity of the tumors but it was related to the age of patients, IGHV and TP53 status of the tumors. In conclusion, our study reveals that both the mutational complexity and subclonal diversity influence the evolution of CLL.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor
- Clonal Evolution/genetics
- DNA Copy Number Variations
- Disease Progression
- Female
- Follow-Up Studies
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/mortality
- Male
- Middle Aged
- Mutation/genetics
- Neoplasm Staging
- Prognosis
- Proportional Hazards Models
- Signal Transduction
- Young Adult
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Affiliation(s)
- F Nadeu
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - G Clot
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - J Delgado
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - D Martín-García
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - T Baumann
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - I Salaverria
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - S Beà
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - M Pinyol
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unitat de Genòmica, IDIBAPS, Barcelona, Spain
| | - P Jares
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - A Navarro
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - M Aymerich
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - M Rozman
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - N Villamor
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - D Colomer
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
| | - M González
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Biología Molecular e Histocompatibilidad, Hospital Universitario, Salamanca, Spain
| | - M Alcoceba
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Biología Molecular e Histocompatibilidad, Hospital Universitario, Salamanca, Spain
| | - M J Terol
- Unidad de Hematología, Hospital Clínico Universitario, Valencia, Spain
| | - B Navarro
- Unidad de Hematología, Hospital Clínico Universitario, Valencia, Spain
| | - E Colado
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - ÁR Payer
- Servicio de Hematología y Hemoterapia, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - X S Puente
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - C López-Otín
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Universidad de Oviedo, Oviedo, Spain
| | - A López-Guillermo
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
- Medical School, Universitat de Barcelona, Barcelona, Spain
| | - A Enjuanes
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Unitat de Genòmica, IDIBAPS, Barcelona, Spain
| | - E Campo
- Lymphoid Neoplasms Program, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Tumores Hematológicos, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Hematology Department, Hospital Clínic, Barcelona, Spain
- Medical School, Universitat de Barcelona, Barcelona, Spain
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3
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Karube K, Enjuanes A, Dlouhy I, Jares P, Martin-Garcia D, Nadeu F, Ordóñez GR, Rovira J, Clot G, Royo C, Navarro A, Gonzalez-Farre B, Vaghefi A, Castellano G, Rubio-Perez C, Tamborero D, Briones J, Salar A, Sancho JM, Mercadal S, Gonzalez-Barca E, Escoda L, Miyoshi H, Ohshima K, Miyawaki K, Kato K, Akashi K, Mozos A, Colomo L, Alcoceba M, Valera A, Carrió A, Costa D, Lopez-Bigas N, Schmitz R, Staudt LM, Salaverria I, López-Guillermo A, Campo E. Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets. Leukemia 2017; 32:675-684. [PMID: 28804123 PMCID: PMC5843901 DOI: 10.1038/leu.2017.251] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 02/08/2023]
Abstract
Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In this study, we have integrated the analysis of targeted next-generation sequencing of 106 genes and genomic copy number alterations (CNA) in 150 DLBCL. The clinically significant findings were validated in an independent cohort of 111 patients. Germinal center B-cell and activated B-cell DLBCL had a differential profile of mutations, altered pathogenic pathways and CNA. Mutations in genes of the NOTCH pathway and tumor suppressor genes (TP53/CDKN2A), but not individual genes, conferred an unfavorable prognosis, confirmed in the independent validation cohort. A gene expression profiling analysis showed that tumors with NOTCH pathway mutations had a significant modulation of downstream target genes, emphasizing the relevance of this pathway in DLBCL. An in silico drug discovery analysis recognized 69 (46%) cases carrying at least one genomic alteration considered a potential target of drug response according to early clinical trials or preclinical assays in DLBCL or other lymphomas. In conclusion, this study identifies relevant pathways and mutated genes in DLBCL and recognizes potential targets for new intervention strategies.
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Affiliation(s)
- K Karube
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,Department of Pathology and Cell Biology, Graduate School of Medicine and Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - A Enjuanes
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - I Dlouhy
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - P Jares
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - D Martin-Garcia
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - F Nadeu
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | | | - J Rovira
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - G Clot
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - C Royo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - A Navarro
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - B Gonzalez-Farre
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - A Vaghefi
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - G Castellano
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - C Rubio-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - D Tamborero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - J Briones
- Servei de Patologia, Hospital de Sant Pau, Barcelona, Spain
| | - A Salar
- Department of Pathology, Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - J M Sancho
- ICO-Hospital Germans Trias i Pujol, Barcelona, Spain
| | - S Mercadal
- ICO-Hospital Duran i Reynals, L'Hospitalet, Barcelona, Spain
| | | | - L Escoda
- Department of Hematology, Hospital Universitari Joan XXIII, Tarragona, Spain
| | - H Miyoshi
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - K Ohshima
- Department of Pathology, Kurume University School of Medicine, Kurume, Japan
| | - K Miyawaki
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - K Kato
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - K Akashi
- Department of Medicine and Biosystemic Science, Graduate School of Medical Science, Kyushu University, Fukuoka, Japan
| | - A Mozos
- Servei de Patologia, Hospital de Sant Pau, Barcelona, Spain
| | - L Colomo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,Department of Pathology, Hospital del Mar, Universitat Pompeu Fabra, Barcelona, Spain
| | - M Alcoceba
- CIBERONC, Madrid, Spain.,Unidad de Biología Molecular/Histocompatibilidad, Servicio de Hematología, Hospital Universitario de Salamanca, Salamanca, Spain
| | - A Valera
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - A Carrió
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - D Costa
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - N Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Research Unit on Biomedical Informatics, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - R Schmitz
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - L M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - I Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - A López-Guillermo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
| | - E Campo
- Institut d'Investigacions Biomèdiques August Pi i Sunyer, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBERONC, Madrid, Spain
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