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Ibáñez M, Such E, Onecha E, Gómez-Seguí I, Liquori A, Sellés J, Hervás-Marín D, Barragán E, Ayala R, LLop M, López-Pavía M, Rapado I, Neef A, Sanjuan-Pla A, Sargas C, Gonzalez-Romero E, Boluda-Navarro M, Andreu R, Senent L, Montesinos P, Martínez-López J, Angel Sanz M, Sanz G, Cervera J. Analysis of SNP Array Abnormalities in Patients with DE NOVO Acute Myeloid Leukemia with Normal Karyotype. Sci Rep 2020; 10:5904. [PMID: 32246042 PMCID: PMC7125150 DOI: 10.1038/s41598-020-61589-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/28/2020] [Indexed: 02/02/2023] Open
Abstract
Nearly 50% of patients with de novo acute myeloid leukemia (AML) harbor an apparently normal karyotype (NK) by conventional cytogenetic techniques showing a very heterogeneous prognosis. This could be related to the presence of cryptic cytogenetic abnormalities (CCA) not detectable by conventional methods. The study of copy number alterations (CNA) and loss of heterozygozity (LOH) in hematological malignancies is possible using a high resolution SNP-array. Recently, in clinical practice the karyotype study has been complemented with the identification of point mutations in an increasing number of genes. We analyzed 252 de novo NK-AML patients from Hospital La Fe (n = 44) and from previously reported cohorts (n = 208) to identify CCA by SNP-array, and to integrate the analysis of CCA with molecular alterations detected by Next-Generation-sequencing. CCA were detected in 58% of patients. In addition, 49% of them harbored CNA or LOH and point mutations, simultaneously. Patients were grouped in 3 sets by their abnormalities: patients carrying several CCA simultaneously, patients with mutations in FLT3, NPM1 and/or DNMT3A and patients with an amalgam of mutations. We found a negative correlation between the number of CCA and the outcome of the patients. This study outlines that CCA are present in up to 50% of NK-AML patients and have a negative impact on the outcome. CCA may contribute to the heterogeneous prognosis.
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Affiliation(s)
- Mariam Ibáñez
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Departamento de Ciencias Biomédicas. Facultad de Ciencias de la Salud. Universidad CEU Cardenal Herrera, Valencia, Spain
| | - Esperanza Such
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Departamento de Ciencias Biomédicas. Facultad de Ciencias de la Salud. Universidad CEU Cardenal Herrera, Valencia, Spain
| | | | - Inés Gómez-Seguí
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Alessandro Liquori
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Grupo de Investigación en Hematología, IIS La Fe, Valencia, Spain
| | - Jorge Sellés
- Array's Unit. Instituto Investigación Sanitaria Fundación La Fe, Valencia, Spain
| | - David Hervás-Marín
- Biostadistic Unit. Instituto Investigación Sanitaria Fundación La Fe, Valencia, Spain
| | - Eva Barragán
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Laboratory of Molecular Biology, Department of Clinical Chemistry, University Hospital La Fe, Valencia, Spain
| | | | - Marta LLop
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Laboratory of Molecular Biology, Department of Clinical Chemistry, University Hospital La Fe, Valencia, Spain
| | | | | | - Alex Neef
- Grupo de Investigación en Hematología, IIS La Fe, Valencia, Spain
| | | | - Claudia Sargas
- Grupo de Investigación en Hematología, IIS La Fe, Valencia, Spain
- Laboratory of Molecular Biology, Department of Clinical Chemistry, University Hospital La Fe, Valencia, Spain
| | - Elisa Gonzalez-Romero
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Grupo de Investigación en Hematología, IIS La Fe, Valencia, Spain
| | | | - Rafa Andreu
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Leonor Senent
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Pau Montesinos
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | | | - Miguel Angel Sanz
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
- Department of Medicine. University of Valencia, Valencia, Spain
| | - Guillermo Sanz
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - José Cervera
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
- Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain.
- Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain.
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Ibáñez M, Carbonell-Caballero J, García-Alonso L, Such E, Jiménez-Almazán J, Vidal E, Barragán E, López-Pavía M, LLop M, Martín I, Gómez-Seguí I, Montesinos P, Sanz MA, Dopazo J, Cervera J. The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations. PLoS One 2016; 11:e0148346. [PMID: 26886259 PMCID: PMC4757557 DOI: 10.1371/journal.pone.0148346] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 12/02/2022] Open
Abstract
Preliminary Acute Promyelocytic Leukemia (APL) whole exome sequencing (WES) studies have identified a huge number of somatic mutations affecting more than a hundred different genes mainly in a non-recurrent manner, suggesting that APL is a heterogeneous disease with secondary relevant changes not yet defined. To extend our knowledge of subtle genetic alterations involved in APL that might cooperate with PML/RARA in the leukemogenic process, we performed a comprehensive analysis of somatic mutations in APL combining WES with sequencing of a custom panel of targeted genes by next-generation sequencing. To select a reduced subset of high confidence candidate driver genes, further in silico analysis were carried out. After prioritization and network analysis we found recurrent deleterious mutations in 8 individual genes (STAG2, U2AF1, SMC1A, USP9X, IKZF1, LYN, MYCBP2 and PTPN11) with a strong potential of being involved in APL pathogenesis. Our network analysis of multiple mutations provides a reliable approach to prioritize genes for additional analysis, improving our knowledge of the leukemogenesis interactome. Additionally, we have defined a functional module in the interactome of APL. The hypothesis is that the number, or the specific combinations, of mutations harbored in each patient might not be as important as the disturbance caused in biological key functions, triggered by several not necessarily recurrent mutations.
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Affiliation(s)
- Mariam Ibáñez
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - Luz García-Alonso
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Esperanza Such
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Jorge Jiménez-Almazán
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Enrique Vidal
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Eva Barragán
- Laboratory of Molecular Biology, Department of Clinical Chemistry, Hospital Universitario La Fe, Valencia, Spain
| | - María López-Pavía
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Marta LLop
- Laboratory of Molecular Biology, Department of Clinical Chemistry, Hospital Universitario La Fe, Valencia, Spain
| | - Iván Martín
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Inés Gómez-Seguí
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Pau Montesinos
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Miguel A. Sanz
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, 46012, Valencia, Spain
- Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
- * E-mail: (JC); (JD)
| | - José Cervera
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- * E-mail: (JC); (JD)
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