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Alors-Pérez E, Pedraza-Arevalo S, Blázquez-Encinas R, García-Vioque V, Agraz-Doblas A, Yubero-Serrano EM, Sánchez-Frías ME, Serrano-Blanch R, Gálvez-Moreno MÁ, Gracia-Navarro F, Gahete MD, Arjona-Sánchez Á, Luque RM, Ibáñez-Costa A, Castaño JP. Altered CELF4 splicing factor enhances pancreatic neuroendocrine tumors aggressiveness influencing mTOR and everolimus response. Mol Ther Nucleic Acids 2024; 35:102090. [PMID: 38187140 PMCID: PMC10767201 DOI: 10.1016/j.omtn.2023.102090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 12/01/2023] [Indexed: 01/09/2024]
Abstract
Pancreatic neuroendocrine tumors (PanNETs) comprise a heterogeneous group of tumors with growing incidence. Recent molecular analyses provided a precise picture of their genomic and epigenomic landscape. Splicing dysregulation is increasingly regarded as a novel cancer hallmark influencing key tumor features. We have previously demonstrated that splicing machinery is markedly dysregulated in PanNETs. Here, we aimed to elucidate the molecular and functional implications of CUGBP ELAV-like family member 4 (CELF4), one of the most altered splicing factors in PanNETs. CELF4 expression was determined in 20 PanNETs, comparing tumor and non-tumoral adjacent tissue. An RNA sequencing (RNA-seq) dataset was analyzed to explore CELF4-linked interrelations among clinical features, gene expression, and splicing events. Two PanNET cell lines were employed to assess CELF4 function in vitro and in vivo. PanNETs display markedly upregulated CELF4 expression, which is closely associated with malignancy features, altered expression of key tumor players, and distinct splicing event profiles. Modulation of CELF4 influenced proliferation in vitro and reduced in vivo xenograft tumor growth. Interestingly, functional assays and RNA-seq analysis revealed that CELF4 silencing altered mTOR signaling pathway, enhancing the effect of everolimus. We demonstrate that CELF4 is dysregulated in PanNETs, where it influences tumor development and aggressiveness, likely by modulating the mTOR pathway, suggesting its potential as therapeutic target.
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Affiliation(s)
- Emilia Alors-Pérez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Sergio Pedraza-Arevalo
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Ricardo Blázquez-Encinas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Víctor García-Vioque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Antonio Agraz-Doblas
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Elena M. Yubero-Serrano
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Unidad de Gestión Clinica Medicina Interna, Lipids and Atherosclerosis Unit, Department of Internal Medicine, Reina Sofia University Hospital, Córdoba, Spain
| | - Marina E. Sánchez-Frías
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Pathology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Raquel Serrano-Blanch
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Medical Oncology Service, Reina Sofia University Hospital, Córdoba, Spain
| | - María Ángeles Gálvez-Moreno
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Francisco Gracia-Navarro
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Manuel D. Gahete
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Álvaro Arjona-Sánchez
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
- Surgery Service, Reina Sofia University Hospital, Córdoba, Spain
| | - Raúl M. Luque
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Alejandro Ibáñez-Costa
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
| | - Justo P. Castaño
- Maimonides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
- Department of Cell Biology, Physiology, and Immunology, University of Córdoba, Córdoba, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), Córdoba, Spain
- Reina Sofia University Hospital, Córdoba, Spain
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2
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Tejedor JR, Bueno C, Vinyoles M, Petazzi P, Agraz-Doblas A, Cobo I, Torres-Ruiz R, Bayón GF, Pérez RF, López-Tamargo S, Gutierrez-Agüera F, Santamarina-Ojeda P, Ramírez-Orellana M, Bardini M, Cazzaniga G, Ballerini P, Schneider P, Stam RW, Varela I, Fraga MF, Fernández AF, Menéndez P. Integrative methylome-transcriptome analysis unravels cancer cell vulnerabilities in infant MLL-rearranged B cell acute lymphoblastic leukemia. J Clin Invest 2021; 131:138833. [PMID: 33983906 DOI: 10.1172/jci138833] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/11/2021] [Indexed: 01/04/2023] Open
Abstract
B cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer. As predicted by its prenatal origin, infant B-ALL (iB-ALL) shows an exceptionally silent DNA mutational landscape, suggesting that alternative epigenetic mechanisms may substantially contribute to its leukemogenesis. Here, we have integrated genome-wide DNA methylome and transcriptome data from 69 patients with de novo MLL-rearranged leukemia (MLLr) and non-MLLr iB-ALL leukemia uniformly treated according to the Interfant-99/06 protocol. iB-ALL methylome signatures display a plethora of common and specific alterations associated with chromatin states related to enhancer and transcriptional control in normal hematopoietic cells. DNA methylation, gene expression, and gene coexpression network analyses segregated MLLr away from non-MLLr iB-ALL and identified a coordinated and enriched expression of the AP-1 complex members FOS and JUN and RUNX factors in MLLr iB-ALL, consistent with the significant enrichment of hypomethylated CpGs in these genes. Integrative methylome-transcriptome analysis identified consistent cancer cell vulnerabilities, revealed a robust iB-ALL-specific gene expression-correlating dmCpG signature, and confirmed an epigenetic control of AP-1 and RUNX members in reshaping the molecular network of MLLr iB-ALL. Finally, pharmacological inhibition or functional ablation of AP-1 dramatically impaired MLLr-leukemic growth in vitro and in vivo using MLLr-iB-ALL patient-derived xenografts, providing rationale for new therapeutic avenues in MLLr-iB-ALL.
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Affiliation(s)
- Juan Ramón Tejedor
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and.,RICORS-TERAV Network, ISCIII, Madrid, Spain
| | - Meritxell Vinyoles
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and
| | - Paolo Petazzi
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Isabel Cobo
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Raúl Torres-Ruiz
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,RICORS-TERAV Network, ISCIII, Madrid, Spain.,Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Gustavo F Bayón
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Raúl F Pérez
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Sara López-Tamargo
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Francisco Gutierrez-Agüera
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,RICORS-TERAV Network, ISCIII, Madrid, Spain
| | - Pablo Santamarina-Ojeda
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain
| | - Manuel Ramírez-Orellana
- RICORS-TERAV Network, ISCIII, Madrid, Spain.,Hematology Diagnostic Laboratory, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Michela Bardini
- Centro Ricerca Tettamanti, Department of Paediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Department of Paediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Paola Ballerini
- Pediatric Hematology, Armand Trousseau Hospital, Paris, France
| | - Pauline Schneider
- Princess Maxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Ronald W Stam
- Princess Maxima Center for Paediatric Oncology, Utrecht, Netherlands
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Mario F Fraga
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Agustín F Fernández
- Fundación para la Investigación Biosanitaria de Asturias (FINBA), Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Instituto Universitario de Oncología de Asturias (IUOPA), Hospital Universitario Central de Asturias (HUCA), Universidad de Oviedo, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Asturias, Spain.,Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, Asturias, Spain
| | - Pablo Menéndez
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC) and.,RICORS-TERAV Network, ISCIII, Madrid, Spain.,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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3
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Moreno T, Monterde B, González-Silva L, Betancor-Fernández I, Revilla C, Agraz-Doblas A, Freire J, Isidro P, Quevedo L, Blanco R, Montes-Moreno S, Cereceda L, Astudillo A, Casar B, Crespo P, Morales Torres C, Scaffidi P, Gómez-Román J, Salido E, Varela I. ARID2 deficiency promotes tumor progression and is associated with higher sensitivity to chemotherapy in lung cancer. Oncogene 2021; 40:2923-2935. [PMID: 33742126 PMCID: PMC7610680 DOI: 10.1038/s41388-021-01748-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/23/2021] [Accepted: 03/04/2021] [Indexed: 12/26/2022]
Abstract
The survival rate in lung cancer remains stubbornly low and there is an urgent need for the identification of new therapeutic targets. In the last decade, several members of the SWI/SNF chromatin remodeling complexes have been described altered in different tumor types. Nevertheless, the precise mechanisms of their impact on cancer progression, as well as the application of this knowledge to cancer patient management are largely unknown. In this study, we performed targeted sequencing of a cohort of lung cancer patients on genes involved in chromatin structure. Additionally, we studied at the protein level the expression of these genes in cancer samples and performed functional experiments to identify the molecular mechanisms linking alterations of chromatin remodeling genes and tumor development. Remarkably, we found that 20% of lung cancer patients show ARID2 protein loss, partially explained by the presence of ARID2 mutations. Additionally, we showed that ARID2-deficiency provokes profound chromatin structural changes altering cell transcriptional programmes which bolsters the proliferative and metastatic potential of the cells both in vitro and in vivo. Moreover, we demonstrated that ARID2 deficiency impairs DNA repair, enhancing the sensitivity of the cells to DNA damaging agents. Our findings support that ARID2 is a bona-fide tumor suppressor gene in lung cancer that may be exploited therapeutically.
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Affiliation(s)
- Thaidy Moreno
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Beatriz Monterde
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Laura González-Silva
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Isabel Betancor-Fernández
- Departamento de Patología, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Tenerife, Spain
| | - Carlos Revilla
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Antonio Agraz-Doblas
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Javier Freire
- Servicio de Anatomía Patológica y Biobanco Valdecilla, HUMV/IDIVAL, Santander, Spain
| | - Pablo Isidro
- Biobanco del Principado de Asturias (BBPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Laura Quevedo
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Rosa Blanco
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | | | - Laura Cereceda
- Servicio de Anatomía Patológica y Biobanco Valdecilla, HUMV/IDIVAL, Santander, Spain
| | - Aurora Astudillo
- Biobanco del Principado de Asturias (BBPA), Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Berta Casar
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Piero Crespo
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Paola Scaffidi
- Cancer Epigenetics Laboratory, The Francis Crick Institute, London, UK
| | - Javier Gómez-Román
- Servicio de Anatomía Patológica y Biobanco Valdecilla, HUMV/IDIVAL, Santander, Spain
| | - Eduardo Salido
- Departamento de Patología, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Tenerife, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain.
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4
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O'Byrne S, Elliott N, Rice S, Buck G, Fordham N, Garnett C, Godfrey L, Crump NT, Wright G, Inglott S, Hua P, Psaila B, Povinelli B, Knapp DJHF, Agraz-Doblas A, Bueno C, Varela I, Bennett P, Koohy H, Watt SM, Karadimitris A, Mead AJ, Ancliff P, Vyas P, Menendez P, Milne TA, Roberts I, Roy A. Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs. Blood 2019; 134:1059-1071. [PMID: 31383639 DOI: 10.1182/blood.2019001289] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 07/05/2019] [Indexed: 12/13/2022] Open
Abstract
Human lymphopoiesis is a dynamic lifelong process that starts in utero 6 weeks postconception. Although fetal B-lymphopoiesis remains poorly defined, it is key to understanding leukemia initiation in early life. Here, we provide a comprehensive analysis of the human fetal B-cell developmental hierarchy. We report the presence in fetal tissues of 2 distinct CD19+ B-progenitors, an adult-type CD10+ve ProB-progenitor and a new CD10-ve PreProB-progenitor, and describe their molecular and functional characteristics. PreProB-progenitors and ProB-progenitors appear early in the first trimester in embryonic liver, followed by a sustained second wave of B-progenitor development in fetal bone marrow (BM), where together they form >40% of the total hematopoietic stem cell/progenitor pool. Almost one-third of fetal B-progenitors are CD10-ve PreProB-progenitors, whereas, by contrast, PreProB-progenitors are almost undetectable (0.53% ± 0.24%) in adult BM. Single-cell transcriptomics and functional assays place fetal PreProB-progenitors upstream of ProB-progenitors, identifying them as the first B-lymphoid-restricted progenitor in human fetal life. Although fetal BM PreProB-progenitors and ProB-progenitors both give rise solely to B-lineage cells, they are transcriptionally distinct. As with their fetal counterparts, adult BM PreProB-progenitors give rise only to B-lineage cells in vitro and express the expected B-lineage gene expression program. However, fetal PreProB-progenitors display a distinct, ontogeny-related gene expression pattern that is not seen in adult PreProB-progenitors, and they share transcriptomic signatures with CD10-ve B-progenitor infant acute lymphoblastic leukemia blast cells. These data identify PreProB-progenitors as the earliest B-lymphoid-restricted progenitor in human fetal life and suggest that this fetal-restricted committed B-progenitor might provide a permissive cellular context for prenatal B-progenitor leukemia initiation.
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Affiliation(s)
| | | | - Siobhan Rice
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gemma Buck
- Department of Paediatrics and
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas Fordham
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Catherine Garnett
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura Godfrey
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicholas T Crump
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Gary Wright
- Department of Haematology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Sarah Inglott
- Department of Haematology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Peng Hua
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Bethan Psaila
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Benjamin Povinelli
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - David J H F Knapp
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Antonio Agraz-Doblas
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria-CSIC, Santander, Spain
| | - Phillip Bennett
- Institute of Reproductive and Developmental Biology, Department of Surgery and Cancer, Hammersmith Hospital Campus, Imperial College London, London, United Kingdom
| | - Hashem Koohy
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Suzanne M Watt
- Stem Cell Research, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anastasios Karadimitris
- Centre for Haematology, Department of Medicine, Hammersmith Hospital, Imperial College London, London, United Kingdom
| | - Adam J Mead
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Phillip Ancliff
- Department of Haematology, Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Paresh Vyas
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
- Institucio Catalana of Recerca i Estudis Avançats, Barcelona, Spain; and
- Centro de Investigación Biomédica en Red en Cancer-ISCIII, Barcelona, Spain
| | - Thomas A Milne
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
| | - Irene Roberts
- Department of Paediatrics and
- Medical Research Council (MRC) Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
- Haematology Theme, Oxford Biomedical Research Centre, Oxford University Hospitals, Oxford, United Kingdom
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5
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Bueno C, Calero-Nieto FJ, Wang X, Valdés-Mas R, Gutiérrez-Agüera F, Roca-Ho H, Ayllon V, Real PJ, Arambilet D, Espinosa L, Torres-Ruiz R, Agraz-Doblas A, Varela I, de Boer J, Bigas A, Gottgens B, Marschalek R, Menendez P. Enhanced hemato-endothelial specification during human embryonic differentiation through developmental cooperation between AF4-MLL and MLL-AF4 fusions. Haematologica 2019; 104:1189-1201. [PMID: 30679325 PMCID: PMC6545840 DOI: 10.3324/haematol.2018.202044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/21/2019] [Indexed: 12/18/2022] Open
Abstract
The t(4;11)(q21;q23) translocation is associated with high-risk infant pro-B-cell acute lymphoblastic leukemia and arises prenatally during embryonic/fetal hematopoiesis. The developmental/pathogenic contribution of the t(4;11)-resulting MLL-AF4 (MA4) and AF4-MLL (A4M) fusions remains unclear; MA4 is always expressed in patients with t(4;11)+ B-cell acute lymphoblastic leukemia, but the reciprocal fusion A4M is expressed in only half of the patients. Because prenatal leukemogenesis manifests as impaired early hematopoietic differentiation, we took advantage of well-established human embryonic stem cell-based hematopoietic differentiation models to study whether the A4M fusion cooperates with MA4 during early human hematopoietic development. Co-expression of A4M and MA4 strongly promoted the emergence of hemato-endothelial precursors, both endothelial- and hemogenic-primed. Double fusion-expressing hemato-endothelial precursors specified into significantly higher numbers of both hematopoietic and endothelial-committed cells, irrespective of the differentiation protocol used and without hijacking survival/proliferation. Functional analysis of differentially expressed genes and differentially enriched H3K79me3 genomic regions by RNA-sequencing and H3K79me3 chromatin immunoprecipitation-sequencing, respectively, confirmed a hematopoietic/endothelial cell differentiation signature in double fusion-expressing hemato-endothelial precursors. Importantly, chromatin immunoprecipitation-sequencing analysis revealed a significant enrichment of H3K79 methylated regions specifically associated with HOX-A cluster genes in double fusion-expressing differentiating hematopoietic cells. Overall, these results establish a functional and molecular cooperation between MA4 and A4M fusions during human hematopoietic development.
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Affiliation(s)
- Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Fernando J Calero-Nieto
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Xiaonan Wang
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | | | - Francisco Gutiérrez-Agüera
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Heleia Roca-Ho
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Veronica Ayllon
- GENyO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government and University of Granada, Department of Biochemistry and Molecular Biology, Granada, Spain
| | - Pedro J Real
- GENyO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government and University of Granada, Department of Biochemistry and Molecular Biology, Granada, Spain
| | - David Arambilet
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
| | - Lluis Espinosa
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Raul Torres-Ruiz
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Jasper de Boer
- Cancer Section, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Anna Bigas
- Programa de Cáncer, Instituto Hospital del Mar de Investigaciones Médicas. Barcelona. Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
| | - Bertie Gottgens
- Department of Hematology, Cambridge Institute for Medical Research and Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Rolf Marschalek
- Institute of Pharmaceutical Biology, Goethe-University, Frankfurt, Germany
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBER-ONC), ISCIII, Barcelona, Spain
- Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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6
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Agraz-Doblas A, Bueno C, Bashford-Rogers R, Roy A, Schneider P, Bardini M, Ballerini P, Cazzaniga G, Moreno T, Revilla C, Gut M, Valsecchi MG, Roberts I, Pieters R, De Lorenzo P, Varela I, Menendez P, Stam RW. Unraveling the cellular origin and clinical prognostic markers of infant B-cell acute lymphoblastic leukemia using genome-wide analysis. Haematologica 2019; 104:1176-1188. [PMID: 30679323 PMCID: PMC6545849 DOI: 10.3324/haematol.2018.206375] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [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: 09/07/2018] [Accepted: 12/20/2018] [Indexed: 02/06/2023] Open
Abstract
B-cell acute lymphoblastic leukemia is the commonest childhood cancer. In infants, B-cell acute lymphoblastic leukemia remains fatal, especially in patients with t(4;11), present in ~80% of cases. The pathogenesis of t(4;11)/KMT2A-AFF1+ (MLL-AF4+) infant B-cell acute lymphoblastic leukemia remains difficult to model, and the pathogenic contribution in cancer of the reciprocal fusions resulting from derivative translocated-chromosomes remains obscure. Here, “multi-layered” genome-wide analyses and validation were performed on a total of 124 de novo cases of infant B-cell acute lymphoblastic leukemia uniformly diagnosed and treated according to the Interfant 99/06 protocol. These patients showed the most silent mutational landscape reported so far for any sequenced pediatric cancer. Recurrent mutations were exclusively found in K-RAS and N-RAS, were subclonal and were frequently lost at relapse, despite a larger number of non-recurrent/non-silent mutations. Unlike non-MLL-rearranged B-cell acute lymphoblastic leukemias, B-cell receptor repertoire analysis revealed minor, non-expanded B-cell clones in t(4;11)+ infant B-cell acute lymphoblastic leukemia, and RNA-sequencing showed transcriptomic similarities between t(4;11)+ infant B-cell acute lymphoblastic leukemias and the most immature human fetal liver hematopoietic stem and progenitor cells, confirming a “pre-VDJ” fetal cellular origin for both t(4;11) and RASmut. The reciprocal fusion AF4-MLL was expressed in only 45% (19/43) of the t(4;11)+ patients, and HOXA cluster genes are exclusively expressed in AF4-MLL-expressing patients. Importantly, AF4-MLL/HOXA-expressing patients had a significantly better 4-year event-free survival (62.4% vs. 11.7%, P=0.001), and overall survival (73.7 vs. 25.2%, P=0.016). AF4-MLL expression retained its prognostic significance when analyzed in a Cox model adjusting for risk stratification according to the Interfant-06 protocol based on age at diagnosis, white blood cell count and response to prednisone. This study has clinical implications for disease outcome and diagnostic risk-stratification of t(4;11)+ infant B-cell acute lymphoblastic leukemia.
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Affiliation(s)
- Antonio Agraz-Doblas
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain.,Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Spain
| | | | - Anindita Roy
- Department of Paediatrics, University of Oxford, UK
| | - Pauline Schneider
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Michela Bardini
- Centro Ricerca Tettamanti, Department of Pediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | | | - Gianni Cazzaniga
- Centro Ricerca Tettamanti, Department of Pediatrics, University of Milano Bicocca, Fondazione MBBM, Monza, Italy
| | - Thaidy Moreno
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Carlos Revilla
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Marta Gut
- CNAG-CRG, Center for Genomic Regulation, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Maria G Valsecchi
- Interfant Trial Data Center, University of Milano-Bicocca, Monza, Italy
| | - Irene Roberts
- Department of Paediatrics, University of Oxford, UK.,MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, UK
| | - Rob Pieters
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Paola De Lorenzo
- Interfant Trial Data Center, University of Milano-Bicocca, Monza, Italy
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute-Campus Clinic, Department of Biomedicine, School of Medicine, University of Barcelona, Spain .,Instituciò Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), ISCIII, Barcelona, Spain
| | - Ronald W Stam
- Princess Maxima Center for Pediatric Oncology, Utrecht, the Netherlands
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7
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Llerena S, García-Díaz N, Curiel-Olmo S, Agraz-Doblas A, García-Blanco A, Pisonero H, Varela M, Santibáñez M, Almaraz C, Cereceda L, Martínez N, Arias-Loste MT, Puente Á, Martín-Ramos L, de Lope CR, Castillo-Suescun F, Cagigas-Fernandez C, Isidro P, Lopez-López C, Lopez-Hoyos M, Llorca J, Agüero J, Crespo-Facorro B, Varela I, Piris MÁ, Crespo J, Vaqué JP. Applied diagnostics in liver cancer. Efficient combinations of sorafenib with targeted inhibitors blocking AKT/mTOR. Oncotarget 2018; 9:30869-30882. [PMID: 30112114 PMCID: PMC6089396 DOI: 10.18632/oncotarget.25766] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third most common cause of cancer-related deaths worldwide. There is increasing interest in developing specific markers to serve as predictors of response to sorafenib and to guide targeted therapy. Using a sequencing platform designed to study somatic mutations in a selection of 112 genes (HepatoExome), we aimed to characterize lesions from HCC patients and cell lines, and to use the data to study the biological and mechanistic effects of case-specific targeted therapies used alone or in combination with sorafenib. We characterized 331 HCC cases in silico and 32 paired samples obtained prospectively from primary tumors of HCC patients. Each case was analyzed in a time compatible with the requirements of the clinic (within 15 days). In 53% of the discovery cohort cases, we detected unique mutational signatures, with up to 34% of them carrying mutated genes with the potential to guide therapy. In a panel of HCC cell lines, each characterized by a specific mutational signature, sorafenib elicited heterogeneous mechanistic and biological responses, whereas targeted therapy provoked the robust inhibition of cell proliferation and DNA synthesis along with the blockage of AKT/mTOR signaling. The combination of sorafenib with targeted therapies exhibited synergistic anti-HCC biological activity concomitantly with highly effective inhibition of MAPK and AKT/mTOR signaling. Thus, somatic mutations may lead to identify case-specific mechanisms of disease in HCC lesions arising from multiple etiologies. Moreover, targeted therapies guided by molecular characterization, used alone or in combination with sorafenib, can effectively block important HCC disease mechanisms.
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Affiliation(s)
- Susana Llerena
- Gastroenterology and Hepatology Unit, Hospital Universitario Marqués de Valdecilla, Santander, Spain.,Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain
| | - Nuria García-Díaz
- Translational Hematopathology Group, IDIVAL, Instituto de Investigación Marqués de Valdecilla, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria (UC-IBBTEC), Santander, Spain
| | - Soraya Curiel-Olmo
- Translational Hematopathology Group, IDIVAL, Instituto de Investigación Marqués de Valdecilla, Santander, Spain
| | - Antonio Agraz-Doblas
- Departamento de Biología Molecular, Universidad de Cantabria (UC-IBBTEC), Santander, Spain.,Josep Carreras Leukemia Research Institute and School of Medicine, University of Barcelona, Barcelona, Spain
| | - Agustín García-Blanco
- Gastroenterology and Hepatology Unit, Hospital Universitario Marqués de Valdecilla, Santander, Spain.,Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain
| | - Helena Pisonero
- Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria (UC-IBBTEC), Santander, Spain
| | - María Varela
- Digestive Service, Hepatology Unit, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - Carmen Almaraz
- Translational Hematopathology Group, IDIVAL, Instituto de Investigación Marqués de Valdecilla, Santander, Spain
| | - Laura Cereceda
- Translational Hematopathology Group, IDIVAL, Instituto de Investigación Marqués de Valdecilla, Santander, Spain
| | - Nerea Martínez
- Translational Hematopathology Group, IDIVAL, Instituto de Investigación Marqués de Valdecilla, Santander, Spain
| | - María Teresa Arias-Loste
- Gastroenterology and Hepatology Unit, Hospital Universitario Marqués de Valdecilla, Santander, Spain.,Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain
| | - Ángela Puente
- Gastroenterology and Hepatology Unit, Hospital Universitario Marqués de Valdecilla, Santander, Spain.,Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain
| | - Luis Martín-Ramos
- Gastroenterology and Hepatology Unit, Hospital Universitario Marqués de Valdecilla, Santander, Spain.,Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain
| | - Carlos Rodríguez de Lope
- Gastroenterology and Hepatology Unit, Hospital Universitario Marqués de Valdecilla, Santander, Spain.,Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain
| | - Federico Castillo-Suescun
- General and Digestive Tract Surgery Service, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Carmen Cagigas-Fernandez
- General and Digestive Tract Surgery Service, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Pablo Isidro
- Biobanco-Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Carlos Lopez-López
- Oncology Service, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Marcos Lopez-Hoyos
- Immunology Service, Hospital Universitario Marqués de Valdecilla, Santander, Spain
| | - Javier Llorca
- Department of Epidemiology and Computational Biology, School of Medicine, University of Cantabria, Santander, Spain.,CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Jesús Agüero
- Microbiology Service, University Hospital Marques de Valdecilla-IDIVAL, Santander, Spain
| | - Benedicto Crespo-Facorro
- Department of Psychiatry, Marqués de Valdecilla University Hospital-IDIVAL, Santander, Spain.,CIBERSAM, Centro de Investigación Biomédica en Red Salud Mental, Madrid, Spain
| | - Ignacio Varela
- Departamento de Biología Molecular, Universidad de Cantabria (UC-IBBTEC), Santander, Spain
| | | | - Javier Crespo
- Gastroenterology and Hepatology Unit, Hospital Universitario Marqués de Valdecilla, Santander, Spain.,Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain
| | - José Pedro Vaqué
- Infection, Immunity and Digestive Pathology Group, IDIVAL, Santander, Spain.,Departamento de Biología Molecular, Universidad de Cantabria (UC-IBBTEC), Santander, Spain
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8
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Moreno T, Gonzalez-Silva L, Revilla C, Monterde B, Agraz-Doblas A, Betancor I, Freire J, Gomez-Roman J, Salido E, Varela I. PO-376 SWI/SNF alterations as markers for prognosis and specific treatments in human cancer. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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9
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Agraz-Doblas A, Bueno C, Schneider P, Revilla C, Moreno T, Ballerini P, Bardini M, Stam R, Menéndez P, Varela I. PO-315 The mutational and transcriptome landscape of infant B-cell acute lymphoblastic leukaemia: the INTERFANT treatment protocol experience. ESMO Open 2018. [DOI: 10.1136/esmoopen-2018-eacr25.345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
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10
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González-Vela MDC, Curiel-Olmo S, Derdak S, Beltran S, Santibañez M, Martínez N, Castillo-Trujillo A, Gut M, Sánchez-Pacheco R, Almaraz C, Cereceda L, Llombart B, Agraz-Doblas A, Revert-Arce J, López Guerrero JA, Mollejo M, Marrón PI, Ortiz-Romero P, Fernandez-Cuesta L, Varela I, Gut I, Cerroni L, Piris MÁ, Vaqué JP. Shared Oncogenic Pathways Implicated in Both Virus-Positive and UV-Induced Merkel Cell Carcinomas. J Invest Dermatol 2017; 137:197-206. [PMID: 27592799 DOI: 10.1016/j.jid.2016.08.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 12/27/2022]
Abstract
Merkel cell carcinoma (MCC) is a highly malignant neuroendocrine tumor of the skin whose molecular pathogenesis is not completely understood, despite the role that Merkel cell polyomavirus can play in 55-90% of cases. To study potential mechanisms driving this disease in clinically characterized cases, we searched for somatic mutations using whole-exome sequencing, and extrapolated our findings to study functional biomarkers reporting on the activity of the mutated pathways. Confirming previous results, Merkel cell polyomavirus-negative tumors had higher mutational loads with UV signatures and more frequent mutations in TP53 and RB compared with their Merkel cell polyomavirus-positive counterparts. Despite important genetic differences, the two Merkel cell carcinoma etiologies both exhibited nuclear accumulation of oncogenic transcription factors such as NFAT or nuclear factor of activated T cells (NFAT), P-CREB, and P-STAT3, indicating commonly deregulated pathogenic mechanisms with the potential to serve as targets for therapy. A multivariable analysis identified phosphorylated CRE-binding protein as an independent survival factor with respect to clinical variables and Merkel cell polyomavirus status in our cohort of Merkel cell carcinoma patients.
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Affiliation(s)
- María Del Carmen González-Vela
- Pathology Department, Hospital Universitario Marqués de Valdecilla, Santander, Spain; Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - Soraya Curiel-Olmo
- Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - Sophia Derdak
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Sergi Beltran
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Nerea Martínez
- Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain
| | | | - Martha Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Carmen Almaraz
- Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - Laura Cereceda
- Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - Beatriz Llombart
- Department of Dermatology, Instituto Valenciano de Oncología, Valencia, Spain
| | - Antonio Agraz-Doblas
- IBBTEC-UC-CSIC-SODERCAN Instituto de Biomedicina y Biotecnología de Cantabria, Santander, Spain; Josep Carreras Leukemia Research Institute and School of Medicine, University of Barcelona, Barcelona, Spain
| | - José Revert-Arce
- Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain
| | | | | | | | - Pablo Ortiz-Romero
- Dermatology Service, Instituto I+12, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Lynnette Fernandez-Cuesta
- International Agency for Research on Cancer (IARC-WHO), Lyon, France; Department of Translational Genomics, Center of Integrated Oncology Cologne-Bonn, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Ignacio Varela
- IBBTEC-UC-CSIC-SODERCAN Instituto de Biomedicina y Biotecnología de Cantabria, Santander, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lorenzo Cerroni
- Department of Dermatology Medical University of Graz, Austria
| | - Miguel Ángel Piris
- Pathology Department, Hospital Universitario Marqués de Valdecilla, Santander, Spain; Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain
| | - José Pedro Vaqué
- Cancer Genomics Laboratory, Instituto de Investigación Marqués de Valdecilla, IDIVAL, Santander, Spain; IBBTEC-UC-CSIC-SODERCAN Instituto de Biomedicina y Biotecnología de Cantabria, Santander, Spain.
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11
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Muñoz-López A, Romero-Moya D, Prieto C, Ramos-Mejía V, Agraz-Doblas A, Varela I, Buschbeck M, Palau A, Carvajal-Vergara X, Giorgetti A, Ford A, Lako M, Granada I, Ruiz-Xivillé N, Rodríguez-Perales S, Torres-Ruíz R, Stam RW, Fuster JL, Fraga MF, Nakanishi M, Cazzaniga G, Bardini M, Cobo I, Bayon GF, Fernandez AF, Bueno C, Menendez P. Development Refractoriness of MLL-Rearranged Human B Cell Acute Leukemias to Reprogramming into Pluripotency. Stem Cell Reports 2016; 7:602-618. [PMID: 27666791 PMCID: PMC5063541 DOI: 10.1016/j.stemcr.2016.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/09/2023] Open
Abstract
Induced pluripotent stem cells (iPSCs) are a powerful tool for disease modeling. They are routinely generated from healthy donors and patients from multiple cell types at different developmental stages. However, reprogramming leukemias is an extremely inefficient process. Few studies generated iPSCs from primary chronic myeloid leukemias, but iPSC generation from acute myeloid or lymphoid leukemias (ALL) has not been achieved. We attempted to generate iPSCs from different subtypes of B-ALL to address the developmental impact of leukemic fusion genes. OKSM(L)-expressing mono/polycistronic-, retroviral/lentiviral/episomal-, and Sendai virus vector-based reprogramming strategies failed to render iPSCs in vitro and in vivo. Addition of transcriptomic-epigenetic reprogramming “boosters” also failed to generate iPSCs from B cell blasts and B-ALL lines, and when iPSCs emerged they lacked leukemic fusion genes, demonstrating non-leukemic myeloid origin. Conversely, MLL-AF4-overexpressing hematopoietic stem cells/B progenitors were successfully reprogrammed, indicating that B cell origin and leukemic fusion gene were not reprogramming barriers. Global transcriptome/DNA methylome profiling suggested a developmental/differentiation refractoriness of MLL-rearranged B-ALL to reprogramming into pluripotency. Neither primary B-ALL blasts nor leukemic B cell lines can be reprogrammed to iPSCs Global transcriptome and DNA methylome suggest a developmental refractoriness
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Affiliation(s)
- Alvaro Muñoz-López
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Damià Romero-Moya
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Cristina Prieto
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Verónica Ramos-Mejía
- Genomic Oncology Department, Centre for Genomics and Oncology GENyO, 18016 Granada, Spain
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain; IBBTEC, CSIC-University of Cantabria, 39011 Santander, Spain
| | - Ignacio Varela
- IBBTEC, CSIC-University of Cantabria, 39011 Santander, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Anna Palau
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Xonia Carvajal-Vergara
- Cell Therapy Department, Centro de Investigación Médica Aplicada (CIMA), 31008 Pamplona, Spain
| | - Alessandra Giorgetti
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain
| | - Anthony Ford
- Centre for Evolution and Cancer, Institute of Cancer Research, London SW7 3RP, UK
| | - Majlinda Lako
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 7RU, UK
| | - Isabel Granada
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Hematology Department, Hospital Germans Trias i Pujol, Institut Català d'Oncología, 08916 Badalona, Spain
| | - Neus Ruiz-Xivillé
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Hematology Department, Hospital Germans Trias i Pujol, Institut Català d'Oncología, 08916 Badalona, Spain
| | | | - Raul Torres-Ruíz
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Cytogenetics Group, Centro Nacional de Investigaciones Oncológicas (CNIO), 28029 Madrid, Spain
| | - Ronald W Stam
- Department of Pediatric Oncology/Hematology, Erasmus Medical Center, Erasmus University, 3015 CN Rotterdam, the Netherlands
| | - Jose Luis Fuster
- Department of Pediatric Oncohematology, Clinical University Hospital Virgen de la Arrixaca, 30120 Murcia, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Mahito Nakanishi
- Research Center for Stem Cell Engineering, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraka 305-0046, Japan
| | - Gianni Cazzaniga
- University di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, 20052 Monza MB, Italy
| | - Michela Bardini
- University di Milano-Bicocca, Ospedale San Gerardo/Fondazione MBBM, 20052 Monza MB, Italy
| | - Isabel Cobo
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Gustavo F Bayon
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Agustin F Fernandez
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA-HUCA), Universidad de Oviedo, 33003 Oviedo, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain.
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; Department of Biomedicine, School of Medicine, University of Barcelona, 08036 Barcelona, Spain; Instituciò Catalana de Recerca i Estudis Avançats (ICREA), 08036 Barcelona, Spain.
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Prieto C, Stam RW, Agraz-Doblas A, Ballerini P, Camos M, Castaño J, Marschalek R, Bursen A, Varela I, Bueno C, Menendez P. Activated KRAS Cooperates with MLL-AF4 to Promote Extramedullary Engraftment and Migration of Cord Blood CD34+ HSPC But Is Insufficient to Initiate Leukemia. Cancer Res 2016; 76:2478-89. [PMID: 26837759 DOI: 10.1158/0008-5472.can-15-2769] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/08/2016] [Indexed: 11/16/2022]
Abstract
The MLL-AF4 (MA4) fusion gene is the genetic hallmark of an aggressive infant pro-B-acute lymphoblastic leukemia (B-ALL). Our understanding of MA4-mediated transformation is very limited. Whole-genome sequencing studies revealed a silent mutational landscape, which contradicts the aggressive clinical outcome of this hematologic malignancy. Only RAS mutations were recurrently detected in patients and found to be associated with poorer outcome. The absence of MA4-driven B-ALL models further questions whether MA4 acts as a single oncogenic driver or requires cooperating mutations to manifest a malignant phenotype. We explored whether KRAS activation cooperates with MA4 to initiate leukemia in cord blood-derived CD34(+) hematopoietic stem/progenitor cells (HSPC). Clonogenic and differentiation/proliferation assays demonstrated that KRAS activation does not cooperate with MA4 to immortalize CD34(+) HSPCs. Intrabone marrow transplantation into immunodeficient mice further showed that MA4 and KRAS(G12V) alone or in combination enhanced hematopoietic repopulation without impairing myeloid-lymphoid differentiation, and that mutated KRAS did not cooperate with MA4 to initiate leukemia. However, KRAS activation enhanced extramedullary hematopoiesis of MA4-expressing cell lines and CD34(+) HSPCs that was associated with leukocytosis and central nervous system infiltration, both hallmarks of infant t(4;11)(+) B-ALL. Transcriptional profiling of MA4-expressing patients supported a cell migration gene signature underlying the mutant KRAS-mediated phenotype. Collectively, our findings demonstrate that KRAS affects the homeostasis of MA4-expressing HSPCs, suggesting that KRAS activation in MA4(+) B-ALL is important for tumor maintenance rather than initiation. Cancer Res; 76(8); 2478-89. ©2016 AACR.
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Affiliation(s)
- Cristina Prieto
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Ronald W Stam
- Pediatric Oncology/Hematology, Erasmus MC-Sophia Children's Hospital, Rotterdam, the Netherlands
| | - Antonio Agraz-Doblas
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain. Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC-CSIC-UNIVERSIDAD DE CANTABRIA-SODERCAN), Santander, Spain
| | - Paola Ballerini
- Pediatric Hematology Department, A. Trousseau Hospital, Paris, France
| | - Mireia Camos
- Hematology Laboratory, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Julio Castaño
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Rolf Marschalek
- Institute Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Aldeheid Bursen
- Institute Pharmaceutical Biology, Goethe-University, Frankfurt/Main, Germany
| | - Ignacio Varela
- Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC-CSIC-UNIVERSIDAD DE CANTABRIA-SODERCAN), Santander, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain.
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona, Spain. Instituciò Catalana Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
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