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Cruzado JM, Manonelles A, Rayego-Mateos S, Doladé N, Amaya-Garrido A, Varela C, Guiteras R, Mosquera JL, Jung M, Codina S, Martínez-Valenzuela L, Draibe J, Couceiro C, Vigués F, Madrid Á, Florian MC, Ruíz-Ortega M, Sola A. Colony stimulating factor-1 receptor drives glomerular parietal epithelial cell activation in focal segmental glomerulosclerosis. Kidney Int 2024:S0085-2538(24)00164-9. [PMID: 38428734 DOI: 10.1016/j.kint.2024.02.010] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 12/19/2023] [Accepted: 02/02/2024] [Indexed: 03/03/2024]
Abstract
Parietal epithelial cells (PECs) are kidney progenitor cells with similarities to a bone marrow stem cell niche. In focal segmental glomerulosclerosis (FSGS) PECs become activated and contribute to extracellular matrix deposition. Colony stimulating factor-1 (CSF-1), a hematopoietic growth factor, acts via its specific receptor, CSF-1R, and has been implicated in several glomerular diseases, although its role on PEC activation is unknown. Here, we found that CSF-1R was upregulated in PECs and podocytes in biopsies from patients with FSGS. Through in vitro studies, PECs were found to constitutively express CSF-1R. Incubation with CSF-1 induced CSF-1R upregulation and significant transcriptional regulation of genes involved in pathways associated with PEC activation. Specifically, CSF-1/CSF-1R activated the ERK1/2 signaling pathway and upregulated CD44 in PECs, while both ERK and CSF-1R inhibitors reduced CD44 expression. Functional studies showed that CSF-1 induced PEC proliferation and migration, while reducing the differentiation of PECs into podocytes. These results were validated in the Adriamycin-induced FSGS experimental mouse model. Importantly, treatment with either the CSF-1R-specific inhibitor GW2580 or Ki20227 provided a robust therapeutic effect. Thus, we provide evidence of the role of the CSF-1/CSF-1R pathway in PEC activation in FSGS, paving the way for future clinical studies investigating the therapeutic effect of CSF-1R inhibitors on patients with FSGS.
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Affiliation(s)
- Josep M Cruzado
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain; Department of Nephrology, Hospital Universitari Bellvitge, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
| | - Anna Manonelles
- Department of Nephrology, Hospital Universitari Bellvitge, Barcelona, Spain; Department of Clinical Sciences, University of Barcelona, Barcelona, Spain
| | - Sandra Rayego-Mateos
- Cellular Biology in Renal Diseases Laboratory, IIS Fundación Jiménez Díaz, Universidad Autónoma, Madrid, Spain
| | - Núria Doladé
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Amaya-Garrido
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Cristian Varela
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Roser Guiteras
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Jose Luis Mosquera
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
| | - Michaela Jung
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Frankfurt am Main, Germany
| | - Sergi Codina
- Department of Nephrology, Hospital Universitari Bellvitge, Barcelona, Spain
| | | | - Juliana Draibe
- Department of Nephrology, Hospital Universitari Bellvitge, Barcelona, Spain
| | - Carlos Couceiro
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain; Department of Nephrology, Hospital Universitari Bellvitge, Barcelona, Spain
| | - Francesc Vigués
- Department of Urology, Hospital Universitari Bellvitge, Barcelona, Spain
| | - Álvaro Madrid
- Pediatric Nephrology Department, Sant Joan de Deu University Hospital, Barcelona, Spain
| | - M Carolina Florian
- Program of Regenerative Medicine, The Bellvitge Institute for Biomedical Research (IDIBELL), Barcelona, Spain; Stem Cell Aging Group, Regenerative Medicine Program, The Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; The Catalan Institution for Research and Advanced Studies (ICREA)
| | - Marta Ruíz-Ortega
- Cellular Biology in Renal Diseases Laboratory, IIS Fundación Jiménez Díaz, Universidad Autónoma, Madrid, Spain
| | - Anna Sola
- Department of Nephrology and Transplantation, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain.
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2
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Munté E, Feliubadaló L, Pineda M, Tornero E, Gonzalez M, Moreno-Cabrera JM, Roca C, Bales Rubio J, Arnaldo L, Capellá G, Mosquera JL, Lázaro C. vaRHC: an R package for semi-automation of variant classification in hereditary cancer genes according to ACMG/AMP and gene-specific ClinGen guidelines. Bioinformatics 2023; 39:7077135. [PMID: 36916756 PMCID: PMC10032633 DOI: 10.1093/bioinformatics/btad128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/10/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
MOTIVATION Germline variant classification allows accurate genetic diagnosis and risk assessment. However, it is a tedious iterative process integrating information from several sources and types of evidence. It should follow gene-specific (if available) or general updated international guidelines. Thus, it is the main burden of the incorporation of next-generation sequencing into the clinical setting. RESULTS We created the vaRiants in HC (vaRHC) R package to assist the process of variant classification in hereditary cancer by: (i) collecting information from diverse databases; (ii) assigning or denying different types of evidence according to updated American College of Molecular Genetics and Genomics/Association of Molecular Pathologist gene-specific criteria for ATM, CDH1, CHEK2, MLH1, MSH2, MSH6, PMS2, PTEN, and TP53 and general criteria for other genes; (iii) providing an automated classification of variants using a Bayesian metastructure and considering CanVIG-UK recommendations; and (iv) optionally printing the output to an .xlsx file. A validation using 659 classified variants demonstrated the robustness of vaRHC, presenting a better criteria assignment than Cancer SIGVAR, an available similar tool. AVAILABILITY AND IMPLEMENTATION The source code can be consulted in the GitHub repository (https://github.com/emunte/vaRHC) Additionally, it will be submitted to CRAN soon.
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Affiliation(s)
- Elisabet Munté
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Eva Tornero
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
| | - Maribel Gonzalez
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
| | - José Marcos Moreno-Cabrera
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
| | - Carla Roca
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
| | - Joan Bales Rubio
- Department of Information Technologies, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat 08908, Spain
| | - Laura Arnaldo
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Jose Luis Mosquera
- Department of Bioinformatics, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat 08908, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, L'Hospitalet de Llobregat 08908, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
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3
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Nogué C, Chong AS, Grau E, Han H, Dorca E, Roca C, Mosquera JL, lazaro C, Foulkes WD, Brunet J, Polo BR. Abstract 1549: The tumorigenesis model in DGCR8 associated schwannomatosis. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Purpose: Schwannomatosis is an inherited disorder that affects Schwann cells from peripheral nerves. It is diagnosed when multiple schwannomas occur in the absence of bilateral vestibular schwannomas. The two main genes associated with this disorder are SMARCB1 and LZTR1 both on chromosome 22q (Chrm22q). Somatic inactivation of NF2, downstream of SMARCB1, is observed in most schwannomas. The accepted model of schwannomatosis involves multiple hits over three steps to inactivate LZTR1 or SMARCB1 together with NF2. Following this pattern, most of the LZTR1/SMARCB1-schwannomas acquire a somatic loss of Chrm22 (thus deleting the three genes) and a somatic mutation affecting the remaining wild-type NF2 copy on the GPV allele. Several studies have postulated the plausible existence of other susceptibility genes predisposing to schwannomatosis and the likelihood of those being localized in Chrm22q. Last year we identified a GPV in the microprocessor DGCR8 (c.1552G>A; p.E518K) located in the Chrm22q11 region, as responsible for a familial form of schwannomatosis and multinodular goiter (Rivera et al JCI, 2020). Our goal is to clarify the role of DGCR8 as a novel tumor susceptibility gene and the tumorigenic mechanisms that lead to DGCR8-schwannomatosis.
Methods: We searched for patients affected of schwannoma and thyroid tumors. By whole exome sequencing we identified the same DGCR8 (c.1552G>A; p.E518K) variant in one patient. We then collected a total of 13 DGCR8-schwannomas from carriers. Eleven tumors were subjected to WES and two tumors were subjected to a NGS targeted panel covering all known schwannoma genes in Chrm22q.
Results: We report the second case of a patient with peripheral schwannomatosis and thyroid alterations caused by the germline pathogenic variant E518K in DGCR8. Loss of Chrm22q was seen in all 13 tumors analyzed. While all tumors had at least one alteration of NF2, 4 tumors had no somatic mutations on the retained (not deleted) allele (30.8%). Given that DGCR8 localizes 5’ of LZTR1, the second step (LOH) leads to the deletion of DGCR8 and the three bona fide schwannoma genes (LZTR1, SMARCB1 and NF2) adding up to a total of 6 hits in a 3-step model. Suggesting that the path to tumorigenesis driven by DGCR8 requires the loss of the wild type allele of Chrm22q and in more than two thirds of the tumors a complete inactivation of NF2 occurs.
Conclusion: Our findings highlight DGCR8 as a schwannomatosis gene mapping to the Chrm22 cluster of tumor suppressors that cooperate to promote tumorigenesis in Schwann cell and pinpoints an important role of miRNA regulation in this process.
Citation Format: Clara Nogué, Anne-Sophie Chong, Elia Grau, HyeRim Han, Eduard Dorca, Carla Roca, Jose Luis Mosquera, Conxi lazaro, William D. Foulkes, Joan Brunet, Bárbara Rivera Polo. The tumorigenesis model in DGCR8 associated schwannomatosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1549.
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Affiliation(s)
- Clara Nogué
- 1IDIBELL, L´Hospitalet de Llobregat, Barcelona, Spain
| | | | - Elia Grau
- 1IDIBELL, L´Hospitalet de Llobregat, Barcelona, Spain
| | - HyeRim Han
- 1IDIBELL, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Eduard Dorca
- 3Hospital de Bellvitge, L´Hospitalet de Llobregat, Barcelona, Spain
| | - Carla Roca
- 1IDIBELL, L´Hospitalet de Llobregat, Barcelona, Spain
| | | | - Conxi lazaro
- 1IDIBELL, L´Hospitalet de Llobregat, Barcelona, Spain
| | | | - Joan Brunet
- 4Instituto Catalán de Oncología, L´Hospitalet de Llobregat, Barcelona, Spain
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Rovira M, Atla G, Maestro MA, Grau V, García-Hurtado J, Maqueda M, Mosquera JL, Yamada Y, Kerr-Conte J, Pattou F, Ferrer J. REST is a major negative regulator of endocrine differentiation during pancreas organogenesis. Genes Dev 2021; 35:1229-1242. [PMID: 34385258 PMCID: PMC8415321 DOI: 10.1101/gad.348501.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 03/24/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
Abstract
In this study, Rovira et al. report that inactivation of the transcriptional repressor REST causes a drastic increase in pancreatic endocrine progenitors and endocrine cells, and establish that REST is a major negative regulator of embryonic pancreas endocrine differentiation in mice and zebrafish. Their findings show that REST-dependent inhibition ensures a balanced production of endocrine cells from embryonic pancreatic progenitors. Multiple transcription factors have been shown to promote pancreatic β-cell differentiation, yet much less is known about negative regulators. Earlier epigenomic studies suggested that the transcriptional repressor REST could be a suppressor of endocrinogenesis in the embryonic pancreas. However, pancreatic Rest knockout mice failed to show abnormal numbers of endocrine cells, suggesting that REST is not a major regulator of endocrine differentiation. Using a different conditional allele that enables profound REST inactivation, we observed a marked increase in pancreatic endocrine cell formation. REST inhibition also promoted endocrinogenesis in zebrafish and mouse early postnatal ducts and induced β-cell-specific genes in human adult duct-derived organoids. We also defined genomic sites that are bound and repressed by REST in the embryonic pancreas. Our findings show that REST-dependent inhibition ensures a balanced production of endocrine cells from embryonic pancreatic progenitors.
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Affiliation(s)
- Meritxell Rovira
- Department of Physiological Science, School of Medicine, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Barcelona 08907, Spain.,Pancreas Regeneration: Pancreatic Progenitors and Their Niche Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona 08908, Spain.,Program for Advancing the Clinical Translation of Regenerative Medicine of Catalonia (P-CMR[C]), L'Hospitalet de Llobregat, Barcelona 08908, Spain.,Center for Networked Biomedical Research on Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid 28029, Spain
| | - Goutham Atla
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Miguel Angel Maestro
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid 28029, Spain
| | - Vane Grau
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid 28029, Spain
| | - Javier García-Hurtado
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid 28029, Spain
| | - Maria Maqueda
- Bioinformatics Unit, Bellvitge Biomedical Research Institute, IDIBELL, L'Hospitalet del Llobregat, Barcelona 08908, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Bellvitge Biomedical Research Institute, IDIBELL, L'Hospitalet del Llobregat, Barcelona 08908, Spain
| | - Yasuhiro Yamada
- Division of Stem Cell Pathology, Center for Experimental Medicine and Systems Biology, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan
| | - Julie Kerr-Conte
- Institute Pasteur Lille, University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), U1190, European Genomic Institute for Diabetes (EGID), Lille F-59000, France
| | - Francois Pattou
- Institute Pasteur Lille, University of Lille, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre Hospitalier Universitaire de Lille (CHU Lille), U1190, European Genomic Institute for Diabetes (EGID), Lille F-59000, France
| | - Jorge Ferrer
- Regulatory Genomics and Diabetes, Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Centro de Investigación Biomédica en Red Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Madrid 28029, Spain.,Department of Metabolism, Digestion, and Reproduction, Section of Genetics and Genomics, Imperial College London, London W12 0NN, United Kingdom
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5
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Garcia P, Fernandez-Hernandez R, Cuadrado A, Coca I, Gomez A, Maqueda M, Latorre-Pellicer A, Puisac B, Ramos FJ, Sandoval J, Esteller M, Mosquera JL, Rodriguez J, Pié J, Losada A, Queralt E. Disruption of NIPBL/Scc2 in Cornelia de Lange Syndrome provokes cohesin genome-wide redistribution with an impact in the transcriptome. Nat Commun 2021; 12:4551. [PMID: 34315879 PMCID: PMC8316422 DOI: 10.1038/s41467-021-24808-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 04/28/2020] [Accepted: 07/05/2021] [Indexed: 12/31/2022] Open
Abstract
Cornelia de Lange syndrome (CdLS) is a rare disease affecting multiple organs and systems during development. Mutations in the cohesin loader, NIPBL/Scc2, were first described and are the most frequent in clinically diagnosed CdLS patients. The molecular mechanisms driving CdLS phenotypes are not understood. In addition to its canonical role in sister chromatid cohesion, cohesin is implicated in the spatial organization of the genome. Here, we investigate the transcriptome of CdLS patient-derived primary fibroblasts and observe the downregulation of genes involved in development and system skeletal organization, providing a link to the developmental alterations and limb abnormalities characteristic of CdLS patients. Genome-wide distribution studies demonstrate a global reduction of NIPBL at the NIPBL-associated high GC content regions in CdLS-derived cells. In addition, cohesin accumulates at NIPBL-occupied sites at CpG islands potentially due to reduced cohesin translocation along chromosomes, and fewer cohesin peaks colocalize with CTCF.
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Affiliation(s)
- Patricia Garcia
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca and Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain.
| | - Rita Fernandez-Hernandez
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Cuadrado
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ignacio Coca
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
- Grup de Recerca de Reumatologia, Parc Científic de Barcelona, Barcelona, Spain
| | - Maria Maqueda
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Ana Latorre-Pellicer
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Beatriz Puisac
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Feliciano J Ramos
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit (UByMP) and Epigenomics Core Facility, Health Research Institute La Fe (IISLaFe), Valencia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain
| | - Jairo Rodriguez
- Research and Development Department, qGenomics Laboratory, Esplugues de Llobregat, Spain
| | - J Pié
- Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology and Paediatrics, School of Medicine, University of Zaragoza, CIBERER-GCV02 and IISAragon, Zaragoza, Spain
| | - Ana Losada
- Chromosome Dynamics Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Ethel Queralt
- Cell Cycle Group, Institut d'Investigacions Biomèdica de Bellvitge (IDIBELL), Av. Gran Via de L'Hospitalet 199-203, Barcelona, Spain.
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.
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6
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Maqueda M, Mosquera JL, García-Arumí J, Veiga A, Duarri A. Repopulation of decellularized retinas with hiPSC-derived retinal pigment epithelial and ocular progenitor cells shows cell engraftment, organization and differentiation. Biomaterials 2021; 276:121049. [PMID: 34332373 DOI: 10.1016/j.biomaterials.2021.121049] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/22/2021] [Accepted: 07/23/2021] [Indexed: 11/18/2022]
Abstract
The retinal extracellular matrix (ECM) provides architectural support, adhesion and signal guidance that controls retinal development. Decellularization of the ECM affords great potential to tissue engineering; however, how structural retinal ECM affects in vitro development, differentiation and maturation of ocular cells remains to be elucidated. Here, mouse and porcine retinas were decellularized and the protein profile analyzed. Acellular retinal ECM (arECM) scaffolds were then repopulated with human iPSC-derived retinal pigment epithelial (RPE) cells or ocular progenitor cells (OPC) to assess their integration, proliferation and organization. 3837 and 2612 unique proteins were identified in mouse and porcine arECM, respectively, of which 93 and 116 proteins belong to the matrisome. GO analysis shows that matrisome-related proteins were associated with the extracellular region and cell junction and KEGG pathways related to signalling transduction, nervous and endocrine systems and cell junctions were enriched. Interestingly, mouse and porcine arECMs were successfully repopulated with both RPE and OPC, the latter exhibiting cell lineage-specific clusters. Retinal cells organized into different layers containing well-defined areas with pigmented cells, photoreceptors, Müller glia, astrocytes, and ganglion cells, whereas in other areas, conjunctival/limbal, corneal and lens cells re-arranged in cell-specific self-organized areas. In conclusion, our results demonstrated that decellularization of both mouse and porcine retinas retains common native ECM components that upon cell repopulation could guide similar ocular cell adhesion, migration and organization.
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Affiliation(s)
- Maria Maqueda
- Bioinformatics Unit, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - José García-Arumí
- Ophthalmology Research Group, Vall d'Hebron Institut de Recerca - VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Anna Veiga
- Pluripotent Stem Cell Therapy Group, Regenerative Medicine Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain; National Stem Cell Bank-Barcelona Node, Biomolecular and Bioinformatics Resources Platform (PRB2), ISCIII, Madrid, Spain
| | - Anna Duarri
- Ophthalmology Research Group, Vall d'Hebron Institut de Recerca - VHIR, Vall d'Hebron Hospital Universitari, Barcelona, Spain; National Stem Cell Bank-Barcelona Node, Biomolecular and Bioinformatics Resources Platform (PRB2), ISCIII, Madrid, Spain.
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7
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Farre L, Sanz G, Ruiz-Xivillé N, Castro de Moura M, Martin-Tejera JF, Gonçalves-Ribeiro S, Martinez-Iniesta M, Calaf M, Luis Mosquera J, Martín-Subero JI, Granada I, Esteller M, Domingo-Domenech E, Climent F, Villanueva A, Sureda A. Extramedullary multiple myeloma patient-derived orthotopic xenograft with a highly altered genome: combined molecular and therapeutic studies. Dis Model Mech 2021; 14:dmm048223. [PMID: 33988237 PMCID: PMC8325009 DOI: 10.1242/dmm.048223] [Citation(s) in RCA: 3] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/05/2021] [Indexed: 12/29/2022] Open
Abstract
Extramedullary multiple myeloma (EMM) has an overall survival of 6 months and occurs in 20% of multiple myeloma (MM) patients. Genetic and epigenetic mechanisms involved in EMM and the therapeutic role of new agents for MM are not well established. Besides, well-characterized preclinical models for EMM are not available. Herein, a patient-derived orthotopic xenograft (PDOX) was generated from a patient with an aggressive EMM to study in-depth genetic and epigenetic events, and drug responses related to extramedullary disease. A fresh punch of an extramedullary cutaneous lesion was orthotopically implanted in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ(NSG) mouse. The PDOX mimicked histologic and phenotypic features of the tumor of the patient. Cytogenetic studies revealed a hyperploid genome with multiple genetic poor-prognosis alterations. Copy number alterations (CNAs) were detected in all chromosomes. The IGH translocation t(14;16)(q32;q23)IGH/MAF was already observed at the medullary stage and a new one, t(10;14)(p?11-12;q32), was observed only with extramedullary disease and could be eventually related to EMM progression in this case. Exome sequencing showed 24 high impact single nucleotide variants and 180 indels. From the genes involved, only TP53 was previously described as a driver in MM. A rather balanced proportion of hyper/hypomethylated sites different to previously reported widespread hypomethylation in MM was also observed. Treatment with lenalidomide, dexamethasone and carfilzomib showed a tumor weight reduction of 90% versus non-treated tumors, whereas treatment with the anti-CD38 antibody daratumumab showed a reduction of 46%. The generation of PDOX from a small EMM biopsy allowed us to investigate in depth the molecular events associated with extramedullary disease in combination with drug testing.
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Affiliation(s)
- Lourdes Farre
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Gabriela Sanz
- Department of Clinical Hematology, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet del Llobregat Barcelona, Spain
| | - Neus Ruiz-Xivillé
- Hematological Laboratory, Germans Trias i Pujol Hospital, Catalan Institute of Oncology, 08916 Badalona, Barcelona, Spain
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
| | - Manuel Castro de Moura
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
| | - Juan Francisco Martin-Tejera
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Samuel Gonçalves-Ribeiro
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Maria Martinez-Iniesta
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Monica Calaf
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Jose Luis Mosquera
- IDIBELL Bioinformatic Unit – Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - José Ignacio Martín-Subero
- Biomedical Epigenomics Group, Institut d'investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Isabel Granada
- Hematological Laboratory, Germans Trias i Pujol Hospital, Catalan Institute of Oncology, 08916 Badalona, Barcelona, Spain
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cancer, Carlos III Institute of Health, 28029 Madrid, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Eva Domingo-Domenech
- Department of Clinical Hematology, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet del Llobregat Barcelona, Spain
| | - Fina Climent
- Centro de Investigación Biomédica en Red de Cancer, Carlos III Institute of Health, 28029 Madrid, Spain
- Department of Pathology, Hospital Universitari de Bellvitge – Bellvitge Biomedical Research Institute, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alberto Villanueva
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
- Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Sureda
- Department of Clinical Hematology, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet del Llobregat Barcelona, Spain
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8
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Castaño J, Aranda S, Bueno C, Calero-Nieto FJ, Mejia-Ramirez E, Mosquera JL, Blanco E, Wang X, Prieto C, Zabaleta L, Mereu E, Rovira M, Jiménez-Delgado S, Matson DR, Heyn H, Bresnick EH, Göttgens B, Di Croce L, Menendez P, Raya A, Giorgetti A. GATA2 Promotes Hematopoietic Development and Represses Cardiac Differentiation of Human Mesoderm. Stem Cell Reports 2019; 13:515-529. [PMID: 31402335 PMCID: PMC6742600 DOI: 10.1016/j.stemcr.2019.07.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 05/03/2018] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 02/02/2023] Open
Abstract
In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo development and in adult life. Although the essential role of GATA2 in mouse hematopoiesis is well established, its involvement during early human hematopoietic development is not clear. By combining time-controlled overexpression of GATA2 with genetic knockout experiments, we found that GATA2, at the mesoderm specification stage, promotes the generation of hemogenic endothelial progenitors and their further differentiation to hematopoietic progenitor cells, and negatively regulates cardiac differentiation. Surprisingly, genome-wide transcriptional and chromatin immunoprecipitation analysis showed that GATA2 bound to regulatory regions, and repressed the expression of cardiac development-related genes. Moreover, genes important for hematopoietic differentiation were upregulated by GATA2 in a mostly indirect manner. Collectively, our data reveal a hitherto unrecognized role of GATA2 as a repressor of cardiac fates, and highlight the importance of coordinating the specification and repression of alternative cell fates.
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Affiliation(s)
- Julio Castaño
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid 28029, Spain
| | - Sergi Aranda
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Clara Bueno
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Fernando J Calero-Nieto
- Department of Hematology, Wellcome and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Eva Mejia-Ramirez
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Jose Luis Mosquera
- Bioinformatics Unit, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, 08908 Spain
| | - Enrique Blanco
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Xiaonan Wang
- Department of Hematology, Wellcome and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Cristina Prieto
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Lorea Zabaleta
- Laboratory of Hematological Diseases, Fundación Inbiomed, San Sebastian, 20009, Spain
| | - Elisabetta Mereu
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Meritxell Rovira
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Senda Jiménez-Delgado
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain
| | - Daniel R Matson
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Holger Heyn
- CNAG-CRG, Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Universitat Pompeu Fabra, Barcelona, Spain
| | - Emery H Bresnick
- Department of Cell and Regenerative Biology, UW-Madison Blood Research Program, Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Berthold Göttgens
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain
| | - Luciano Di Croce
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Universitat Pompeu Fabra, Barcelona 08003, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Pablo Menendez
- Josep Carreras Leukemia Research Institute and Department of Biomedicine, School of Medicine, University of Barcelona, Barcelona 08036, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain; Centro de Investigación Biomedica en Red en Cancer (CIBERONIC) ISCIII, Barcelona, Spain
| | - Angel Raya
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain; Center for Networked Biomedical Research on Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid 28029, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Alessandra Giorgetti
- Center of Regenerative Medicine in Barcelona (CMRB), Hospital Duran i Reynals, Gran Via de L'Hospitalet, 199-203, Hospitalet de Llobregat, Barcelona 08908, Spain.
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9
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Garcia-Puig A, Mosquera JL, Jiménez-Delgado S, García-Pastor C, Jorba I, Navajas D, Canals F, Raya A. Proteomics Analysis of Extracellular Matrix Remodeling During Zebrafish Heart Regeneration. Mol Cell Proteomics 2019; 18:1745-1755. [PMID: 31221719 PMCID: PMC6731076 DOI: 10.1074/mcp.ra118.001193] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [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: 11/20/2018] [Revised: 06/03/2019] [Indexed: 12/13/2022] Open
Abstract
Adult zebrafish, in contrast to mammals, are able to regenerate their hearts in response to injury or experimental amputation. Our understanding of the cellular and molecular bases that underlie this process, although fragmentary, has increased significantly over the last years. However, the role of the extracellular matrix (ECM) during zebrafish heart regeneration has been comparatively rarely explored. Here, we set out to characterize the ECM protein composition in adult zebrafish hearts, and whether it changed during the regenerative response. For this purpose, we first established a decellularization protocol of adult zebrafish ventricles that significantly enriched the yield of ECM proteins. We then performed proteomic analyses of decellularized control hearts and at different times of regeneration. Our results show a dynamic change in ECM protein composition, most evident at the earliest (7 days postamputation) time point analyzed. Regeneration associated with sharp increases in specific ECM proteins, and with an overall decrease in collagens and cytoskeletal proteins. We finally tested by atomic force microscopy that the changes in ECM composition translated to decreased ECM stiffness. Our cumulative results identify changes in the protein composition and mechanical properties of the zebrafish heart ECM during regeneration.
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Affiliation(s)
- Anna Garcia-Puig
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain; §Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Jose Luis Mosquera
- ¶Bioinformatics Unit, Institut d'Investigació Biomèdica de Bellvitge IDIBELL), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Senda Jiménez-Delgado
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Cristina García-Pastor
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain
| | - Ignasi Jorba
- ‖Institute for Bioengineering of Catalonia (IBEC), Barcelona Science Park, Baldiri Reixac 15-21, 08028 Barcelona, Spain; **Unit of Biophysics and Bioengineering, Department of Physiological Sciences I, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; ‡‡Center for Networked Biomedical Research on Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Daniel Navajas
- ‖Institute for Bioengineering of Catalonia (IBEC), Barcelona Science Park, Baldiri Reixac 15-21, 08028 Barcelona, Spain; **Unit of Biophysics and Bioengineering, Department of Physiological Sciences I, School of Medicine, University of Barcelona, Casanova 143, 08036 Barcelona, Spain; ‡‡Center for Networked Biomedical Research on Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Francesc Canals
- §§Proteomics group, Vall d'Hebron Institut of Oncology (VHIO), Cellex center, Natzaret 115-117, 08035 Barcelona, Spain
| | - Angel Raya
- ‡Center of Regenerative Medicine in Barcelona (CMRB), 3rd Floor Hospital Duran i Reynals, Avinguda de la Gran Via 199-203, 08908 Hospitalet de Llobregat (Barcelona), Spain; §Center for Networked Biomedical Research on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 08908 Hospitalet de Llobregat (Barcelona), Spain; ¶¶Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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10
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Rossi F, Attolini CSO, Mosquera JL, Gonzalez C. Drosophila Larval Brain Neoplasms Present Tumour-Type Dependent Genome Instability. G3 (Bethesda) 2018; 8:1205-1214. [PMID: 29467187 PMCID: PMC5873911 DOI: 10.1534/g3.117.300489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/01/2018] [Indexed: 12/30/2022]
Abstract
Single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) are found at different rates in human cancer. To determine if these genetic lesions appear in Drosophila tumors we have sequenced the genomes of 17 malignant neoplasms caused by mutations in l(3)mbt, brat, aurA, or lgl We have found CNVs and SNPs in all the tumors. Tumor-linked CNVs range between 11 and 80 per sample, affecting between 92 and 1546 coding sequences. CNVs are in average less frequent in l(3)mbt than in brat lines. Nearly half of the CNVs fall within the 10 to 100Kb range, all tumor samples contain CNVs larger that 100 Kb and some have CNVs larger than 1Mb. The rates of tumor-linked SNPs change more than 20-fold depending on the tumor type: at late time points brat, l(3)mbt, and aurA and lgl lines present median values of SNPs/Mb of exome of 0.16, 0.48, and 3.6, respectively. Higher SNP rates are mostly accounted for by C > A transversions, which likely reflect enhanced oxidative stress conditions in the affected tumors. Both CNVs and SNPs turn over rapidly. We found no evidence for selection of a gene signature affected by CNVs or SNPs in the cohort. Altogether, our results show that the rates of CNVs and SNPs, as well as the distribution of CNV sizes in this cohort of Drosophila tumors are well within the range of those reported for human cancer. Genome instability is therefore inherent to Drosophila malignant neoplastic growth at a variable extent that is tumor type dependent.
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Affiliation(s)
- Fabrizio Rossi
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Camille Stephan-Otto Attolini
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Jose Luis Mosquera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Cayetano Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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11
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Blanch M, Mosquera JL, Ansoleaga B, Ferrer I, Barrachina M. Altered Mitochondrial DNA Methylation Pattern in Alzheimer Disease-Related Pathology and in Parkinson Disease. Am J Pathol 2016; 186:385-97. [PMID: 26776077 DOI: 10.1016/j.ajpath.2015.10.004] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 09/30/2015] [Accepted: 10/13/2015] [Indexed: 12/28/2022]
Abstract
Mitochondrial dysfunction is linked with the etiopathogenesis of Alzheimer disease and Parkinson disease. Mitochondria are intracellular organelles essential for cell viability and are characterized by the presence of the mitochondrial (mt)DNA. DNA methylation is a well-known epigenetic mechanism that regulates nuclear gene transcription. However, mtDNA methylation is not the subject of the same research attention. The present study shows the presence of mitochondrial 5-methylcytosine in CpG and non-CpG sites in the entorhinal cortex and substantia nigra of control human postmortem brains, using the 454 GS FLX Titanium pyrosequencer. Moreover, increased mitochondrial 5-methylcytosine levels are found in the D-loop region of mtDNA in the entorhinal cortex in brain samples with Alzheimer disease-related pathology (stages I to II and stages III to IV of Braak and Braak; n = 8) with respect to control cases. Interestingly, this region shows a dynamic pattern in the content of mitochondrial 5-methylcytosine in amyloid precursor protein/presenilin 1 mice along with Alzheimer disease pathology progression (3, 6, and 12 months of age). Finally, a loss of mitochondrial 5-methylcytosine levels in the D-loop region is found in the substantia nigra in Parkinson disease (n = 10) with respect to control cases. In summary, the present findings suggest mtDNA epigenetic modulation in human brain is vulnerable to neurodegenerative disease states.
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Affiliation(s)
- Marta Blanch
- Institute of Neuropathology, Bellvitge University Hospital (Bellvitge Biomedical Research Institute) IDIBELL, L'Hospitalet de Llobregat, Spain
| | | | - Belén Ansoleaga
- Institute of Neuropathology, Bellvitge University Hospital (Bellvitge Biomedical Research Institute) IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Bellvitge University Hospital (Bellvitge Biomedical Research Institute) IDIBELL, L'Hospitalet de Llobregat, Spain; Networked Biomedical Research Centre for NeuroDegenerative Disorders (CIBERNED), Madrid, Spain; Departament of Pathology and Experimental Therapeutics, University of Barcelona, L'Hospitalet de Llobregat, Spain
| | - Marta Barrachina
- Institute of Neuropathology, Bellvitge University Hospital (Bellvitge Biomedical Research Institute) IDIBELL, L'Hospitalet de Llobregat, Spain; Networked Biomedical Research Centre for NeuroDegenerative Disorders (CIBERNED), Madrid, Spain.
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12
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Nogales-Gadea G, Ramos-Fransi A, Suárez-Calvet X, Navas M, Rojas-García R, Mosquera JL, Díaz-Manera J, Querol L, Gallardo E, Illa I. Analysis of serum miRNA profiles of myasthenia gravis patients. PLoS One 2014; 9:e91927. [PMID: 24637658 PMCID: PMC3956820 DOI: 10.1371/journal.pone.0091927] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [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: 11/15/2013] [Accepted: 02/17/2014] [Indexed: 12/14/2022] Open
Abstract
Myasthenia gravis (MG) is an autoimmune disease characterized by the presence of autoantibodies, mainly against the acetylcholine receptor (AChR). The mechanisms triggering and maintaining this chronic disease are unknown. MiRNAs are regulatory molecules that play a key role in the immune system and are altered in many autoimmune diseases. The aim of this study was to evaluate miRNA profiles in serum of 61 AChR MG patients. We studied serum from patients with early onset MG (n = 22), late onset MG (n = 27) and thymoma (n = 12), to identify alterations in the specific subgroups. In a discovery cohort, we analysed 381 miRNA arrays from 5 patients from each subgroup, and 5 healthy controls. The 15 patients had not received any treatment. We found 32 miRNAs in different levels in MG and analysed 8 of these in a validation cohort that included 46 of the MG patients. MiR15b, miR122, miR-140-3p, miR185, miR192, miR20b and miR-885-5p were in lower levels in MG patients than in controls. Our study suggests that different clinical phenotypes in MG share common altered mechanisms in circulating miRNAs, with no additional contribution of the thymoma. MG treatment intervention does not modify the profile of these miRNAs. Novel insights into the pathogenesis of MG can be reached by the analysis of circulating miRNAs since some of these miRNAs have also been found low in MG peripheral mononuclear cells, and have targets with important roles in B cell survival and antibody production.
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Affiliation(s)
- Gisela Nogales-Gadea
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Alba Ramos-Fransi
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Xavier Suárez-Calvet
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Miquel Navas
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Ricard Rojas-García
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | | | - Jordi Díaz-Manera
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Luis Querol
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Eduard Gallardo
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Illa
- Neuromuscular Diseases Unit, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain
- CIBER de enfermedades neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
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13
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Martínez C, Vicario M, Ramos L, Lobo B, Mosquera JL, Alonso C, Sánchez A, Guilarte M, Antolín M, de Torres I, González-Castro AM, Pigrau M, Saperas E, Azpiroz F, Santos J. The jejunum of diarrhea-predominant irritable bowel syndrome shows molecular alterations in the tight junction signaling pathway that are associated with mucosal pathobiology and clinical manifestations. Am J Gastroenterol 2012; 107:736-46. [PMID: 22415197 DOI: 10.1038/ajg.2011.472] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVES Diarrhea-predominant irritable bowel syndrome (IBS-D) patients show altered epithelial permeability and mucosal micro-inflammation in both proximal and distal regions of the intestine. The objective of this study was to determine the molecular events and mechanisms and the clinical role of upper small intestinal alterations. METHODS Clinical assessment and a jejunal biopsy was obtained in IBS-D patients and healthy subjects. Routine histology and immunohistochemistry was performed in all participants to assess the number of mast cells (MCs) and intraepithelial lymphocytes. RNA in tissue samples was isolated to identify genes showing consistent differential expression by microarray analysis followed by pathway and network analysis in order to identify the biological functions of the differentially expressed genes in IBS-D. Gene and protein expression of tight junction (TJ) components was also assessed by quantitative real-time polymerase chain reaction and confocal microscopy to evaluate the pathways identified by gene expression analysis. RESULTS The analysis reveals a strong association between the transcript signature of the jejunal mucosa of IBS-D and intestinal permeability, MC biology, and TJ signaling. The expression of zonula occludens 1 (ZO-1) was reduced in IBS-D at both gene and protein level, with protein redistribution from the TJ to the cytoplasm. Remarkably, our analysis disclosed significant correlation between ZO proteins, MC activation, and clinical symptoms. CONCLUSIONS IBS-D manifestations are linked to molecular alterations involving MC-related dysregulation of TJ functioning in the jejunal mucosa.
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Affiliation(s)
- Cristina Martínez
- Department of Gastroenterology, Digestive System Research Unit, Hospital Universitari Vall d'Hebron, Institut de Recerca Vall d'Hebron, Universitat Autònoma de Barcelona-Departmento de Medicina, Barcelona, Spain
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Abstract
In recent years, the scientific community has provided many tools to assist with pathway analysis. Some of these programs can be used to manage functional annotation of gene products, others are oriented to exploring and analyzing data sets and many allow both possibilities. Potential users of these tools are faced with the necessity to decide which of the existing programs are the most appropriate for their needs. SerbGO is a user-friendly web tool created to facilitate this task. It can be used (i) to search for specific functionalities and determine which applications provide them and (ii) to compare several applications on the basis of different types of functionalities. Iterating and combining both functionalities can easily lead to selecting an appropriate tool. Data required by SerbGO is either the desired capabilities within a defined Standard Functionalities Set or the list of the tools to be compared. The analysis performed carries out a cross-classification that produces an easily readable output with the list of tools that implement the capabilities demanded or a table with the categorization of the GO tools that one wishes to compare. SerbGO is freely available and does not require a login. It can be accessed either directly at our server (http://estbioinfo.stat.ub.es/apli/serbgo) or at the GO Consortium website (http://www.geneontology.org/GO.tools.microarray.shtml#serbgo).
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Affiliation(s)
- J L Mosquera
- Statistics and Bioinformatics Research Group, Departament d'Estadística, Universitat de Barcelona. Av. Diagonal 645, 08028 Barcelona, Spain.
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Mosquera JL. [Radiology: foreign body due to digestion of kakis]. Prensa Med Argent 1970; 57:1984-1985. [PMID: 5509784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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