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Ribeiro M, Jager J, Furtado M, Carvalho T, Cabral JMS, Brito D, Carmo-Fonseca M, Martins S, da Rocha ST. Generation of induced pluripotent stem cell lines from two unrelated individuals with familial hypertrophic cardiomyopathy carrying MYBPC3 nonsense mutations. Stem Cell Res 2024; 76:103362. [PMID: 38417376 DOI: 10.1016/j.scr.2024.103362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 02/01/2024] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024] Open
Abstract
Familial hypertrophic cardiomyopathy (HCM) stands as a predominant heart condition, characterised by left ventricle hypertrophy in the absence of any associated loading conditions, with affected individuals having an increased risk of developing heart failure and sudden cardiac death (SCD). Two induced pluripotent stem cell (iPSC) lines were derived from peripheral blood mononuclear cells obtained from two unrelated individuals with previously reported nonsense mutations in the MYBPC3 gene. The first individual is a 48-year-old male (F26) with the MYBPC3 c.1731G > A HCM mutation, whereas the second individual is a 43-year-old female (F82) carrying the MYBPC3 c.2670G > A HCM mutation. The generated iPSCs exhibit appropriate expression of pluripotency markers, trilineage differentiation capacity and a normal karyotype. This resource contributes to gaining deeper insights into the pathophysiological mechanisms that underlie HCM.
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Affiliation(s)
- Marta Ribeiro
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joanna Jager
- Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, United Kingdom
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Joaquim M S Cabral
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Dulce Brito
- Heart and Vessels Department, Cardiology Division, Centro Hospitalar Universitário de Lisboa Norte, Lisboa Portugal; Centro Cardiovascular da Universidade de Lisboa (CCUL@RISE), Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal.
| | - Simão Teixeira da Rocha
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal.
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2
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Ribeiro M, Martins S, Carvalho T, Furtado M, Sampaio Cabral J, Brito D, Carmo-Fonseca M, da Rocha ST. Generation of induced pluripotent stem cell lines from two unrelated individuals with familial hypertrophic cardiomyopathy carrying the MYBPC3 missense c.1484G>A mutation. Stem Cell Res 2024; 74:103282. [PMID: 38104429 DOI: 10.1016/j.scr.2023.103282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 11/03/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023] Open
Abstract
Familial hypertrophic cardiomyopathy (HCM) is the most common inherited heart condition. HCM patients show left ventricle hypertrophy without any associated loading conditions, being at risk for heart failure and sudden cardiac death. Two induced pluripotent stem cell (iPSC) lines were generated from peripheral blood mononuclear cells obtained from two unrelated individuals, a 54-year-old male (F81) and a 44-year-old female (F93), both carrying the MYBPC3 c.1484G>A HCM mutation. iPSCs show expression of pluripotency markers, trilineage differentiation capacity and a normal karyotype. This resource enables further assessment of the pathophysiological development of HCM.
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Affiliation(s)
- Marta Ribeiro
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal.
| | - Teresa Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Joaquim Sampaio Cabral
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Dulce Brito
- Heart and Vessels Department, Cardiology Division, Centro Hospitalar Universitário de Lisboa Norte, Lisboa Portugal; Centro Cardiovascular da Universidade de Lisboa (CCUL@RISE), Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Simão Teixeira da Rocha
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal.
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3
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Carmo-Fonseca M. A twist to splicing regulation in haematopoiesis. Nat Cell Biol 2023; 25:516-517. [PMID: 37024682 DOI: 10.1038/s41556-022-01043-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, Lisboa, Portugal.
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4
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Gotthardt M, Badillo-Lisakowski V, Parikh VN, Ashley E, Furtado M, Carmo-Fonseca M, Schudy S, Meder B, Grosch M, Steinmetz L, Crocini C, Leinwand L. Cardiac splicing as a diagnostic and therapeutic target. Nat Rev Cardiol 2023:10.1038/s41569-022-00828-0. [PMID: 36653465 DOI: 10.1038/s41569-022-00828-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 01/19/2023]
Abstract
Despite advances in therapeutics for heart failure and arrhythmias, a substantial proportion of patients with cardiomyopathy do not respond to interventions, indicating a need to identify novel modifiable myocardial pathobiology. Human genetic variation associated with severe forms of cardiomyopathy and arrhythmias has highlighted the crucial role of alternative splicing in myocardial health and disease, given that it determines which mature RNA transcripts drive the mechanical, structural, signalling and metabolic properties of the heart. In this Review, we discuss how the analysis of cardiac isoform expression has been facilitated by technical advances in multiomics and long-read and single-cell sequencing technologies. The resulting insights into the regulation of alternative splicing - including the identification of cardiac splice regulators as therapeutic targets and the development of a translational pipeline to evaluate splice modulators in human engineered heart tissue, animal models and clinical trials - provide a basis for improved diagnosis and therapy. Finally, we consider how the medical and scientific communities can benefit from facilitated acquisition and interpretation of splicing data towards improved clinical decision-making and patient care.
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Affiliation(s)
- Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany. .,DZHK (German Center for Cardiovascular Research Partner Site Berlin), Berlin, Germany. .,Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Victor Badillo-Lisakowski
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,DZHK (German Center for Cardiovascular Research Partner Site Berlin), Berlin, Germany
| | - Victoria Nicole Parikh
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Euan Ashley
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Palo Alto, CA, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sarah Schudy
- Institute for Cardiomyopathies, Department of Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies, Department of Medicine III, University of Heidelberg, Heidelberg, Germany.,DZHK (German Center for Cardiovascular Research Partner Site Heidelberg-Mannheim), Heidelberg, Germany
| | - Markus Grosch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Lars Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Claudia Crocini
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Leslie Leinwand
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
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Abstract
Glucose is the main source of energy for cells. In this issue of Cell, a study now shows that glucose has additional non-energetic functions, acting as a biomolecular cue that regulates alternative splicing during epidermal differentiation. As keratinocytes differentiate, glucose associates with RNA-binding protein DDX21 and modulates its interaction properties, which modifies splicing decisions.
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Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal.
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6
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Barbosa P, Savisaar R, Carmo-Fonseca M, Fonseca A. Computational prediction of human deep intronic variation. Gigascience 2022; 12:giad085. [PMID: 37878682 PMCID: PMC10599398 DOI: 10.1093/gigascience/giad085] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND The adoption of whole-genome sequencing in genetic screens has facilitated the detection of genetic variation in the intronic regions of genes, far from annotated splice sites. However, selecting an appropriate computational tool to discriminate functionally relevant genetic variants from those with no effect is challenging, particularly for deep intronic regions where independent benchmarks are scarce. RESULTS In this study, we have provided an overview of the computational methods available and the extent to which they can be used to analyze deep intronic variation. We leveraged diverse datasets to extensively evaluate tool performance across different intronic regions, distinguishing between variants that are expected to disrupt splicing through different molecular mechanisms. Notably, we compared the performance of SpliceAI, a widely used sequence-based deep learning model, with that of more recent methods that extend its original implementation. We observed considerable differences in tool performance depending on the region considered, with variants generating cryptic splice sites being better predicted than those that potentially affect splicing regulatory elements. Finally, we devised a novel quantitative assessment of tool interpretability and found that tools providing mechanistic explanations of their predictions are often correct with respect to the ground - information, but the use of these tools results in decreased predictive power when compared to black box methods. CONCLUSIONS Our findings translate into practical recommendations for tool usage and provide a reference framework for applying prediction tools in deep intronic regions, enabling more informed decision-making by practitioners.
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Affiliation(s)
- Pedro Barbosa
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016,, Lisboa, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | | | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisboa, Portugal
| | - Alcides Fonseca
- LASIGE, Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, 1749-016,, Lisboa, Portugal
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7
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Silveira C, Sousa AC, Corredeira P, Martins M, Sousa AR, Da Cruz Paula A, Selenica P, Brown DN, Golkaram M, Kaplan S, Zhang S, Liu L, Weigelt B, Reis-Filho JS, Costa L, Carmo-Fonseca M. Comprehensive Genomic Profiling of Cell-Free Circulating Tumor DNA Detects Response to Ribociclib Plus Letrozole in a Patient with Metastatic Breast Cancer. Biomolecules 2022; 12:biom12121818. [PMID: 36551247 PMCID: PMC9775495 DOI: 10.3390/biom12121818] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/28/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Analysis of cell-free circulating tumor DNA obtained by liquid biopsy is a non-invasive approach that may provide clinically actionable information when conventional tissue biopsy is inaccessible or infeasible. Here, we followed a patient with hormone receptor-positive and human epidermal growth factor receptor (HER) 2-negative breast cancer who developed bone metastases seven years after mastectomy. We analyzed circulating cell-free DNA (cfDNA) extracted from plasma using high-depth massively parallel sequencing targeting 468 cancer-associated genes, and we identified a clonal hotspot missense mutation in the PIK3CA gene (3:178952085, A > G, H1047R) and amplification of the CCND1 gene. Whole-exome sequencing revealed that both alterations were present in the primary tumor. After treatment with ribociclib plus letrozole, the genetic abnormalities were no longer detected in cfDNA. These results underscore the clinical utility of combining liquid biopsy and comprehensive genomic profiling to monitor treatment response in patients with metastasized breast cancer.
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Affiliation(s)
- Catarina Silveira
- GenoMed—Diagnósticos de Medicina Molecular, S.A., Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Carla Sousa
- GenoMed—Diagnósticos de Medicina Molecular, S.A., Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Patrícia Corredeira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Marta Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Ana Rita Sousa
- Serviço de Oncologia Médica, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Arnaud Da Cruz Paula
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - David N. Brown
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mahdi Golkaram
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Shannon Kaplan
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Shile Zhang
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Li Liu
- Illumina Inc., 5200 Illumina Way, San Diego, CA 92122, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Jorge S. Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Luís Costa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Serviço de Oncologia Médica, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Avenida Professor Egas Moniz, 1649-035 Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Correspondence:
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8
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Barbosa P, Ribeiro M, Carmo-Fonseca M, Fonseca A. Clinical significance of genetic variation in hypertrophic cardiomyopathy: comparison of computational tools to prioritize missense variants. Front Cardiovasc Med 2022; 9:975478. [PMID: 36061567 PMCID: PMC9433717 DOI: 10.3389/fcvm.2022.975478] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a common heart disease associated with sudden cardiac death. Early diagnosis is critical to identify patients who may benefit from implantable cardioverter defibrillator therapy. Although genetic testing is an integral part of the clinical evaluation and management of patients with HCM and their families, in many cases the genetic analysis fails to identify a disease-causing mutation. This is in part due to difficulties in classifying newly detected rare genetic variants as well as variants-of-unknown-significance (VUS). Multiple computational algorithms have been developed to predict the potential pathogenicity of genetic variants, but their relative performance in HCM has not been comprehensively assessed. Here, we compared the performance of 39 currently available prediction tools in distinguishing between high-confidence HCM-causing missense variants and benign variants, and we developed an easy-to-use-tool to perform variant prediction benchmarks based on annotated VCF files (VETA). Our results show that tool performance increases after HCM-specific calibration of thresholds. After excluding potential biases due to circularity type I issues, we identified ClinPred, MISTIC, FATHMM, MPC and MetaLR as the five best performer tools in discriminating HCM-associated variants. We propose combining these tools in order to prioritize unknown HCM missense variants that should be closely followed-up in the clinic.
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Affiliation(s)
- Pedro Barbosa
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Marta Ribeiro
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- *Correspondence: Maria Carmo-Fonseca
| | - Alcides Fonseca
- LASIGE, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
- GenoMed - Diagnósticos de Medicina Molecular, Lisboa, Portugal
- Alcides Fonseca
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9
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Marín T, Dulcey AE, Campos F, de la Fuente C, Acuña M, Castro J, Pinto C, Yañez MJ, Cortez C, McGrath DW, Sáez PJ, Gorshkov K, Zheng W, Southall N, Carmo-Fonseca M, Marugán J, Alvarez AR, Zanlungo S. c-Abl Activation Linked to Autophagy-Lysosomal Dysfunction Contributes to Neurological Impairment in Niemann-Pick Type A Disease. Front Cell Dev Biol 2022; 10:844297. [PMID: 35399514 PMCID: PMC8985125 DOI: 10.3389/fcell.2022.844297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/25/2022] [Indexed: 12/05/2022] Open
Abstract
Niemann-Pick type A (NPA) disease is a fatal lysosomal neurodegenerative disorder caused by the deficiency in acid sphingomyelinase (ASM) activity. NPA patients present severe and progressive neurodegeneration starting at an early age. Currently, there is no effective treatment for this disease and NPA patients die between 2 and 3 years of age. NPA is characterized by an accumulation of sphingomyelin in lysosomes and dysfunction in the autophagy-lysosomal pathway. Recent studies show that c-Abl tyrosine kinase activity downregulates autophagy and the lysosomal pathway. Interestingly, this kinase is also activated in other lysosomal neurodegenerative disorders. Here, we describe that c-Abl activation contributes to the mechanisms of neuronal damage and death in NPA disease. Our data demonstrate that: 1) c-Abl is activated in-vitro as well as in-vivo NPA models; 2) imatinib, a clinical c-Abl inhibitor, reduces autophagy-lysosomal pathway alterations, restores autophagy flux, and lowers sphingomyelin accumulation in NPA patient fibroblasts and NPA neuronal models and 3) chronic treatment with nilotinib and neurotinib, two c-Abl inhibitors with differences in blood-brain barrier penetrance and target binding mode, show further benefits. While nilotinib treatment reduces neuronal death in the cerebellum and improves locomotor functions, neurotinib decreases glial activation, neuronal disorganization, and loss in hippocampus and cortex, as well as the cognitive decline of NPA mice. Our results support the participation of c-Abl signaling in NPA neurodegeneration and autophagy-lysosomal alterations, supporting the potential use of c-Abl inhibitors for the clinical treatment of NPA patients.
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Affiliation(s)
- Tamara Marín
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrés E. Dulcey
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Fabián Campos
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Catalina de la Fuente
- Laboratory of Cell Signaling, Center for Aging and Regeneration (CARE), Millennium Institute on Immunology and Immunotherapy (IMII), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Mariana Acuña
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Juan Castro
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudio Pinto
- Laboratory of Cell Signaling, Center for Aging and Regeneration (CARE), Millennium Institute on Immunology and Immunotherapy (IMII), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - María José Yañez
- School of Medical Technology, Health Sciences Faculty, Universidad San Sebastián, Santiago, Chile
| | - Cristian Cortez
- Center for Genomics and Bioinformatics, Faculty of Science, Universidad Mayor, Santiago, Chile
| | - David W. McGrath
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Pablo J. Sáez
- Cell Communication and Migration Laboratory, Institute of Biochemistry and Molecular Cell Biology, Center for Experimental Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirill Gorshkov
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Wei Zheng
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Noel Southall
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular Joȧo Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Juan Marugán
- Early Translation Branch, National Center for Advancing Translational Sciences (NCATS), NIH, Rockville, MD, United States
- *Correspondence: Juan Marugán, ; Alejandra R. Alvarez, ; Silvana Zanlungo,
| | - Alejandra R. Alvarez
- Laboratory of Cell Signaling, Center for Aging and Regeneration (CARE), Millennium Institute on Immunology and Immunotherapy (IMII), Department of Cellular and Molecular Biology, Biological Sciences Faculty, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Juan Marugán, ; Alejandra R. Alvarez, ; Silvana Zanlungo,
| | - Silvana Zanlungo
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
- *Correspondence: Juan Marugán, ; Alejandra R. Alvarez, ; Silvana Zanlungo,
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10
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Tammer L, Hameiri O, Keydar I, Roy VR, Ashkenazy-Titelman A, Custódio N, Sason I, Shayevitch R, Rodríguez-Vaello V, Rino J, Lev Maor G, Leader Y, Khair D, Aiden EL, Elkon R, Irimia M, Sharan R, Shav-Tal Y, Carmo-Fonseca M, Ast G. Gene architecture directs splicing outcome in separate nuclear spatial regions. Mol Cell 2022; 82:1021-1034.e8. [PMID: 35182478 DOI: 10.1016/j.molcel.2022.02.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 04/12/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 12/13/2022]
Abstract
How the splicing machinery defines exons or introns as the spliced unit has remained a puzzle for 30 years. Here, we demonstrate that peripheral and central regions of the nucleus harbor genes with two distinct exon-intron GC content architectures that differ in the splicing outcome. Genes with low GC content exons, flanked by long introns with lower GC content, are localized in the periphery, and the exons are defined as the spliced unit. Alternative splicing of these genes results in exon skipping. In contrast, the nuclear center contains genes with a high GC content in the exons and short flanking introns. Most splicing of these genes occurs via intron definition, and aberrant splicing leads to intron retention. We demonstrate that the nuclear periphery and center generate different environments for the regulation of alternative splicing and that two sets of splicing factors form discrete regulatory subnetworks for the two gene architectures. Our study connects 3D genome organization and splicing, thus demonstrating that exon and intron definition modes of splicing occur in different nuclear regions.
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Affiliation(s)
- Luna Tammer
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ofir Hameiri
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Ifat Keydar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Vanessa Rachel Roy
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Asaf Ashkenazy-Titelman
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Itay Sason
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ronna Shayevitch
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Victoria Rodríguez-Vaello
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain, ICREA, Barcelona, Spain
| | - José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Galit Lev Maor
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Yodfat Leader
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Doha Khair
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain. Universitat Pompeu Fabra (UPF), Barcelona, Spain, ICREA, Barcelona, Spain
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv 69978, Israel.
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11
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Abstract
Martinez et al. (2022) uncovered a novel function for the most abundant modified nucleoside in RNA. The study shows that uridines at splice sites and splicing regulatory motifs in the pre-mRNA may be converted to pseudouridine during transcription and impact splicing decisions.
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Affiliation(s)
- Rui Sousa-Luís
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal.
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12
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Prudêncio P, Savisaar R, Rebelo K, Martinho RG, Carmo-Fonseca M. Transcription and splicing dynamics during early Drosophila development. RNA 2022; 28:139-161. [PMID: 34667107 PMCID: PMC8906543 DOI: 10.1261/rna.078933.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/23/2021] [Indexed: 05/03/2023]
Abstract
Widespread cotranscriptional splicing has been demonstrated from yeast to human. However, most studies to date addressing the kinetics of splicing relative to transcription used either Saccharomyces cerevisiae or metazoan cultured cell lines. Here, we adapted native elongating transcript sequencing technology (NET-seq) to measure cotranscriptional splicing dynamics during the early developmental stages of Drosophila melanogaster embryos. Our results reveal the position of RNA polymerase II (Pol II) when both canonical and recursive splicing occur. We found heterogeneity in splicing dynamics, with some RNAs spliced immediately after intron transcription, whereas for other transcripts no splicing was observed over the first 100 nt of the downstream exon. Introns that show splicing completion before Pol II has reached the end of the downstream exon are necessarily intron-defined. We studied the splicing dynamics of both nascent pre-mRNAs transcribed in the early embryo, which have few and short introns, as well as pre-mRNAs transcribed later in embryonic development, which contain multiple long introns. As expected, we found a relationship between the proportion of spliced reads and intron size. However, intron definition was observed at all intron sizes. We further observed that genes transcribed in the early embryo tend to be isolated in the genome whereas genes transcribed later are often overlapped by a neighboring convergent gene. In isolated genes, transcription termination occurred soon after the polyadenylation site, while in overlapped genes, Pol II persisted associated with the DNA template after cleavage and polyadenylation of the nascent transcript. Taken together, our data unravel novel dynamic features of Pol II transcription and splicing in the developing Drosophila embryo.
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Affiliation(s)
- Pedro Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Kenny Rebelo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Rui Gonçalo Martinho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Medical Sciences and Institute for Biomedicine (iBiMED), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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13
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Custódio N, Savisaar R, Carvalho C, Bak-Gordon P, Ribeiro MI, Tavares J, Nunes PB, Peixoto A, Pinto C, Escudeiro C, Teixeira MR, Carmo-Fonseca M. Expression Profiling in Ovarian Cancer Reveals Coordinated Regulation of BRCA1/2 and Homologous Recombination Genes. Biomedicines 2022; 10:biomedicines10020199. [PMID: 35203410 PMCID: PMC8868827 DOI: 10.3390/biomedicines10020199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Predictive biomarkers are crucial in clarifying the best strategy to use poly(ADP-ribose) polymerase inhibitors (PARPi) for the greatest benefit to ovarian cancer patients. PARPi are specifically lethal to cancer cells that cannot repair DNA damage by homologous recombination (HR), and HR deficiency is frequently associated with BRCA1/2 mutations. Genetic tests for BRCA1/2 mutations are currently used in the clinic, but results can be inconclusive due to the high prevalence of rare DNA sequence variants of unknown significance. Most tests also fail to detect epigenetic modifications and mutations located deep within introns that may alter the mRNA. The aim of this study was to investigate whether quantitation of BRCA1/2 mRNAs in ovarian cancer can provide information beyond the DNA tests. Using the nCounter assay from NanoString Technologies, we analyzed RNA isolated from 38 ovarian cancer specimens and 11 normal fallopian tube samples. We found that BRCA1/2 expression was highly variable among tumors. We further observed that tumors with lower levels of BRCA1/2 mRNA showed downregulated expression of 12 additional HR genes. Analysis of 299 ovarian cancer samples from The Cancer Genome Atlas (TCGA) confirmed the coordinated expression of BRCA1/2 and HR genes. To facilitate the routine analysis of BRCA1/2 mRNA in the clinical setting, we developed a targeted droplet digital PCR approach that can be used with FFPE samples. In conclusion, this study underscores the potential clinical benefit of measuring mRNA levels in tumors when BRCA1/2 DNA tests are negative or inconclusive.
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Affiliation(s)
- Noélia Custódio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
- Correspondence: ; Tel.: +35-121-799-9411
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Célia Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Maria I. Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
| | - Joana Tavares
- Serviço de Anatomia Patológica, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-028 Lisboa, Portugal;
| | - Paula B. Nunes
- Hospital CUF Descobertas, 1998-018 Lisboa, Portugal;
- Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Peixoto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Pinto
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Carla Escudeiro
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Manuel R. Teixeira
- Serviço de Genética, Instituto Português de Oncologia do Porto Francisco Gentil, 4200-072 Porto, Portugal; (A.P.); (C.P.); (C.E.); (M.R.T.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal; (R.S.); (C.C.); (P.B.-G.); (M.I.R.); (M.C.-F.)
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14
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Fernández-Alvarez AJ, Thomas MG, Pascual ML, Habif M, Pimentel J, Corbat AA, Pessoa JP, La Spina PE, Boscaglia L, Plessis A, Carmo-Fonseca M, Grecco HE, Casado M, Boccaccio GL. Smaug1 membrane-less organelles respond to AMPK/mTOR and affect mitochondrial function‡. J Cell Sci 2021; 135:273619. [PMID: 34859817 DOI: 10.1242/jcs.253591] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 09/09/2020] [Accepted: 11/15/2021] [Indexed: 11/20/2022] Open
Abstract
Smaug is a conserved translational regulator that binds numerous mRNAs, including nuclear transcripts that encode mitochondrial enzymes. Smaug orthologs form cytosolic membrane-less organelles (MLOs) in several organisms and cell types. We have performed single-molecule FISH assays that revealed that SDHB and UQCRC1 mRNAs associate with Smaug1 bodies in U2OS cells. Loss of function of Smaug1 and Smaug2 affected both mitochondrial respiration and morphology of the mitochondrial network. Phenotype rescue by Smaug1 transfection depends on the presence of its RNA binding domain. Moreover, we identified specific Smaug1 domains involved in MLO formation, and found that impaired Smaug1 MLO condensation correlates with mitochondrial defects. Mitochondrial Complex I inhibition by rotenone -but not strong mitochondrial uncoupling by CCCP- rapidly induced Smaug1 MLOs dissolution. Metformin and rapamycin elicited similar effects, which were blocked by pharmacological inhibition of AMPK. Finally, we found that Smaug1 MLO dissolution weakens the interaction with target mRNAs, thus enabling their release. We propose that mitochondrial respiration and the AMPK/mTOR balance controls the condensation and dissolution of Smaug1 MLOs, thus regulating nuclear mRNAs that encode key mitochondrial proteins.
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Affiliation(s)
- Ana J Fernández-Alvarez
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - María Gabriela Thomas
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Malena L Pascual
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Martín Habif
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Jerónimo Pimentel
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | - Agustín A Corbat
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - João P Pessoa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Pablo E La Spina
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina
| | | | - Anne Plessis
- Institut Jacques Monod, CNRS, UMR 7592, University Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Hernán E Grecco
- Department of Physics, Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, and IFIBA, CONICET, C1428EHA Buenos Aires, Argentina
| | - Marta Casado
- Instituto de Biomedicina de Valencia, IBV-CSIC, Valencia 46010, Spain, and Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Madrid 28029, Spain
| | - Graciela L Boccaccio
- Fundación Instituto Leloir (FIL).,Instituto de Investigaciones Bioquímicas de Buenos Aires (IIBBA) - Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), C1405BWE Buenos Aires, Argentina.,Department of Molecular and Cellular Biology and Physiology (FBMyC), Facultad de Ciencias Exactas y Naturales (FCEN), University of Buenos Aires, C1428EHA Buenos Aires, Argentina
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15
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Guo K, Shao C, Han L, Liu H, Ma Z, Yang Y, Feng Y, Pan M, Santarpia M, Carmo-Fonseca M, Silveira C, Lee KY, Han J, Li X, Yan X. Detection of epidermal growth factor receptor ( EGFR) mutations from preoperative circulating tumor DNA (ctDNA) as a prognostic predictor for stage I-III non-small cell lung cancer (NSCLC) patients with baseline tissue EGFR mutations. Transl Lung Cancer Res 2021; 10:3213-3225. [PMID: 34430359 PMCID: PMC8350110 DOI: 10.21037/tlcr-21-530] [Citation(s) in RCA: 4] [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: 04/22/2021] [Accepted: 07/19/2021] [Indexed: 12/24/2022]
Abstract
Background Plasma circulating tumor DNA (ctDNA) may be a surrogate, minimally invasive approach to tissue-based epidermal growth factor receptor (EGFR) mutation detection in non-small cell lung cancer (NSCLC) patients. However, the predictive ability of preoperative ctDNA EGFR mutation test on long-term postoperative survival and tumor metastasis development has not been extensively investigated. Methods Stage I–III NSCLC patients with tissue EGFR mutations were enrolled in this study (n=174). The ctDNA EGFR mutations were identified in paired preoperative plasma samples. EGFR mutation testing was performed using Scorpion amplified refractory mutation system (ARMS) technology. The correlation between ctDNA EGFR mutation status and clinicopathologic parameters was analyzed. By combining at least 5 years of follow-up data, we assessed the relationship between ctDNA EGFR mutation status and disease-free survival (DFS) and overall survival (OS). Results Plasma-based ctDNA EGFR mutations were detected in 27 patients. The mutation types were exactly matched with those in paired tissue samples. Blood test sensitivity was closely associated with N stages, tumor-node-metastasis (TNM) stages and tumor differentiation (P<0.001). The overall 5-year survival rate was 18.5% versus 76.9% for ctDNA EGFR mutation-positive and ctDNA EGFR mutation-negative patients, respectively. For patients with ctDNA EGFR mutation positive, the median OS and DFS were 29.00±2.55 and 19.00±2.50 months, respectively, which were both significantly better than those in the ctDNA EGFR mutation-negative subgroup (P<0.001). ctDNA EGFR mutation was an independent risk factor of OS and DFS [hazard ratio (HR) 3.289, 95% confidence interval (CI), 1.816–5.956, P<0.001; HR, 4.860, 95% CI, 2.660–8.880, P<0.001]. For stage III patients with exon 19 deletion or L858R mutations in both tissue and plasma samples, tyrosine kinase inhibitor (TKI) therapy showed significantly better OS (P=0.025) and possible DFS benefit (P=0.060) than did chemotherapy. Conclusions EGFR mutation testing using the Scorpion-ARMS method in preoperative plasma could be a strong predictor for postoperative survival and metastasis of NSCLC patients. Thus, the subset of this population may be benefit from targeted strategies and management.
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Affiliation(s)
- Kai Guo
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China.,Department of Thoracic Surgery, Shaanxi Provincial People's Hospital, Xi'an, China.,The Third Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Changjian Shao
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Lu Han
- Department of Ultrasound, Xi'an Central Hospital, Xi'an Jiaotong University, Xi'an, China
| | - Honggang Liu
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Zhiqiang Ma
- Department of Oncology, Chinese PLA General Hospital, Beijing, China
| | - Yang Yang
- Department of Neurosurgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yingtong Feng
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Minghong Pan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Patology "G. Barresi", University of Messina, Messina, Italy
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon Medical School, Lisbon, Portugal
| | | | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul, Korea
| | - Jing Han
- Department of Ophthalmology, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Xiaofei Li
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Xiaolong Yan
- Department of Thoracic Surgery, Tangdu Hospital, Air Force Medical University, Xi'an, China
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16
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Silva TP, Sousa-Luís R, Fernandes TG, Bekman EP, Rodrigues CAV, Vaz SH, Moreira LM, Hashimura Y, Jung S, Lee B, Carmo-Fonseca M, Cabral JMS. Transcriptome profiling of human pluripotent stem cell-derived cerebellar organoids reveals faster commitment under dynamic conditions. Biotechnol Bioeng 2021; 118:2781-2803. [PMID: 33871054 DOI: 10.1002/bit.27797] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 12/29/2020] [Revised: 03/30/2021] [Accepted: 04/14/2021] [Indexed: 12/14/2022]
Abstract
Human-induced pluripotent stem cells (iPSCs) have great potential for disease modeling. However, generating iPSC-derived models to study brain diseases remains a challenge. In particular, the ability to recapitulate cerebellar development in vitro is still limited. We presented a reproducible and scalable production of cerebellar organoids by using the novel single-use Vertical-Wheel bioreactors, in which functional cerebellar neurons were obtained. Here, we evaluate the global gene expression profiles by RNA sequencing (RNA-seq) across cerebellar differentiation, demonstrating a faster cerebellar commitment in this novel dynamic differentiation protocol. Furthermore, transcriptomic profiles suggest a significant enrichment of extracellular matrix (ECM) in dynamic-derived cerebellar organoids, which can better mimic the neural microenvironment and support a consistent neuronal network. Thus, an efficient generation of organoids with cerebellar identity was achieved for the first time in a continuous process using a dynamic system without the need of organoids encapsulation in ECM-based hydrogels, allowing the possibility of large-scale production and application in high-throughput processes. The presence of factors that favors angiogenesis onset was also detected in dynamic conditions, which can enhance functional maturation of cerebellar organoids. We anticipate that large-scale production of cerebellar organoids may help developing models for drug screening, toxicological tests, and studying pathological pathways involved in cerebellar degeneration.
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Affiliation(s)
- Teresa P Silva
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Rui Sousa-Luís
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Tiago G Fernandes
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Evguenia P Bekman
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos A V Rodrigues
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Sandra H Vaz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto de Farmacologia e Neurociências, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal, Portugal
| | - Leonilde M Moreira
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | | | - Brian Lee
- PBS Biotech, Camarillo, California, USA
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Joaquim M S Cabral
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
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17
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Silva TP, Pereira CA, Raposo AC, Oliveira AR, Arez M, Cabral JMS, Milagre I, Carmo-Fonseca M, Rocha STD. Generation and characterization of induced pluripotent stem cells heterozygous for the Portuguese BRCA2 founder mutation. Stem Cell Res 2021; 53:102364. [PMID: 34087993 DOI: 10.1016/j.scr.2021.102364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/05/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022] Open
Abstract
Women who inherit heterozygous mutations in the BRCA2 gene have an increased risk of developing cancer, mainly breast and ovarian tumors. A particular BRCA2 mutation (c.156_157insAlu) is exclusively found in families of Portuguese ancestry and is present in approximately 30% of all Portuguese families with hereditary breast and ovarian cancers. We report the generation and characterization of the first iPSC line from a female donor harboring the Portuguese BRCA2 founder mutation. Skin fibroblasts were reprogrammed using a non-integrative Sendai virus. These iPSCs are a valuable tool to study the origin of BRCA2-associated cancer in its earliest phases.
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Affiliation(s)
- Teresa P Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | | | - Ana Cláudia Raposo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Ana Rita Oliveira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Maria Arez
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joaquim M S Cabral
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Inês Milagre
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Simão Teixeira da Rocha
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Portugal.
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Sousa-Luís R, Dujardin G, Zukher I, Kimura H, Weldon C, Carmo-Fonseca M, Proudfoot NJ, Nojima T. POINT technology illuminates the processing of polymerase-associated intact nascent transcripts. Mol Cell 2021; 81:1935-1950.e6. [PMID: 33735606 PMCID: PMC8122139 DOI: 10.1016/j.molcel.2021.02.034] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/21/2020] [Accepted: 02/24/2021] [Indexed: 12/29/2022]
Abstract
Mammalian chromatin is the site of both RNA polymerase II (Pol II) transcription and coupled RNA processing. However, molecular details of such co-transcriptional mechanisms remain obscure, partly because of technical limitations in purifying authentic nascent transcripts. We present a new approach to characterize nascent RNA, called polymerase intact nascent transcript (POINT) technology. This three-pronged methodology maps nascent RNA 5′ ends (POINT-5), establishes the kinetics of co-transcriptional splicing patterns (POINT-nano), and profiles whole transcription units (POINT-seq). In particular, we show by depletion of the nuclear exonuclease Xrn2 that this activity acts selectively on cleaved 5′ P-RNA at polyadenylation sites. Furthermore, POINT-nano reveals that co-transcriptional splicing either occurs immediately after splice site transcription or is delayed until Pol II transcribes downstream sequences. Finally, we connect RNA cleavage and splicing with either premature or full-length transcript termination. We anticipate that POINT technology will afford full dissection of the complexity of co-transcriptional RNA processing. POINT methodology dissects intact nascent RNA processing Specificity of Xrn2 exonuclease in co-transcriptional RNA degradation Splicing suppresses Xrn2-dependent premature termination Different kinetic classes of co-transcriptional splicing in human genes
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Affiliation(s)
- Rui Sousa-Luís
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal
| | - Gwendal Dujardin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Inna Zukher
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Hiroshi Kimura
- Cell Biology Centre, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Carika Weldon
- Wellcome Trust Center for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisbon, Portugal.
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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19
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Silveira C, Sousa AC, Janeiro A, Malveiro S, Teixeira E, Brysch E, Pantarotto M, Felizardo M, Madureira R, Nogueira F, Guimarães C, Matos C, Canário D, Bruges-Armas J, Carmo-Fonseca M. Detection and quantification of EGFR T790M mutation in liquid biopsies by droplet digital PCR. Transl Lung Cancer Res 2021; 10:1200-1208. [PMID: 33889502 PMCID: PMC8044487 DOI: 10.21037/tlcr-20-1010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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] [Indexed: 01/05/2023]
Abstract
Background Liquid biopsy allows the identification of targetable cancer mutations in a minimally invasive manner. In patients with advanced non-small cell lung cancer (NSCLC), droplet digital PCR (ddPCR) is increasingly used to genotype the epidermal growth factor receptor (EGFR) gene in circulating cell-free DNA (cfDNA). However, the sensitivity of this method is still under debate. The aim of this study was to implement and assess the performance of a ddPCR assay for detecting the EGFR T790M mutation in liquid biopsies. Methods A ddPCR assay was optimized to detect the EGFR T790M mutation in plasma samples from 77 patients with NSCLC in progression. Results Our ddPCR assay enabled the detection and quantification of the EGFR T790M mutation at cfDNA allele frequency as low as 0.5%. The mutation was detected in 40 plasma samples, corresponding to a positivity rate of 52%. The number of mutant molecules per mL of plasma ranged from 1 to 6,000. A re-biopsy was analyzed for 12 patients that had a negative plasma test and the mutation was detected in 2 cases. A second liquid biopsy was performed for 6 patients and the mutation was detected in 3 cases. Conclusions This study highlights the value of ddPCR to detect and quantify the EGFR T790M mutation in liquid biopsies in a real-world clinical setting. Our results suggest that repeated ddPCR tests in cfDNA may obviate tissue re-biopsy in patients unable to provide a tumor tissue sample suitable for molecular analysis.
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Affiliation(s)
| | - Ana Carla Sousa
- GenoMed - Molecular Medicine Diagnostics, S.A., Lisbon, Portugal
| | - André Janeiro
- GenoMed - Molecular Medicine Diagnostics, S.A., Lisbon, Portugal
| | - Sara Malveiro
- GenoMed - Molecular Medicine Diagnostics, S.A., Lisbon, Portugal
| | | | - Eva Brysch
- Hospital Pulido Valente, Department of Pulmonary Oncology, Lisbon, Portugal
| | | | | | - Rosa Madureira
- Hospital Beatriz Ângelo, Department of Pathology, Lisbon, Portugal
| | | | - Cátia Guimarães
- Hospital Egas Moniz, Department of Pulmonology, Lisbon, Portugal
| | - Cristina Matos
- Hospital Egas Moniz, Department of Pulmonology, Lisbon, Portugal
| | - Dolores Canário
- Hospital Garcia de Orta, Department of Pulmonology, Almada, Portugal
| | - Jácome Bruges-Armas
- Hospital de Santo Espírito, Department of Specialized Service of Epidemiology and Molecular Biology (SEEBMO), Angra do Heroísmo, Azores, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, University of Lisbon Medical School, Lisbon, Portugal
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20
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Silva TP, Pereira CA, Oliveira AR, Raposo AC, Arez M, Cabral JMS, Milagre I, Carmo-Fonseca M, da Rocha ST. Generation and characterization of induced pluripotent stem cells from a family carrying the BRCA1 mutation c.3612delA. Stem Cell Res 2021; 52:102242. [PMID: 33631522 DOI: 10.1016/j.scr.2021.102242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/02/2021] [Indexed: 10/22/2022] Open
Abstract
How BRCA1 germline mutations predispose to cancer remains poorly understood. Induced pluripotent stem cells (iPSCs) represent an emerging model to investigate the molecular mechanisms underlying malignant transformation in primary cells from individuals who are carriers of deleterious mutations in the BRCA1 gene. Here we report the generation and characterization of iPSC lines from a female donor harboring a germline c.3612delA mutation in the BRCA1 gene and her daughter who does not carry the mutation. Skin fibroblasts were reprogrammed using non-integrative Sendai virus and characterized for their pluripotent properties. These iPSCs are a valuable cellular model for personalized pre-clinical research in the context of BRCA1 mutant hereditary cancers.
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Affiliation(s)
- Teresa P Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | | | - Ana Rita Oliveira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Ana Cláudia Raposo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Maria Arez
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Joaquim M S Cabral
- Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal
| | - Inês Milagre
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal
| | - Simão T da Rocha
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Portugal; Departamento de Bioengenharia e Instituto de Bioengenharia e Biociências, Instituto Superior Técnico, Universidade de Lisboa, Portugal.
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21
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Silva TP, Fernandes TG, Nogueira DES, Rodrigues CAV, Bekman EP, Hashimura Y, Jung S, Lee B, Carmo-Fonseca M, Cabral JMS. Scalable Generation of Mature Cerebellar Organoids from Human Pluripotent Stem Cells and Characterization by Immunostaining. J Vis Exp 2020. [PMID: 32597849 DOI: 10.3791/61143] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The cerebellum plays a critical role in the maintenance of balance and motor coordination, and a functional defect in different cerebellar neurons can trigger cerebellar dysfunction. Most of the current knowledge about disease-related neuronal phenotypes is based on postmortem tissues, which makes understanding of disease progression and development difficult. Animal models and immortalized cell lines have also been used as models for neurodegenerative disorders. However, they do not fully recapitulate human disease. Human induced pluripotent stem cells (iPSCs) have great potential for disease modeling and provide a valuable source for regenerative approaches. In recent years, the generation of cerebral organoids from patient-derived iPSCs improved the prospects for neurodegenerative disease modeling. However, protocols that produce large numbers of organoids and a high yield of mature neurons in 3D culture systems are lacking. The protocol presented is a new approach for reproducible and scalable generation of human iPSC-derived organoids under chemically-defined conditions using scalable single-use bioreactors, in which organoids acquire cerebellar identity. The generated organoids are characterized by the expression of specific markers at both mRNA and protein level. The analysis of specific groups of proteins allows the detection of different cerebellar cell populations, whose localization is important for the evaluation of organoid structure. Organoid cryosectioning and further immunostaining of organoid slices are used to evaluate the presence of specific cerebellar cell populations and their spatial organization.
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Affiliation(s)
- Teresa P Silva
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa
| | - Tiago G Fernandes
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa
| | - Diogo E S Nogueira
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa
| | - Carlos A V Rodrigues
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa
| | - Evguenia P Bekman
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa; Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa; The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Universidade de Lisboa
| | | | | | - Brian Lee
- PBS Biotech, Inc, Camarillo, CA, USA
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa
| | - Joaquim M S Cabral
- iBB - Institute for Bioengineering and Biosciences and Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa;
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22
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Prudêncio P, Rebelo K, Grosso AR, Martinho RG, Carmo-Fonseca M. Analysis of Mammalian Native Elongating Transcript sequencing (mNET-seq) high-throughput data. Methods 2020; 178:89-95. [PMID: 31493517 DOI: 10.1016/j.ymeth.2019.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 05/03/2019] [Revised: 07/17/2019] [Accepted: 09/01/2019] [Indexed: 11/28/2022] Open
Abstract
Mammalian Native Elongating Transcript sequencing (mNET-seq) is a recently developed technique that generates genome-wide profiles of nascent transcripts associated with RNA polymerase II (Pol II) elongation complexes. The ternary transcription complexes formed by Pol II, DNA template and nascent RNA are first isolated, without crosslinking, by immunoprecipitation with antibodies that specifically recognize the different phosphorylation states of the polymerase large subunit C-terminal domain (CTD). The coordinate of the 3' end of the RNA in the complexes is then identified by high-throughput sequencing. The main advantage of mNET-seq is that it provides global, bidirectional maps of Pol II CTD phosphorylation-specific nascent transcripts and coupled RNA processing at single nucleotide resolution. Here we describe the general pipeline to prepare and analyse high-throughput data from mNET-seq experiments.
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Affiliation(s)
- Pedro Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Center for Biomedical Research, Universidade do Algarve, Faro, Portugal.
| | - Kenny Rebelo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana Rita Grosso
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Rui Gonçalo Martinho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal; Center for Biomedical Research, Universidade do Algarve, Faro, Portugal; iBiMED, Departamento de Ciências Médicas, Universidade de Aveiro, Aveiro, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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23
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Robinson EL, Pedrosa da Costa Gomes C, Potočnjak I, Hellemans J, Betsou F, de Gonzalo-Calvo D, Stoll M, Birhan Yilmaz M, Ágg B, Beis D, Carmo-Fonseca M, Enguita FJ, Dogan S, Tuna BG, Schroen B, Ammerlaan W, Kuster GM, Carpusca I, Pedrazzini T, Emanueli C, Martelli F, Devaux Y. A Year in the Life of the EU-CardioRNA COST Action: CA17129 Catalysing Transcriptomics Research in Cardiovascular Disease. Noncoding RNA 2020; 6:E17. [PMID: 32443579 PMCID: PMC7345156 DOI: 10.3390/ncrna6020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
The EU-CardioRNA Cooperation in Science and Technology (COST) Action is a European-wide consortium established in 2018 with 31 European country members and four associate member countries to build bridges between translational researchers from academia and industry who conduct research on non-coding RNAs, cardiovascular diseases and similar research areas. EU-CardioRNA comprises four core working groups (WG1-4). In the first year since its launch, EU-CardioRNA met biannually to exchange and discuss recent findings in related fields of scientific research, with scientific sessions broadly divided up according to WG. These meetings are also an opportunity to establish interdisciplinary discussion groups, brainstorm ideas and make plans to apply for joint research grants and conduct other scientific activities, including knowledge transfer. Following its launch in Brussels in 2018, three WG meetings have taken place. The first of these in Lisbon, Portugal, the second in Istanbul, Turkey, and the most recent in Maastricht, The Netherlands. Each meeting includes a scientific session from each WG. This meeting report briefly describes the highlights and key take-home messages from each WG session in this first successful year of the EU-CardioRNA COST Action.
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Affiliation(s)
- Emma Louise Robinson
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | | | - Ines Potočnjak
- Institute for Clinical Medical Research and Education, University Hospital Centre Sisters of Charity, Zagreb 10 000, Croatia;
| | | | - Fay Betsou
- Integrated BioBank of Luxembourg, L-3555 Dudelange, Luxembourg; (F.B.); (W.A.)
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, 25198 Lleida, Spain;
| | - Monika Stoll
- Institute of Human Genetics, Genetic Epidemiology, University of Münster, 48149 Münster, Germany;
| | - Mehmet Birhan Yilmaz
- Department of Cardiology, Faculty of Medicine, Dokuz Eylül University, İzmir 35330, Turkey;
| | - Bence Ágg
- Department of Pharmacology and Pharmacotherapy, Semmelweis University, H-1085 Budapest, Hungary;
- Pharmahungary Group, H-6722 Szeged, Hungary
| | - Dimitris Beis
- Centre for Clinical, Experimental Surgery, & Translational Research, Biomedical Research Foundation, Academy of Athens, 115 27 Athens, Greece;
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.C.-F.); (F.J.E.)
| | - Francisco J. Enguita
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (M.C.-F.); (F.J.E.)
| | - Soner Dogan
- Department of Medical Biology, School of Medicine, Yeditepe University, Istanbul 34755, Turkey;
| | - Bilge G. Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul 34755, Turkey
| | - Blanche Schroen
- Department of Cardiology, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, 6229 ER Maastricht, The Netherlands;
| | - Wim Ammerlaan
- Integrated BioBank of Luxembourg, L-3555 Dudelange, Luxembourg; (F.B.); (W.A.)
| | - Gabriela M. Kuster
- Department of Biomedicine, University Hospital Basel and University of Basel, 4031 Basel, Switzerland;
| | - Irina Carpusca
- Cardiovascular Research Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (C.P.d.C.G.); (I.C.)
| | - Thierry Pedrazzini
- Department of Medicine, University of Lausanne Medical School, 1005 Lausanne, Switzerland;
| | - Costanza Emanueli
- National Heart and Lung Institute, Imperial College London, London SW3 6LY, UK;
| | - Fabio Martelli
- Molecular Cardiology Laboratory, Policlinico San Donato IRCCS, San Donato Milanese, 20097 Milan, Italy;
| | - Yvan Devaux
- Cardiovascular Research Unit, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg; (C.P.d.C.G.); (I.C.)
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24
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Lopes LR, Barbosa P, Torrado M, Quinn E, Merino A, Ochoa JP, Jager J, Futema M, Carmo-Fonseca M, Monserrat L, Syrris P, Elliott PM. Cryptic Splice-Altering Variants in MYBPC3 Are a Prevalent Cause of Hypertrophic Cardiomyopathy. Circ Genom Precis Med 2020; 13:e002905. [PMID: 32396390 DOI: 10.1161/circgen.120.002905] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Luis R Lopes
- Inherited Cardiovascular Disease Unit, St Bartholomew's Hospital, Barts Health NHS Trust (L.R.L., E.Q., P.M.E.).,UCL Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, United Kingdom (L.R.L., J.J., M.F., P.S., P.M.E.).,European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART; http://guardheart.ern-net.eu/) (L.R.L., P.M.E.)
| | - Pedro Barbosa
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina (P.B., M.C.-F.), Universidade de Lisboa, Portugal.,LASIGE, Faculdade de Ciências (P.B.), Universidade de Lisboa, Portugal
| | - Mario Torrado
- Institute of Health Sciences, University of A Coruña (M.T.)
| | - Ellie Quinn
- Inherited Cardiovascular Disease Unit, St Bartholomew's Hospital, Barts Health NHS Trust (L.R.L., E.Q., P.M.E.)
| | - Ana Merino
- Cardiology Department, University Hospital of Burgos (A.M.)
| | - Juan Pablo Ochoa
- Cardiology Department, Health in Code, A Coruña, Spain (J.P.O., L.M.)
| | - Joanna Jager
- UCL Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, United Kingdom (L.R.L., J.J., M.F., P.S., P.M.E.)
| | - Marta Futema
- UCL Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, United Kingdom (L.R.L., J.J., M.F., P.S., P.M.E.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina (P.B., M.C.-F.), Universidade de Lisboa, Portugal
| | - Lorenzo Monserrat
- Cardiology Department, Health in Code, A Coruña, Spain (J.P.O., L.M.)
| | - Petros Syrris
- UCL Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, United Kingdom (L.R.L., J.J., M.F., P.S., P.M.E.)
| | - Perry M Elliott
- Inherited Cardiovascular Disease Unit, St Bartholomew's Hospital, Barts Health NHS Trust (L.R.L., E.Q., P.M.E.).,UCL Centre for Heart Muscle Disease, Institute of Cardiovascular Science, University College London, United Kingdom (L.R.L., J.J., M.F., P.S., P.M.E.).,European Reference Network for Rare and Low Prevalence Complex Diseases of the Heart (ERN GUARD-HEART; http://guardheart.ern-net.eu/) (L.R.L., P.M.E.)
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25
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Gomes AC, Barbosa PS, Coutinho A, Cruz I, Carmo-Fonseca M, Lopes LR. Whole-genome DNA sequencing: The key to detecting a sarcomeric mutation in a ‘false genotype-negative’ family with hypertrophic cardiomyopathy. Revista Portuguesa de Cardiologia (English Edition) 2020. [DOI: 10.1016/j.repce.2019.03.015] [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: 10/23/2022] Open
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Ribeiro M, Furtado M, Martins S, Carvalho T, Carmo-Fonseca M. RNA Splicing Defects in Hypertrophic Cardiomyopathy: Implications for Diagnosis and Therapy. Int J Mol Sci 2020; 21:ijms21041329. [PMID: 32079122 PMCID: PMC7072897 DOI: 10.3390/ijms21041329] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/10/2020] [Accepted: 02/13/2020] [Indexed: 12/27/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM), the most common inherited heart disease, is predominantly caused by mutations in genes that encode sarcomere-associated proteins. Effective gene-based diagnosis is critical for the accurate clinical management of patients and their family members. However, the introduction of high-throughput DNA sequencing approaches for clinical diagnostics has vastly expanded the number of variants of uncertain significance, leading to many inconclusive results that limit the clinical utility of genetic testing. More recently, developments in RNA analysis have been improving diagnostic outcomes by identifying new variants that interfere with splicing. This review summarizes recent discoveries of RNA mis-splicing in HCM and provides an overview of research that aims to apply the concept of RNA therapeutics to HCM.
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Affiliation(s)
- Marta Ribeiro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
- Department of Bioengineering and iBB–Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Sandra Martins
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Teresa Carvalho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal; (M.R.); (M.F.); (S.M.); (T.C.)
- Correspondence:
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Silva TP, Bekman EP, Fernandes TG, Vaz SH, Rodrigues CAV, Diogo MM, Cabral JMS, Carmo-Fonseca M. Maturation of Human Pluripotent Stem Cell-Derived Cerebellar Neurons in the Absence of Co-culture. Front Bioeng Biotechnol 2020; 8:70. [PMID: 32117945 PMCID: PMC7033648 DOI: 10.3389/fbioe.2020.00070] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 10/23/2019] [Accepted: 01/27/2020] [Indexed: 11/29/2022] Open
Abstract
The cerebellum plays a critical role in all vertebrates, and many neurological disorders are associated with cerebellum dysfunction. A major limitation in cerebellar research has been the lack of adequate disease models. As an alternative to animal models, cerebellar neurons differentiated from pluripotent stem cells have been used. However, previous studies only produced limited amounts of Purkinje cells. Moreover, in vitro generation of Purkinje cells required co-culture systems, which may introduce unknown components to the system. Here we describe a novel differentiation strategy that uses defined medium to generate Purkinje cells, granule cells, interneurons, and deep cerebellar nuclei projection neurons, that self-formed and differentiated into electrically active cells. Using a defined basal medium optimized for neuronal cell culture, we successfully promoted the differentiation of cerebellar precursors without the need for co-culturing. We anticipate that our findings may help developing better models for the study of cerebellar dysfunctions, while providing an advance toward the development of autologous replacement strategies for treating cerebellar degenerative diseases.
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Affiliation(s)
- Teresa P Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Evguenia P Bekman
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal.,The Discoveries Centre for Regenerative and Precision Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - Tiago G Fernandes
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra H Vaz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.,Instituto de Farmacologia e Neurociências, Faculdade de Medicina da Universidade de Lisboa, Lisbon, Portugal
| | - Carlos A V Rodrigues
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Margarida Diogo
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Joaquim M S Cabral
- Department of Bioengineering and Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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Abstract
Discoveries in the past decade have highlighted the potential of mRNA as a therapeutic target for cancer. Specifically, RNA sequencing revealed that, in addition to gene mutations, alterations in mRNA can contribute to the initiation and progression of cancer. Indeed, precursor mRNA processing, which includes the removal of introns by splicing and the formation of 3' ends by cleavage and polyadenylation, is frequently altered in tumours. These alterations result in numerous cancer-specific mRNAs that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumour-suppressor genes. Abnormally spliced and polyadenylated mRNAs are also associated with resistance to cancer treatment and, unexpectedly, certain cancers are highly sensitive to the pharmacological inhibition of splicing. This Review summarizes recent progress in our understanding of how splicing and polyadenylation are altered in cancer and highlights how this knowledge has been translated for drug discovery, resulting in the production of small molecules and oligonucleotides that modulate the spliceosome and are in clinical trials for the treatment of cancer.
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Affiliation(s)
- Joana Desterro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Português de Oncologia de Lisboa, Serviço de Hematologia, Lisboa, Portugal
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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Silva TP, Cotovio JP, Bekman E, Carmo-Fonseca M, Cabral JMS, Fernandes TG. Design Principles for Pluripotent Stem Cell-Derived Organoid Engineering. Stem Cells Int 2019; 2019:4508470. [PMID: 31149014 PMCID: PMC6501244 DOI: 10.1155/2019/4508470] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 10/18/2018] [Revised: 02/12/2019] [Accepted: 02/24/2019] [Indexed: 12/17/2022] Open
Abstract
Human morphogenesis is a complex process involving distinct microenvironmental and physical signals that are manipulated in space and time to give rise to complex tissues and organs. Advances in pluripotent stem cell (PSC) technology have promoted the in vitro recreation of processes involved in human morphogenesis. The development of organoids from human PSCs represents one reliable source for modeling a large spectrum of human disorders, as well as a promising approach for drug screening and toxicological tests. Based on the "self-organization" capacity of stem cells, different PSC-derived organoids have been created; however, considerable differences between in vitro-generated PSC-derived organoids and their in vivo counterparts have been reported. Advances in the bioengineering field have allowed the manipulation of different components, including cellular and noncellular factors, to better mimic the in vivo microenvironment. In this review, we focus on different examples of bioengineering approaches used to promote the self-organization of stem cells, including assembly, patterning, and morphogenesis in vitro, contributing to tissue-like structure formation.
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Affiliation(s)
- Teresa P. Silva
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal
| | - João P. Cotovio
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Universidade de Lisboa, Lisboa, Portugal
| | - Evguenia Bekman
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal
| | - Maria Carmo-Fonseca
- The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Universidade de Lisboa, Lisboa, Portugal
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av Prof Egas Moniz, Edificio Egas Moniz, 1649-028 Lisboa, Portugal
| | - Joaquim M. S. Cabral
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Universidade de Lisboa, Lisboa, Portugal
| | - Tiago G. Fernandes
- Department of Bioengineering and iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
- The Discoveries Centre for Regenerative and Precision Medicine, Lisbon Campus, Universidade de Lisboa, Lisboa, Portugal
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Mendes de Almeida R, Tavares J, Martins S, Carvalho T, Enguita FJ, Brito D, Carmo-Fonseca M, Lopes LR. Whole gene sequencing identifies deep-intronic variants with potential functional impact in patients with hypertrophic cardiomyopathy. PLoS One 2017; 12:e0182946. [PMID: 28797094 PMCID: PMC5552324 DOI: 10.1371/journal.pone.0182946] [Citation(s) in RCA: 21] [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: 04/10/2017] [Accepted: 07/27/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND High throughput sequencing technologies have revolutionized the identification of mutations responsible for genetic diseases such as hypertrophic cardiomyopathy (HCM). However, approximately 50% of individuals with a clinical diagnosis of HCM have no causal mutation identified. This may be due to the presence of pathogenic mutations located deep within the introns, which are not detected by conventional sequencing analysis restricted to exons and exon-intron boundaries. OBJECTIVE The aim of this study was to develop a whole-gene sequencing strategy to prioritize deep intronic variants that may play a role in HCM pathogenesis. METHODS AND RESULTS The full genomic DNA sequence of 26 genes previously associated with HCM was analysed in 16 unrelated patients. We identified likely pathogenic deep intronic variants in VCL, PRKAG2 and TTN genes. These variants, which are predicted to act through disruption of either splicing or transcription factor binding sites, are 3-fold more frequent in our cohort of probands than in normal European populations. Moreover, we found a patient that is compound heterozygous for a splice site mutation in MYBPC3 and the deep intronic VCL variant. Analysis of family members revealed that carriers of the MYBPC3 mutation alone do not manifest the disease, while family members that are compound heterozygous are clinically affected. CONCLUSION This study provides a framework for scrutinizing variation along the complete intronic sequence of HCM-associated genes and prioritizing candidates for mechanistic and functional analysis. Our data suggest that deep intronic variation contributes to HCM phenotype.
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Affiliation(s)
- Rita Mendes de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Joana Tavares
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Francisco J. Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Dulce Brito
- Departamento de Cardiologia, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Centro Académico de Medicina de Lisboa, Lisbon, Portugal
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Luís Rocha Lopes
- Centro Cardiovascular da Universidade de Lisboa, Lisbon, Portugal
- Institute of Cardiovascular Science, University College London, London, United Kingdom
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Carvalho T, Martins S, Rino J, Marinho S, Carmo-Fonseca M. Pharmacological inhibition of the spliceosome subunit SF3b triggers exon junction complex-independent nonsense-mediated decay. J Cell Sci 2017; 130:1519-1531. [PMID: 28302904 DOI: 10.1242/jcs.202200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 02/06/2017] [Accepted: 03/06/2017] [Indexed: 12/12/2022] Open
Abstract
Spliceostatin A, meayamycin, and pladienolide B are small molecules that target the SF3b subunit of the spliceosomal U2 small nuclear ribonucleoprotein (snRNP). These compounds are attracting much attention as tools to manipulate splicing and for use as potential anti-cancer drugs. We investigated the effects of these inhibitors on mRNA transport and stability in human cells. Upon splicing inhibition, unspliced pre-mRNAs accumulated in the nucleus, particularly within enlarged nuclear speckles. However, a small fraction of the pre-mRNA molecules were exported to the cytoplasm. We identified the export adaptor ALYREF as being associated with intron-containing transcripts and show its requirement for the nucleo-cytoplasmic transport of unspliced pre-mRNA. In contrast, the exon junction complex (EJC) core protein eIF4AIII failed to form a stable complex with intron-containing transcripts. Despite the absence of EJC, unspliced transcripts in the cytoplasm were degraded by nonsense-mediated decay (NMD), suggesting that unspliced transcripts are degraded by an EJC-independent NMD pathway. Collectively, our results indicate that although blocking the function of SF3b elicits a massive accumulation of unspliced pre-mRNAs in the nucleus, intron-containing transcripts can still bind the ALYREF export factor and be transported to the cytoplasm, where they trigger an alternative NMD pathway.
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Affiliation(s)
- Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sérgio Marinho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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32
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Sridhara SC, Carvalho S, Grosso AR, Gallego-Paez LM, Carmo-Fonseca M, de Almeida SF. Transcription Dynamics Prevent RNA-Mediated Genomic Instability through SRPK2-Dependent DDX23 Phosphorylation. Cell Rep 2017; 18:334-343. [DOI: 10.1016/j.celrep.2016.12.050] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/13/2016] [Accepted: 12/14/2016] [Indexed: 10/20/2022] Open
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Schlackow M, Nojima T, Gomes T, Dhir A, Carmo-Fonseca M, Proudfoot NJ. Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs. Mol Cell 2016; 65:25-38. [PMID: 28017589 PMCID: PMC5222723 DOI: 10.1016/j.molcel.2016.11.029] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 07/19/2016] [Accepted: 11/17/2016] [Indexed: 12/27/2022]
Abstract
Numerous long intervening noncoding RNAs (lincRNAs) are generated from the mammalian genome by RNA polymerase II (Pol II) transcription. Although multiple functions have been ascribed to lincRNAs, their synthesis and turnover remain poorly characterized. Here, we define systematic differences in transcription and RNA processing between protein-coding and lincRNA genes in human HeLa cells. This is based on a range of nascent transcriptomic approaches applied to different nuclear fractions, including mammalian native elongating transcript sequencing (mNET-seq). Notably, mNET-seq patterns specific for different Pol II CTD phosphorylation states reveal weak co-transcriptional splicing and poly(A) signal-independent Pol II termination of lincRNAs as compared to pre-mRNAs. In addition, lincRNAs are mostly restricted to chromatin, since they are rapidly degraded by the RNA exosome. We also show that a lincRNA-specific co-transcriptional RNA cleavage mechanism acts to induce premature termination. In effect, functional lincRNAs must escape from this targeted nuclear surveillance process.
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Affiliation(s)
- Margarita Schlackow
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
| | - Tomas Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ashish Dhir
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Nick J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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34
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Abstract
Transcription and splicing are fundamental steps in gene expression. These processes have been studied intensively over the past four decades, and very recent findings are challenging some of the formerly established ideas. In particular, splicing was shown to occur much faster than previously thought, with the first spliced products observed as soon as splice junctions emerge from RNA polymerase II (Pol II). Splicing was also found coupled to a specific phosphorylation pattern of Pol II carboxyl-terminal domain (CTD), suggesting a new layer of complexity in the CTD code. Moreover, phosphorylation of the CTD may be scarcer than expected, and other post-translational modifications of the CTD are emerging with unanticipated roles in gene expression regulation.
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Affiliation(s)
- Noélia Custódio
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
| | - Maria Carmo-Fonseca
- a Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa , Lisboa , Portugal
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35
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Martins AF, Martins JM, do Vale S, Dias T, Silveira C, da Silva IR, Carmo-Fonseca M. A rare missense variant in RET exon 8 in a Portuguese family with atypical multiple endocrine neoplasia type 2A. Hormones (Athens) 2016; 15:435-440. [PMID: 27838608 DOI: 10.14310/horm.2002.1691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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] [Received: 02/16/2016] [Accepted: 05/31/2016] [Indexed: 11/20/2022]
Abstract
BACKGROUND AND OBJECTIVE Multiple Endocrine Neoplasia type 2 (MEN2) is a rare genetic disorder characterized by medullary thyroid carcinoma (MTC), pheochromocytoma and primary hyperparathyroidism. MEN2 is an autosomal dominant syndrome caused by mutations in the RET proto-oncogene. In the vast majority of patients, the mutations are localized in exons 10, 11 and 13-15 of the RET gene. Rare variants located in exon 8 were recently identified but their clinical significance remains unclear. DESIGN AND METHODS We studied two sisters presenting with pheochromocytoma as the first tumor. One of the sisters was diagnosed with a right pheochromocytoma at the age of 44 and at age 53 she developed an invasive left pheochromocytoma with no other endocrine neoplasia. The other sister was diagnosed with a left pheochromocytoma at age 50 and at age 64 she had a right phemochromocytoma and MTC. Neither of the two sisters presented evidence of primary hyperparathyroidism. Mutations of the RET proto-oncogene were investigated by DNA sequencing. RESULTS We detected a germline missense variant in RET exon 8 (p.Cys531Arg) in both sisters. The p.Cys531Arg variant was not present in a third 50-year-old sister who has remained to date clinically unaffected. CONCLUSION This is the first case showing the p.Cys531Arg variant in RET exon 8 co-segregating with family members affected by a syndrome reminiscent of MEN2A. Our results suggest that this variant has a specific genotype-phenotype correlation as it is associated with the development of pheochromocytoma before the onset of MTC.
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Affiliation(s)
| | - João Martin Martins
- Serviço de Endocrinologia, Hospital de Santa Maria, Lisboa, Portugal
- Faculdade de Mediana, Universidade de Lisboa, Lisboa, Portugal
| | - Sónia do Vale
- Serviço de Endocrinologia, Hospital de Santa Maria, Lisboa, Portugal
- Faculdade de Mediana, Universidade de Lisboa, Lisboa, Portugal
| | - Teresa Dias
- Serviço de Endocrinologia, Hospital de Santa Maria, Lisboa, Portugal
| | - Catarina Silveira
- Genomed, Instituto de Medicina Molecular, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Inês Rodrigues da Silva
- Genomed, Instituto de Medicina Molecular, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Faculdade de Mediana, Universidade de Lisboa, Lisboa, Portugal
- Genomed, Instituto de Medicina Molecular, Centro Académico de Medicina de Lisboa, Lisboa, Portugal
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Rino J, de Jesus AC, Carmo-Fonseca M. STaQTool: Spot tracking and quantification tool for monitoring splicing of single pre-mRNA molecules in living cells. Methods 2016; 98:143-149. [PMID: 26855377 DOI: 10.1016/j.ymeth.2016.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 11/02/2015] [Revised: 02/02/2016] [Accepted: 02/04/2016] [Indexed: 10/22/2022] Open
Abstract
The vast majority of human protein-coding genes contain up to 90% of non-coding sequence in the form of introns that must be removed from the primary transcripts or pre-mRNAs. Diverse forms of mRNAs encoded from a single gene are created by the differential use of splice sites and alternative splicing is rapidly evolving. Although the kinetic properties of splicing are thought to be critical for proofreading and regulatory mechanisms, tools for making direct experimental measurements of splicing rates are still limited. We recently developed a strategy that permits real-time imaging of fluorescent-labelled introns in single pre-mRNA molecules. Here we describe the software tool that we created for automatic tracking and quantification of intronic fluorescence at the site of transcription in live human cells.
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Affiliation(s)
- José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Ana C de Jesus
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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37
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Nojima T, Gomes T, Carmo-Fonseca M, Proudfoot NJ. Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide. Nat Protoc 2016; 11:413-28. [PMID: 26844429 DOI: 10.1038/nprot.2016.012] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The transcription cycle of RNA polymerase II (Pol II) correlates with changes to the phosphorylation state of its large subunit C-terminal domain (CTD). We recently developed Native Elongation Transcript sequencing using mammalian cells (mNET-seq), which generates single-nucleotide-resolution genome-wide profiles of nascent RNA and co-transcriptional RNA processing that are associated with different CTD phosphorylation states. Here we provide a detailed protocol for mNET-seq. First, Pol II elongation complexes are isolated with specific phospho-CTD antibodies from chromatin solubilized by micrococcal nuclease digestion. Next, RNA derived from within the Pol II complex is size fractionated and Illumina sequenced. Using mNET-seq, we have previously shown that Pol II pauses at both ends of protein-coding genes but with different CTD phosphorylation patterns, and we have also detected phosphorylation at serine 5 (Ser5-P) CTD-specific splicing intermediates and Pol II accumulation over co-transcriptionally spliced exons. With moderate biochemical and bioinformatic skills, mNET-seq can be completed in ∼6 d, not including sequencing and data analysis.
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Affiliation(s)
- Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Tomás Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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38
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Abstract
Microscopy protocols that allow live-cell imaging of molecules and subcellular components tagged with fluorescent conjugates are indispensable in modern biological research. A breakthrough was recently introduced by the development of genetically encoded fluorescent tags that combined with fluorescence-based microscopic approaches of increasingly higher spatial and temporal resolution made it possible to detect single protein and nucleic acid molecules inside living cells. Here, we describe an approach to visualize single nascent pre-mRNA molecules and to measure in real time the dynamics of intron synthesis and excision.
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Affiliation(s)
- Robert M Martin
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - José Rino
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Ana C de Jesus
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Faculdade de Medicina, Instituto de Medicina Molecular, Universidade de Lisboa, Av. Prof. Egas Moniz, 1649-028, Lisbon, Portugal.
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39
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Grosso AR, Leite AP, Carvalho S, Matos MR, Martins FB, Vítor AC, Desterro JMP, Carmo-Fonseca M, de Almeida SF. Pervasive transcription read-through promotes aberrant expression of oncogenes and RNA chimeras in renal carcinoma. eLife 2015; 4. [PMID: 26575290 PMCID: PMC4744188 DOI: 10.7554/elife.09214] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [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: 06/03/2015] [Accepted: 11/16/2015] [Indexed: 12/18/2022] Open
Abstract
Aberrant expression of cancer genes and non-canonical RNA species is a hallmark of cancer. However, the mechanisms driving such atypical gene expression programs are incompletely understood. Here, our transcriptional profiling of a cohort of 50 primary clear cell renal cell carcinoma (ccRCC) samples from The Cancer Genome Atlas (TCGA) reveals that transcription read-through beyond the termination site is a source of transcriptome diversity in cancer cells. Amongst the genes most frequently mutated in ccRCC, we identified SETD2 inactivation as a potent enhancer of transcription read-through. We further show that invasion of neighbouring genes and generation of RNA chimeras are functional outcomes of transcription read-through. We identified the BCL2 oncogene as one of such invaded genes and detected a novel chimera, the CTSC-RAB38, in 20% of ccRCC samples. Collectively, our data highlight a novel link between transcription read-through and aberrant expression of oncogenes and chimeric transcripts that is prevalent in cancer. DOI:http://dx.doi.org/10.7554/eLife.09214.001 Mutations in genes play important roles in many types of cancer. However, mutations alone cannot explain all the biological changes that occur to cancer cells. For example, very few mutations have been linked with a type of kidney cancer called clear cell renal cell carcinoma (or ccRCC for short). Instead, scientists suspect that this cancer is largely caused by changes in the expression of particular genes so that certain cancer-promoting genes are more highly expressed, while other genes that would prevent tumor growth become less active. One of the few genes that is often mutated in ccRCC is called SETD2. This gene is involved in processes that alter the structure of DNA, but do not alter the genes themselves. These “epigenetic” changes can alter how the instructions in genes are used to make proteins. The first step in making proteins is to use a section of DNA as a template to make molecules of messenger ribonucleic acid (mRNA) in a process called transcription. There are markers within a gene that show where transcription should start and stop to produce the mRNA required to make a particular protein. Epigenetic changes can mask these markers so that the cell produces longer mRNAs that incorporate instructions from neighboring genes. It was not known how often these stop signs are ignored in ccRCC cells. Here, Grosso et al. compared transcription in normal cells and in ccRCC tumor cells from 50 different patients. The experiments show that more stop signs were ignored in many of the cancer cells, especially in cells with mutations in SETD2. This caused all or parts of neighboring genes to be transcribed along with the target gene and led to changes in the expression levels of these genes. For example, a cancer-promoting gene called BCL2 was more highly expressed in these cells. Furthermore, some of the mRNA molecules produced in these cancer cells may make “fusion” proteins that combine elements from several proteins. These fusion proteins may work differently to normal cell proteins and therefore might also promote the development of tumors. Grosso et al.’s findings reveal a new link between epigenetic changes and cancer. DOI:http://dx.doi.org/10.7554/eLife.09214.002
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Affiliation(s)
- Ana R Grosso
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Ana P Leite
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sílvia Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mafalda R Matos
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Filipa B Martins
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Alexandra C Vítor
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Joana M P Desterro
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Sérgio F de Almeida
- Instituto de Medicina Molecular, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
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40
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Abstract
Our current view of the nucleolus has been shaped by the concept that the organization of this prominent compartment within the nucleus is primarily dictated by its function, the making of ribosome subunits. Whether ribosome biogenesis is framed by a dedicated nucleolar scaffold has remained unclear. In this issue of The EMBO Journal, Caudron‐Herger and colleagues present evidence for a nucleolar skeleton composed of non‐coding RNA enriched in Alu repeat elements.
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Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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41
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Nojima T, Gomes T, Grosso ARF, Kimura H, Dye MJ, Dhir S, Carmo-Fonseca M, Proudfoot NJ. Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing. Cell 2015; 161:526-540. [PMID: 25910207 PMCID: PMC4410947 DOI: 10.1016/j.cell.2015.03.027] [Citation(s) in RCA: 365] [Impact Index Per Article: 40.6] [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: 08/12/2014] [Revised: 12/24/2014] [Accepted: 02/25/2015] [Indexed: 11/18/2022]
Abstract
Transcription is a highly dynamic process. Consequently, we have developed native elongating transcript sequencing technology for mammalian chromatin (mNET-seq), which generates single-nucleotide resolution, nascent transcription profiles. Nascent RNA was detected in the active site of RNA polymerase II (Pol II) along with associated RNA processing intermediates. In particular, we detected 5'splice site cleavage by the spliceosome, showing that cleaved upstream exon transcripts are associated with Pol II CTD phosphorylated on the serine 5 position (S5P), which is accumulated over downstream exons. Also, depletion of termination factors substantially reduces Pol II pausing at gene ends, leading to termination defects. Notably, termination factors play an additional promoter role by restricting non-productive RNA synthesis in a Pol II CTD S2P-specific manner. Our results suggest that CTD phosphorylation patterns established for yeast transcription are significantly different in mammals. Taken together, mNET-seq provides dynamic and detailed snapshots of the complex events underlying transcription in mammals.
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Affiliation(s)
- Takayuki Nojima
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Tomás Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Ana Rita Fialho Grosso
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Hiroshi Kimura
- Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 226-8501Yokohama, Japan
| | - Michael J Dye
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Somdutta Dhir
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
| | - Nicholas J Proudfoot
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK.
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42
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Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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43
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Abstract
Expression of genetic information in eukaryotes involves a series of interconnected processes that ultimately determine the quality and amount of proteins in the cell. Many individual steps in gene expression are kinetically coupled, but tools are lacking to determine how temporal relationships between chemical reactions contribute to the output of the final gene product. Here, we describe a strategy that permits direct measurements of intron dynamics in single pre-mRNA molecules in live cells. This approach reveals that splicing can occur much faster than previously proposed and opens new avenues for studying how kinetic mechanisms impact on RNA biogenesis.
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Affiliation(s)
- José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Robert M Martin
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Célia Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Ana C de Jesus
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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44
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Vaz-Drago R, Pinheiro MT, Martins S, Enguita FJ, Carmo-Fonseca M, Custódio N. Transcription-coupled RNA surveillance in human genetic diseases caused by splice site mutations. Hum Mol Genet 2015; 24:2784-95. [PMID: 25652404 DOI: 10.1093/hmg/ddv039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 01/31/2015] [Indexed: 12/15/2022] Open
Abstract
Current estimates indicate that approximately one-third of all disease-causing mutations are expected to disrupt splicing. Abnormal splicing often leads to disruption of the reading frame with introduction of a premature termination codon (PTC) that targets the mRNA for degradation in the cytoplasm by nonsense mediated decay (NMD). In addition to NMD there are RNA surveillance mechanisms that act in the nucleus while transcripts are still associated with the chromatin template. However, the significance of nuclear RNA quality control in the context of human genetic diseases is unknown. Here we used patient-derived lymphoblastoid cell lines as disease models to address how biogenesis of mRNAs is affected by splice site mutations. We observed that most of the mutations analyzed introduce PTCs and trigger mRNA degradation in the cytoplasm. However, for some mutant transcripts, RNA levels associated with chromatin were found down-regulated. Quantification of nascent transcripts further revealed that a subset of genes containing splicing mutations (SM) have reduced transcriptional activity. Following treatment with the translation inhibitor cycloheximide the cytoplasmic levels of mutant RNAs increased, while the levels of chromatin-associated transcripts remained unaltered. These results suggest that transcription-coupled surveillance mechanisms operate independently from NMD to reduce cellular levels of abnormal RNAs caused by SM.
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Affiliation(s)
- Rita Vaz-Drago
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Marco T Pinheiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Sandra Martins
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Francisco J Enguita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Noélia Custódio
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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45
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Pena AC, Pimentel MR, Manso H, Vaz-Drago R, Pinto-Neves D, Aresta-Branco F, Rijo-Ferreira F, Guegan F, Pedro Coelho L, Carmo-Fonseca M, Barbosa-Morais NL, Figueiredo LM. Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo. Mol Microbiol 2014; 93:645-63. [PMID: 24946224 PMCID: PMC4285223 DOI: 10.1111/mmi.12677] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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] [Accepted: 06/15/2014] [Indexed: 11/30/2022]
Abstract
Trypanosoma brucei is a unicellular parasite that causes sleeping sickness in humans. Most of its transcription is constitutive and driven by RNA polymerase II. RNA polymerase I (Pol I) transcribes not only ribosomal RNA genes, but also protein-encoding genes, including variant surface glycoproteins (VSGs) and procyclins. In T. brucei, histone H1 (H1) is required for VSG silencing and chromatin condensation. However, whether H1 has a genome-wide role in transcription is unknown. Here, using RNA sequencing we show that H1 depletion changes the expression of a specific cohort of genes. Interestingly, the predominant effect is partial loss of silencing of Pol I loci, such as VSG and procyclin genes. Labelling of nascent transcripts with 4-thiouridine showed that H1 depletion does not alter the level of labelled Pol II transcripts. In contrast, the levels of 4sU-labelled Pol I transcripts were increased by two- to sixfold, suggesting that H1 preferentially blocks transcription at Pol I loci. Finally, we observed that parasites depleted of H1 grow almost normally in culture but they have a reduced fitness in mice, suggesting that H1 is important for host-pathogen interactions.
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Affiliation(s)
- Ana C Pena
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Av. Prof. Egas Moniz, Edifício Egas Moniz, 1649-028, Lisboa, Portugal
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46
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Costa L, Casimiro S, Gupta S, Knapp S, Pillai MR, Toi M, Badwe R, Carmo-Fonseca M, Kumar R. The global cancer genomics consortium's third annual symposium: from oncogenomics to cancer care. Genes Cancer 2014. [DOI: 10.18632/genesandcancer.7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Luis Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Hospital de Santa Maria – CHLN, Lisbon, Portugal
| | - Sandra Casimiro
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | | | - Stefan Knapp
- Structural Genomic Consortium, University of Oxford, Oxford, UK
| | | | - Masakazu Toi
- Kyoto University Graduate School of Medicine, Japan
| | | | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Rakesh Kumar
- The George Washington University, Washington, DC, USA
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47
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de Almeida SF, Carmo-Fonseca M. Reciprocal regulatory links between cotranscriptional splicing and chromatin. Semin Cell Dev Biol 2014; 32:2-10. [PMID: 24657193 DOI: 10.1016/j.semcdb.2014.03.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [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: 02/26/2014] [Accepted: 03/11/2014] [Indexed: 10/25/2022]
Abstract
Here we review recent findings showing that chromatin organization adds another layer of complexity to the already intricate network of splicing regulatory mechanisms. Chromatin structure can impact splicing by either affecting the elongation rate of RNA polymerase II or by signaling the recruitment of splicing regulatory proteins. The C-terminal domain of the RNA polymerase II largest subunit serves as a coordination platform that binds factors required for adapting chromatin structure to both efficient transcription and processing of the newly synthesized RNA. Reciprocal interconnectivity of steps required for gene activation plays a critical role ensuring efficiency and fidelity of gene expression.
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Affiliation(s)
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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48
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Rino J, Martin RM, Carvalho T, Carmo-Fonseca M. Imaging dynamic interactions between spliceosomal proteins and pre-mRNA in living cells. Methods 2014; 65:359-66. [PMID: 23969316 DOI: 10.1016/j.ymeth.2013.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 06/11/2013] [Revised: 08/07/2013] [Accepted: 08/08/2013] [Indexed: 11/22/2022] Open
Abstract
The ability to observe protein dynamics in living cells is critical for the mechanistic understanding of highly flexible biological processes such as pre-mRNA splicing by the spliceosome. Splicing relies on intricate RNA and protein networks that are repeatedly rearranged during spliceosome assembly. Here we describe a method based on fluorescence microscopy that has been used by our and other laboratories to study interaction of spliceosomal proteins with nascent pre-mRNA in living cells. The method involves co-expressing in mammalian cells the target pre-mRNA labeled with one color, and the spliceosomal protein tagged with another color. The diffusion coefficient of the protein as well as its association and dissociation rates with the pre-mRNA are estimated by fluorescence recovery after photobleaching (FRAP) or photoactivation.
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Affiliation(s)
- José Rino
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Robert M Martin
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Teresa Carvalho
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal.
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49
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Abstract
Since it became clear that intervening sequences or introns are spliced out from precursor pre-mRNA molecules in the nucleus before mature mRNAs are exported to the cytoplasm, questions were raised about the timing of splicing. Does splicing start while RNA polymerase II is still transcribing? Is splicing a slow or a fast process? Is timing important to control the splicing reaction? Although our understanding on the mechanism and function of splicing is largely based on data obtained using biochemical and large-scale "omic" approaches, microscopy has been instrumental to address questions related to timing. Experiments done with the electron microscope paved the way to the discovery of splicing and provided unequivocal evidence that splicing can occur co-transcriptionally. More recently, live-cell microscopy introduced a technical breakthrough that allows real-time visualization of splicing dynamics. We discuss here some of the microscopy advances that provided the basis for the current conceptual view of the splicing process and we outline a most recent development that permits direct measurement, in living cells, of the time it takes to synthesize and excise an intron from individual pre-mRNA molecules.
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Affiliation(s)
- Maria Carmo-Fonseca
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisboa, Portugal
| | - Tomas Kirchhausen
- Departments of Cell Biology and Pediatrics; Harvard Medical School and Program in Molecular and Cellular Medicine at Boston Children's Hospital; Boston, MA USA
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50
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Martin RM, Rino J, Carvalho C, Kirchhausen T, Carmo-Fonseca M. Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep 2013; 4:1144-55. [PMID: 24035393 DOI: 10.1016/j.celrep.2013.08.013] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 05/20/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022] Open
Abstract
Removal of introns from pre-messenger RNAs (pre-mRNAs) via splicing provides a versatile means of genetic regulation that is often disrupted in human diseases. To decipher how splicing occurs in real time, we directly examined with single-molecule sensitivity the kinetics of intron excision from pre-mRNA in the nucleus of living human cells. By using two different RNA labeling methods, MS2 and λN, we show that β-globin introns are transcribed and excised in 20-30 s. Furthermore, we show that replacing the weak polypyrimidine (Py) tract in mouse immunoglobulin μ (IgM) pre-mRNA by a U-rich Py decreases the intron lifetime, thus providing direct evidence that splice-site strength influences splicing kinetics. We also found that RNA polymerase II transcribes at elongation rates ranging between 3 and 6 kb min(-1) and that transcription can be rate limiting for splicing. These results have important implications for a mechanistic understanding of cotranscriptional splicing regulation in the live-cell context.
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Affiliation(s)
- Robert M Martin
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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