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Doria-Borrell P, Moya-Navamuel M, Hemberger M, Pérez-García V. Generation of Knockout Mouse Trophoblast Stem Cells by CRISPR/Cas9. Methods Mol Biol 2024; 2781:81-91. [PMID: 38502445 DOI: 10.1007/978-1-0716-3746-3_8] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The placenta is the organ that dictates the reproductive outcome of mammalian pregnancy by supplying nutrients and oxygen to the developing fetus to sustain its normal growth. During early mammalian development, trophoblast cells are the earliest cell type to differentiate with multipotent capacity to generate the trophoblast components of the placenta. The isolation and use of mouse trophoblast stem cells (mTSCs) to model in vitro trophoblast differentiation, in combination with CRISPR/Cas9 genome editing technology, has provided tremendous insight into the molecular mechanisms governing early mouse placentation. By knocking out a specific gene of interest in mTSCs, researchers are shedding light onto the molecular pathways involved in normal placental development and pregnancy disorders associated with abnormal placentation. In this chapter, we provide a detailed protocol for the genetic modification of mTSCs by using CRISPR/Cas9 genome editing system.
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Affiliation(s)
- Paula Doria-Borrell
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, Valencia, Spain
| | - Maria Moya-Navamuel
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, Valencia, Spain
| | - Myriam Hemberger
- Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
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2
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Pérez-García I, Pérez-García V. CRISPR Activation in Mouse Trophoblast Stem Cells. Methods Mol Biol 2024; 2781:93-103. [PMID: 38502446 DOI: 10.1007/978-1-0716-3746-3_9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
The placenta is a vital organ that regulates nutrient supply to the developing embryo during gestation. In mice, the placenta is composed of trophoblast lineage and mesodermal derivatives, which merge through the chorioallantoic fusion process in a critical event for the progression of placenta development. The trophoblast lineage is derived from self-renewing, multipotent cells known as mouse trophoblast stem cells (mTSCs). These cells are a valuable tool that allows scientists to comprehend the signals regulating major placental cell types' self-renewal and differentiation capacity. Recent advances in CRISPR-Cas9 genome editing applied in mTSCs have provided novel insights into the molecular networks involved in placentation. Here, we present a comprehensive CRISPR activation (CRISPRa) protocol based on the CRISPR/gRNA-directed synergistic activation mediator (SAM) method to overexpress specific target genes in mTSCs.
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3
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Gonzalez-Aguilar AM, Pérez-García V, Riesco-Ávila JM. A Thermo-Catalytic Pyrolysis of Polystyrene Waste Review: A Systematic, Statistical, and Bibliometric Approach. Polymers (Basel) 2023; 15:polym15061582. [PMID: 36987361 PMCID: PMC10054604 DOI: 10.3390/polym15061582] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 03/30/2023] Open
Abstract
Global polystyrene (PS) production has been influenced by the lightness and heat resistance this material offers in different applications, such as construction and packaging. However, population growth and the lack of PS recycling lead to a large waste generation, affecting the environment. Pyrolysis has been recognized as an effective recycling method, converting PS waste into valuable products in the chemical industry. The present work addresses a systematic, bibliometric, and statistical analysis of results carried out from 2015 to 2022, making an extensive critique of the most influential operation parameters in the thermo-catalytic pyrolysis of PS and its waste. The systematic study showed that the conversion of PS into a liquid with high aromatic content (84.75% of styrene) can be achieved by pyrolysis. Discussion of PS as fuel is described compared to commercial fuels. In addition, PS favors the production of liquid fuel when subjected to co-pyrolysis with biomass, improving its properties such as viscosity and energy content. A statistical analysis of the data compilation was also discussed, evaluating the influence of temperature, reactor design, and catalysts on product yield.
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Affiliation(s)
- Arantxa M Gonzalez-Aguilar
- Mechanical Engineering Department, Engineering Division, Campus Irapuato-Salamanca, University of Guanajuato, Salamanca Gto. 36885, Mexico
| | - Vicente Pérez-García
- Mechanical Engineering Department, Engineering Division, Campus Irapuato-Salamanca, University of Guanajuato, Salamanca Gto. 36885, Mexico
| | - José M Riesco-Ávila
- Mechanical Engineering Department, Engineering Division, Campus Irapuato-Salamanca, University of Guanajuato, Salamanca Gto. 36885, Mexico
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Yadav S, Garrido A, Hernández MC, Oliveros JC, Pérez-García V, Fraga MF, Carrera AC. PI3Kβ-regulated β-catenin mediates EZH2 removal from promoters controlling primed human ESC stemness and primitive streak gene expression. Stem Cell Reports 2022; 17:2239-2255. [PMID: 36179694 PMCID: PMC9561645 DOI: 10.1016/j.stemcr.2022.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/24/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
The mechanism governing the transition of human embryonic stem cells (hESCs) toward differentiated cells is only partially understood. To explore this transition, the activity and expression of the ubiquitous phosphatidylinositol 3-kinase (PI3Kα and PI3Kβ) were modulated in primed hESCs. The study reports a pathway that dismantles the restraint imposed by the EZH2 polycomb repressor on an essential stemness gene, NODAL, and on transcription factors required to trigger primitive streak formation. The primitive streak is the site where gastrulation begins to give rise to the three embryonic cell layers from which all human tissues derive. The pathway involves a PI3Kβ non-catalytic action that controls nuclear/active RAC1 levels, activation of JNK (Jun N-terminal kinase) and nuclear β-catenin accumulation. β-Catenin deposition at promoters triggers release of the EZH2 repressor, permitting stemness maintenance (through control of NODAL) and correct differentiation by allowing primitive streak master gene expression. PI3Kβ epigenetic control of EZH2/β-catenin might be modulated to direct stem cell differentiation. PI3Kβ directs epigenetic control of stemness and primitive streak (PS) essential genes PI3Kβ directs RAC1/JNK/β-catenin activation and induces EZH2 promoter displacement β-Catenin/EZH2 control NODAL, a gene essential for stemness and the master PS genes PI3Kβ/PI3K activities cooperate at stemness; PI3Kβ directs PS gene expression
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Affiliation(s)
- Sudhanshu Yadav
- Department of Immunology and Oncology, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Antonio Garrido
- Department of Immunology and Oncology, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - M Carmen Hernández
- Department of Immunology and Oncology, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Juan C Oliveros
- Department of Systems Biology, Bioinformatics, Centro Nacional de Biotecnología/CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Vicente Pérez-García
- Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, 46013 Valencia, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center/CSIC, Health Research Institute of Asturias (ISPA), Institute of Oncology of Asturias (IUOPA), Research Center for Rare Diseases (CIBERER), 33011 Oviedo, Asturias, Spain
| | - Ana C Carrera
- Department of Immunology and Oncology, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain.
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Sandovici I, Georgopoulou A, Pérez-García V, Hufnagel A, López-Tello J, Lam BYH, Schiefer SN, Gaudreau C, Santos F, Hoelle K, Yeo GSH, Burling K, Reiterer M, Fowden AL, Burton GJ, Branco CM, Sferruzzi-Perri AN, Constância M. The imprinted Igf2-Igf2r axis is critical for matching placental microvasculature expansion to fetal growth. Dev Cell 2021; 57:63-79.e8. [PMID: 34963058 PMCID: PMC8751640 DOI: 10.1016/j.devcel.2021.12.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [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: 12/20/2019] [Revised: 09/30/2021] [Accepted: 12/03/2021] [Indexed: 11/21/2022]
Abstract
In all eutherian mammals, growth of the fetus is dependent upon a functional placenta, but whether and how the latter adapts to putative fetal signals is currently unknown. Here, we demonstrate, through fetal, endothelial, hematopoietic, and trophoblast-specific genetic manipulations in the mouse, that endothelial and fetus-derived IGF2 is required for the continuous expansion of the feto-placental microvasculature in late pregnancy. The angiocrine effects of IGF2 on placental microvasculature expansion are mediated, in part, through IGF2R and angiopoietin-Tie2/TEK signaling. Additionally, IGF2 exerts IGF2R-ERK1/2-dependent pro-proliferative and angiogenic effects on primary feto-placental endothelial cells ex vivo. Endothelial and fetus-derived IGF2 also plays an important role in trophoblast morphogenesis, acting through Gcm1 and Synb. Thus, our study reveals a direct role for the imprinted Igf2-Igf2r axis on matching placental development to fetal growth and establishes the principle that hormone-like signals from the fetus play important roles in controlling placental microvasculature and trophoblast morphogenesis. Fetus-derived IGF2 controls placental microvasculature expansion in late gestation The angiocrine effects of IGF2 are mediated via angiopoietins/Tek and IGF2R-ERK1/2 Fetus-derived IGF2 also regulates trophoblast morphogenesis via Gcm1 and Synb The imprinted Igf2-Igf2r axis matches placental development to fetal demand
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Affiliation(s)
- Ionel Sandovici
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK; Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
| | - Aikaterini Georgopoulou
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Vicente Pérez-García
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, 46012 Valencia, Spain
| | - Antonia Hufnagel
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK
| | - Jorge López-Tello
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Brian Y H Lam
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Samira N Schiefer
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK
| | - Chelsea Gaudreau
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Fátima Santos
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Katharina Hoelle
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK
| | - Giles S H Yeo
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Keith Burling
- Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Moritz Reiterer
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Abigail L Fowden
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Graham J Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Cristina M Branco
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Center for Cancer Research and Cell Biology, Queen's University Belfast, Belfast BT9 7AE, UK
| | - Amanda N Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - Miguel Constância
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge CB2 0SW, UK; Wellcome-MRC Institute of Metabolic Science and Medical Research Council Metabolic Diseases Unit, University of Cambridge, Cambridge CB2 0QQ, UK; Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK.
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6
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López-Tello J, Pérez-García V, Khaira J, Kusinski LC, Cooper WN, Andreani A, Grant I, Fernández de Liger E, Lam BY, Hemberger M, Sandovici I, Constancia M, Sferruzzi-Perri AN. Fetal and trophoblast PI3K p110α have distinct roles in regulating resource supply to the growing fetus in mice. eLife 2019; 8:45282. [PMID: 31241463 PMCID: PMC6634971 DOI: 10.7554/elife.45282] [Citation(s) in RCA: 25] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 06/25/2019] [Indexed: 01/07/2023] Open
Abstract
Studies suggest that placental nutrient supply adapts according to fetal demands. However, signaling events underlying placental adaptations remain unknown. Here we demonstrate that phosphoinositide 3-kinase p110α in the fetus and the trophoblast interplay to regulate placental nutrient supply and fetal growth. Complete loss of fetal p110α caused embryonic death, whilst heterozygous loss resulted in fetal growth restriction and impaired placental formation and nutrient transport. Loss of trophoblast p110α resulted in viable fetuses, abnormal placental development and a failure of the placenta to transport sufficient nutrients to match fetal demands for growth. Using RNA-seq we identified genes downstream of p110α in the trophoblast that are important in adapting placental phenotype. Using CRISPR/Cas9 we showed loss of p110α differentially affects gene expression in trophoblast and embryonic stem cells. Our findings reveal important, but distinct roles for p110α in the different compartments of the conceptus, which control fetal resource acquisition and growth.
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Affiliation(s)
- Jorge López-Tello
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Vicente Pérez-García
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Jaspreet Khaira
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Laura C Kusinski
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Metabolic Research Laboratories, MRC Metabolic Diseases Unit, Department of Obstetrics and Gynaecology, The Rosie Hospital, Cambridge, United Kingdom
| | - Wendy N Cooper
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit, Department of Obstetrics and Gynaecology, The Rosie Hospital, Cambridge, United Kingdom
| | - Adam Andreani
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Imogen Grant
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Edurne Fernández de Liger
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Brian Yh Lam
- Metabolic Research Laboratories, MRC Metabolic Diseases Unit, Department of Obstetrics and Gynaecology, The Rosie Hospital, Cambridge, United Kingdom
| | - Myriam Hemberger
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom.,Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Canada.,Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Ionel Sandovici
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Metabolic Research Laboratories, MRC Metabolic Diseases Unit, Department of Obstetrics and Gynaecology, The Rosie Hospital, Cambridge, United Kingdom
| | - Miguel Constancia
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.,Metabolic Research Laboratories, MRC Metabolic Diseases Unit, Department of Obstetrics and Gynaecology, The Rosie Hospital, Cambridge, United Kingdom
| | - Amanda N Sferruzzi-Perri
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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Ituna-Yudonago J, Belman-Flores J, Elizalde-Blancas F, Pérez-García V, García-Valladares O, Carvajal-Mariscal I. NUMERICAL ANALYSIS OF CO2 TRANSIENT BEHAVIOR IN THE GAS COOLER DURING VARIABLE START-UP CONDITIONS OF A TRANSCRITICAL REFRIGERATION SYSTEM. Rev Mex Ing Quim 2019. [DOI: 10.24275/uam/izt/dcbi/revmexingquim/2019v18n3/ituna] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Henares-Molina A, Benzekry S, Lara P, García-Rojo M, Pérez-García V, Martínez-González A. OS06.6 Optimized radiotherapy protocols delay the malignant transformation of low-grade gliomas in-silico. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox036.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Wang Z, Monteiro CD, Jagodnik KM, Fernandez NF, Gundersen GW, Rouillard AD, Jenkins SL, Feldmann AS, Hu KS, McDermott MG, Duan Q, Clark NR, Jones MR, Kou Y, Goff T, Woodland H, Amaral FMR, Szeto GL, Fuchs O, Schüssler-Fiorenza Rose SM, Sharma S, Schwartz U, Bausela XB, Szymkiewicz M, Maroulis V, Salykin A, Barra CM, Kruth CD, Bongio NJ, Mathur V, Todoric RD, Rubin UE, Malatras A, Fulp CT, Galindo JA, Motiejunaite R, Jüschke C, Dishuck PC, Lahl K, Jafari M, Aibar S, Zaravinos A, Steenhuizen LH, Allison LR, Gamallo P, de Andres Segura F, Dae Devlin T, Pérez-García V, Ma'ayan A. Extraction and analysis of signatures from the Gene Expression Omnibus by the crowd. Nat Commun 2016; 7:12846. [PMID: 27667448 PMCID: PMC5052684 DOI: 10.1038/ncomms12846] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [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: 12/07/2015] [Accepted: 08/05/2016] [Indexed: 12/14/2022] Open
Abstract
Gene expression data are accumulating exponentially in public repositories. Reanalysis and integration of themed collections from these studies may provide new insights, but requires further human curation. Here we report a crowdsourcing project to annotate and reanalyse a large number of gene expression profiles from Gene Expression Omnibus (GEO). Through a massive open online course on Coursera, over 70 participants from over 25 countries identify and annotate 2,460 single-gene perturbation signatures, 839 disease versus normal signatures, and 906 drug perturbation signatures. All these signatures are unique and are manually validated for quality. Global analysis of these signatures confirms known associations and identifies novel associations between genes, diseases and drugs. The manually curated signatures are used as a training set to develop classifiers for extracting similar signatures from the entire GEO repository. We develop a web portal to serve these signatures for query, download and visualization.
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Affiliation(s)
- Zichen Wang
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Caroline D. Monteiro
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Kathleen M. Jagodnik
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
- Fluid Physics and Transport Processes Branch, NASA Glenn Research Center, 21000 Brookpark Rd, Cleveland, Ohio 44135, USA
- Center for Space Medicine, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
| | - Nicolas F. Fernandez
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Gregory W. Gundersen
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Andrew D. Rouillard
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Sherry L. Jenkins
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Axel S. Feldmann
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Kevin S. Hu
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Michael G. McDermott
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Qiaonan Duan
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Neil R. Clark
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Matthew R. Jones
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Yan Kou
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | - Troy Goff
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
| | | | - Fabio M R. Amaral
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Gregory L. Szeto
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Materials Science & Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- The Ragon Institute of MGH, MIT, and Harvard, 400 Technology Square, Cambridge, Massachusetts 02139, USA
| | - Oliver Fuchs
- Paediatric Allergology and Pulmonology, Dr von Hauner University Children's Hospital, Ludwig-Maximilians-University of Munich, Member of the German Centre for Lung Research (DZL), Lindwurmstrasse 4, Munich 80337, Germany
| | - Sophia M. Schüssler-Fiorenza Rose
- Spinal Cord Injury Service, Veteran Affairs Palo Alto Health Care System, Palo Alto, California 94304, USA
- Department of Neurosurgery, Stanford School of Medicine, Stanford, California 94304, USA
| | - Shvetank Sharma
- Department of Research, Institute of Liver & Biliary Sciences, D1, Vasant Kunj, New Delhi 110070, India
| | - Uwe Schwartz
- Department of Biochemistry III, University of Regensburg, Universitätsstrasse 31, Regensburg 93053, Germany
| | - Xabier Bengoetxea Bausela
- Department of Pharmacology and Toxicology, University of Navarra, Pamplona, Irunlarrea 1, Pamplona 31008, Spain
| | - Maciej Szymkiewicz
- Warsaw School of Information Technology under the auspices of the Polish Academy of Sciences, 6 Newelska St, Warsaw 01–447, Poland
| | | | - Anton Salykin
- Department of Biology, Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Carolina M. Barra
- IMIM-Hospital Del Mar, PRBB Barcelona, Dr Aiguader, Barcelona 88.08003, Spain
| | | | - Nicholas J. Bongio
- Department of Biology, Shenandoah University, 1460 University Dr Winchester, Winchester, Virginia 22601, USA
| | | | | | - Udi E. Rubin
- Department of Biological Sciences, 600 Fairchild Center, Mail Code 2402, Columbia University, New York, New York 10032, USA
| | - Apostolos Malatras
- Center for Research in Myology, Sorbonne Universités, UPMC Univ Paris 06, INSERM UMRS975, CNRS FRE3617, 47 Boulevard de l'hôpital, Paris 75013, France
| | - Carl T. Fulp
- 13-1, Higashi 4-chome Shibuya-ku, Tokyo 150-0011, Japan
| | - John A. Galindo
- Department of Biology and Institute of Genetics, Universidad Nacional de Colombia, Bogota, Cr. 30 # 45-08, Colombia
| | - Ruta Motiejunaite
- Center for Interdisciplinary Cardiovascular Sciences, Brigham and Women's Hospital, 3 Blackfan Circle, Boston, Massachusetts 02115, USA
| | - Christoph Jüschke
- Department of Human Genetics, Faculty of Medicine and Health Sciences, University of Oldenburg, Ammerländer Heerstrasse 114-118, Oldenburg 26129, Germany
| | | | - Katharina Lahl
- Technical University of Denmark, National Veterinary Institute, Bülowsvej 27 Building 2-3, Frederiksberg C 1870, Denmark
| | - Mohieddin Jafari
- Protein Chemistry and Proteomics Unit, Biotechnology Research Center, Pasteur Institute of Iran, No. 358, 12th Farwardin Ave, Jomhhoori St, Tehran 13164, Iran
- School of Biological Sciences, Institute for Researches in Fundamental Sciences, Niavaran Square, P.O.Box, Tehran 19395-5746, Iran
| | - Sara Aibar
- University of Salamanca, Salamanca, Madrid 37008, Spain
| | - Apostolos Zaravinos
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute, Alfred Nobels Allé 8, level 7, Stockholm SE141 86, Sweden
- Department of Life Sciences, School of Sciences, European University Cyprus, 6 Diogenes Str. Engomi, P.O.Box 22006, Nicosia 1516, Cyprus
| | | | | | | | - Fernando de Andres Segura
- CICAB, Clinical Research Centre, Extremadura University Hospital, Elvas Av., s/n. 06006 Badajoz 06006, Spain
| | | | - Vicente Pérez-García
- Consejo Superior de Investigaciones Científicas, Centro Nacional de Biotecnología, Department of Immunology and Oncology, c/Darwin, 3 Madrid 28049, Spain
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, BD2K-LINCS Data Coordination and Integration Center, Illuminating the Druggable Genome Knowledge Management Center, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place Box 1215, New York, New York 10029, USA
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Ramírez-Minguela J, Rodríguez-Muñoz J, Pérez-García V, Mendoza-Miranda J, Muñoz-Carpio V, Alfaro-Ayala J. Solid oxide fuel cell numerical study: modified MOLB-type and simple planar geometries with internal reforming. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.01.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Cariaga-Martínez AE, Cortés I, García E, Pérez-García V, Pajares MJ, Idoate MA, Redondo-Muñóz J, Antón IM, Carrera AC. Phosphoinositide 3-kinase p85beta regulates invadopodium formation. Biol Open 2014; 3:924-36. [PMID: 25217619 PMCID: PMC4197441 DOI: 10.1242/bio.20148185] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The acquisition of invasiveness is characteristic of tumor progression. Numerous genetic changes are associated with metastasis, but the mechanism by which a cell becomes invasive remains unclear. Expression of p85β, a regulatory subunit of phosphoinositide-3-kinase, markedly increases in advanced carcinoma, but its mode of action is unknown. We postulated that p85β might facilitate cell invasion. We show that p85β localized at cell adhesions in complex with focal adhesion kinase and enhanced stability and maturation of cell adhesions. In addition, p85β induced development at cell adhesions of an F-actin core that extended several microns into the cell z-axis resembling the skeleton of invadopodia. p85β lead to F-actin polymerization at cell adhesions by recruiting active Cdc42/Rac at these structures. In accordance with p85β function in invadopodium-like formation, p85β levels increased in metastatic melanoma and p85β depletion reduced invadopodium formation and invasion. These results show that p85β enhances invasion by inducing cell adhesion development into invadopodia-like structures explaining the metastatic potential of tumors with increased p85β levels.
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Affiliation(s)
- Ariel E Cariaga-Martínez
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid E-28049, Spain
| | - Isabel Cortés
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid E-28049, Spain
| | - Esther García
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid E-28049, Spain
| | - Vicente Pérez-García
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid E-28049, Spain
| | - María J Pajares
- Biomarkers Laboratory, Division of Oncology, Center for Applied Biomedical Research (CIMA), University of Navarra, Pamplona E-31008, Spain
| | - Miguel A Idoate
- Pathology Department, Hospital Clinic of Navarra, University of Navarra, Pamplona, E-31008, Spain
| | - Javier Redondo-Muñóz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid E-28049, Spain
| | - Inés M Antón
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid E-28049, Spain
| | - Ana C Carrera
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid E-28049, Spain
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12
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Redondo-Muñoz J, Rodríguez MJ, Silió V, Pérez-García V, Valpuesta JM, Carrera AC. Phosphoinositide 3-kinase beta controls replication factor C assembly and function. Nucleic Acids Res 2012; 41:855-68. [PMID: 23175608 PMCID: PMC3553946 DOI: 10.1093/nar/gks1095] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [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] [Indexed: 01/29/2023] Open
Abstract
Genomic integrity is preserved by the action of protein complexes that control DNA homeostasis. These include the sliding clamps, trimeric protein rings that are arranged around DNA by clamp loaders. Replication factor C (RFC) is the clamp loader for proliferating cell nuclear antigen, which acts on DNA replication. Other processes that require mobile contact of proteins with DNA use alternative RFC complexes that exchange RFC1 for CTF18 or RAD17. Phosphoinositide 3-kinases (PI3K) are lipid kinases that generate 3-poly-phosphorylated-phosphoinositides at the plasma membrane following receptor stimulation. The two ubiquitous isoforms, PI3Kalpha and PI3Kbeta, have been extensively studied due to their involvement in cancer and nuclear PI3Kbeta has been found to regulate DNA replication and repair, processes controlled by molecular clamps. We studied here whether PI3Kbeta directly controls the process of molecular clamps loading. We show that PI3Kbeta associated with RFC1 and RFC1-like subunits. Only when in complex with PI3Kbeta, RFC1 bound to Ran GTPase and localized to the nucleus, suggesting that PI3Kbeta regulates RFC1 nuclear import. PI3Kbeta controlled not only RFC1- and RFC-RAD17 complexes, but also RFC-CTF18, in turn affecting CTF18-mediated chromatid cohesion. PI3Kbeta thus has a general function in genomic stability by controlling the localization and function of RFC complexes.
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Affiliation(s)
- Javier Redondo-Muñoz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Darwin 3, Campus de Cantoblanco, Madrid E-28049, Spain
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13
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Calvanese V, Fernández AF, Urdinguio RG, Suárez-Alvarez B, Mangas C, Pérez-García V, Bueno C, Montes R, Ramos-Mejía V, Martínez-Camblor P, Ferrero C, Assenov Y, Bock C, Menendez P, Carrera AC, Lopez-Larrea C, Fraga MF. A promoter DNA demethylation landscape of human hematopoietic differentiation. Nucleic Acids Res 2011; 40:116-31. [PMID: 21911366 PMCID: PMC3245917 DOI: 10.1093/nar/gkr685] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [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] [Indexed: 02/02/2023] Open
Abstract
Global mechanisms defining the gene expression programs specific for hematopoiesis are still not fully understood. Here, we show that promoter DNA demethylation is associated with the activation of hematopoietic-specific genes. Using genome-wide promoter methylation arrays, we identified 694 hematopoietic-specific genes repressed by promoter DNA methylation in human embryonic stem cells and whose loss of methylation in hematopoietic can be associated with gene expression. The association between promoter methylation and gene expression was studied for many hematopoietic-specific genes including CD45, CD34, CD28, CD19, the T cell receptor (TCR), the MHC class II gene HLA-DR, perforin 1 and the phosphoinositide 3-kinase (PI3K) and results indicated that DNA demethylation was not always sufficient for gene activation. Promoter demethylation occurred either early during embryonic development or later on during hematopoietic differentiation. Analysis of the genome-wide promoter methylation status of induced pluripotent stem cells (iPSCs) generated from somatic CD34+ HSPCs and differentiated derivatives from CD34+ HSPCs confirmed the role of DNA methylation in regulating the expression of genes of the hemato-immune system, and indicated that promoter methylation of these genes may be associated to stemness. Together, these data suggest that promoter DNA demethylation might play a role in the tissue/cell-specific genome-wide gene regulation within the hematopoietic compartment.
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Affiliation(s)
- Vincenzo Calvanese
- Department of Immunology and Oncology, Centro Nacional de Biotecnologia (CNB-CSIC), Darwin 3, Cantoblanco, Madrid E-28049, Spain
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Sempere-Ortells JM, Pérez-García V, Marín-Alberca G, Peris-Pertusa A, Benito JM, Marco FM, Zubcoff JJ, Navarro-Blasco FJ. Quantification and phenotype of regulatory T cells in rheumatoid arthritis according to disease activity score-28. Autoimmunity 2010; 42:636-45. [PMID: 19886735 DOI: 10.3109/08916930903061491] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Here we studied and characterized different peripheral blood (PB) regulatory T cell (Treg) subsets in rheumatoid arthritis (RA) patients and tested the hypothesis that changes in these cells can be linked to the degree of inflammation and relapsing/remission periods. PB cells were examined from RA subjects (n = 60) with different disease activity score-28 (DAS28) and from healthy controls (n = 40). Frequencies of Treg subsets expressing characteristic membrane antigens, FoxP3 or intracellular cytokines were quantified by flow cytometry. We observed a decrease in the percentages of CD4(+)CD25(high), CD4(+)CD25(int), CD4(+)CD25(int/high)FoxP3(+), CD4(+)CD38(+), CD4(+)CD62L(+), CD8(+)CD25(high)CD45RA(+) and CD8(+)CD25(int)CD45RA(+) T cells in PB of RA patients compared to healthy controls. In addition, we found increased percentages of cells expressing membrane/intracellular regulatory antigens such as OX40 (CD134), CD45RB(low) or CTLA-4 (CD152), and a higher proportion of other T cell subsets including CD4(+)CTLA-4(+), CD4(+)IL10(+), CD4(+)CD25(int)IL10(+), CD4(+)CD25(int) TGFbeta(+), CD4(+)CD25(low) TGFbeta(+) and CD8(+)CD28(- ). We show that most of these changes parallel the intensity of inflammation, with lowest or highest values in patients with moderately/very active disease compared to healthy controls and at times to patients with inactive RA. The balance between these cell subsets and their antigen expression would determine the inflammation levels and could thus be linked to the relapsing/remission periods of the disease.
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Cano M, Campo J, Pérez-García V, Gutiérrez-Puebla E, Alvarez-Ibarra C. Molybdenum tricarbonyl complexes containing unidentate diphosphine. NMR study of fac-mer isomers and crystal structure of fac-Mo(CO)3(η2-phen)(η1-dppm). J Organomet Chem 1990. [DOI: 10.1016/0022-328x(90)80217-n] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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