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Dong Z, He W, Lin G, Chen X, Cao S, Guan T, Sun Y, Zhang Y, Qi M, Guo B, Zhou Z, Zhuo R, Wu R, Liu M, Liu Y. Histone acetyltransferase KAT2A modulates neural stem cell differentiation and proliferation by inducing degradation of the transcription factor PAX6. J Biol Chem 2023; 299:103020. [PMID: 36791914 PMCID: PMC10011063 DOI: 10.1016/j.jbc.2023.103020] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
Neural stem cells (NSCs) proliferation and differentiation rely on proper expression and post-translational modification of transcription factors involved in the determination of cell fate. Further characterization is needed to connect modifying enzymes with their transcription factor substrates in the regulation of these processes. Here, we demonstrated that the inhibition of KAT2A, a histone acetyltransferase, leads to a phenotype of small eyes in the developing embryo of zebrafish, which is associated with enhanced proliferation and apoptosis of NSCs in zebrafish eyes. We confirmed that this phenotype is mediated by the evaluated level of PAX6 protein. We further verified that KAT2A negatively regulates PAX6 at the protein level in cultured neural stem cells of rat cerebral cortex. We revealed that PAX6 is a novel acetylation substrate of KAT2A, and the acetylation of PAX6 promotes its ubiquitination mediated by the E3 ligase RNF8 that facilitated PAX6 degradation. Our study proposes that KAT2A inhibition results in accelerated proliferation, delayed differentiation, or apoptosis, depending on the context of PAX6 dosage. Thus, the KAT2A/PAX6 axis plays an essential role to keep a balance between the self-renewal and differentiation of NSCs.
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Affiliation(s)
- Zhangji Dong
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Wei He
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Ge Lin
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Xu Chen
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Sixian Cao
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Tuchen Guan
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Ying Sun
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Yufang Zhang
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Mengwei Qi
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Beibei Guo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Zhihao Zhou
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Run Zhuo
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Ronghua Wu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China
| | - Mei Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China.
| | - Yan Liu
- Key Laboratory of Neuroregeneration of Jiangsu and Ministry of Education, Co-innovation Center of Neuroregeneration, NMPA Key Laboratory for Research and Evaluation of Tissue Engineering Technology Products, Nantong University, China.
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2
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Gupta S, Polit LD, Fitzgerald M, Rowland HA, Murali D, Buckley NJ, Subramaniam S. Temporal transcriptional control of neural induction in human induced pluripotent stem cells. Front Mol Neurosci 2023; 16:1139287. [PMID: 37213689 PMCID: PMC10195998 DOI: 10.3389/fnmol.2023.1139287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 04/14/2023] [Indexed: 05/23/2023] Open
Abstract
Introduction Neural induction of human induced pluripotent stem cells represents a critical switch in cell state during which pluripotency is lost and commitment to a neural lineage is initiated. Although many of the key transcription factors involved in neural induction are known, we know little of the temporal and causal relationships that are required for this state transition. Methods Here, we have carried out a longitudinal analysis of the transcriptome of human iPSCs undergoing neural induction. Using the temporal relationships between the changing profile of key transcription factors and subsequent changes in their target gene expression profiles, we have identified distinct functional modules operative throughout neural induction. Results In addition to modules that govern loss of pluripotency and gain of neural ectoderm identity, we discover other modules governing cell cycle and metabolism. Strikingly, some of these functional modules are retained throughout neural induction, even though the gene membership of the module changes. Systems analysis identifies other modules associated with cell fate commitment, genome integrity, stress response and lineage specification. We then focussed on OTX2, one of the most precociously activated transcription factors during neural induction. Our temporal analysis of OTX2 target gene expression identified several OTX2 regulated gene modules representing protein remodelling, RNA splicing and RNA processing. Further CRISPRi inhibition of OTX2 prior to neural induction promotes an accelerated loss of pluripotency and a precocious and aberrant neural induction disrupting some of the previously identified modules. Discussion We infer that OTX2 has a diverse role during neural induction and regulates many of the biological processes that are required for loss of pluripotency and gain of neural identity. This dynamical analysis of transcriptional changes provides a unique perspective of the widespread remodelling of the cell machinery that occurs during neural induction of human iPSCs.
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Affiliation(s)
- Shakti Gupta
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Lucia Dutan Polit
- Maurice Wohl Clinical Neuroscience Institute, King’s College London, London, United Kingdom
| | - Michael Fitzgerald
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Helen A. Rowland
- Department of Psychiatry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
| | - Divya Murali
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
| | - Noel J. Buckley
- Department of Psychiatry and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, United Kingdom
- *Correspondence: Noel J. Buckley, ; Shankar Subramaniam,
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, San Diego, CA, United States
- Departments of Computer Science and Engineering, and Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, United States
- *Correspondence: Noel J. Buckley, ; Shankar Subramaniam,
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3
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Samara A, Spildrejorde M, Sharma A, Falck M, Leithaug M, Modafferi S, Bjørnstad PM, Acharya G, Gervin K, Lyle R, Eskeland R. A multi-omics approach to visualize early neuronal differentiation from hESCs in 4D. iScience 2022; 25:105279. [PMID: 36304110 PMCID: PMC9593815 DOI: 10.1016/j.isci.2022.105279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 08/22/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
Neuronal differentiation of pluripotent stem cells is an established method to study physiology, disease, and medication safety. However, the sequence of events in human neuronal differentiation and the ability of in vitro models to recapitulate early brain development are poorly understood. We developed a protocol optimized for the study of early human brain development and neuropharmacological applications. We comprehensively characterized gene expression and epigenetic profiles at four timepoints, because the cells differentiate from embryonic stem cells towards a heterogeneous population of progenitors, immature and mature neurons bearing telencephalic signatures. A multi-omics roadmap of neuronal differentiation, combined with searchable interactive gene analysis tools, allows for extensive exploration of early neuronal development and the effect of medications.
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Affiliation(s)
- Athina Samara
- Division of Clinical Paediatrics, Department of Women’s and Children’s Health, Karolinska Institutet, Solna, Sweden
- Astrid Lindgren Children′s Hospital Karolinska University Hospital, Stockholm, Sweden
| | - Mari Spildrejorde
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ankush Sharma
- Department of Informatics, University of Oslo, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Martin Falck
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Magnus Leithaug
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Stefania Modafferi
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Pål Marius Bjørnstad
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Ganesh Acharya
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Alfred Nobels Allé 8, SE-14152 Stockholm, Sweden
- Center for Fetal Medicine, Karolinska University Hospital Huddinge, SE-14186 Stockholm, Sweden
| | - Kristina Gervin
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, School of Pharmacy, University of Oslo, Oslo, Norway
- Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway
| | - Robert Lyle
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ragnhild Eskeland
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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Bai M, Li G, Jiapaer Z, Guo X, Xi J, Wang G, Ye D, Chen W, Duan B, Kang J. Linc1548 promotes the transition of epiblast stem cells into neural progenitors by engaging OCT6 and SOX2. Stem Cells 2022; 40:22-34. [DOI: 10.1093/stmcls/sxab003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/17/2021] [Indexed: 11/12/2022]
Abstract
Abstract
The transition of embryonic stem cells from the epiblast stem cells (EpiSCs) to neural progenitor cells (NPCs), name as the neural induction process, is crucial for cell fate determination of neural differentiation. However, the mechanism of this transition is unclear. Here, we identified a long non-coding RNA (linc1548) as a critical regulator of neural differentiation of mouse embryonic stem cells (mESCs). Knockout of linc1548 did not affect the conversion of mESCs to EpiSCs, but delayed the transition from EpiSCs to NPCs. Moreover, linc1548 interacts with the transcription factors OCT6 and SOX2 forming an RNA-protein complex to regulate the transition from EpiSCs to NPCs. Finally, we showed that Zfp521 is an important target gene of this RNA-protein complex regulating neural differentiation. Our findings prove how the intrinsic transcription complex mediated by a lncRNA linc1548 and can better understand the intrinsic mechanism of neural fate determination.
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Affiliation(s)
- Mingliang Bai
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guoping Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zeyidan Jiapaer
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Xinjiang Key Laboratory of Biology Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, China
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Institute for Advanced Study, Tongji University, Shanghai, China
| | - Jiajie Xi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guiying Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Dan Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wen Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Baoyu Duan
- College of Medical Technology, Shanghai University of Medical and Health Sciences, Shanghai, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
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5
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Different Flavors of Astrocytes: Revising the Origins of Astrocyte Diversity and Epigenetic Signatures to Understand Heterogeneity after Injury. Int J Mol Sci 2021; 22:ijms22136867. [PMID: 34206710 PMCID: PMC8268487 DOI: 10.3390/ijms22136867] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/11/2022] Open
Abstract
Astrocytes are a specific type of neuroglial cells that confer metabolic and structural support to neurons. Astrocytes populate all regions of the nervous system and adopt a variety of phenotypes depending on their location and their respective functions, which are also pleiotropic in nature. For example, astrocytes adapt to pathological conditions with a specific cellular response known as reactive astrogliosis, which includes extensive phenotypic and transcriptional changes. Reactive astrocytes may lose some of their homeostatic functions and gain protective or detrimental properties with great impact on damage propagation. Different astrocyte subpopulations seemingly coexist in reactive astrogliosis, however, the source of such heterogeneity is not completely understood. Altered cellular signaling in pathological compared to healthy conditions might be one source fueling astrocyte heterogeneity. Moreover, diversity might also be encoded cell-autonomously, for example as a result of astrocyte subtype specification during development. We hypothesize and propose here that elucidating the epigenetic signature underlying the phenotype of each astrocyte subtype is of high relevance to understand another regulative layer of astrocyte heterogeneity, in general as well as after injury or as a result of other pathological conditions. High resolution methods should allow enlightening diverse cell states and subtypes of astrocyte, their adaptation to pathological conditions and ultimately allow controlling and manipulating astrocyte functions in disease states. Here, we review novel literature reporting on astrocyte diversity from a developmental perspective and we focus on epigenetic signatures that might account for cell type specification.
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6
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Menuchin-Lasowski Y, Dagan B, Conidi A, Cohen-Gulkar M, David A, Ehrlich M, Giladi PO, Clark BS, Blackshaw S, Shapira K, Huylebroeck D, Henis YI, Ashery-Padan R. Zeb2 regulates the balance between retinal interneurons and Müller glia by inhibition of BMP-Smad signaling. Dev Biol 2020; 468:80-92. [PMID: 32950463 DOI: 10.1016/j.ydbio.2020.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/24/2020] [Accepted: 09/10/2020] [Indexed: 12/27/2022]
Abstract
The interplay between signaling molecules and transcription factors during retinal development is key to controlling the correct number of retinal cell types. Zeb2 (Sip1) is a zinc-finger multidomain transcription factor that plays multiple roles in central and peripheral nervous system development. Haploinsufficiency of ZEB2 causes Mowat-Wilson syndrome, a congenital disease characterized by intellectual disability, epilepsy and Hirschsprung disease. In the developing retina, Zeb2 is required for generation of horizontal cells and the correct number of interneurons; however, its potential function in controlling gliogenic versus neurogenic decisions remains unresolved. Here we present cellular and molecular evidence of the inhibition of Müller glia cell fate by Zeb2 in late stages of retinogenesis. Unbiased transcriptomic profiling of control and Zeb2-deficient early-postnatal retina revealed that Zeb2 functions in inhibiting Id1/2/4 and Hes1 gene expression. These neural progenitor factors normally inhibit neural differentiation and promote Müller glia cell fate. Chromatin immunoprecipitation (ChIP) supported direct regulation of Id1 by Zeb2 in the postnatal retina. Reporter assays and ChIP analyses in differentiating neural progenitors provided further evidence that Zeb2 inhibits Id1 through inhibition of Smad-mediated activation of Id1 transcription. Together, the results suggest that Zeb2 promotes the timely differentiation of retinal interneurons at least in part by repressing BMP-Smad/Notch target genes that inhibit neurogenesis. These findings show that Zeb2 integrates extrinsic cues to regulate the balance between neuronal and glial cell types in the developing murine retina.
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Affiliation(s)
- Yotam Menuchin-Lasowski
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Bar Dagan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, the Netherlands
| | - Mazal Cohen-Gulkar
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ahuvit David
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Marcelo Ehrlich
- Shumins School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Pazit Oren Giladi
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Brian S Clark
- John F Hardesty, MD Department of Ophthalmology and Visual Sciences and Department of Developmental Biology, Washington University, St. Louis, MO 63110, USA
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Baltimore, MD 21205, USA; Department of Ophthalmology, Baltimore, MD 21205, USA; Department of Neurology, Baltimore, MD 21205, USA; Center for Human Systems Biology, Baltimore, MD 21205, USA; Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Keren Shapira
- Shumins School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam 3015 CN, the Netherlands; Department of Development and Regeneration, KU Leuven, Leuven 3000, Belgium
| | - Yoav I Henis
- Shumins School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 69978, Israel.
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7
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Dries R, Stryjewska A, Coddens K, Okawa S, Notelaers T, Birkhoff J, Dekker M, Verfaillie CM, Del Sol A, Mulugeta E, Conidi A, Grosveld FG, Huylebroeck D. Integrative and perturbation-based analysis of the transcriptional dynamics of TGFβ/BMP system components in transition from embryonic stem cells to neural progenitors. Stem Cells 2019; 38:202-217. [PMID: 31675135 PMCID: PMC7027912 DOI: 10.1002/stem.3111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 10/09/2019] [Indexed: 01/05/2023]
Abstract
Cooperative actions of extrinsic signals and cell‐intrinsic transcription factors alter gene regulatory networks enabling cells to respond appropriately to environmental cues. Signaling by transforming growth factor type β (TGFβ) family ligands (eg, bone morphogenetic proteins [BMPs] and Activin/Nodal) exerts cell‐type specific and context‐dependent transcriptional changes, thereby steering cellular transitions throughout embryogenesis. Little is known about coordinated regulation and transcriptional interplay of the TGFβ system. To understand intrafamily transcriptional regulation as part of this system's actions during development, we selected 95 of its components and investigated their mRNA‐expression dynamics, gene‐gene interactions, and single‐cell expression heterogeneity in mouse embryonic stem cells transiting to neural progenitors. Interrogation at 24 hour intervals identified four types of temporal gene transcription profiles that capture all stages, that is, pluripotency, epiblast formation, and neural commitment. Then, between each stage we performed esiRNA‐based perturbation of each individual component and documented the effect on steady‐state mRNA levels of the remaining 94 components. This exposed an intricate system of multilevel regulation whereby the majority of gene‐gene interactions display a marked cell‐stage specific behavior. Furthermore, single‐cell RNA‐profiling at individual stages demonstrated the presence of detailed co‐expression modules and subpopulations showing stable co‐expression modules such as that of the core pluripotency genes at all stages. Our combinatorial experimental approach demonstrates how intrinsically complex transcriptional regulation within a given pathway is during cell fate/state transitions.
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Affiliation(s)
- Ruben Dries
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Agata Stryjewska
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Kathleen Coddens
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Satoshi Okawa
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Tineke Notelaers
- Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Judith Birkhoff
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Antonio Del Sol
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg.,CIC bioGUNE, Bizkaia Technology Park, Derio, Spain.,IKERBASQUE, Basque, Foundation for Science, Bilbao, Spain
| | - Eskeatnaf Mulugeta
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andrea Conidi
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Frank G Grosveld
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Danny Huylebroeck
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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8
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Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state. Nat Cell Biol 2019; 21:1518-1531. [PMID: 31792383 DOI: 10.1038/s41556-019-0423-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022]
Abstract
The first lineage specification of pluripotent mouse epiblast segregates neuroectoderm (NE) from mesoderm and definitive endoderm (ME) by mechanisms that are not well understood. Here we demonstrate that the induction of ME gene programs critically relies on the T-box transcription factors Eomesodermin (also known as Eomes) and Brachyury, which concomitantly repress pluripotency and NE gene programs. Cells deficient in these T-box transcription factors retain pluripotency and differentiate to NE lineages despite the presence of ME-inducing signals transforming growth factor β (TGF-β)/Nodal and Wnt. Pluripotency and NE gene networks are additionally repressed by ME factors downstream of T-box factor induction, demonstrating a redundancy in program regulation to safeguard mutually exclusive lineage specification. Analyses of chromatin revealed that accessibility of ME enhancers depends on T-box factor binding, whereas NE enhancers are accessible and already activation primed at pluripotency. This asymmetry of the chromatin landscape thus explains the default differentiation of pluripotent cells to NE in the absence of ME induction that depends on activating and repressive functions of Eomes and Brachyury.
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9
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Cui G, Suo S, Wang R, Qian Y, Han JDJ, Peng G, Tam PPL, Jing N. Mouse gastrulation: Attributes of transcription factor regulatory network for epiblast patterning. Dev Growth Differ 2018; 60:463-472. [DOI: 10.1111/dgd.12568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 08/23/2018] [Accepted: 08/23/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Guizhong Cui
- State Key Laboratory of Cell Biology; CAS Center for Excellence in Molecular Cell Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai China
| | - Shengbao Suo
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai China
| | - Ran Wang
- State Key Laboratory of Cell Biology; CAS Center for Excellence in Molecular Cell Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai China
| | - Yun Qian
- State Key Laboratory of Cell Biology; CAS Center for Excellence in Molecular Cell Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai China
| | - Jing-Dong J. Han
- Key Laboratory of Computational Biology; CAS Center for Excellence in Molecular Cell Science; Collaborative Innovation Center for Genetics and Developmental Biology; Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology; Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai China
| | - Guangdun Peng
- State Key Laboratory of Cell Biology; CAS Center for Excellence in Molecular Cell Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai China
| | - Patrick P. L. Tam
- Embryology Unit; Children's Medical Research Institute; University of Sydney; Sydney New South Wales Australia
- School of Medical Sciences; Faculty of Medicine and Health; University of Sydney; Sydney New South Wales Australia
| | - Naihe Jing
- State Key Laboratory of Cell Biology; CAS Center for Excellence in Molecular Cell Science; Shanghai Institute of Biochemistry and Cell Biology; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai China
- School of Life Science and Technology; ShanghaiTech University; Shanghai China
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10
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Schliermann A, Nickel J. Unraveling the Connection between Fibroblast Growth Factor and Bone Morphogenetic Protein Signaling. Int J Mol Sci 2018; 19:ijms19103220. [PMID: 30340367 PMCID: PMC6214098 DOI: 10.3390/ijms19103220] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 10/07/2018] [Accepted: 10/16/2018] [Indexed: 12/19/2022] Open
Abstract
Ontogeny of higher organisms as well the regulation of tissue homeostasis in adult individuals requires a fine-balanced interplay of regulating factors that individually trigger the fate of particular cells to either stay undifferentiated or to differentiate towards distinct tissue specific lineages. In some cases, these factors act synergistically to promote certain cellular responses, whereas in other tissues the same factors antagonize each other. However, the molecular basis of this obvious dual signaling activity is still only poorly understood. Bone morphogenetic proteins (BMPs) and fibroblast growth factors (FGFs) are two major signal protein families that have a lot in common: They are both highly preserved between different species, involved in essential cellular functions, and their ligands vastly outnumber their receptors, making extensive signal regulation necessary. In this review we discuss where and how BMP and FGF signaling cross paths. The compiled data reflect that both factors synchronously act in many tissues, and that antagonism and synergism both exist in a context-dependent manner. Therefore, by challenging a generalization of the connection between these two pathways a new chapter in BMP FGF signaling research will be introduced.
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Affiliation(s)
- Anna Schliermann
- Lehrstuhl für Tissue Engineering und Regenerative Medizin, Universitätsklinikum Würzburg, Röntgenring 11, 97222 Würzburg, Germany.
| | - Joachim Nickel
- Lehrstuhl für Tissue Engineering und Regenerative Medizin, Universitätsklinikum Würzburg, Röntgenring 11, 97222 Würzburg, Germany.
- Fraunhofer Institut für Silicatforschung, Translationszentrum TLZ-RT, Röntgenring 11, 97222 Würzburg, Germany.
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11
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Abstract
Embryonic development and stem cell differentiation, during which coordinated cell fate specification takes place in a spatial and temporal context, serve as a paradigm for studying the orderly assembly of gene regulatory networks (GRNs) and the fundamental mechanism of GRNs in driving lineage determination. However, knowledge of reliable GRN annotation for dynamic development regulation, particularly for unveiling the complex temporal and spatial architecture of tissue stem cells, remains inadequate. With the advent of single-cell RNA sequencing technology, elucidating GRNs in development and stem cell processes poses both new challenges and unprecedented opportunities. This review takes a snapshot of some of this work and its implication in the regulative nature of early mammalian development and specification of the distinct cell types during embryogenesis.
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Affiliation(s)
- Guangdun Peng
- CAS Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, China
| | - Jing-Dong J. Han
- Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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12
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Ibarra-Soria X, Jawaid W, Pijuan-Sala B, Ladopoulos V, Scialdone A, Jörg DJ, Tyser RCV, Calero-Nieto FJ, Mulas C, Nichols J, Vallier L, Srinivas S, Simons BD, Göttgens B, Marioni JC. Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation. Nat Cell Biol 2018; 20:127-134. [PMID: 29311656 PMCID: PMC5787369 DOI: 10.1038/s41556-017-0013-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/21/2017] [Indexed: 02/02/2023]
Abstract
During gastrulation, cell types from all three germ layers are specified and the basic body plan is established 1 . However, molecular analysis of this key developmental stage has been hampered by limited cell numbers and a paucity of markers. Single-cell RNA sequencing circumvents these problems, but has so far been limited to specific organ systems 2 . Here, we report single-cell transcriptomic characterization of >20,000 cells immediately following gastrulation at E8.25 of mouse development. We identify 20 major cell types, which frequently contain substructure, including three distinct signatures in early foregut cells. Pseudo-space ordering of somitic progenitor cells identifies dynamic waves of transcription and candidate regulators, which are validated by molecular characterization of spatially resolved regions of the embryo. Within the endothelial population, cells that transition from haemogenic endothelial to erythro-myeloid progenitors specifically express Alox5 and its co-factor Alox5ap, which control leukotriene production. Functional assays using mouse embryonic stem cells demonstrate that leukotrienes promote haematopoietic progenitor cell generation. Thus, this comprehensive single-cell map can be exploited to reveal previously unrecognized pathways that contribute to tissue development.
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Affiliation(s)
- Ximena Ibarra-Soria
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Wajid Jawaid
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Department of Paediatric Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Blanca Pijuan-Sala
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Vasileios Ladopoulos
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Antonio Scialdone
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - David J Jörg
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Richard C V Tyser
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Carla Mulas
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Ludovic Vallier
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, UK
- Department of Surgery, University of Cambridge, Cambridge, UK
| | - Shankar Srinivas
- Department of Physiology Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Benjamin D Simons
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
- The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - John C Marioni
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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13
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Peng G, Tam PPL, Jing N. Lineage specification of early embryos and embryonic stem cells at the dawn of enabling technologies. Natl Sci Rev 2017. [DOI: 10.1093/nsr/nwx093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Abstract
Establishment of progenitor cell populations and lineage diversity during embryogenesis and the differentiation of pluripotent stem cells is a fascinating and intricate biological process. Conceptually, an understanding of this developmental process provides a framework to integrate stem-cell pluripotency, cell competence and differentiating potential with the activity of extrinsic and intrinsic molecular determinants. The recent advent of enabling technologies of high-resolution transcriptome analysis at the cellular, population and spatial levels proffers the capability of gaining deeper insights into the attributes of the gene regulatory network and molecular signaling in lineage specification and differentiation. In this review, we provide a snapshot of the emerging enabling genomic technologies that contribute to the study of development and stem-cell biology.
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Affiliation(s)
- Guangdun Peng
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Patrick P. L. Tam
- Embryology Unit, Children's Medical Research Institute, School of Medical Sciences, Sydney Medical School, University of Sydney, NSW 2145, Australia
| | - Naihe Jing
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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14
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van der Stijl R, Withoff S, Verbeek DS. Spinocerebellar ataxia: miRNAs expose biological pathways underlying pervasive Purkinje cell degeneration. Neurobiol Dis 2017; 108:148-158. [PMID: 28823930 DOI: 10.1016/j.nbd.2017.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/21/2017] [Accepted: 08/16/2017] [Indexed: 01/09/2023] Open
Abstract
Recent work has demonstrated the importance of miRNAs in the pathogenesis of various brain disorders including the neurodegenerative disorder spinocerebellar ataxia (SCA). This review focuses on the role of miRNAs in the shared pathogenesis of the different SCA types. We examine the novel findings of a recent cell-type-specific RNA-sequencing study in mouse brain and discuss how the identification of Purkinje-cell-enriched miRNAs highlights biological pathways that expose the mechanisms behind pervasive Purkinje cell degeneration in SCA. These key pathways are likely to contain targets for therapeutic development and represent potential candidate genes for genetically unsolved SCAs.
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Affiliation(s)
- Rogier van der Stijl
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Sebo Withoff
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Dineke S Verbeek
- Department of Genetics, University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands.
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15
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López-García I, Gerő D, Szczesny B, Szoleczky P, Olah G, Módis K, Zhang K, Gao J, Wu P, Sowers LC, DeWitt D, Prough DS, Szabo C. Development of a stretch-induced neurotrauma model for medium-throughput screening in vitro: identification of rifampicin as a neuroprotectant. Br J Pharmacol 2016; 175:284-300. [PMID: 27723079 DOI: 10.1111/bph.13642] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND AND PURPOSE We hypothesized that an in vitro, stretch-based model of neural injury may be useful to identify compounds that decrease the cellular damage in neurotrauma. EXPERIMENTAL APPROACH We screened three neural cell lines (B35, RN33B and SH-SY5Y) subjected to two differentiation methods and selected all-trans-retinoic acid-differentiated B35 rat neuroblastoma cells subjected to rapid stretch injury, coupled with a subthreshold concentration of H2 O2 , for the screen. The model induced marked alterations in gene expression and proteomic signature of the cells and culminated in delayed cell death (LDH release) and mitochondrial dysfunction [reduced 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) conversion]. Follow-up studies utilized human stem cell-derived neurons subjected to rapid stretch injury. KEY RESULTS From screening of a composite library of 3500 drugs, five drugs (when applied in a post-treatment regimen relative to stretch injury) improved both LDH and MTT responses. The effects of rifampicin were investigated in further detail. Rifampicin reduced cell necrosis and apoptosis and improved cellular bioenergetics. In a second model (stretch injury in human stem cell-derived neurons), rifampicin pretreatment attenuated LDH release, protected against the loss of neurite length and maintained neuron-specific class III β-tubulin immunoreactivity. CONCLUSIONS AND IMPLICATIONS We conclude that the current model is suitable for medium-throughput screening to identify compounds with neuroprotective potential. Rifampicin, when applied either in pre- or post-treatment, improves the viability of neurons subjected to stretch injury and protects against neurite loss. Rifampicin may be a candidate for repurposing for the therapy of traumatic brain injury. LINKED ARTICLES This article is part of a themed section on Inventing New Therapies Without Reinventing the Wheel: The Power of Drug Repurposing. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.2/issuetoc.
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Affiliation(s)
- Isabel López-García
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Domokos Gerő
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Bartosz Szczesny
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Petra Szoleczky
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gabor Olah
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Katalin Módis
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Kangling Zhang
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jungling Gao
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Wu
- Department of Neuroscience & Cell Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Lawrence C Sowers
- Department of Pharmacology, University of Texas Medical Branch, Galveston, TX, USA
| | - Doug DeWitt
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Donald S Prough
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
| | - Csaba Szabo
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, TX, USA
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16
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Yu M, Al-Dallal S, Al-Haj L, Panjwani S, McCartney AS, Edwards SM, Manjunath P, Walker C, Awgulewitsch A, Hentges KE. Transcriptional regulation of the proto-oncogene Zfp521 by SPI1 (PU.1) and HOXC13. Genesis 2016; 54:519-533. [PMID: 27506447 PMCID: PMC5073027 DOI: 10.1002/dvg.22963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 08/08/2016] [Accepted: 08/08/2016] [Indexed: 12/19/2022]
Abstract
The mouse zinc‐finger gene Zfp521 (also known as ecotropic viral insertion site 3; Evi3; and ZNF521 in humans) has been identified as a B‐cell proto‐oncogene, causing leukemia in mice following retroviral insertions in its promoter region that drive Zfp521 over‐expression. Furthermore, ZNF521 is expressed in human hematopoietic cells, and translocations between ZNF521 and PAX5 are associated with pediatric acute lymphoblastic leukemia. However, the regulatory factors that control Zfp521 expression directly have not been characterized. Here we demonstrate that the transcription factors SPI1 (PU.1) and HOXC13 synergistically regulate Zfp521 expression, and identify the regions of the Zfp521 promoter required for this transcriptional activity. We also show that SPI1 and HOXC13 activate Zfp521 in a dose‐dependent manner. Our data support a role for this regulatory mechanism in vivo, as transgenic mice over‐expressing Hoxc13 in the fetal liver show a strong correlation between Hoxc13 expression levels and Zfp521 expression. Overall these experiments provide insights into the regulation of Zfp521 expression in a nononcogenic context. The identification of transcription factors capable of activating Zfp521 provides a foundation for further investigation of the regulatory mechanisms involved in ZFP521‐driven cell differentiation processes and diseases linked to Zfp521 mis‐expression.
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Affiliation(s)
- Ming Yu
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.,The Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Molecular and Clinical Medicine, Kunming Medical University, Kunming, Yunnan Province, 650500, People's Republic of China
| | - Salma Al-Dallal
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Latifa Al-Haj
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.,Molecular Biomedicine Program, Program in Biomolecular Research, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Shiraj Panjwani
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Akina S McCartney
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Sarah M Edwards
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Pooja Manjunath
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | - Catherine Walker
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
| | | | - Kathryn E Hentges
- Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK.
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17
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Qiao Y, Yang X, Jing N. Epigenetic regulation of early neural fate commitment. Cell Mol Life Sci 2016; 73:1399-411. [PMID: 26801220 PMCID: PMC11108527 DOI: 10.1007/s00018-015-2125-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/01/2015] [Accepted: 12/22/2015] [Indexed: 12/18/2022]
Abstract
Early neural fate commitment is a key process in neural development and establishment of the central nervous system, and this process is tightly controlled by extrinsic signals, intrinsic factors, and epigenetic regulation. Here, we summarize the main findings regarding the regulatory network of epigenetic mechanisms that play important roles during early neural fate determination and embryonic development, including histone modifications, chromatin remodeling, DNA modifications, and RNA-level regulation. These regulatory mechanisms coordinate to play essential roles in silencing of pluripotency genes and activating key neurodevelopmental genes during cell fate commitment at DNA, histone, chromatin, and RNA levels. Moreover, we discuss the relationship between epigenetic regulation, signaling pathways, and intrinsic factors during early neural fate specification.
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Affiliation(s)
- Yunbo Qiao
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
| | - Xianfa Yang
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 200031, China
| | - Naihe Jing
- State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- School of Life Science and Technology, Shanghai Tech University, Shanghai, 200031, China.
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18
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Chen X, Du Z, Li X, Wang L, Wang F, Shi W, Hao A. Protein Palmitoylation Regulates Neural Stem Cell Differentiation by Modulation of EID1 Activity. Mol Neurobiol 2015; 53:5722-36. [PMID: 26497028 DOI: 10.1007/s12035-015-9481-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/08/2015] [Indexed: 01/13/2023]
Abstract
The functional significance of palmitoylation in the switch between self-renewal and differentiation of neural stem cells (NSCs) is not well defined, and the underlying mechanisms of protein palmitoylation are not well understood. Here, mouse NSCs were used as a model system and cell behavior was monitored in the presence of the protein palmitoylation inhibitor 2-bromopalmitate (2BRO). Our data show that 2BRO impaired the differentiation of NSCs into both neurons and glia and impaired NSC cell cycle exit. Moreover, the results show that palmitoylation modified E1A-like inhibitor of differentiation one (EID1) and this modification regulated EID1 degradation and CREB-binding protein (CBP)/p300 histone acetyltransferase activity at the switch between self-renewal and differentiation of NSCs. Our results extended the cellular role of palmitoylation, suggesting that it acts as a regulator in the acetylation-dependent gene expression network, and established the epigenetic regulatory function of palmitoylation in the switch between maintenance of multipotency and differentiation in NSCs.
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Affiliation(s)
- Xueran Chen
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Histology and Embryology, Shandong University School of Medicine, No. 44, Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.,Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, No. 350, Shushan Hu Road, Hefei, Anhui, 230031, People's Republic of China
| | - Zhaoxia Du
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Histology and Embryology, Shandong University School of Medicine, No. 44, Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Xian Li
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Histology and Embryology, Shandong University School of Medicine, No. 44, Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Liyan Wang
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Histology and Embryology, Shandong University School of Medicine, No. 44, Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Fuwu Wang
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Histology and Embryology, Shandong University School of Medicine, No. 44, Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Wei Shi
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Histology and Embryology, Shandong University School of Medicine, No. 44, Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China
| | - Aijun Hao
- Key Laboratory of the Ministry of Education for Experimental Teratology, Shandong Provincial Key Laboratory of Mental Disorders, Department of Histology and Embryology, Shandong University School of Medicine, No. 44, Wenhua Xi Road, Jinan, Shandong, 250012, People's Republic of China.
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