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Gao Y, He Y, Tang Y, Chen ZS, Qu M. VISTA: A Novel Checkpoint for Cancer Immunotherapy. Drug Discov Today 2024; 29:104045. [PMID: 38797321 DOI: 10.1016/j.drudis.2024.104045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/20/2024] [Accepted: 05/21/2024] [Indexed: 05/29/2024]
Abstract
V-domain Ig suppressor of T cell activation (VISTA) is a recently identified member of the B7 family of immunoregulatory proteins. It is pivotal for maintaining T cell quiescence and exerts a significant regulatory influence on the immune response to tumors. Accumulating clinical evidence suggests that the influence of VISTA on tumor immunity is more nuanced than initially postulated. Although these revelations add layers of complexity to our understanding of the function of VISTA, they also offer novel avenues for scientific inquiry and potential therapeutic targets. In this review, we scrutinize the current literature pertaining to the expression of VISTA in various of malignancies, aiming to elucidate its intricate roles within the tumor microenvironment and in cancer immunotherapy.
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Affiliation(s)
- Yu Gao
- Translational Medical Center, Weifang Second People's Hospital, Weifang 261041, Shandong, China
| | - Yanting He
- Department of Pathology, The Affiliated Hospital of Qingdao University, Pingdu 266700, Shandong, China
| | - Yuanyuan Tang
- Translational Medical Center, Weifang Second People's Hospital, Weifang 261041, Shandong, China
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, Queens, NY 11439, USA.
| | - Meihua Qu
- Translational Medical Center, Weifang Second People's Hospital, Weifang 261041, Shandong, China; School of Life Science and Technology, Weifang Medical University, Weifang 261053, Shandon, China.
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2
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López-Ayllón BD, Marin S, Fernández MF, García-García T, Fernández-Rodríguez R, de Lucas-Rius A, Redondo N, Mendoza-García L, Foguet C, Grigas J, Calvet A, Villalba JM, Gómez MJR, Megías D, Mandracchia B, Luque D, Lozano JJ, Calvo C, Herrán UM, Thomson TM, Garrido JJ, Cascante M, Montoya M. Metabolic and mitochondria alterations induced by SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10. J Med Virol 2024; 96:e29752. [PMID: 38949191 DOI: 10.1002/jmv.29752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
Antiviral signaling, immune response and cell metabolism are dysregulated by SARS-CoV-2, the causative agent of COVID-19. Here, we show that SARS-CoV-2 accessory proteins ORF3a, ORF9b, ORF9c and ORF10 induce a significant mitochondrial and metabolic reprogramming in A549 lung epithelial cells. While ORF9b, ORF9c and ORF10 induced largely overlapping transcriptomes, ORF3a induced a distinct transcriptome, including the downregulation of numerous genes with critical roles in mitochondrial function and morphology. On the other hand, all four ORFs altered mitochondrial dynamics and function, but only ORF3a and ORF9c induced a marked alteration in mitochondrial cristae structure. Genome-Scale Metabolic Models identified both metabolic flux reprogramming features both shared across all accessory proteins and specific for each accessory protein. Notably, a downregulated amino acid metabolism was observed in ORF9b, ORF9c and ORF10, while an upregulated lipid metabolism was distinctly induced by ORF3a. These findings reveal metabolic dependencies and vulnerabilities prompted by SARS-CoV-2 accessory proteins that may be exploited to identify new targets for intervention.
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Affiliation(s)
- Blanca D López-Ayllón
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - Marco Fariñas Fernández
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Ana de Lucas-Rius
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Natalia Redondo
- Unit of Infectious Diseases, University Hospital '12 de Octubre', Institute for Health Research Hospital '12 de Octubre' (imas12), Madrid, Spain
- Centre for Biomedical Research Network on Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Laura Mendoza-García
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Carles Foguet
- British Heart Foundation Cardiovascular Epidemiology Unit and Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Juozas Grigas
- Laboratory of Immunology, Department of Anatomy and Physiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alba Calvet
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - José Manuel Villalba
- Department of Cell Biology, Physiology and Immunology, Agrifood Campus of International Excellence, University of Córdoba, Córdoba, Spain
| | - María Josefa Rodríguez Gómez
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Diego Megías
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
| | - Biagio Mandracchia
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- ETSI Telecommunication, University of Valladolid, Valladolid, Spain
| | - Daniel Luque
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
- School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Juan José Lozano
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Cristina Calvo
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
| | - Unai Merino Herrán
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Timothy M Thomson
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Barcelona Institute for Molecular Biology (IBMB-CSIC), Barcelona, Spain
- Translational Research and Computational Biology Laboratory, Faculty of Science and Engineering, Peruvian University Cayetano Heredia, Lima, Perú
| | - Juan J Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research, Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona (UB), Barcelona, Spain
- CIBER of Hepatic and Digestive Diseases (CIBEREHD), Institute of Health Carlos III (ISCIII), Madrid, Spain
- Institute of Biomedicine of University of Barcelona (IBUB), University of Barcelona (UB), Barcelona, Spain
| | - María Montoya
- Viral Immunology Lab, Molecular Biomedicine Department, BICS Unit. Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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3
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Hoffman JA, Muse GW, Langer LF, Patterson AI, Gandara I, Ward JM, Archer TK. BRG1 establishes the neuroectodermal chromatin landscape to restrict dorsal cell fates. SCIENCE ADVANCES 2024; 10:eadj5107. [PMID: 38427725 PMCID: PMC10906928 DOI: 10.1126/sciadv.adj5107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
Cell fate decisions are achieved with gene expression changes driven by lineage-specific transcription factors (TFs). These TFs depend on chromatin remodelers including the Brahma-related gene 1 (BRG1)-associated factor (BAF) complex to activate target genes. BAF complex subunits are essential for development and frequently mutated in cancer. Thus, interrogating how BAF complexes contribute to cell fate decisions is critical for human health. We examined the requirement for the catalytic BAF subunit BRG1 in neural progenitor cell (NPC) specification from human embryonic stem cells. During the earliest stages of differentiation, BRG1 was required to establish chromatin accessibility at neuroectoderm-specific enhancers. Depletion of BRG1 dorsalized NPCs and promoted precocious neural crest specification and enhanced neuronal differentiation. These findings demonstrate that BRG1 mediates NPC specification by ensuring proper expression of lineage-specific TFs and appropriate activation of their transcriptional programs.
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Affiliation(s)
- Jackson A. Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Ginger W. Muse
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Lee F. Langer
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - A. Isabella Patterson
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
- University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Isabella Gandara
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - James M. Ward
- Integrative Bioinformatics, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Trevor K. Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institutes of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
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4
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Fatima N, Saif Ur Rahman M, Qasim M, Ali Ashfaq U, Ahmed U, Masoud MS. Transcriptional Factors Mediated Reprogramming to Pluripotency. Curr Stem Cell Res Ther 2024; 19:367-388. [PMID: 37073151 DOI: 10.2174/1574888x18666230417084518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 04/20/2023]
Abstract
A unique kind of pluripotent cell, i.e., Induced pluripotent stem cells (iPSCs), now being targeted for iPSC synthesis, are produced by reprogramming animal and human differentiated cells (with no change in genetic makeup for the sake of high efficacy iPSCs formation). The conversion of specific cells to iPSCs has revolutionized stem cell research by making pluripotent cells more controllable for regenerative therapy. For the past 15 years, somatic cell reprogramming to pluripotency with force expression of specified factors has been a fascinating field of biomedical study. For that technological primary viewpoint reprogramming method, a cocktail of four transcription factors (TF) has required: Kruppel-like factor 4 (KLF4), four-octamer binding protein 34 (OCT3/4), MYC and SOX2 (together referred to as OSKM) and host cells. IPS cells have great potential for future tissue replacement treatments because of their ability to self-renew and specialize in all adult cell types, although factor-mediated reprogramming mechanisms are still poorly understood medically. This technique has dramatically improved performance and efficiency, making it more useful in drug discovery, disease remodeling, and regenerative medicine. Moreover, in these four TF cocktails, more than 30 reprogramming combinations were proposed, but for reprogramming effectiveness, only a few numbers have been demonstrated for the somatic cells of humans and mice. Stoichiometry, a combination of reprogramming agents and chromatin remodeling compounds, impacts kinetics, quality, and efficiency in stem cell research.
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Affiliation(s)
- Nazira Fatima
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Muhammad Saif Ur Rahman
- Institute of Advanced Studies, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Uzair Ahmed
- EMBL Partnership Institute for Genome Editing Technologies, Vilnius University, Vilnius, 10257, Lithuania
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, 38000, Pakistan
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5
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Gökbuget D, Boileau RM, Lenshoek K, Blelloch R. MLL3/MLL4 enzymatic activity shapes DNA replication timing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.569680. [PMID: 38106216 PMCID: PMC10723431 DOI: 10.1101/2023.12.07.569680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mammalian genomes are replicated in a precise order during S phase, which is cell-type-specific1-3 and correlates with local transcriptional activity2,4-8, chromatin modifications9 and chromatin architecture1,10,11,12. However, the causal relationships between these features and the key regulators of DNA replication timing (RT) are largely unknown. Here, machine learning was applied to quantify chromatin features, including epigenetic marks, histone variants and chromatin architectural factors, best predicting local RT under steady-state and RT changes during early embryonic stem (ES) cell differentiation. About one-third of genome exhibited RT changes during the differentiation. Combined, chromatin features predicted steady-state RT and RT changes with high accuracy. Of these features, histone H3 lysine 4 monomethylation (H3K4me1) catalyzed by MLL3/4 (also known as KMT2C/D) emerged as a top predictor. Loss of Mll3/4 (but not Mll3 alone) or their enzymatic activity resulted in erasure of genome-wide RT dynamics during ES cell differentiation. Sites that normally gain H3K4me1 in a MLL3/4-dependent fashion during the transition failed to transition towards earlier RT, often with transcriptional activation unaffected. Further analysis revealed a requirement for MLL3/4 in promoting DNA replication initiation zones through MCM2 recruitment, providing a direct link for its role in regulating RT. Our results uncover MLL3/4-dependent H3K4me1 as a functional regulator of RT and highlight a causal relationship between the epigenome and RT that is largely uncoupled from transcription. These findings uncover a previously unknown role for MLL3/4-dependent chromatin functions which is likely relevant to the numerous diseases associated with MLL3/4 mutations.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ryan M. Boileau
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Present address: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Kayla Lenshoek
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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6
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Choi S, Whitman MA, Shimpi AA, Sempertegui ND, Chiou AE, Druso JE, Verma A, Lux SC, Cheng Z, Paszek M, Elemento O, Estroff LA, Fischbach C. Bone-matrix mineralization dampens integrin-mediated mechanosignalling and metastatic progression in breast cancer. Nat Biomed Eng 2023; 7:1455-1472. [PMID: 37550422 DOI: 10.1038/s41551-023-01077-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/30/2023] [Indexed: 08/09/2023]
Abstract
In patients with breast cancer, lower bone mineral density increases the risk of bone metastasis. Although the relationship between bone-matrix mineralization and tumour-cell phenotype in breast cancer is not well understood, mineralization-induced rigidity is thought to drive metastatic progression via increased cell-adhesion forces. Here, by using collagen-based matrices with adjustable intrafibrillar mineralization, we show that, unexpectedly, matrix mineralization dampens integrin-mediated mechanosignalling and induces a less proliferative stem-cell-like phenotype in breast cancer cells. In mice with xenografted decellularized physiological bone matrices seeded with human breast tumour cells, the presence of bone mineral reduced tumour growth and upregulated a gene-expression signature that is associated with longer metastasis-free survival in patients with breast cancer. Our findings suggest that bone-matrix changes in osteogenic niches regulate metastatic progression in breast cancer and that in vitro models of bone metastasis should integrate organic and inorganic matrix components to mimic physiological and pathologic mineralization.
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Affiliation(s)
- Siyoung Choi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew A Whitman
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Adrian A Shimpi
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Nicole D Sempertegui
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Aaron E Chiou
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Joseph E Druso
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Akanksha Verma
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie C Lux
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Zhu Cheng
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Matthew Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Lara A Estroff
- Department of Materials Science and Engineering, Cornell University, Ithaca, NY, USA.
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA.
| | - Claudia Fischbach
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY, USA.
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7
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Gökbuget D, Lenshoek K, Boileau RM, Bayerl J, Huang H, Wiita AP, Laird DJ, Blelloch R. Transcriptional repression upon S phase entry protects genome integrity in pluripotent cells. Nat Struct Mol Biol 2023; 30:1561-1570. [PMID: 37696959 DOI: 10.1038/s41594-023-01092-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/07/2023] [Indexed: 09/13/2023]
Abstract
Coincident transcription and DNA replication causes replication stress and genome instability. Rapidly dividing mouse pluripotent stem cells are highly transcriptionally active and experience elevated replication stress, yet paradoxically maintain genome integrity. Here, we study FOXD3, a transcriptional repressor enriched in pluripotent stem cells, and show that its repression of transcription upon S phase entry is critical to minimizing replication stress and preserving genome integrity. Acutely deleting Foxd3 leads to immediate replication stress, G2/M phase arrest, genome instability and p53-dependent apoptosis. FOXD3 binds near highly transcribed genes during S phase entry, and its loss increases the expression of these genes. Transient inhibition of RNA polymerase II in S phase reduces observed replication stress and cell cycle defects. Loss of FOXD3-interacting histone deacetylases induces replication stress, while transient inhibition of histone acetylation opposes it. These results show how a transcriptional repressor can play a central role in maintaining genome integrity through the transient inhibition of transcription during S phase, enabling faithful DNA replication.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Kayla Lenshoek
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan M Boileau
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan Bayerl
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, San Francisco, CA, USA
| | - Hector Huang
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Arun P Wiita
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Diana J Laird
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Science, University of California, San Francisco, San Francisco, CA, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
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8
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Selleri L, Rijli FM. Shaping faces: genetic and epigenetic control of craniofacial morphogenesis. Nat Rev Genet 2023; 24:610-626. [PMID: 37095271 DOI: 10.1038/s41576-023-00594-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2023] [Indexed: 04/26/2023]
Abstract
Major differences in facial morphology distinguish vertebrate species. Variation of facial traits underlies the uniqueness of human individuals, and abnormal craniofacial morphogenesis during development leads to birth defects that significantly affect quality of life. Studies during the past 40 years have advanced our understanding of the molecular mechanisms that establish facial form during development, highlighting the crucial roles in this process of a multipotent cell type known as the cranial neural crest cell. In this Review, we discuss recent advances in multi-omics and single-cell technologies that enable genes, transcriptional regulatory networks and epigenetic landscapes to be closely linked to the establishment of facial patterning and its variation, with an emphasis on normal and abnormal craniofacial morphogenesis. Advancing our knowledge of these processes will support important developments in tissue engineering, as well as the repair and reconstruction of the abnormal craniofacial complex.
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Affiliation(s)
- Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences, School of Dentistry, University of California, San Francisco, CA, USA.
- Department of Anatomy, School of Medicine, University of California, San Francisco, CA, USA.
| | - Filippo M Rijli
- Laboratory of Developmental Neuroepigenetics, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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9
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Ishibashi R. Multidimensional scaling methods can reconstruct genomic DNA loops using Hi-C data properties. PLoS One 2023; 18:e0289651. [PMID: 37590265 PMCID: PMC10434948 DOI: 10.1371/journal.pone.0289651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/23/2023] [Indexed: 08/19/2023] Open
Abstract
This paper proposes multidimensional scaling (MDS) applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Currently, the mechanisms underlying the regulation of gene expression are poorly understood, and where and when DNA loops are formed remains undetermined. Previous studies have focused on reproducing the entire three-dimensional structure of chromatin; however, identifying DNA loops using these data is time-consuming and difficult. MDS is an unsupervised method for reconstructing the original coordinates from a distance matrix. Here, MDS was applied to high-throughput chromosome conformation capture (Hi-C) data on genomic interactions to visualize DNA loops. Hi-C data were converted to distances by taking the inverse to reproduce loops via MDS, and the missing values were set to zero. Using the converted data, MDS was applied to the log-transformed genomic coordinate distances and this process successfully reproduced the DNA loops in the given structure. Consequently, the reconstructed DNA loops revealed significantly more DNA-transcription factor interactions involved in DNA loop formation than those obtained from previously applied methods. Furthermore, the reconstructed DNA loops were significantly consistent with chromatin immunoprecipitation followed by sequencing (ChIP-seq) peak positions. In conclusion, the proposed method is an improvement over previous methods for identifying DNA loops.
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Affiliation(s)
- Ryo Ishibashi
- Department of Physics, Chuo University, Tokyo, Japan
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10
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Saha D, Hailu S, Hada A, Lee J, Luo J, Ranish JA, Lin YC, Feola K, Persinger J, Jain A, Liu B, Lu Y, Sen P, Bartholomew B. The AT-hook is an evolutionarily conserved auto-regulatory domain of SWI/SNF required for cell lineage priming. Nat Commun 2023; 14:4682. [PMID: 37542049 PMCID: PMC10403523 DOI: 10.1038/s41467-023-40386-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The SWI/SNF ATP-dependent chromatin remodeler is a master regulator of the epigenome, controlling pluripotency and differentiation. Towards the C-terminus of the catalytic subunit of SWI/SNF is a motif called the AT-hook that is evolutionary conserved. The AT-hook is present in many chromatin modifiers and generally thought to help anchor them to DNA. We observe however that the AT-hook regulates the intrinsic DNA-stimulated ATPase activity aside from promoting SWI/SNF recruitment to DNA or nucleosomes by increasing the reaction velocity a factor of 13 with no accompanying change in substrate affinity (KM). The changes in ATP hydrolysis causes an equivalent change in nucleosome movement, confirming they are tightly coupled. The catalytic subunit's AT-hook is required in vivo for SWI/SNF remodeling activity in yeast and mouse embryonic stem cells. The AT-hook in SWI/SNF is required for transcription regulation and activation of stage-specific enhancers critical in cell lineage priming. Similarly, growth assays suggest the AT-hook is required in yeast SWI/SNF for activation of genes involved in amino acid biosynthesis and metabolizing ethanol. Our findings highlight the importance of studying SWI/SNF attenuation versus eliminating the catalytic subunit or completely shutting down its enzymatic activity.
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Affiliation(s)
- Dhurjhoti Saha
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Solomon Hailu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- Illumina, 5200 Illumina Way, San Diego, CA, 92122, USA
| | - Arjan Hada
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Junwoo Lee
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Jie Luo
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Jeff A Ranish
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Yuan-Chi Lin
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
- BioAgilytix, Durham, NC, 27713, USA
| | - Kyle Feola
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- Department of Internal Medicine (Nephrology) and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jim Persinger
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Abhinav Jain
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA
| | - Bin Liu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA
| | - Payel Sen
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD, 21224, USA
| | - Blaine Bartholomew
- Department of Epigenetics and Molecular Carcinogenesis, Univ. of Texas MD Anderson Cancer Center, Houston, TX, 77230, USA.
- University of Texas MD Anderson Cancer Center, Center for Cancer Epigenetics, Houston, TX, 77230, USA.
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11
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Pulecio J, Tayyebi Z, Liu D, Wong W, Luo R, Damodaran JR, Kaplan S, Cho H, Yan J, Murphy D, Rickert RW, Shukla A, Zhong A, González F, Yang D, Li W, Zhou T, Apostolou E, Leslie CS, Huangfu D. Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544990. [PMID: 37398096 PMCID: PMC10312725 DOI: 10.1101/2023.06.14.544990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
The mechanisms underlying the ability of embryonic stem cells (ESCs) to rapidly activate lineage-specific genes during differentiation remain largely unknown. Through multiple CRISPR-activation screens, we discovered human ESCs have pre-established transcriptionally competent chromatin regions (CCRs) that support lineage-specific gene expression at levels comparable to differentiated cells. CCRs reside in the same topological domains as their target genes. They lack typical enhancer-associated histone modifications but show enriched occupancy of pluripotent transcription factors, DNA demethylation factors, and histone deacetylases. TET1 and QSER1 protect CCRs from excessive DNA methylation, while HDAC1 family members prevent premature activation. This "push and pull" feature resembles bivalent domains at developmental gene promoters but involves distinct molecular mechanisms. Our study provides new insights into pluripotency regulation and cellular plasticity in development and disease. One sentence summary We report a class of distal regulatory regions distinct from enhancers that confer human embryonic stem cells with the competence to rapidly activate the expression of lineage-specific genes.
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12
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Smits JG, Arts JA, Frölich S, Snabel RR, Heuts BM, Martens JH, van Heeringen SJ, Zhou H. scANANSE gene regulatory network and motif analysis of single-cell clusters. F1000Res 2023; 12:243. [PMID: 38116584 PMCID: PMC10728588 DOI: 10.12688/f1000research.130530.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/03/2023] [Indexed: 12/21/2023] Open
Abstract
The recent development of single-cell techniques is essential to unravel complex biological systems. By measuring the transcriptome and the accessible genome on a single-cell level, cellular heterogeneity in a biological environment can be deciphered. Transcription factors act as key regulators activating and repressing downstream target genes, and together they constitute gene regulatory networks that govern cell morphology and identity. Dissecting these gene regulatory networks is crucial for understanding molecular mechanisms and disease, especially within highly complex biological systems. The gene regulatory network analysis software ANANSE and the motif enrichment software GimmeMotifs were both developed to analyse bulk datasets. We developed scANANSE, a software pipeline for gene regulatory network analysis and motif enrichment using single-cell RNA and ATAC datasets. The scANANSE pipeline can be run from either R or Python. First, it exports data from standard single-cell objects. Next, it automatically runs multiple comparisons of cell cluster data. Finally, it imports the results back to the single-cell object, where the result can be further visualised, integrated, and interpreted. Here, we demonstrate our scANANSE pipeline on a publicly available PBMC multi-omics dataset. It identifies well-known cell type-specific hematopoietic factors. Importantly, we also demonstrated that scANANSE combined with GimmeMotifs is able to predict transcription factors with both activating and repressing roles in gene regulation.
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Affiliation(s)
- Jos G.A. Smits
- Molecular Developmental Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
| | - Julian A. Arts
- Molecular Developmental Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
| | - Siebren Frölich
- Molecular Developmental Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
| | - Rebecca R. Snabel
- Molecular Developmental Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
| | - Branco M.H. Heuts
- Molecular Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
| | - Joost H.A. Martens
- Molecular Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
| | - Simon J. van Heeringen
- Molecular Developmental Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
| | - Huiqing Zhou
- Molecular Developmental Biology, Radboud University, Nijmegen, Gelderland, The Netherlands
- Human Genetics, Radboud University Medical Centre, Nijmegen, Gelderland, The Netherlands
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13
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Boileau RM, Chen KX, Blelloch R. Loss of MLL3/4 decouples enhancer H3K4 monomethylation, H3K27 acetylation, and gene activation during embryonic stem cell differentiation. Genome Biol 2023; 24:41. [PMID: 36869380 PMCID: PMC9983171 DOI: 10.1186/s13059-023-02883-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 02/19/2023] [Indexed: 03/05/2023] Open
Abstract
BACKGROUND Enhancers are essential in defining cell fates through the control of cell-type-specific gene expression. Enhancer activation is a multi-step process involving chromatin remodelers and histone modifiers including the monomethylation of H3K4 (H3K4me1) by MLL3 (KMT2C) and MLL4 (KMT2D). MLL3/4 are thought to be critical for enhancer activation and cognate gene expression including through the recruitment of acetyltransferases for H3K27. RESULTS Here we test this model by evaluating the impact of MLL3/4 loss on chromatin and transcription during early differentiation of mouse embryonic stem cells. We find that MLL3/4 activity is required at most if not all sites that gain or lose H3K4me1 but is largely dispensable at sites that remain stably methylated during this transition. This requirement extends to H3K27 acetylation (H3K27ac) at most transitional sites. However, many sites gain H3K27ac independent of MLL3/4 or H3K4me1 including enhancers regulating key factors in early differentiation. Furthermore, despite the failure to gain active histone marks at thousands of enhancers, transcriptional activation of nearby genes is largely unaffected, thus uncoupling the regulation of these chromatin events from transcriptional changes during this transition. These data challenge current models of enhancer activation and imply distinct mechanisms between stable and dynamically changing enhancers. CONCLUSIONS Collectively, our study highlights gaps in knowledge about the steps and epistatic relationships of enzymes necessary for enhancer activation and cognate gene transcription.
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Affiliation(s)
- Ryan M. Boileau
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program , University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
| | - Kevin X. Chen
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, and Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
- Developmental and Stem Cell Biology Graduate Program , University of California San Francisco, San Francisco, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA USA
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14
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Wen F, Tan Z, Huang D, Jiang Y, Xiang J. LncRNA PVT1 Promotes Neuronal Cell Apoptosis and Neuroinflammation by Regulating miR-488-3p/FOXD3/SCN2A Axis in Epilepsy. Neurochem Res 2023; 48:895-908. [PMID: 36378391 DOI: 10.1007/s11064-022-03801-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/08/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022]
Abstract
It is vital to understand the mechanism of epilepsy onset and development. Dysregulated lncRNAs are closely associated with epilepsy. Our work probed the role of lncRNA PVT1/miR-488-3p/FOXD3/SCN2A axis in epilepsy. The mRNA and protein expressions were assessed using qRT-PCR and western blot. MTT assay and TUNEL staining were conducted to assess cell viability and apoptosis, respectively. TNFα, IL-1β and IL-6 levels were analyzed using ELISA. LDH level was tested by Assay Kit. The binding relationship between PVT1, miR-488-3p and FOXD3 were verified using dual luciferase reporter gene assay. The epilepsy model of rats was established by lithium-pilocarpine injection. Nissl staining was performed to evaluate neuronal damage. PVT1 was markedly upregulated in epilepsy model cells. Knockdown of PVT1 increased the viability, while repressed the apoptosis and inflammatory cytokines secretion as well as LDH level in epilepsy cell model. MiR-488-3p alleviated neuronal injury and neuroinflammation in model cells. MiR-488-3p functioned as the direct target of PVT1, and its inhibition neutralized the effects of PVT1 silencing on neuronal cell injury and neuroinflammation in model cells. Furthermore, miR-488-3p inhibited neuronal cell injury and neuroinflammation in model cells by regulating FOXD3/SCN2A pathway. Finally, animal experiments proved that PVT1 promoted epilepsy-induced neuronal cell injury and neuroinflammation by regulating miR-488-3p-mediated FOXD3/SCN2A pathway. PVT1 promoted neuronal cell injury and inflammatory response in epilepsy via inhibiting miR-488-3p and further regulating FOXD3/SCN2A pathway.
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Affiliation(s)
- Fang Wen
- Department of Neurology, The Second Xiangya Hospital of Central South University, Changsha, 410011, Hunan, People's Republic of China
| | - Zhigang Tan
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139, Renmin Road, Changsha, 410011, Hunan, People's Republic of China
| | - Dezhi Huang
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139, Renmin Road, Changsha, 410011, Hunan, People's Republic of China
| | - Yugang Jiang
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139, Renmin Road, Changsha, 410011, Hunan, People's Republic of China
| | - Jun Xiang
- Department of Neurosurgery, The Second Xiangya Hospital of Central South University, No. 139, Renmin Road, Changsha, 410011, Hunan, People's Republic of China.
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15
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Furlan G, Huyghe A, Combémorel N, Lavial F. Molecular versatility during pluripotency progression. Nat Commun 2023; 14:68. [PMID: 36604434 PMCID: PMC9814743 DOI: 10.1038/s41467-022-35775-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 12/22/2022] [Indexed: 01/07/2023] Open
Abstract
A challenge during development is to ensure lineage segregation while preserving plasticity. Using pluripotency progression as a paradigm, we review how developmental transitions are coordinated by redeployments, rather than global resettings, of cellular components. We highlight how changes in response to extrinsic cues (FGF, WNT, Activin/Nodal, Netrin-1), context- and stoichiometry-dependent action of transcription factors (Oct4, Nanog) and reconfigurations of epigenetic regulators (enhancers, promoters, TrxG, PRC) may confer robustness to naïve to primed pluripotency transition. We propose the notion of Molecular Versatility to regroup mechanisms by which molecules are repurposed to exert different, sometimes opposite, functions in close stem cell configurations.
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Affiliation(s)
- Giacomo Furlan
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.,Lunenfeld-Tanenbaum Research Institute, University of Toronto, Toronto, ON, Canada
| | - Aurélia Huyghe
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Noémie Combémorel
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France
| | - Fabrice Lavial
- Cellular reprogramming, stem cells and oncogenesis laboratory - Equipe labellisée La Ligue Contre le Cancer - LabEx Dev2Can - Univ Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Lyon, 69008, France.
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16
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The pioneering function of the hox transcription factors. Semin Cell Dev Biol 2022:S1084-9521(22)00354-8. [PMID: 36517345 DOI: 10.1016/j.semcdb.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/13/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
Ever since the discovery that the Hox family of transcription factors establish morphological diversity in the developing embryo, major efforts have been directed towards understanding Hox-dependent patterning. This has led to important discoveries, notably on the mechanisms underlying the collinear expression of Hox genes and Hox binding specificity. More recently, several studies have provided evidence that Hox factors have the capacity to bind their targets in an inaccessible chromatin context and trigger the switch to an accessible, transcriptional permissive, chromatin state. In this review, we provide an overview of the evidences supporting that Hox factors behave as pioneer factors and discuss the potential mechanisms implicated in Hox pioneer activity as well as the significance of this functional property in Hox-dependent patterning.
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17
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Giannopoulou AI, Kanakoglou DS, Papavassiliou AG, Piperi C. Insights into the multi-faceted role of Pioneer transcription factors in glioma formation and progression with targeting options. Biochim Biophys Acta Rev Cancer 2022; 1877:188801. [PMID: 36113627 DOI: 10.1016/j.bbcan.2022.188801] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/30/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022]
Abstract
Pioneer transcription factors (TFs) present an important subtype of transcription factors which are vital for cell programming during embryonic development and cellular memory during mitotic growth, as well as cell fate reprogramming. Pioneer TFs can engage specific target binding sites on nucleosomal DNA to attract chromatin remodeling complexes, cofactors, and other transcription factors, ultimately controlling gene expression by shaping locally the epigenome. The priority of binding that they exhibit in contrast to other transcription factors and their involvement in crucial events regarding cell fate, has implicated their aberrant function in the pathogenesis of several disorders including carcinogenesis. Emerging experimental data indicate that certain Pioneer TFs are highly implicated in gliomas development, in neoplastic cell proliferation, angiogenic processes, resistance to therapy, and patient survival. Herein, we describe the main structural characteristics and functional mechanisms of pioneer TFs, focusing on their central role in the pathogenesis and progression of gliomas. We further highlight the current treatment options ranging from natural agents (oleanolic acid) to a variety of chemical compounds (APR-246, COTI-2) and discuss potential delivery systems, including nanoparticles, viral vectors, and intracellular protein delivery techniques.
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Affiliation(s)
- Angeliki-Ioanna Giannopoulou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Dimitrios S Kanakoglou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Athanasios G Papavassiliou
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece,.
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18
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Candido-Ferreira IL, Lukoseviciute M, Sauka-Spengler T. Multi-layered transcriptional control of cranial neural crest development. Semin Cell Dev Biol 2022; 138:1-14. [PMID: 35941042 DOI: 10.1016/j.semcdb.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
Abstract
The neural crest (NC) is an emblematic population of embryonic stem-like cells with remarkable migratory ability. These distinctive attributes have inspired the curiosity of developmental biologists for over 150 years, however only recently the regulatory mechanisms controlling the complex features of the NC have started to become elucidated at genomic scales. Regulatory control of NC development is achieved through combinatorial transcription factor binding and recruitment of associated transcriptional complexes to distal cis-regulatory elements. Together, they regulate when, where and to what extent transcriptional programmes are actively deployed, ultimately shaping ontogenetic processes. Here, we discuss how transcriptional networks control NC ontogeny, with a special emphasis on the molecular mechanisms underlying specification of the cephalic NC. We also cover emerging properties of transcriptional regulation revealed in diverse developmental systems, such as the role of three-dimensional conformation of chromatin, and how they are involved in the regulation of NC ontogeny. Finally, we highlight how advances in deciphering the NC transcriptional network have afforded new insights into the molecular basis of human diseases.
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Affiliation(s)
- Ivan L Candido-Ferreira
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Martyna Lukoseviciute
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford OX3 9DS, UK.
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19
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Kobayashi Y, Nouet J, Baljinnyam E, Siddiqui Z, Fine DH, Fraidenraich D, Kumar VA, Shimizu E. iPSC-derived cranial neural crest-like cells can replicate dental pulp tissue with the aid of angiogenic hydrogel. Bioact Mater 2022; 14:290-301. [PMID: 35310357 PMCID: PMC8897656 DOI: 10.1016/j.bioactmat.2021.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 12/18/2022] Open
Abstract
The dental pulp has irreplaceable roles in maintaining healthy teeth and its regeneration is a primary aim of regenerative endodontics. This study aimed to replicate the characteristics of dental pulp tissue by using cranial neural crest (CNC)-like cells (CNCLCs); these cells were generated by modifying several steps of a previously established method for deriving NC-like cells from induced pluripotent stem cells (iPSCs). CNC is the anterior region of the neural crest in vertebrate embryos, which contains the primordium of dental pulp cells or odontoblasts. The produced CNCLCs showed approximately 2.5–12,000-fold upregulations of major CNC marker genes. Furthermore, the CNCLCs exhibited remarkable odontoblastic differentiation ability, especially when treated with a combination of the fibroblast growth factors (FGFs) FGF4 and FGF9. The FGFs induced odontoblast marker genes by 1.7–5.0-fold, as compared to bone morphogenetic protein 4 (BMP4) treatment. In a mouse subcutaneous implant model, the CNCLCs briefly fated with FGF4 + FGF9 replicated dental pulp tissue characteristics, such as harboring odontoblast-like cells, a dentin-like layer, and vast neovascularization, induced by the angiogenic self-assembling peptide hydrogel (SAPH), SLan. SLan acts as a versatile biocompatible scaffold in the canal space. This study demonstrated a successful collaboration between regenerative medicine and SAPH technology. Cranial neural crest like cells (CNCLCs) were generated by simplifying a previously established method for deriving neural crest-like cells from iPSCs. The produced CNCLCs showed approximately ∼12,000-fold upregulations of major CNC marker genes. The combination of fibroblast growth factors, FGF4 and FGF9, induced the CNCLCs toward odontoblastic differentiation more effectively than BMP4. In a mice subcutaneous implant model, the CNCLCs replicated the characteristics of dental pulp harboring vast neovascularization with the aid of the angiogenic hydrogel, SLan.
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20
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Epigenetics as "conductor" in "orchestra" of pluripotent states. Cell Tissue Res 2022; 390:141-172. [PMID: 35838826 DOI: 10.1007/s00441-022-03667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 07/01/2022] [Indexed: 11/02/2022]
Abstract
Pluripotent character is described as the potency of cells to differentiate into all three germ layers. The best example to reinstate the term lies in the context of embryonic stem cells (ESCs). Pluripotent ESC describes the in vitro status of those cells that originate during the complex process of embryogenesis. Pre-implantation to post-implantation development of embryo embrace cells with different levels of stemness. Currently, four states of pluripotency have been recognized, in the progressing order of "naïve," "poised," "formative," and "primed." Epigenetics act as the "conductor" in this "orchestra" of transition in pluripotent states. With a distinguishable gene expression profile, these four states associate with different epigenetic signatures, sometimes distinct while otherwise overlapping. The present review focuses on how epigenetic factors, including DNA methylation, bivalent chromatin, chromatin remodelers, chromatin/nuclear architecture, and microRNA, could dictate pluripotent states and their transition among themselves.
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21
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Schock EN, York JR, LaBonne C. The developmental and evolutionary origins of cellular pluripotency in the vertebrate neural crest. Semin Cell Dev Biol 2022; 138:36-44. [PMID: 35534333 DOI: 10.1016/j.semcdb.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/28/2022] [Accepted: 04/10/2022] [Indexed: 11/30/2022]
Abstract
Neural crest cells are central to vertebrate development and evolution, endowing vertebrates with a "new head" that resulted in morphological, physiological, and behavioral features that allowed vertebrates to become active predators. One remarkable feature of neural crest cells is their multi-germ layer potential that allows for the formation of both ectodermal (pigmentation, peripheral glia, sensory neurons) and mesenchymal (connective tissue, cartilage/bone, dermis) cell types. Understanding the cellular and evolutionary origins of this broad cellular potential in the neural crest has been a long-standing focus for developmental biologists. Here, we review recent work that has demonstrated that neural crest cells share key features with pluripotent blastula stem cells, including expression of the Yamanaka stem cell factors (Oct3/4, Klf4, Sox2, c-Myc). These shared features suggest that pluripotency is either retained in the neural crest from blastula stages or subsequently reactivated as the neural crest forms. We highlight the cellular and molecular parallels between blastula stem cells and neural crest cells and discuss the work that has led to current models for the cellular origins of broad potential in the crest. Finally, we explore how these themes can provide new insights into how and when neural crest cells and pluripotency evolved in vertebrates and the evolutionary relationship between these populations.
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Affiliation(s)
| | | | - Carole LaBonne
- Dept. of Molecular Biosciences; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, United States.
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22
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Coronel-Córdoba P, Molina MD, Cardona G, Fraguas S, Pascual-Carreras E, Saló E, Cebrià F, Adell T. FoxK1 is Required for Ectodermal Cell Differentiation During Planarian Regeneration. Front Cell Dev Biol 2022; 10:808045. [PMID: 35273960 PMCID: PMC8901602 DOI: 10.3389/fcell.2022.808045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Forkhead box (Fox) genes belong to the “winged helix” transcription factor superfamily. The function of some Fox genes is well known, such as the role of foxO in controlling metabolism and longevity and foxA in controlling differentiation of endodermal tissues. However, the role of some Fox factors is not yet well characterized. Such is the case of FoxK genes, which are mainly studied in mammals and have been implicated in diverse processes including cell proliferation, tissue differentiation and carcinogenesis. Planarians are free-living flatworms, whose importance in biomedical research lies in their regeneration capacity. Planarians possess a wide population of pluripotent adult stem cells, called neoblasts, which allow them to regenerate any body part after injury. In a recent study, we identified three foxK paralogs in the genome of Schmidtea mediterranea. In this study, we demonstrate that foxK1 inhibition prevents regeneration of the ectodermal tissues, including the nervous system and the epidermis. These results correlate with foxK1 expression in neoblasts and in neural progenitors. Although the triggering of wound genes expression, polarity reestablishment and proliferation was not affected after foxK1 silencing, the apoptotic response was decreased. Altogether, these results suggest that foxK1 would be required for differentiation and maintenance of ectodermal tissues.
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Affiliation(s)
- Pablo Coronel-Córdoba
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - M Dolores Molina
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Gemma Cardona
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Susanna Fraguas
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Eudald Pascual-Carreras
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Emili Saló
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Francesc Cebrià
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
| | - Teresa Adell
- Department of Genetics, Microbiology and Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), Barcelona, Spain
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23
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Preimplantation Endometrial Transcriptomics in Natural Conception Cycle of the Rhesus Monkey. REPRODUCTIVE MEDICINE 2022. [DOI: 10.3390/reprodmed3010003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There is no report on preimplantation phase endometrial transcriptomics in natural conception cycles of primates. In the present study, the whole-genome expression array of endometrium on Days 2, 4, and 6 post-ovulation (pov) in proven natural conception (Group 1; n = 12) and non-mated, ovulatory (Group 2; n = 12) cycles of rhesus monkeys was examined, compared, and validated. Of fifteen (15) genes showing differential expression (>2-fold; pFDR < 0.05), six genes (CHRND, FOXD3, GJD4, MAPK8IP3, MKS1, and NUP50) were upregulated, while eight genes (ADCY5, ADIPOR1, NNMT, PATL1, PIGV, TGFBR2, TOX2, and VWA5B1) were down regulated on Day 6 pov as compared to Day 2 pov in conception cycles. On Day 6 pov, four genes (ADCY5, NNMT, TOX2, and VWA5B1) were down regulated, and AVEN was upregulated in conception cycles compared with the non-conception cycle. These observations were orthogonally validated at protein expression level. Group-specifically expressed unique genes in conception cycles influence the process of induction of immune-tolerance, while the genes expressed in both groups influence processes of protein targeting and metabolism. A triad of timed-actions of progesterone, seminal plasma, and preimplantation embryo putatively regulate several input molecules to CREB, NF-kB, and STAT regulatory networks during secretory phase towards evolution of endometrial receptivity in the rhesus monkey.
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24
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Boesmans W, Nash A, Tasnády KR, Yang W, Stamp LA, Hao MM. Development, Diversity, and Neurogenic Capacity of Enteric Glia. Front Cell Dev Biol 2022; 9:775102. [PMID: 35111752 PMCID: PMC8801887 DOI: 10.3389/fcell.2021.775102] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
Enteric glia are a fascinating population of cells. Initially identified in the gut wall as the "support" cells of the enteric nervous system, studies over the past 20 years have unveiled a vast array of functions carried out by enteric glia. They mediate enteric nervous system signalling and play a vital role in the local regulation of gut functions. Enteric glial cells interact with other gastrointestinal cell types such as those of the epithelium and immune system to preserve homeostasis, and are perceptive to luminal content. Their functional versatility and phenotypic heterogeneity are mirrored by an extensive level of plasticity, illustrated by their reactivity in conditions associated with enteric nervous system dysfunction and disease. As one of the hallmarks of their plasticity and extending their operative relationship with enteric neurons, enteric glia also display neurogenic potential. In this review, we focus on the development of enteric glial cells, and the mechanisms behind their heterogeneity in the adult gut. In addition, we discuss what is currently known about the role of enteric glia as neural precursors in the enteric nervous system.
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Affiliation(s)
- Werend Boesmans
- Biomedical Research Institute (BIOMED), Hasselt University, Hasselt, Belgium
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Amelia Nash
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kinga R. Tasnády
- Biomedical Research Institute (BIOMED), Hasselt University, Hasselt, Belgium
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Wendy Yang
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taiwan, Taiwan
| | - Lincon A. Stamp
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marlene M. Hao
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
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25
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Sangokoya C. Measuring Endocytosis and Endosomal Uptake at Single Cell Resolution. Methods Mol Biol 2022; 2490:57-67. [PMID: 35486239 DOI: 10.1007/978-1-0716-2281-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Endocytosis impacts many cell biological functions, including in embryonic stem cells (ESCs). It has been shown that endocytosis is necessary for adequate FGF-signaling within the preimplantation ESC to post-implantation epiblast (EpiLC) pluripotency continuum and is required for proper levels of ERK activation. Quantitative methods at single cell resolution are needed to study endocytosis as well as its regulation and roles in these transitioning populations. The methods in this chapter provide an easily adaptable, multiplexable platform to monitor and quantify endosomal uptake at single cell resolution in live cells following receptor-mediated and non-receptor-mediated endocytosis, including nonspecific mechanisms such as pinocytosis.
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Affiliation(s)
- Carolyn Sangokoya
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA.
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26
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Puri D, Koschorz B, Engist B, Onishi-Seebacher M, Ryan D, Soujanya M, Montavon T. Foxd3 controls heterochromatin-mediated repression of repeat elements and 2-cell state transcription. EMBO Rep 2021; 22:e53180. [PMID: 34605600 PMCID: PMC8647145 DOI: 10.15252/embr.202153180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/18/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Repeat element transcription plays a vital role in early embryonic development. The expression of repeats such as MERVL characterises mouse embryos at the 2‐cell stage and defines a 2‐cell‐like cell (2CLC) population in a mouse embryonic stem cell culture. Repeat element sequences contain binding sites for numerous transcription factors. We identify the forkhead domain transcription factor FOXD3 as a regulator of major satellite repeats and MERVL transcription in mouse embryonic stem cells. FOXD3 binds to and recruits the histone methyltransferase SUV39H1 to MERVL and major satellite repeats, consequentially repressing the transcription of these repeats by the establishment of the H3K9me3 heterochromatin modification. Notably, depletion of FOXD3 leads to the de‐repression of MERVL and major satellite repeats as well as a subset of genes expressed in the 2‐cell state, shifting the balance between the stem cell and 2‐cell‐like population in culture. Thus, FOXD3 acts as a negative regulator of repeat transcription, ascribing a novel function to this transcription factor.
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Affiliation(s)
- Deepika Puri
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Birgit Koschorz
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Bettina Engist
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Megumi Onishi-Seebacher
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Devon Ryan
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Thomas Montavon
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
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27
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Abstract
Transcription factors (TFs) are essential mediators of epigenetic regulation and modifiers of penetrance. Studies from the past decades have revealed a sub-class of TF that is capable of remodeling closed chromatin states through targeting nucleosomal motifs. This pioneer factor (PF) class of chromatin remodeler is ATP independent in its roles in epigenetic initiation, with nucleosome-motif recognition and association with repressive chromatin regions. Increasing evidence suggests that the fundamental properties of PFs can be coopted in human cancers. We explore the role of PFs in the larger context of tissue-specific epigenetic regulation. Moreover, we highlight an emerging class of chimeric PF derived from translocation partners in human disease and PFs associated with rare tumors. In the age of site-directed genome editing and targeted protein degradation, increasing our understanding of PFs will provide access to next-generation therapy for human disease driven from altered transcriptional circuitry.
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28
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Mizeracka K, Rogers JM, Rumley JD, Shaham S, Bulyk ML, Murray JI, Heiman MG. Lineage-specific control of convergent differentiation by a Forkhead repressor. Development 2021; 148:272306. [PMID: 34423346 DOI: 10.1242/dev.199493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 08/17/2021] [Indexed: 12/14/2022]
Abstract
During convergent differentiation, multiple developmental lineages produce a highly similar or identical cell type. However, few molecular players that drive convergent differentiation are known. Here, we show that the C. elegans Forkhead transcription factor UNC-130 is required in only one of three convergent lineages that produce the same glial cell type. UNC-130 acts transiently as a repressor in progenitors and newly-born terminal cells to allow the proper specification of cells related by lineage rather than by cell type or function. Specification defects correlate with UNC-130:DNA binding, and UNC-130 can be functionally replaced by its human homolog, the neural crest lineage determinant FoxD3. We propose that, in contrast to terminal selectors that activate cell type-specific transcriptional programs in terminally differentiating cells, UNC-130 acts early and specifically in one convergent lineage to produce a cell type that also arises from molecularly distinct progenitors in other lineages.
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Affiliation(s)
- Karolina Mizeracka
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Julia M Rogers
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Jonathan D Rumley
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shai Shaham
- The Rockefeller University, New York, NY 10065, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.,Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - John I Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maxwell G Heiman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA
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29
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Sui Y, Hu W, Zhang W, Li D, Zhu H, You Q, Zhu R, Yi Q, Tang T, Gao L, Zhu S, Yang T. Insights into homeobox B9: a propeller for metastasis in dormant prostate cancer progenitor cells. Br J Cancer 2021; 125:1003-1015. [PMID: 34247196 PMCID: PMC8476533 DOI: 10.1038/s41416-021-01482-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 05/30/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Metastasis is the major cause of treatment failure and cancer-related deaths in prostate cancer (PCa) patients. Our previous study demonstrated that a CD44+ subpopulation isolated from PCa cells or tumours possesses both stem cell properties and metastatic potential, serving as metastatic prostate cancer stem cells (mPCSCs) in PCa metastasis. However, the underlying mechanisms remain unknown. METHODS In this study, we established PCa models via the orthotopic and subcutaneous implantation of different human PCa cancer cell lines, and compared the metastatic efficacy, after which process function analysis of target genes was pinpointed. RESULTS Several novel differentially expressed genes (DEGs) between orthotopic and ectopic tumours were identified. Among them, human homeobox B9 (HOXB9) transcription factor was found to be essential for PCa metastasis, as evidenced by the diminished number of lung metastatic foci derived from orthotopic implantation with HOXB9-deficient CWR22 cells, compared with the control. In addition, HOXB9 protein expression was upregulated in PCa tissues, compared with paracancer and benign prostate hyperplasia tissues. It was also positively correlated with Gleason scores. Gain- and loss-of-function assays showed that HOXB9 altered the expression of various tumour metastasis- and cancer stem cell (CSC) growth-related genes in a transforming growth factor beta (TGFβ)-dependent manner. Moreover, HOXB9 was overexpressed in an ALDH+CD44+CXCR4+CD24+ subpopulation of PCa cells that exhibited enhanced TGFβ-dependent tumorigenic and metastatic abilities, compared with other isogenic PCa cells. This suggests that HOXB9 may contribute to PCa tumorigenesis and metastasis via TGFβ signalling. Of note, ALDH+CD44+CXCR4+CD24+-PCa cells exhibited resistance to castration and antiandrogen therapy and were present in human PCa tissues. CONCLUSION Taken together, our study identified HOXB9 as a critical regulator of metastatic mPCSC behaviour. This occurs through altering the expression of a panel of CSC growth- and invasion/metastasis-related genes via TGFβ signalling. Thus, targeting HOXB9 is a potential novel therapeutic PCa treatment strategy.
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Affiliation(s)
- Yi Sui
- grid.412615.5Department of Nutrition, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Wei Hu
- grid.477929.6Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Wei Zhang
- grid.488206.00000 0004 4912 1751Department of Pharmacology, School of Basic Medicine, Hebei University of Chinese Medicine, Shijiazhuang, China
| | - Dejian Li
- grid.477929.6Department of Othopedics, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Hongbo Zhu
- grid.477929.6Department of Pathology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Qinghua You
- grid.477929.6Department of Pathology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Rujian Zhu
- grid.477929.6Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Qingtong Yi
- grid.477929.6Department of Urology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Tao Tang
- grid.10784.3a0000 0004 1937 0482Department of Obstetrics and Gynaecology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Lili Gao
- grid.477929.6Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Shengjuan Zhu
- grid.477929.6Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Tao Yang
- grid.477929.6Center for Medical Research and Innovation, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
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30
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Antonio Urrutia G, Ramachandran H, Cauchy P, Boo K, Ramamoorthy S, Boller S, Dogan E, Clapes T, Trompouki E, Torres-Padilla ME, Palvimo JJ, Pichler A, Grosschedl R. ZFP451-mediated SUMOylation of SATB2 drives embryonic stem cell differentiation. Genes Dev 2021; 35:1142-1160. [PMID: 34244292 PMCID: PMC8336893 DOI: 10.1101/gad.345843.120] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/08/2021] [Indexed: 12/15/2022]
Abstract
Here, Urrutia et al. set out to study the mechanism that regulates the choice between pluripotency and differentiation in embryonic stem cells (ESCs). Using biochemical and genomic analyses, the authors identify SUMO2 modification of Satb2 by the E3 ligase Zfp451 as a driver of ESC differentiation. The establishment of cell fates involves alterations of transcription factor repertoires and repurposing of transcription factors by post-translational modifications. In embryonic stem cells (ESCs), the chromatin organizers SATB2 and SATB1 balance pluripotency and differentiation by activating and repressing pluripotency genes, respectively. Here, we show that conditional Satb2 gene inactivation weakens ESC pluripotency, and we identify SUMO2 modification of SATB2 by the E3 ligase ZFP451 as a potential driver of ESC differentiation. Mutations of two SUMO-acceptor lysines of Satb2 (Satb2K →R) or knockout of Zfp451 impair the ability of ESCs to silence pluripotency genes and activate differentiation-associated genes in response to retinoic acid (RA) treatment. Notably, the forced expression of a SUMO2-SATB2 fusion protein in either Satb2K →R or Zfp451−/− ESCs rescues, in part, their impaired differentiation potential and enhances the down-regulation of Nanog. The differentiation defect of Satb2K →R ESCs correlates with altered higher-order chromatin interactions relative to Satb2wt ESCs. Upon RA treatment of Satb2wt ESCs, SATB2 interacts with ZFP451 and the LSD1/CoREST complex and gains binding at differentiation genes, which is not observed in RA-treated Satb2K →R cells. Thus, SATB2 SUMOylation may contribute to the rewiring of transcriptional networks and the chromatin interactome of ESCs in the transition of pluripotency to differentiation.
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Affiliation(s)
- Gustavo Antonio Urrutia
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Haribaskar Ramachandran
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Pierre Cauchy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Kyungjin Boo
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Senthilkumar Ramamoorthy
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Soeren Boller
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Esen Dogan
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | | | - Jorma J Palvimo
- Institute of Biomedicine, University of Eastern Finland, 70210 Kuopio, Finland
| | - Andrea Pichler
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
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31
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Dilshat R, Vu HN, Steingrímsson E. Epigenetic regulation during melanocyte development and homeostasis. Exp Dermatol 2021; 30:1033-1050. [PMID: 34003523 DOI: 10.1111/exd.14391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/09/2021] [Accepted: 05/09/2021] [Indexed: 12/26/2022]
Abstract
Melanocytes originate in the neural crest as precursor cells which then migrate and proliferate to reach their destination where they differentiate into pigment-producing cells. Melanocytes not only determine the colour of hair, skin and eyes but also protect against the harmful effects of UV irradiation. The establishment of the melanocyte lineage is regulated by a defined set of transcription factors and signalling pathways that direct the specific gene expression programmes underpinning melanoblast specification, survival, migration, proliferation and differentiation. In addition, epigenetic modifiers and replacement histones play key roles in regulating gene expression and its timing during the different steps of this process. Here, we discuss the evidence for the role of epigenetic regulators in melanocyte development and function and how they interact with transcription factors and signalling pathways to establish and maintain this important cell lineage.
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Affiliation(s)
- Ramile Dilshat
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Hong Nhung Vu
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, BioMedical Center, University of Iceland, Reykjavik, Iceland
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32
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Hosseinkhani N, Derakhshani A, Shadbad MA, Argentiero A, Racanelli V, Kazemi T, Mokhtarzadeh A, Brunetti O, Silvestris N, Baradaran B. The Role of V-Domain Ig Suppressor of T Cell Activation (VISTA) in Cancer Therapy: Lessons Learned and the Road Ahead. Front Immunol 2021; 12:676181. [PMID: 34093577 PMCID: PMC8172140 DOI: 10.3389/fimmu.2021.676181] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/29/2021] [Indexed: 12/12/2022] Open
Abstract
Immune checkpoints (ICs) have pivotal roles in regulating immune responses. The inhibitory ICs in the tumor microenvironment (TME) have been implicated in the immune evasion of tumoral cells. Therefore, identifying and targeting these inhibitory ICs might be critical for eliminating tumoral cells. V-domain immunoglobulin suppressor of T cell activation (VISTA) is a novel inhibitory IC that is expressed on myeloid cells, lymphoid cells, and tumoral cells; therefore, VISTA can substantially regulate innate and adaptive anti-tumoral immune responses. Besides, growing evidence indicates that VISTA blockade can enhance the sensitivity of tumoral cells to conventional IC-based immunotherapy, e.g., cytotoxic T lymphocyte antigen 4 (CTLA-4) inhibitors. In this regard, the current study aimed to review the current evidence about the structure and expression pattern of VISTA, its role in TME, the clinicopathological significance of VISTA, and its prognostic values in various cancers. Besides, this review intended to collect the lessons from the recent pre-clinical and clinical studies and propose a strategy to overcome tumor immune-resistance states.
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Affiliation(s)
- Negar Hosseinkhani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Afshin Derakhshani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Mahdi Abdoli Shadbad
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Antonella Argentiero
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Vito Racanelli
- Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Tohid Kazemi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Oronzo Brunetti
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy
| | - Nicola Silvestris
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Tumori "Giovanni Paolo II" of Bari, Bari, Italy.,Department of Biomedical Sciences and Human Oncology, Aldo Moro University of Bari, Bari, Italy
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.,Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
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33
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Wang X, Xiang Y, Yu Y, Wang R, Zhang Y, Xu Q, Sun H, Zhao ZA, Jiang X, Wang X, Lu X, Qin D, Quan Y, Zhang J, Shyh-Chang N, Wang H, Jing N, Xie W, Li L. Formative pluripotent stem cells show features of epiblast cells poised for gastrulation. Cell Res 2021; 31:526-541. [PMID: 33608671 PMCID: PMC8089102 DOI: 10.1038/s41422-021-00477-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/22/2021] [Indexed: 01/29/2023] Open
Abstract
The pluripotency of mammalian early and late epiblast could be recapitulated by naïve embryonic stem cells (ESCs) and primed epiblast stem cells (EpiSCs), respectively. However, these two states of pluripotency may not be sufficient to reflect the full complexity and developmental potency of the epiblast during mammalian early development. Here we report the establishment of self-renewing formative pluripotent stem cells (fPSCs) which manifest features of epiblast cells poised for gastrulation. fPSCs can be established from different mouse ESCs, pre-/early-gastrula epiblasts and induced PSCs. Similar to pre-/early-gastrula epiblasts, fPSCs show the transcriptomic features of formative pluripotency, which are distinct from naïve ESCs and primed EpiSCs. fPSCs show the unique epigenetic states of E6.5 epiblast, including the super-bivalency of a large set of developmental genes. Just like epiblast cells immediately before gastrulation, fPSCs can efficiently differentiate into three germ layers and primordial germ cells (PGCs) in vitro. Thus, fPSCs highlight the feasibility of using PSCs to explore the development of mammalian epiblast.
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Affiliation(s)
- Xiaoxiao Wang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yunlong Xiang
- grid.203458.80000 0000 8653 0555Department of Cell Biology and Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016 China
| | - Yang Yu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ran Wang
- grid.9227.e0000000119573309State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031 China
| | - Yu Zhang
- grid.12527.330000 0001 0662 3178Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Qianhua Xu
- grid.12527.330000 0001 0662 3178Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Hao Sun
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhen-Ao Zhao
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiangxiang Jiang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xiaoqing Wang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Xukun Lu
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Dandan Qin
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yujun Quan
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Jiaqi Zhang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ng Shyh-Chang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Hongmei Wang
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
| | - Naihe Jing
- grid.9227.e0000000119573309State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, 200031 China ,grid.9227.e0000000119573309Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, Guangdong 510530 China
| | - Wei Xie
- grid.12527.330000 0001 0662 3178Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, THU-PKU Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Lei Li
- grid.410726.60000 0004 1797 8419State Key Laboratory of Stem Cell and Reproductive Biology, Innovation Academy for Stem Cell and Regeneration, Beijing Institute for Stem Cell and Regenerative Medicine, Institute of Zoology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100101 China
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34
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Zheng K, Hu F, Zhou Y, Zhang J, Zheng J, Lai C, Xiong W, Cui K, Hu YZ, Han ZT, Zhang HH, Chen JG, Man HY, Liu D, Lu Y, Zhu LQ. miR-135a-5p mediates memory and synaptic impairments via the Rock2/Adducin1 signaling pathway in a mouse model of Alzheimer's disease. Nat Commun 2021; 12:1903. [PMID: 33771994 PMCID: PMC7998005 DOI: 10.1038/s41467-021-22196-y] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 02/25/2021] [Indexed: 12/13/2022] Open
Abstract
Aberrant regulation of microRNAs (miRNAs) has been implicated in the pathogenesis of Alzheimer's disease (AD), but most abnormally expressed miRNAs found in AD are not regulated by synaptic activity. Here we report that dysfunction of miR-135a-5p/Rock2/Add1 results in memory/synaptic disorder in a mouse model of AD. miR-135a-5p levels are significantly reduced in excitatory hippocampal neurons of AD model mice. This decrease is tau dependent and mediated by Foxd3. Inhibition of miR-135a-5p leads to synaptic disorder and memory impairments. Furthermore, excess Rock2 levels caused by loss of miR-135a-5p plays an important role in the synaptic disorder of AD via phosphorylation of Ser726 on adducin 1 (Add1). Blocking the phosphorylation of Ser726 on Add1 with a membrane-permeable peptide effectively rescues the memory impairments in AD mice. Taken together, these findings demonstrate that synaptic-related miR-135a-5p mediates synaptic/memory deficits in AD via the Rock2/Add1 signaling pathway, illuminating a potential therapeutic strategy for AD.
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Affiliation(s)
- Kai Zheng
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fan Hu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Yang Zhou
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Juan Zhang
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Jie Zheng
- Department of Geriatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chuan Lai
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Wan Xiong
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Ke Cui
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Ya-Zhuo Hu
- Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Disease, Institute of Geriatrics, Chinese PLA General Hospital and Chinese PLA Medical Academy, Beijing, P. R. China
| | - Zhi-Tao Han
- Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Disease, Institute of Geriatrics, Chinese PLA General Hospital and Chinese PLA Medical Academy, Beijing, P. R. China
| | - Hong-Hong Zhang
- Beijing Key Laboratory of Aging and Geriatrics, National Clinical Research Center for Geriatric Disease, Institute of Geriatrics, Chinese PLA General Hospital and Chinese PLA Medical Academy, Beijing, P. R. China
| | - Jian-Guo Chen
- The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA, USA
| | - Dan Liu
- The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Youming Lu
- The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P. R. China.
| | - Ling-Qiang Zhu
- Department of Pathophysiology, Key Lab of Neurological Disorder of Education Ministry, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China.
- The Institute of Brain Research, Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, P. R. China.
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35
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Ji Z, Li Y, Liu SX, Sharrocks AD. The forkhead transcription factor FOXK2 premarks lineage-specific genes in human embryonic stem cells for activation during differentiation. Nucleic Acids Res 2021; 49:1345-1363. [PMID: 33434264 PMCID: PMC7897486 DOI: 10.1093/nar/gkaa1281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 12/13/2022] Open
Abstract
Enhancers play important roles in controlling gene expression in a choreographed spatial and temporal manner during development. However, it is unclear how these regulatory regions are established during differentiation. Here we investigated the genome-wide binding profile of the forkhead transcription factor FOXK2 in human embryonic stem cells (ESCs) and downstream cell types. This transcription factor is bound to thousands of regulatory regions in human ESCs, and binding at many sites is maintained as cells differentiate to mesendodermal and neural precursor cell (NPC) types, alongside the emergence of new binding regions. FOXK2 binding is generally associated with active histone marks in any given cell type. Furthermore newly acquired, or retained FOXK2 binding regions show elevated levels of activating histone marks following differentiation to NPCs. In keeping with this association with activating marks, we demonstrate a role for FOXK transcription factors in gene activation during NPC differentiation. FOXK2 occupancy in ESCs is therefore an early mark for delineating the regulatory regions, which become activated in later lineages.
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Affiliation(s)
- Zongling Ji
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Yaoyong Li
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Sean X Liu
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | - Andrew D Sharrocks
- Faculty of Biology, Medicine and Health, University of Manchester, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
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36
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Rosenbaum SR, Knecht M, Mollaee M, Zhong Z, Erkes DA, McCue PA, Chervoneva I, Berger AC, Lo JA, Fisher DE, Gershenwald JE, Davies MA, Purwin TJ, Aplin AE. FOXD3 Regulates VISTA Expression in Melanoma. Cell Rep 2021; 30:510-524.e6. [PMID: 31940493 PMCID: PMC6995351 DOI: 10.1016/j.celrep.2019.12.036] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 11/01/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022] Open
Abstract
Immune checkpoint inhibitors have improved patient survival in melanoma, but the innate resistance of many patients necessitates the investigation of alternative immune targets. Many immune checkpoint proteins lack proper characterization, including V-domain Ig suppressor of T cell activation (VISTA). VISTA expression on immune cells can suppress T cell activity; however, few studies have investigated its expression and regulation in cancer cells. In this study, we observe that VISTA is expressed in melanoma patient samples and cell lines. Tumor cell-specific expression of VISTA promotes tumor onset in vivo, associated with increased intratumoral T regulatory cells, and enhanced PDL-1 expression on tumor-infiltrating macrophages. VISTA transcript levels are regulated by the stemness factor Forkhead box D3 (FOXD3). BRAF inhibition upregulates FOXD3 and reduces VISTA expression. Overall, this study demonstrates melanoma cell expression of VISTA and its regulation by FOXD3, contributing to the rationale for therapeutic strategies that combine targeted inhibitors with immune checkpoint blockade. VISTA is an understudied immune checkpoint protein. Through the analysis of patient samples and studies in mouse models, Rosenbaum et al. investigate the functional consequences of VISTA expression on melanoma cells. Furthermore, they demonstrate that the BRAF-regulated transcription factor FOXD3 negatively regulates VISTA expression.
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Affiliation(s)
- Sheera R Rosenbaum
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Meghan Knecht
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Mehri Mollaee
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Zhijiu Zhong
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Dan A Erkes
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Peter A McCue
- Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Inna Chervoneva
- Division of Biostatistics in the Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Adam C Berger
- Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA; Department of Surgery, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Jennifer A Lo
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - David E Fisher
- Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Jeffrey E Gershenwald
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael A Davies
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Timothy J Purwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Andrew E Aplin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA; Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA.
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37
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Chong-Morrison V, Sauka-Spengler T. The Cranial Neural Crest in a Multiomics Era. Front Physiol 2021; 12:634440. [PMID: 33732166 PMCID: PMC7956944 DOI: 10.3389/fphys.2021.634440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023] Open
Abstract
Neural crest ontogeny plays a prominent role in craniofacial development. In this Perspective article, we discuss recent advances to the understanding of mechanisms underlying the cranial neural crest gene regulatory network (cNC-GRN) stemming from omics-based studies. We briefly summarize how parallel considerations of transcriptome, interactome, and epigenome data significantly elaborated the roles of key players derived from pre-omics era studies. Furthermore, the growing cohort of cNC multiomics data revealed contribution of the non-coding genomic landscape. As technological improvements are constantly being developed, we reflect on key questions we are poised to address by taking advantage of the unique perspective a multiomics approach has to offer.
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38
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Costa R, Muccioli S, Brillo V, Bachmann M, Szabò I, Leanza L. Mitochondrial dysfunction interferes with neural crest specification through the FoxD3 transcription factor. Pharmacol Res 2020; 164:105385. [PMID: 33348025 DOI: 10.1016/j.phrs.2020.105385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 11/28/2022]
Abstract
The neural crest is an important group of cells with pluripotency and migratory ability that is crucially involved in tissue and cell specification during development. Craniofacial shaping, sensory neurons, body asymmetry, and pigmentation are linked to neural crest functionality. Despite its prominent role in embryogenesis, neural crest specification as well as the possible part mitochondria play in such a process remains unclarified. Mitochondria are important organelles not only for respiration, but also for regulation of cell proliferation, differentiation and death. Modulation of mitochondrial fitness and depletion of mitochondrial ATP synthesis has been shown to down-regulate Wnt signaling, both in vitro and in vivo. Since Wnt signaling is one of the crucial players during neural crest induction/specification, we hypothesized a signaling cascade connecting mitochondria to embryonic development and neural crest migration and differentiation. Here, by using pharmacological and genetic modulators of mitochondrial function, we provide evidence that a crosstalk between mitochondrial energy homeostasis and Wnt signaling is important in the development of neural crest-derived tissues. Furthermore, our results highlight the possibility to modulate neural crest cell specification by tuning mitochondrial metabolism via FoxD3, an important transcription factor that is regulated by Wnt. FoxD3 ensures the correct embryonic development and contributes to the maintenance of cell stemness and to the induction of epithelial-to-mesenchymal transition. In summary, our work offers new insights into the molecular mechanism of action of FoxD3 and demonstrates that mitochondrial fitness is linked to the regulation of this important transcription factor via Wnt signaling in the context of neural crest specification.
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Affiliation(s)
- Roberto Costa
- Department of Biology, University of Padova, Padova, Italy
| | | | | | | | - Ildikò Szabò
- Department of Biology, University of Padova, Padova, Italy
| | - Luigi Leanza
- Department of Biology, University of Padova, Padova, Italy.
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39
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Perera SN, Kerosuo L. On the road again: Establishment and maintenance of stemness in the neural crest from embryo to adulthood. STEM CELLS (DAYTON, OHIO) 2020; 39:7-25. [PMID: 33017496 PMCID: PMC7821161 DOI: 10.1002/stem.3283] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 09/08/2020] [Accepted: 09/11/2020] [Indexed: 12/22/2022]
Abstract
Unique to vertebrates, the neural crest (NC) is an embryonic stem cell population that contributes to a greatly expanding list of derivatives ranging from neurons and glia of the peripheral nervous system, facial cartilage and bone, pigment cells of the skin to secretory cells of the endocrine system. Here, we focus on what is specifically known about establishment and maintenance of NC stemness and ultimate fate commitment mechanisms, which could help explain its exceptionally high stem cell potential that exceeds the "rules set during gastrulation." In fact, recent discoveries have shed light on the existence of NC cells that coexpress commonly accepted pluripotency factors like Nanog, Oct4/PouV, and Klf4. The coexpression of pluripotency factors together with the exceptional array of diverse NC derivatives encouraged us to propose a new term "pleistopotent" (Greek for abundant, a substantial amount) to be used to reflect the uniqueness of the NC as compared to other post-gastrulation stem cell populations in the vertebrate body, and to differentiate them from multipotent lineage restricted stem cells. We also discuss studies related to the maintenance of NC stemness within the challenging context of being a transient and thus a constantly changing population of stem cells without a permanent niche. The discovery of the stem cell potential of Schwann cell precursors as well as multiple adult NC-derived stem cell reservoirs during the past decade has greatly increased our understanding of how NC cells contribute to tissues formed after its initial migration stage in young embryos.
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Affiliation(s)
- Surangi N Perera
- Neural Crest Development and Disease Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura Kerosuo
- Neural Crest Development and Disease Unit, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, Maryland, USA
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40
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Peng T, Zhai Y, Atlasi Y, Ter Huurne M, Marks H, Stunnenberg HG, Megchelenbrink W. STARR-seq identifies active, chromatin-masked, and dormant enhancers in pluripotent mouse embryonic stem cells. Genome Biol 2020; 21:243. [PMID: 32912294 PMCID: PMC7488044 DOI: 10.1186/s13059-020-02156-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 08/26/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Enhancers are distal regulators of gene expression that shape cell identity and control cell fate transitions. In mouse embryonic stem cells (mESCs), the pluripotency network is maintained by the function of a complex network of enhancers, that are drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for identifying putative enhancers and for describing their activity levels and dynamics. RESULTS Here, we applied STARR-seq, a genome-wide plasmid-based assay, as a read-out for the enhancer landscape in "ground-state" (2i+LIF; 2iL) and "metastable" (serum+LIF; SL) mESCs. This analysis reveals that active STARR-seq loci show modest overlap with enhancer locations derived from peak calling of ChIP-seq libraries for common enhancer marks. We unveil ZIC3-bound loci with significant STARR-seq activity in SL-ESCs. Knock-out of Zic3 removes STARR-seq activity only in SL-ESCs and increases their propensity to differentiate towards the endodermal fate. STARR-seq also reveals enhancers that are not accessible, masked by a repressive chromatin signature. We describe a class of dormant, p53 bound enhancers that gain H3K27ac under specific conditions, such as after treatment with Nocodazol, or transiently during reprogramming from fibroblasts to pluripotency. CONCLUSIONS In conclusion, loci identified as active by STARR-seq often overlap with those identified by chromatin accessibility and active epigenetic marking, yet a significant fraction is epigenetically repressed or display condition-specific enhancer activity.
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Affiliation(s)
- Tianran Peng
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
| | - Yanan Zhai
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Vico L. De Crecchio 7, 80138, Naples, Italy
| | - Yaser Atlasi
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
| | - Menno Ter Huurne
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
| | - Hendrik Marks
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands.
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
| | - Wout Megchelenbrink
- Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Geert Grooteplein Zuid 28, 6525 GA, Nijmegen, The Netherlands.
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS, Utrecht, The Netherlands.
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Vico L. De Crecchio 7, 80138, Naples, Italy.
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41
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Abstract
Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA sequence motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inaccessible to other transcription factors. Pioneer factors subsequently enable other transcription factors, nucleosome remodeling complexes, and histone modifiers to engage chromatin, thereby initiating the formation of an activating or repressive regulatory sequence. Thus, pioneer factors endow the competence for fate changes in embryonic development, are essential for cellular reprogramming, and rewire gene networks in cancer cells. Recent studies with reconstituted nucleosomes in vitro and chromatin binding in vivo reveal that pioneer factors can directly perturb nucleosome structure and chromatin accessibility in different ways. This review focuses on our current understanding of the mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to our ability to control cell fates at will.
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Affiliation(s)
- Kenneth S Zaret
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5157, USA;
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42
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MicroRNA-dependent inhibition of PFN2 orchestrates ERK activation and pluripotent state transitions by regulating endocytosis. Proc Natl Acad Sci U S A 2020; 117:20625-20635. [PMID: 32788350 DOI: 10.1073/pnas.2002750117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Profilin2 (PFN2) is a target of the embryonic stem cell (ESC)-enriched miR-290 family of microRNAs (miRNAs) and an actin/dynamin-binding protein implicated in endocytosis. Here we show that the miR-290-PFN2 pathway regulates many aspects of ESC biology. In the absence of miRNAs, PFN2 is up-regulated in ESCs, with a resulting decrease in endocytosis. Reintroduction of miR-290, knockout of Pfn2, or disruption of the PFN2-dynamin interaction domain in miRNA-deficient cells reverses the endocytosis defect. The reduced endocytosis is associated with impaired extracellular signal-regulated kinase (ERK) signaling, delayed ESC cell cycle progression, and repressed ESC differentiation. Mutagenesis of the single canonical conserved 3' UTR miR-290-binding site of Pfn2 or overexpression of the Pfn2 open reading frame alone in otherwise wild-type cells largely recapitulates these phenotypes. Taken together, these findings define an axis of posttranscriptional control, endocytosis, and signal transduction that is important for ESC proliferation and differentiation.
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43
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Huang J, Sachdeva M, Xu E, Robinson TJ, Luo L, Ma Y, Williams NT, Lopez O, Cervia LD, Yuan F, Qin X, Zhang D, Owzar K, Gokgoz N, Seto A, Okada T, Singer S, Andrulis IL, Wunder JS, Lazar AJ, Rubin BP, Pipho K, Mello SS, Giudice J, Kirsch DG. The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways. Mol Cancer Res 2020; 18:1534-1544. [PMID: 32561656 DOI: 10.1158/1541-7786.mcr-19-1170] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/09/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022]
Abstract
Soft-tissue sarcomas (STS) are rare malignancies showing lineage differentiation toward diverse mesenchymal tissues. Half of all high-grade STSs develop lung metastasis with a median survival of 15 months. Here, we used a genetically engineered mouse model that mimics undifferentiated pleomorphic sarcoma (UPS) to study the molecular mechanisms driving metastasis. High-grade sarcomas were generated with Cre recombinase technology using mice with conditional mutations in Kras and Trp53 (KP) genes. After amputation of the limb bearing the primary tumor, mice were followed for the development of lung metastasis. Using RNA-sequencing of matched primary KP tumors and lung metastases, we found that the long noncoding RNA (lncRNA) Nuclear Enriched Abundant Transcript 1 (Neat1) is significantly upregulated in lung metastases. Furthermore, NEAT1 RNA ISH of human UPS showed that NEAT1 is upregulated within a subset of lung metastases compared with paired primary UPS. Remarkably, CRISPR/Cas9-mediated knockout of Neat1 suppressed the ability of KP tumor cells to colonize the lungs. To gain insight into the underlying mechanisms by which the lncRNA Neat1 promotes sarcoma metastasis, we pulled down Neat1 RNA and used mass spectrometry to identify interacting proteins. Interestingly, most Neat1 interacting proteins are involved in RNA splicing regulation. In particular, KH-Type Splicing Regulatory Protein (KHSRP) interacts with Neat1 and is associated with poor prognosis of human STS. Moreover, depletion of KHSRP suppressed the ability of KP tumor cells to colonize the lungs. Collectively, these results suggest that Neat1 and its interacting proteins, which regulate RNA splicing, are involved in mediating sarcoma metastasis. IMPLICATIONS: Understanding that lncRNA NEAT1 promotes sarcoma metastasis, at least in part, through interacting with the RNA splicing regulator KHSRP may translate into new therapeutic approaches for sarcoma.
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Affiliation(s)
- Jianguo Huang
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Mohit Sachdeva
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Eric Xu
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Timothy J Robinson
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Nerissa T Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Omar Lopez
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
| | - Lisa D Cervia
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Fan Yuan
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Xiaodi Qin
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Dadong Zhang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.,Department of Biostatistics & Bioinformatics, Duke University, Durham, North Carolina
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Andrew Seto
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Tomoyo Okada
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel Singer
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jay S Wunder
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.,University of Toronto Musculoskeletal Oncology Unit, and Department of Surgery, University of Toronto, Toronto, Canada
| | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Krista Pipho
- University of Rochester Medical Center, Rochester, New York
| | | | - Jimena Giudice
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina.,McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina. .,Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
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44
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Ho PJ, Lloyd SM, Bao X. Unwinding chromatin at the right places: how BAF is targeted to specific genomic locations during development. Development 2019; 146:146/19/dev178780. [PMID: 31570369 DOI: 10.1242/dev.178780] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The BAF (SWI/SNF) chromatin remodeling complex plays a crucial role in modulating spatiotemporal gene expression during mammalian development. Although its remodeling activity was characterized in vitro decades ago, the complex actions of BAF in vivo have only recently begun to be unraveled. In living cells, BAF only binds to and remodels a subset of genomic locations. This selectivity of BAF genomic targeting is crucial for cell-type specification and for mediating precise responses to environmental signals. Here, we provide an overview of the distinct molecular mechanisms modulating BAF chromatin binding, including its combinatory assemblies, DNA/histone modification-binding modules and post-translational modifications, as well as its interactions with proteins, RNA and lipids. This Review aims to serve as a primer for future studies to decode the actions of BAF in developmental processes.
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Affiliation(s)
- Patric J Ho
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Sarah M Lloyd
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Xiaomin Bao
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA .,Department of Dermatology, Northwestern University, Evanston, IL 60208, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, IL 60208, USA
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45
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Gökbuget D, Blelloch R. Epigenetic control of transcriptional regulation in pluripotency and early differentiation. Development 2019; 146:dev164772. [PMID: 31554624 PMCID: PMC6803368 DOI: 10.1242/dev.164772] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pluripotent stem cells give rise to all cells of the adult organism, making them an invaluable tool in regenerative medicine. In response to differentiation cues, they can activate markedly distinct lineage-specific gene networks while turning off or rewiring pluripotency networks. Recent innovations in chromatin and nuclear structure analyses combined with classical genetics have led to novel insights into the transcriptional and epigenetic mechanisms underlying these networks. Here, we review these findings in relation to their impact on the maintenance of and exit from pluripotency and highlight the many factors that drive these processes, including histone modifying enzymes, DNA methylation and demethylation, nucleosome remodeling complexes and transcription factor-mediated enhancer switching.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94143, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94143, USA
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46
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Xiao L, Shan Y, Ma L, Dunk C, Yu Y, Wei Y. Tuning FOXD3 expression dose-dependently balances human embryonic stem cells between pluripotency and meso-endoderm fates. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118531. [PMID: 31415841 DOI: 10.1016/j.bbamcr.2019.118531] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 07/31/2019] [Accepted: 08/05/2019] [Indexed: 02/07/2023]
Abstract
Forkhead box D3 (FOXD3) is a key transcription factor maintaining pluripotency in mouse embryonic stem cells (ESCs). Yet to date studies on its role in human ESCs are quite limited. In this study, we report that deletion of FOXD3 in human ESCs results in loss of pluripotency and spontaneous differentiation toward meso-endoderm. Ectopic overexpression of FOXD3 in hESCs leads to two different phenotypes: Human ESCs expressing high levels of FOXD3 undergo spontaneous meso-endoderm differentiation, whereas those with lower levels of FOXD3 maintain pluripotency. Next we deleted endogenous FOXD3 in the low ectopic expression model and find that addition of exogenous FOXD3 at a low level could rescue FOXD3-deficiency phenotype in hESCs. In summary, our findings suggest that FOXD3 dose-dependently regulates the balance of human ESCs between pluripotency and meso-endoderm fates, which adds to our understanding of the role of FOXD3 in humans.
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Affiliation(s)
- Lu Xiao
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Yongli Shan
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China; CAS Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, Guangdong, China
| | - Lishi Ma
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Caroline Dunk
- Research Centre for Women's and Infants' Health, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON, Canada
| | - Yanhong Yu
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China.
| | - Yanxing Wei
- Department of Obstetrics and Gynecology, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China.
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47
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Stage-dependent differential gene expression profiles of cranial neural crest-like cells derived from mouse-induced pluripotent stem cells. Med Mol Morphol 2019; 53:28-41. [PMID: 31297611 PMCID: PMC7033077 DOI: 10.1007/s00795-019-00229-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 06/26/2019] [Indexed: 12/13/2022]
Abstract
Cranial neural crest cells are multipotent cells that migrate into the pharyngeal arches of the vertebrate embryo and differentiate into various craniofacial organ derivatives. Therefore, migrating cranial neural crest cells are considered one of the most attractive candidate cell sources in regenerative medicine. We generated cranial neural crest like cell (cNCCs) using mouse-induced pluripotent stem cells cultured in neural crest-inducing medium for 14 days. Subsequently, we conducted RNA sequencing experiments to analyze gene expression profiles of cNCCs at different time points after induction. cNCCs expressed several neural crest specifier genes; however, some previously reported specifier genes such as paired box 3 and Forkhead box D3, which are essential for embryonic neural crest development, were not expressed. Moreover, ETS proto-oncogene 1, transcription factor and sex-determining region Y-box 10 were only expressed after 14 days of induction. Finally, cNCCs expressed multiple protocadherins and a disintegrin and metalloproteinase with thrombospondin motifs enzymes, which may be crucial for their migration.
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48
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Lukoseviciute M, Gavriouchkina D, Williams RM, Hochgreb-Hagele T, Senanayake U, Chong-Morrison V, Thongjuea S, Repapi E, Mead A, Sauka-Spengler T. From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo. Dev Cell 2019; 47:608-628.e6. [PMID: 30513303 PMCID: PMC6286384 DOI: 10.1016/j.devcel.2018.11.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 08/15/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023]
Abstract
The neural crest (NC) is a transient embryonic stem cell-like population characterized by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that, during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes. Strikingly, foxd3 then gradually switches from an activator to its well-described role as a transcriptional repressor and potentially uses differential partners for each role. Taken together, these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from “permissive” to “repressive” nucleosome and chromatin organization to maintain multipotency and define cell fates. FoxD3 primes neural crest specification by modulating distal enhancers FoxD3 represses a number of neural crest migration and differentiation genes In neural crest, FoxD3 acts to switch chromatin from “permissive” to “repressive” Distinctive gene regulatory mechanisms underlie the bimodal action of FoxD3
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Affiliation(s)
- Martyna Lukoseviciute
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Daria Gavriouchkina
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Ruth M Williams
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatiana Hochgreb-Hagele
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Upeka Senanayake
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Vanessa Chong-Morrison
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Supat Thongjuea
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Emmanouela Repapi
- MRC WIMM Centre for Computational Biology Research Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Adam Mead
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK.
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49
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Xu W, Li J, Li L, Hou T, Cai X, Liu T, Yang X, Wei H, Jiang C, Xiao J. FOXD3 Suppresses Tumor-Initiating Features in Lung Cancer via Transcriptional Repression of WDR5. Stem Cells 2019; 37:582-592. [PMID: 30703266 DOI: 10.1002/stem.2984] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 12/13/2018] [Accepted: 12/19/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Wei Xu
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
| | - Jialin Li
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
| | - Lei Li
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences; East China Normal University; Shanghai People's Republic of China
| | - Tianhui Hou
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
- The School of Sports and Health; East China Normal University; Shanghai People's Republic of China
| | - Xiaopan Cai
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
| | - Tielong Liu
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
| | - Xinghai Yang
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
| | - Haifeng Wei
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
| | - Cong Jiang
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
| | - Jianru Xiao
- Department of Orthopedic Oncology; Changzheng Hospital, Second Military Medical University; Shanghai People's Republic of China
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50
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Viiri LE, Rantapero T, Kiamehr M, Alexanova A, Oittinen M, Viiri K, Niskanen H, Nykter M, Kaikkonen MU, Aalto-Setälä K. Extensive reprogramming of the nascent transcriptome during iPSC to hepatocyte differentiation. Sci Rep 2019; 9:3562. [PMID: 30837492 PMCID: PMC6401154 DOI: 10.1038/s41598-019-39215-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatocyte-like cells (HLCs) derived from induced pluripotent stem cells (iPSCs) provide a renewable source of cells for drug discovery, disease modelling and cell-based therapies. Here, by using GRO-Seq we provide the first genome-wide analysis of the nascent RNAs in iPSCs, HLCs and primary hepatocytes to extend our understanding of the transcriptional changes occurring during hepatic differentiation process. We demonstrate that a large fraction of hepatocyte-specific genes are regulated at transcriptional level and identify hundreds of differentially expressed non-coding RNAs (ncRNAs), including primary miRNAs (pri-miRNAs) and long non-coding RNAs (lncRNAs). Differentiation induced alternative transcription start site (TSS) usage between the cell types as evidenced for miR-221/222 and miR-3613/15a/16-1 clusters. We demonstrate that lncRNAs and coding genes are tightly co-expressed and could thus be co-regulated. Finally, we identified sets of transcriptional regulators that might drive transcriptional changes during hepatocyte differentiation. These included RARG, E2F1, SP1 and FOXH1, which were associated with the down-regulated transcripts, and hepatocyte-specific TFs such as FOXA1, FOXA2, HNF1B, HNF4A and CEBPA, as well as RXR, PPAR, AP-1, JUNB, JUND and BATF, which were associated with up-regulated transcripts. In summary, this study clarifies the role of regulatory ncRNAs and TFs in differentiation of HLCs from iPSCs.
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Affiliation(s)
- Leena E Viiri
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland.
| | - Tommi Rantapero
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Mostafa Kiamehr
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Anna Alexanova
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Mikko Oittinen
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Keijo Viiri
- Tampere Center for Child Health Research, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland
| | - Minna U Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Katriina Aalto-Setälä
- Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, 33014, Finland.,Heart Center, Tampere University Hospital, Tampere, 33520, Finland
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