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Cui Z, Wei H, Goding C, Cui R. Stem cell heterogeneity, plasticity, and regulation. Life Sci 2023; 334:122240. [PMID: 37925141 DOI: 10.1016/j.lfs.2023.122240] [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: 09/08/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/06/2023]
Abstract
As a population of homogeneous cells with both self-renewal and differentiation potential, stem cell pools are highly compartmentalized and contain distinct subsets that exhibit stable but limited heterogeneity during homeostasis. However, their striking plasticity is showcased under natural or artificial stress, such as injury, transplantation, cancer, and aging, leading to changes in their phenotype, constitution, metabolism, and function. The complex and diverse network of cell-extrinsic niches and signaling pathways, together with cell-intrinsic genetic and epigenetic regulators, tightly regulate both the heterogeneity during homeostasis and the plasticity under perturbation. Manipulating these factors offers better control of stem cell behavior and a potential revolution in the current state of regenerative medicine. However, disruptions of normal regulation by genetic mutation or excessive plasticity acquisition may contribute to the formation of tumors. By harnessing innovative techniques that enhance our understanding of stem cell heterogeneity and employing novel approaches to maximize the utilization of stem cell plasticity, stem cell therapy holds immense promise for revolutionizing the future of medicine.
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Affiliation(s)
- Ziyang Cui
- Department of Dermatology and Venerology, Peking University First Hospital, Beijing 100034, China.
| | - Hope Wei
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, United States of America
| | - Colin Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX37DQ, UK
| | - Rutao Cui
- Skin Disease Research Institute, The 2nd Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
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2
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Wormser O, Perez Y, Dolgin V, Kamali B, Tangeman JA, Gradstein L, Yogev Y, Hadar N, Freund O, Drabkin M, Halperin D, Irron I, Grajales-Esquivel E, Del Rio-Tsonis K, Birnbaum RY, Akler G, Birk OS. IHH enhancer variant within neighboring NHEJ1 intron causes microphthalmia anophthalmia and coloboma. NPJ Genom Med 2023; 8:22. [PMID: 37580330 PMCID: PMC10425348 DOI: 10.1038/s41525-023-00364-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
Genomic sequences residing within introns of few genes have been shown to act as enhancers affecting expression of neighboring genes. We studied an autosomal recessive phenotypic continuum of microphthalmia, anophthalmia and ocular coloboma, with no apparent coding-region disease-causing mutation. Homozygosity mapping of several affected Jewish Iranian families, combined with whole genome sequence analysis, identified a 0.5 Mb disease-associated chromosome 2q35 locus (maximal LOD score 6.8) harboring an intronic founder variant in NHEJ1, not predicted to affect NHEJ1. The human NHEJ1 intronic variant lies within a known specifically limb-development enhancer of a neighboring gene, Indian hedgehog (Ihh), known to be involved in eye development in mice and chickens. Through mouse and chicken molecular development studies, we demonstrated that this variant is within an Ihh enhancer that drives gene expression in the developing eye and that the identified variant affects this eye-specific enhancer activity. We thus delineate an Ihh enhancer active in mammalian eye development whose variant causes human microphthalmia, anophthalmia and ocular coloboma. The findings highlight disease causation by an intronic variant affecting the expression of a neighboring gene, delineating molecular pathways of eye development.
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Affiliation(s)
- Ohad Wormser
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yonatan Perez
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Vadim Dolgin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bahman Kamali
- Medical Advisory Committee, United Mashhadi Jewish Community of America, 54 Steamboat Rd., Great Neck, NY, 11024, USA
| | - Jared A Tangeman
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Libe Gradstein
- Department of Ophthalmology, Soroka Medical Center and Clalit Health Services, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Yuval Yogev
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Noam Hadar
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Ofek Freund
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Max Drabkin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Daniel Halperin
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Inbar Irron
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Erika Grajales-Esquivel
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Katia Del Rio-Tsonis
- Department of Biology and Center for Visual Sciences, Miami University, Oxford, OH, 45056, USA
| | - Ramon Y Birnbaum
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gidon Akler
- TOVANA Health, Houston, TX, USA.
- Precision Medicine Insights, P.C., Great Neck, NY, USA.
| | - Ohad S Birk
- The Morris Kahn Laboratory of Human Genetics, National Institute for Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
- Genetics Institute, Soroka Medical Center affiliated to Ben-Gurion University of the Negev, Beer-Sheva, Israel.
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Hong H, Yoon SB, Park JE, Lee JI, Kim HY, Nam HJ, Cho H. MeCP2 dysfunction prevents proper BMP signaling and neural progenitor expansion in brain organoid. Ann Clin Transl Neurol 2023. [PMID: 37302988 DOI: 10.1002/acn3.51799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/26/2023] [Accepted: 05/10/2023] [Indexed: 06/13/2023] Open
Abstract
OBJECTIVES Sporadic mutations in MeCP2 are a hallmark of Rett syndrome (RTT). Many RTT brain organoid models have exhibited pathogenic phenotypes such as decreased spine density and small size of soma with altered electrophysiological signals. However, previous models are mainly focused on the phenotypes observed in the late phase and rarely provide clues for the defect of neural progenitors which generate different types of neurons and glial cells. METHODS We newly established the RTT brain organoid model derived from MeCP2-truncated iPS cells which were genetically engineered by CRISPR/Cas9 technology. By immunofluorescence imaging, we studied the development of NPC pool and its fate specification into glutamatergic neurons or astrocytes in RTT organoids. By total RNA sequencing, we investigated which signaling pathways were altered during the early brain development in RTT organoids. RESULTS Dysfunction of MeCP2 caused the defect of neural rosette formation in the early phase of cortical development. In total transcriptome analysis, BMP pathway-related genes are highly associated with MeCP2 depletion. Moreover, levels of pSMAD1/5 and BMP target genes are excessively increased, and treatment of BMP inhibitors partially rescues the cell cycle progression of neural progenitors. Subsequently, MeCP2 dysfunction reduced the glutamatergic neurogenesis and induced overproduction of astrocytes. Nevertheless, early inhibition of BMP pathway rescued VGLUT1 expression and suppressed astrocyte maturation. INTERPRETATION Our results demonstrate that MeCP2 is required for the expansion of neural progenitor cells by modulating BMP pathway at early stages of development, and this influence persists during neurogenesis and gliogenesis at later stages of brain organoid development.
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Affiliation(s)
- Hyowon Hong
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sae-Bom Yoon
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung Eun Park
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jung In Lee
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun Young Kim
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hye Jin Nam
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Heeyeong Cho
- Therapeutics & Biotechnology Division, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea
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Ferdaos N, Lowell S, Mason JO. Pax6 mutant cerebral organoids partially recapitulate phenotypes of Pax6 mutant mouse strains. PLoS One 2022; 17:e0278147. [PMID: 36441708 PMCID: PMC9704552 DOI: 10.1371/journal.pone.0278147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 11/10/2022] [Indexed: 11/30/2022] Open
Abstract
Cerebral organoids show great promise as tools to unravel the complex mechanisms by which the mammalian brain develops during embryogenesis. We generated mouse cerebral organoids harbouring constitutive or conditional mutations in Pax6, which encodes a transcription factor with multiple important roles in brain development. By comparing the phenotypes of mutant organoids with the well-described phenotypes of Pax6 mutant mouse embryos, we evaluated the extent to which cerebral organoids reproduce phenotypes previously described in vivo. Organoids lacking Pax6 showed multiple phenotypes associated with its activity in mice, including precocious neural differentiation, altered cell cycle and an increase in abventricular mitoses. Neural progenitors in both Pax6 mutant and wild type control organoids cycled more slowly than their in vivo counterparts, but nonetheless we were able to identify clear changes to cell cycle attributable to the absence of Pax6. Our findings support the value of cerebral organoids as tools to explore mechanisms of brain development, complementing the use of mouse models.
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Affiliation(s)
- Nurfarhana Ferdaos
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Department of Pharmacology and Chemistry, Faculty of Pharmacy, UiTM Selangor, Shah Alam, Malaysia
| | - Sally Lowell
- Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - John O. Mason
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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Diacou R, Nandigrami P, Fiser A, Liu W, Ashery-Padan R, Cvekl A. Cell fate decisions, transcription factors and signaling during early retinal development. Prog Retin Eye Res 2022; 91:101093. [PMID: 35817658 PMCID: PMC9669153 DOI: 10.1016/j.preteyeres.2022.101093] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 12/30/2022]
Abstract
The development of the vertebrate eyes is a complex process starting from anterior-posterior and dorso-ventral patterning of the anterior neural tube, resulting in the formation of the eye field. Symmetrical separation of the eye field at the anterior neural plate is followed by two symmetrical evaginations to generate a pair of optic vesicles. Next, reciprocal invagination of the optic vesicles with surface ectoderm-derived lens placodes generates double-layered optic cups. The inner and outer layers of the optic cups develop into the neural retina and retinal pigment epithelium (RPE), respectively. In vitro produced retinal tissues, called retinal organoids, are formed from human pluripotent stem cells, mimicking major steps of retinal differentiation in vivo. This review article summarizes recent progress in our understanding of early eye development, focusing on the formation the eye field, optic vesicles, and early optic cups. Recent single-cell transcriptomic studies are integrated with classical in vivo genetic and functional studies to uncover a range of cellular mechanisms underlying early eye development. The functions of signal transduction pathways and lineage-specific DNA-binding transcription factors are dissected to explain cell-specific regulatory mechanisms underlying cell fate determination during early eye development. The functions of homeodomain (HD) transcription factors Otx2, Pax6, Lhx2, Six3 and Six6, which are required for early eye development, are discussed in detail. Comprehensive understanding of the mechanisms of early eye development provides insight into the molecular and cellular basis of developmental ocular anomalies, such as optic cup coloboma. Lastly, modeling human development and inherited retinal diseases using stem cell-derived retinal organoids generates opportunities to discover novel therapies for retinal diseases.
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Affiliation(s)
- Raven Diacou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Prithviraj Nandigrami
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Andras Fiser
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Wei Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
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Camargo Ortega G, Götz M. Centrosome heterogeneity in stem cells regulates cell diversity. Trends Cell Biol 2022; 32:707-719. [PMID: 35750615 DOI: 10.1016/j.tcb.2022.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 11/27/2022]
Abstract
Stem cells are at the source of creating cellular diversity. Multiple mechanisms, including basic cell biological processes, regulate their fate. The centrosome is at the core of many stem cell functions and recent work highlights the association of distinct proteins at the centrosome in stem cell differentiation. As showcased by a novel centrosome protein regulating neural stem cell differentiation, it is timely to review the heterogeneity of the centrosome at protein and RNA levels and how this impacts their function in stem and progenitor cells. Together with evidence for heterogeneity of other organelles so far considered as similar between cells, we call for exploring the cell type-specific composition of organelles as a way to expand protein function in development with relevance to regenerative medicine.
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Affiliation(s)
- Germán Camargo Ortega
- Department of Biosystems Science and Engineering, ETH, Zurich, 4058 Basel, Switzerland.
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, 82152 Planegg-Martinsried, Germany; Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, 82152 Planegg-Martinsried, Germany; 4 SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany.
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7
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Ochi S, Manabe S, Kikkawa T, Osumi N. Thirty Years' History since the Discovery of Pax6: From Central Nervous System Development to Neurodevelopmental Disorders. Int J Mol Sci 2022; 23:ijms23116115. [PMID: 35682795 PMCID: PMC9181425 DOI: 10.3390/ijms23116115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/19/2022] [Accepted: 05/27/2022] [Indexed: 12/23/2022] Open
Abstract
Pax6 is a sequence-specific DNA binding transcription factor that positively and negatively regulates transcription and is expressed in multiple cell types in the developing and adult central nervous system (CNS). As indicated by the morphological and functional abnormalities in spontaneous Pax6 mutant rodents, Pax6 plays pivotal roles in various biological processes in the CNS. At the initial stage of CNS development, Pax6 is responsible for brain patterning along the anteroposterior and dorsoventral axes of the telencephalon. Regarding the anteroposterior axis, Pax6 is expressed inversely to Emx2 and Coup-TF1, and Pax6 mutant mice exhibit a rostral shift, resulting in an alteration of the size of certain cortical areas. Pax6 and its downstream genes play important roles in balancing the proliferation and differentiation of neural stem cells. The Pax6 gene was originally identified in mice and humans 30 years ago via genetic analyses of the eye phenotypes. The human PAX6 gene was discovered in patients who suffer from WAGR syndrome (i.e., Wilms tumor, aniridia, genital ridge defects, mental retardation). Mutations of the human PAX6 gene have also been reported to be associated with autism spectrum disorder (ASD) and intellectual disability. Rodents that lack the Pax6 gene exhibit diverse neural phenotypes, which might lead to a better understanding of human pathology and neurodevelopmental disorders. This review describes the expression and function of Pax6 during brain development, and their implications for neuropathology.
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8
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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Ghrelin Regulates Expression of the Transcription Factor Pax6 in Hypoxic Brain Progenitor Cells and Neurons. Cells 2022; 11:cells11050782. [PMID: 35269403 PMCID: PMC8909042 DOI: 10.3390/cells11050782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 12/04/2022] Open
Abstract
The nature of brain impairment after hypoxia is complex and recovery harnesses different mechanisms, including neuroprotection and neurogenesis. Experimental evidence suggests that hypoxia may trigger neurogenesis postnatally by influencing the expression of a variety of transcription factors. However, the existing data are controversial. As a proof-of-principle, we subjected cultured cerebral cortex neurons, cerebellar granule neurons and organotypic cerebral cortex slices from rat brains to hypoxia and treated these cultures with the hormone ghrelin, which is well-known for its neuroprotective functions. We found that hypoxia elevated the expression levels and stimulated nuclear translocation of ghrelin’s receptor GHSR1 in the cultured neurons and the acute organotypic slices, whereas ghrelin treatment reduced the receptor expression to normoxic levels. GHSR1 expression was also increased in cerebral cortex neurons of mice with induced experimental stroke. Additional quantitative analyses of immunostainings for neuronal proliferation and differentiation markers revealed that hypoxia stimulated the proliferation of neuronal progenitors, whereas ghrelin application during the phase of recovery from hypoxia counteracted these effects. At the mechanistic level, we provide a link between the described post-ischemic phenomena and the expression of the transcription factor Pax6, an important regulator of neural progenitor cell fate. In contrast to the neurogenic niches in the brain where hypoxia is known to increase Pax6 expression, the levels of the transcription factor in cultured hypoxic cerebral cortex cells were downregulated. Moreover, the application of ghrelin to hypoxic neurons normalised the expression levels of these factors. Our findings suggest that ghrelin stimulates neurogenic factors for the protection of neurons in a GHSR1-dependent manner in non-neurogenic brain areas such as the cerebral cortex after exposure to hypoxia.
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Sanchez-Gonzalez R, Koupourtidou C, Lepko T, Zambusi A, Novoselc KT, Durovic T, Aschenbroich S, Schwarz V, Breunig CT, Straka H, Huttner HB, Irmler M, Beckers J, Wurst W, Zwergal A, Schauer T, Straub T, Czopka T, Trümbach D, Götz M, Stricker SH, Ninkovic J. Innate Immune Pathways Promote Oligodendrocyte Progenitor Cell Recruitment to the Injury Site in Adult Zebrafish Brain. Cells 2022; 11:cells11030520. [PMID: 35159329 PMCID: PMC8834209 DOI: 10.3390/cells11030520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 01/13/2023] Open
Abstract
The oligodendrocyte progenitors (OPCs) are at the front of the glial reaction to the traumatic brain injury. However, regulatory pathways steering the OPC reaction as well as the role of reactive OPCs remain largely unknown. Here, we compared a long-lasting, exacerbated reaction of OPCs to the adult zebrafish brain injury with a timely restricted OPC activation to identify the specific molecular mechanisms regulating OPC reactivity and their contribution to regeneration. We demonstrated that the influx of the cerebrospinal fluid into the brain parenchyma after injury simultaneously activates the toll-like receptor 2 (Tlr2) and the chemokine receptor 3 (Cxcr3) innate immunity pathways, leading to increased OPC proliferation and thereby exacerbated glial reactivity. These pathways were critical for long-lasting OPC accumulation even after the ablation of microglia and infiltrating monocytes. Importantly, interference with the Tlr1/2 and Cxcr3 pathways after injury alleviated reactive gliosis, increased new neuron recruitment, and improved tissue restoration.
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Affiliation(s)
- Rosario Sanchez-Gonzalez
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Department Biology II, University of Munich, 80539 München, Germany;
| | - Christina Koupourtidou
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Tjasa Lepko
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Alessandro Zambusi
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Klara Tereza Novoselc
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Tamara Durovic
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Sven Aschenbroich
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Veronika Schwarz
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Christopher T. Breunig
- Reprogramming and Regeneration, Biomedical Center (BMC), Physiological Genomics, Faculty of Medicine, LMU Munich, 80539 München, Germany; (C.T.B.); (S.H.S.)
- Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany
| | - Hans Straka
- Department Biology II, University of Munich, 80539 München, Germany;
| | - Hagen B. Huttner
- Department of Neurology, Justus-Liebig-University Giessen, Klinikstrasse 33, 35392 Giessen, Germany;
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (M.I.); (J.B.)
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (M.I.); (J.B.)
- German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Sciences Weihenstephan, Technical University Munich, 80333 München, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (W.W.); (D.T.)
- Munich Cluster for Systems Neurology SYNERGY, LMU, 80539 Munich, Germany
- Chair of Developmental Genetics c/o Helmholtz Zentrum München, School of Life Sciences Weihenstephan, Technical University Munich, 80333 München, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Munich, 80539 Munich, Germany
| | - Andreas Zwergal
- Department of Neurology, Ludwig-Maximilians University, Campus Grosshadern, 81377 Munich, Germany;
| | - Tamas Schauer
- Biomedical Center (BMC), Bioinformatic Core Facility, Faculty of Medicine, LMU Munich, 80539 München, Germany; (T.S.); (T.S.)
| | - Tobias Straub
- Biomedical Center (BMC), Bioinformatic Core Facility, Faculty of Medicine, LMU Munich, 80539 München, Germany; (T.S.); (T.S.)
| | - Tim Czopka
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9YL, UK;
| | - Dietrich Trümbach
- Institute of Developmental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (W.W.); (D.T.)
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Munich Cluster for Systems Neurology SYNERGY, LMU, 80539 Munich, Germany
- Biomedical Center (BMC), Division of Physiological Genomics, Faculty of Medicine, LMU Munich, 80539 München, Germany
| | - Stefan H. Stricker
- Reprogramming and Regeneration, Biomedical Center (BMC), Physiological Genomics, Faculty of Medicine, LMU Munich, 80539 München, Germany; (C.T.B.); (S.H.S.)
- Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany
| | - Jovica Ninkovic
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Munich Cluster for Systems Neurology SYNERGY, LMU, 80539 Munich, Germany
- Correspondence:
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11
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Heng JIT, Viti L, Pugh K, Marshall OJ, Agostino M. Understanding the impact of ZBTB18 missense variation on transcription factor function in neurodevelopment and disease. J Neurochem 2022; 161:219-235. [PMID: 35083747 PMCID: PMC9302683 DOI: 10.1111/jnc.15572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 12/01/2022]
Abstract
Mutations to genes that encode DNA‐binding transcription factors (TFs) underlie a broad spectrum of human neurodevelopmental disorders. Here, we highlight the pathological mechanisms arising from mutations to TF genes that influence the development of mammalian cerebral cortex neurons. Drawing on recent findings for TF genes including ZBTB18, we discuss how functional missense mutations to such genes confer non‐native gene regulatory actions in developing neurons, leading to cell‐morphological defects, neuroanatomical abnormalities during foetal brain development and functional impairment. Further, we discuss how missense variation to human TF genes documented in the general population endow quantifiable changes to transcriptional regulation, with potential cell biological effects on the temporal progression of cerebral cortex neuron development and homeostasis. We offer a systematic approach to investigate the functional impact of missense variation in brain TFs and define their direct molecular and cellular actions in foetal neurodevelopment, tissue homeostasis and disease states.![]()
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Affiliation(s)
- Julian I-T Heng
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Neuroscience Laboratories, Sarich Neuroscience Institute, Crawley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Leon Viti
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Kye Pugh
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Owen J Marshall
- Menzies Institute for Medical Research, The University of Tasmania, Hobart, Australia
| | - Mark Agostino
- Curtin Health Innovation Research Institute, Bentley, WA, Australia.,Curtin Institute for Computation, Curtin University, Bentley, Western Australia, Australia
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12
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Kikkawa T, Osumi N. Multiple Functions of the Dmrt Genes in the Development of the Central Nervous System. Front Neurosci 2021; 15:789583. [PMID: 34955736 PMCID: PMC8695973 DOI: 10.3389/fnins.2021.789583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The Dmrt genes encode the transcription factor containing the DM (doublesex and mab-3) domain, an intertwined zinc finger-like DNA binding module. While Dmrt genes are mainly involved in the sexual development of various species, recent studies have revealed that Dmrt genes, which belong to the DmrtA subfamily, are differentially expressed in the embryonic brain and spinal cord and are essential for the development of the central nervous system. Herein, we summarize recent studies that reveal the multiple functions of the Dmrt genes in various aspects of vertebrate neural development, including brain patterning, neurogenesis, and the specification of neurons.
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Affiliation(s)
- Takako Kikkawa
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, United Centers for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan
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13
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Chu ECP, Morin A, Chang THC, Nguyen T, Tsai YC, Sharma A, Liu CC, Pavlidis P. Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PLoS Comput Biol 2021; 17:e1009484. [PMID: 34665801 PMCID: PMC8565786 DOI: 10.1371/journal.pcbi.1009484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 11/03/2021] [Accepted: 09/28/2021] [Indexed: 11/23/2022] Open
Abstract
To facilitate the development of large-scale transcriptional regulatory networks (TRNs) that may enable in-silico analyses of disease mechanisms, a reliable catalogue of experimentally verified direct transcriptional regulatory interactions (DTRIs) is needed for training and validation. There has been a long history of using low-throughput experiments to validate single DTRIs. Therefore, we reason that a reliable set of DTRIs could be produced by curating the published literature for such evidence. In our survey of previous curation efforts, we identified the lack of details about the quantity and the types of experimental evidence to be a major gap, despite the theoretical importance of such details for the identification of bona fide DTRIs. We developed a curation protocol to inspect the published literature for support of DTRIs at the experiment level, focusing on genes important to the development of the mammalian nervous system. We sought to record three types of low-throughput experiments: Transcription factor (TF) perturbation, TF-DNA binding, and TF-reporter assays. Using this protocol, we examined a total of 1,310 papers to assemble a collection of 1,499 unique DTRIs, involving 251 TFs and 825 target genes, many of which were not reported in any other DTRI resource. The majority of DTRIs (965; 64%) were supported by two or more types of experimental evidence and 27% were supported by all three. Of the DTRIs with all three types of evidence, 170 had been tested using primary tissues or cells and 44 had been tested directly in the central nervous system. We used our resource to document research biases among reports towards a small number of well-studied TFs. To demonstrate a use case for this resource, we compared our curation to a previously published high-throughput perturbation screen and found significant enrichment of the curated targets among genes differentially expressed in the developing brain in response to Pax6 deletion. This study demonstrates a proof-of-concept for the assembly of a high resolution DTRI resource to support the development of large-scale TRNs. The capacity to computationally reconstruct gene regulatory networks using large-scale biological data is currently limited by the absence of a high confidence set of one-to-one regulatory interactions. Given the lengthy history of using small scale experimental assays to investigate individual interactions, we reason that a reliable collection of gene regulatory interactions could be compiled by systematically inspecting the published literature. To this end, we developed a curation protocol to examine and record evidence of regulatory interactions at the individual experiment level. Focusing on the area of brain development, we applied our pipeline to 1,310 publications. We identified 3,601 individual experiments, providing detailed information about 1,499 regulatory interactions. Many of these interactions have verified activity specifically in the embryonic brain. By capturing reports of regulatory interactions at this level of detail, we equip the users with more granular information than other similar resources, enabling more informed assessments of reliability.
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Affiliation(s)
- Eric Ching-Pan Chu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Morin
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tak Hou Calvin Chang
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tue Nguyen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yi-Cheng Tsai
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aman Sharma
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chao Chun Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Paul Pavlidis
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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14
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Samoilova EM, Belopasov VV, Baklaushev VP. Transcription Factors of Direct Neuronal Reprogramming in Ontogenesis and Ex Vivo. Mol Biol 2021. [DOI: 10.1134/s0026893321040087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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15
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Xu Y, Xi J, Wang G, Guo Z, Sun Q, Lu C, Ma L, Wu Y, Jia W, Zhu S, Guo X, Bian S, Kang J. PAUPAR and PAX6 sequentially regulate human embryonic stem cell cortical differentiation. Nucleic Acids Res 2021; 49:1935-1950. [PMID: 33544864 PMCID: PMC7913681 DOI: 10.1093/nar/gkab030] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 01/12/2021] [Indexed: 01/08/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play a wide range of roles in the epigenetic regulation of crucial biological processes, but the functions of lncRNAs in cortical development are poorly understood. Using human embryonic stem cell (hESC)-based 2D neural differentiation approach and 3D cerebral organoid system, we identified that the lncRNA PAUPAR, which is adjacent to PAX6, plays essential roles in cortical differentiation by interacting with PAX6 to regulate the expression of a large number of neural genes. Mechanistic studies showed that PAUPAR confers PAX6 proper binding sites on the target neural genes by directly binding the genomic regions of these genes. Moreover, PAX6 recruits the histone methyltransferase NSD1 through its C-terminal PST enrichment domain, then regulate H3K36 methylation and the expression of target genes. Collectively, our data reveal that the PAUPAR/PAX6/NSD1 complex plays a critical role in the epigenetic regulation of hESC cortical differentiation and highlight the importance of PAUPAR as an intrinsic regulator of cortical differentiation.
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Affiliation(s)
- Yanxin Xu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jiajie Xi
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Guiying Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhenming Guo
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China.,Bio-X Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Qiaoyi Sun
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Chenqi Lu
- Department of Biostatistics and Computational Biology, State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Ma
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Wenwen Jia
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Songcheng Zhu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Shan Bian
- Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Sciences and Technology, Frontier Science Center for Stem Cell Research, Tongji University, Shanghai, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, Collaborative Innovation Center for Brain Science, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai, China
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16
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Abstract
The mammalian cerebral cortex is the pinnacle of brain evolution, reaching its maximum complexity in terms of neuron number, diversity and functional circuitry. The emergence of this outstanding complexity begins during embryonic development, when a limited number of neural stem and progenitor cells manage to generate myriads of neurons in the appropriate numbers, types and proportions, in a process called neurogenesis. Here we review the current knowledge on the regulation of cortical neurogenesis, beginning with a description of the types of progenitor cells and their lineage relationships. This is followed by a review of the determinants of neuron fate, the molecular and genetic regulatory mechanisms, and considerations on the evolution of cortical neurogenesis in vertebrates leading to humans. We finish with an overview on how dysregulation of neurogenesis is a leading cause of human brain malformations and functional disabilities.
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Affiliation(s)
- Ana Villalba
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Magdalena Götz
- Institute for Stem Cell Research, Helmholtz Zentrum München & Biomedical Center, Ludwig-Maximilians Universitaet, Planegg-Martinsried, Germany
| | - Víctor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas & Universidad Miguel Hernández, Sant Joan d'Alacant, Spain.
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17
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Russo GL, Sonsalla G, Natarajan P, Breunig CT, Bulli G, Merl-Pham J, Schmitt S, Giehrl-Schwab J, Giesert F, Jastroch M, Zischka H, Wurst W, Stricker SH, Hauck SM, Masserdotti G, Götz M. CRISPR-Mediated Induction of Neuron-Enriched Mitochondrial Proteins Boosts Direct Glia-to-Neuron Conversion. Cell Stem Cell 2020; 28:524-534.e7. [PMID: 33202244 PMCID: PMC7939544 DOI: 10.1016/j.stem.2020.10.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/11/2020] [Accepted: 08/20/2020] [Indexed: 12/17/2022]
Abstract
Astrocyte-to-neuron conversion is a promising avenue for neuronal replacement therapy. Neurons are particularly dependent on mitochondrial function, but how well mitochondria adapt to the new fate is unknown. Here, we determined the comprehensive mitochondrial proteome of cortical astrocytes and neurons, identifying about 150 significantly enriched mitochondrial proteins for each cell type, including transporters, metabolic enzymes, and cell-type-specific antioxidants. Monitoring their transition during reprogramming revealed late and only partial adaptation to the neuronal identity. Early dCas9-mediated activation of genes encoding mitochondrial proteins significantly improved conversion efficiency, particularly for neuron-enriched but not astrocyte-enriched antioxidant proteins. For example, Sod1 not only improves the survival of the converted neurons but also elicits a faster conversion pace, indicating that mitochondrial proteins act as enablers and drivers in this process. Transcriptional engineering of mitochondrial proteins with other functions improved reprogramming as well, demonstrating a broader role of mitochondrial proteins during fate conversion. Mitochondrial proteomes of cortical astrocytes and neurons are distinct Astrocyte-enriched mitochondrial proteins are downregulated late in neuronal conversion Neuron-enriched mitochondrial proteins are upregulated late in neuronal conversion Early induction of neuronal mitochondrial proteins improves neuronal reprogramming
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Affiliation(s)
- Gianluca L Russo
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, BMC LMU, Planegg-Martinsried, Germany; Graduate School of Systemic Neurosciences, BMC, LMU, Planegg-Martinsried, Germany
| | - Giovanna Sonsalla
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, BMC LMU, Planegg-Martinsried, Germany; Graduate School of Systemic Neurosciences, BMC, LMU, Planegg-Martinsried, Germany
| | - Poornemaa Natarajan
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, BMC LMU, Planegg-Martinsried, Germany; Graduate School of Systemic Neurosciences, BMC, LMU, Planegg-Martinsried, Germany
| | - Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, BMC, LMU, Planegg-Martinsried, Germany; Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, Planegg-Martinsried, Germany
| | - Giorgia Bulli
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, BMC LMU, Planegg-Martinsried, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Center Munich, Neuherberg, Germany
| | - Sabine Schmitt
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University Munich (TUM), Munich, Germany
| | | | - Florian Giesert
- Institute of Developmental Genetics, Helmholtz Center Munich, Neuherberg, Germany; Developmental Genetics, TUM, Munich-Weihenstephan, Germany
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, The Arrhenius Laboratories F3, Stockholm University, Stockholm, Sweden
| | - Hans Zischka
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University Munich (TUM), Munich, Germany; Institute of Molecular Toxicology and Pharmacology, Helmholtz Center Munich, Neuherberg, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, Neuherberg, Germany; Developmental Genetics, TUM, Munich-Weihenstephan, Germany; German Center for Neurodegenerative Diseases (DZNE) Site Munich, Munich, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, BMC, LMU, Planegg-Martinsried, Germany; Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, Planegg-Martinsried, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, Neuherberg, Germany
| | - Giacomo Masserdotti
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, BMC LMU, Planegg-Martinsried, Germany
| | - Magdalena Götz
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians-Universität (LMU), Planegg-Martinsried, Germany; Institute for Stem Cell Research, Helmholtz Center Munich, BMC LMU, Planegg-Martinsried, Germany; Excellence Cluster of Systems Neurology (SYNERGY), Munich, Germany.
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18
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Chhabra NF, Amarie OV, Wu M, Amend AL, Rubey M, Gradinger D, Irmler M, Beckers J, Rathkolb B, Wolf E, Feuchtinger A, Huypens P, Teperino R, Rozman J, Przemeck GKH, Hrabě de Angelis M. PAX6 mutation alters circadian rhythm and β cell function in mice without affecting glucose tolerance. Commun Biol 2020; 3:628. [PMID: 33127955 PMCID: PMC7599253 DOI: 10.1038/s42003-020-01337-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 09/25/2020] [Indexed: 11/09/2022] Open
Abstract
The transcription factor PAX6 is involved in the development of the eye and pancreatic islets, besides being associated with sleep–wake cycles. Here, we investigated a point mutation in the RED subdomain of PAX6, previously described in a human patient, to present a comprehensive study of a homozygous Pax6 mutation in the context of adult mammalian metabolism and circadian rhythm. Pax6Leca2 mice lack appropriate retinal structures for light perception and do not display normal daily rhythmic changes in energy metabolism. Despite β cell dysfunction and decreased insulin secretion, mutant mice have normal glucose tolerance. This is associated with reduced hepatic glucose production possibly due to altered circadian variation in expression of clock and metabolic genes, thereby evading hyperglycemia. Hence, our findings show that while the RED subdomain is important for β cell functional maturity, the Leca2 mutation impacts peripheral metabolism via loss of circadian rhythm, thus revealing pleiotropic effects of PAX6. Nirav Chhabra et al. characterize adult mice carrying a homozygous mutation in Pax6 that was identified in a patient with foveal hypoplasia. They find that the Pax6 point mutation has pleiotropic effects, including defects in the mouse retinal structures, loss of the optic nerve, changes in energy metabolism and circadian rhythms, and dysregulation of genes expressed in the pancreas.
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Affiliation(s)
- Nirav Florian Chhabra
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Oana Veronica Amarie
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Moya Wu
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Anna-Lena Amend
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Marina Rubey
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Daniel Gradinger
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martin Irmler
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany
| | - Johannes Beckers
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Chair of Experimental Genetics, Center of Life and Food Sciences, Weihenstephan, Technische Universität München, Freising, Germany
| | - Birgit Rathkolb
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany.,Ludwig-Maximilians-Universität München, Gene Center, Chair for Molecular Animal Breeding and Biotechnology, Munich, Germany
| | - Eckhard Wolf
- German Center for Diabetes Research (DZD), Neuherberg, Germany.,Ludwig-Maximilians-Universität München, Gene Center, Chair for Molecular Animal Breeding and Biotechnology, Munich, Germany
| | - Annette Feuchtinger
- Helmholtz Zentrum München, Research Unit Analytical Pathology, Neuherberg, Germany
| | - Peter Huypens
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Raffaele Teperino
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Jan Rozman
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Gerhard K H Przemeck
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Martin Hrabě de Angelis
- Helmholtz Zentrum München, Institute of Experimental Genetics and German Mouse Clinic, Neuherberg, Germany. .,German Center for Diabetes Research (DZD), Neuherberg, Germany. .,Chair of Experimental Genetics, Center of Life and Food Sciences, Weihenstephan, Technische Universität München, Freising, Germany.
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19
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Handara G, Kröger S. Alternative Splicing and the Intracellular Domain Mediate TM-agrin's Ability to Differentially Regulate the Density of Excitatory and Inhibitory Synapse-like Specializations in Developing CNS Neurons. Neuroscience 2019; 419:60-71. [PMID: 31672640 DOI: 10.1016/j.neuroscience.2019.09.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 01/26/2023]
Abstract
Agrin is a multi-domain protein best known for its essential function during formation of the neuromuscular junction. Alternative mRNA splicing at sites named y and z in the C-terminal part of agrin regulates its interaction with a receptor complex consisting of the agrin-binding low-density lipoprotein receptor-related protein 4 (Lrp4) and the muscle-specific kinase (MuSK). Isoforms with inserts at both splice sites bind to Lrp4, activate MuSK and are synaptogenic at the neuromuscular junction. Agrin is also expressed as a transmembrane protein in the central nervous system (CNS) but its function during interneuronal synapse formation is unclear. Recently we demonstrated that transfection of a full-length cDNA coding for transmembrane agrin (TM-agrin) in cultured embryonic cortical neurons induced an Lrp4-dependent but MuSK-independent increase in dendritic glutamatergic synapses and an Lrp4- and MuSK-independent reduction of inhibitory synapses. Here we show that presynaptic specializations were similarly affected by TM-agrin overexpression. In addition, we mapped the regions within TM-agrin responsible for TM-agrin's effects on dendritic aggregates of synapse-associated proteins. We show that the presence of a four amino acid insert at splice site y is essential for the increase in the density of puncta containing the postsynaptic density protein 95 kDa. This effect was independent of splice site z. The reduction of the gephyrin puncta density was independent of the entire extracellular part of TM-agrin but required a highly conserved serine residue in the intracellular domain of TM-agrin. These results provide further evidence for a function of TM-agrin during CNS synaptogenesis and demonstrate that different domains and alternative splicing of TM-agrin differentially affect excitatory and inhibitory synapse formation in cultured embryonic CNS neurons.
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Affiliation(s)
- Gerry Handara
- Department of Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University, Großhaderner Str. 9, D-82152 Planegg-Martinsried, Germany; Institute for Stem Cell Research, German Research Center for Environmental Health, Helmholtz Centre Munich, Ingolstädter Landstraße 1, D-85764 Neuherberg, Germany
| | - Stephan Kröger
- Department of Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University, Großhaderner Str. 9, D-82152 Planegg-Martinsried, Germany.
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20
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Klann M, Seaver EC. Functional role of pax6 during eye and nervous system development in the annelid Capitella teleta. Dev Biol 2019; 456:86-103. [PMID: 31445008 DOI: 10.1016/j.ydbio.2019.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/16/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022]
Abstract
The transcription factor Pax6 is an important regulator of early animal development. Loss of function mutations of pax6 in a range of animals result in a reduction or complete loss of the eye, a reduction of a subset of neurons, and defects in axon growth. There are no studies focusing on the role of pax6 during development of any lophotrochozoan representative, however, expression of pax6 in the developing eye and nervous system in a number of species suggest that pax6 plays a highly conserved role in eye and nervous system formation. We investigated the functional role of pax6 during development of the marine annelid Capitella teleta. Expression of pax6 transcripts in C. teleta larvae is similar to patterns found in other animals, with distinct subdomains in the brain and ventral nerve cord as well as in the larval and juvenile eye. To perturb pax6 function, two different splice-blocking morpholinos and a translation-blocking morpholino were used. Larvae resulting from microinjections with either splice-blocking morpholino show a reduction of the pax6 transcript. Development of both the larval eyes and the central nervous system architecture are highly disrupted following microinjection of each of the three morpholinos. The less severe phenotype observed when only the homeodomain is disrupted suggests that presence of the paired domain is sufficient for partial function of the Pax6 protein. Preliminary downstream target analysis confirms disruption in expression of some components of the retinal gene regulatory network, as well as disruption of genes involved in nervous system development. Results from this study, taken together with studies from other species, reveal an evolutionarily conserved role for pax6 in eye and neural specification and development.
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Affiliation(s)
- Marleen Klann
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, Fl, 32080, USA
| | - Elaine C Seaver
- Whitney Laboratory for Marine Bioscience, University of Florida, 9505 Ocean Shore Blvd, St. Augustine, Fl, 32080, USA.
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21
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The role of Pax6 in brain development and its impact on pathogenesis of autism spectrum disorder. Brain Res 2019; 1705:95-103. [DOI: 10.1016/j.brainres.2018.02.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 02/23/2018] [Accepted: 02/24/2018] [Indexed: 12/14/2022]
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22
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Signaling within the pineal gland: A parallelism with the central nervous system. Semin Cell Dev Biol 2018; 95:151-159. [PMID: 30502386 DOI: 10.1016/j.semcdb.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/15/2018] [Accepted: 11/27/2018] [Indexed: 12/22/2022]
Abstract
The pineal gland (PG) derives from the neural tube, like the rest of the central nervous system (CNS). The PG is specialized in synthesizing and secreting melatonin in a circadian fashion. The nocturnal elevation of melatonin is a highly conserved feature among species which proves its importance in nature. Here, we review a limited set of intrinsic and extrinsic regulatory elements that have been shown or proposed to influence the PG's melatonin production, as well as pineal ontogeny and homeostasis. Intrinsic regulators include the transcription factors CREB, Pax6 and NeuroD1. In addition, microglia within the PG participate as extrinsic regulators of these functions. We further discuss how these same elements work in other parts of the CNS, and note similarities and differences to their roles in the PG. Since the PG is a relatively well-defined and highly specialized organ within the CNS, we suggest that applying this comparative approach to additional PG regulators may be a useful tool for understanding complex areas of the brain, as well as the influence of the PG in both health and disease, including circadian functions and disorders.
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23
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May M, Denecke B, Schroeder T, Götz M, Faissner A. Cell tracking in vitro reveals that the extracellular matrix glycoprotein Tenascin-C modulates cell cycle length and differentiation in neural stem/progenitor cells of the developing mouse spinal cord. Biol Open 2018; 7:7/7/bio027730. [PMID: 30045859 PMCID: PMC6078350 DOI: 10.1242/bio.027730] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Generation of astrocytes during the development of the mammalian spinal cord is poorly understood. Previously, we have shown that the glycoprotein of the extracellular matrix (ECM) tenascin-C (Tnc) modulates the expression territories of the patterning genes Nkx6.1 and Nkx2.2 in the developing ventral spinal cord, tunes the responsiveness of neural stem/progenitor cells towards the cytokines FGF2 and EGF and thereby promotes astrocyte maturation. In order to obtain further mechanistic insight into these processes, we have compared embryonic day-15 spinal cord neural progenitor cells (NPCs) from wild-type and Tnc knockout mice using continuous single-cell live imaging and cell lineage analysis in vitroTnc knockout cells displayed a significantly reduced rate of cell division both in response to FGF2 and EGF. When individual clones of dividing cells were investigated with regard to their cell lineage trees using the tTt tracking software, it appeared that the cell cycle length in response to growth factors was reduced in the knockout. Furthermore, when Tnc knockout NPCs were induced to differentiate by the removal of FGF2 and EGF glial differentiation was enhanced. We conclude that the constituent of the stem cell niche Tnc contributes to preserve stemness of NPCs.
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Affiliation(s)
- Marcus May
- Department for Cell Morphology and Molecular Neurobiology, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Bernd Denecke
- Aachen Interdisciplinary Center for Clinical Research, Faculty of Medicine, Rheinisch-Westfälische Technische Hochschule Aachen, 52074 Aachen, Germany
| | - Timm Schroeder
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
| | - Magdalena Götz
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians University Munich, 82152 Planegg/Martinsried, Germany.,Department of Physiological Genomics, Biomedical Center, Ludwig-Maximilians University Munich, 82152 Planegg/Martinsried, Germany.,Munich Cluster for Systems Neurology (SyNergy), Ludwig-Maximilians University Munich, 81377 Munich, Germany
| | - Andreas Faissner
- Department for Cell Morphology and Molecular Neurobiology, Ruhr-University Bochum, 44780 Bochum, Germany
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24
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Drosophila Pax6 promotes development of the entire eye-antennal disc, thereby ensuring proper adult head formation. Proc Natl Acad Sci U S A 2018; 114:5846-5853. [PMID: 28584125 DOI: 10.1073/pnas.1610614114] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Paired box 6 (Pax6) is considered to be the master control gene for eye development in all seeing animals studied so far. In vertebrates, it is required not only for lens/retina formation but also for the development of the CNS, olfactory system, and pancreas. Although Pax6 plays important roles in cell differentiation, proliferation, and patterning during the development of these systems, the underlying mechanism remains poorly understood. In the fruit fly, Drosophila melanogaster, Pax6 also functions in a range of tissues, including the eye and brain. In this report, we describe the function of Pax6 in Drosophila eye-antennal disc development. Previous studies have suggested that the two fly Pax6 genes, eyeless (ey) and twin of eyeless (toy), initiate eye specification, whereas eyegone (eyg) and the Notch (N) pathway independently regulate cell proliferation. Here, we show that Pax6 controls eye progenitor cell survival and proliferation through the activation of teashirt (tsh) and eyg, thereby indicating that Pax6 initiates both eye specification and proliferation. Although simultaneous loss of ey and toy during early eye-antennal disc development disrupts the development of all head structures derived from the eye-antennal disc, overexpression of N or tsh in the absence of Pax6 rescues only antennal and head epidermis development. Furthermore, overexpression of tsh induces a homeotic transformation of the fly head into thoracic structures. Taking these data together, we demonstrate that Pax6 promotes development of the entire eye-antennal disc and that the retinal determination network works to repress alternative tissue fates, which ensures proper development of adult head structures.
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25
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Florio M, Heide M, Pinson A, Brandl H, Albert M, Winkler S, Wimberger P, Huttner WB, Hiller M. Evolution and cell-type specificity of human-specific genes preferentially expressed in progenitors of fetal neocortex. eLife 2018; 7:32332. [PMID: 29561261 PMCID: PMC5898914 DOI: 10.7554/elife.32332] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/09/2018] [Indexed: 01/21/2023] Open
Abstract
Understanding the molecular basis that underlies the expansion of the neocortex during primate, and notably human, evolution requires the identification of genes that are particularly active in the neural stem and progenitor cells of the developing neocortex. Here, we have used existing transcriptome datasets to carry out a comprehensive screen for protein-coding genes preferentially expressed in progenitors of fetal human neocortex. We show that 15 human-specific genes exhibit such expression, and many of them evolved distinct neural progenitor cell-type expression profiles and levels compared to their ancestral paralogs. Functional studies on one such gene, NOTCH2NL, demonstrate its ability to promote basal progenitor proliferation in mice. An additional 35 human genes with progenitor-enriched expression are shown to have orthologs only in primates. Our study provides a resource of genes that are promising candidates to exert specific, and novel, roles in neocortical development during primate, and notably human, evolution.
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Affiliation(s)
- Marta Florio
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Heide
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Anneline Pinson
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Holger Brandl
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mareike Albert
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Pauline Wimberger
- Klinik und Poliklinik für Frauenheilkunde und Geburtshilfe, Universitätsklinikum Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
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26
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Remez LA, Onishi A, Menuchin-Lasowski Y, Biran A, Blackshaw S, Wahlin KJ, Zack DJ, Ashery-Padan R. Pax6 is essential for the generation of late-born retinal neurons and for inhibition of photoreceptor-fate during late stages of retinogenesis. Dev Biol 2017; 432:140-150. [PMID: 28993200 DOI: 10.1016/j.ydbio.2017.09.030] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 12/08/2016] [Accepted: 09/23/2017] [Indexed: 12/16/2022]
Abstract
In the developing retina, as in other regions of the CNS, neural progenitors give rise to individual cell types during discrete temporal windows. Pax6 is expressed in retinal progenitor cells (RPCs) throughout the course of retinogenesis, and has been shown to be required during early retinogenesis for generation of most early-born cell types. In this study, we examined the function of Pax6 in postnatal mouse retinal development. We found that Pax6 is essential for the generation of late-born interneurons, while inhibiting photoreceptor differentiation. Generation of bipolar interneurons requires Pax6 expression in RPCs, while Pax6 is required for the generation of glycinergic, but not for GABAergic or non-GABAergic-non-glycinergic (nGnG) amacrine cell subtypes. In contrast, overexpression of either full-length Pax6 or its 5a isoform in RPCs induces formation of cells with nGnG amacrine features, and suppresses generation of other inner retinal cell types. Moreover, overexpression of both Pax6 variants prevents photoreceptor differentiation, most likely by inhibiting Crx expression. Taken together, these data show that Pax6 acts in RPCs to control differentiation of multiple late-born neuronal cell types.
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Affiliation(s)
- Liv Aleen Remez
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Akishi Onishi
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Yotam Menuchin-Lasowski
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Assaf Biran
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel
| | - Seth Blackshaw
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Karl J Wahlin
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, United States
| | - Donlad J Zack
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States; Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel-Aviv University, Tel Aviv, Israel.
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27
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Subpallial Enhancer Transgenic Lines: a Data and Tool Resource to Study Transcriptional Regulation of GABAergic Cell Fate. Neuron 2017; 92:59-74. [PMID: 27710791 DOI: 10.1016/j.neuron.2016.09.027] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/22/2016] [Accepted: 09/02/2016] [Indexed: 01/08/2023]
Abstract
Elucidating the transcriptional circuitry controlling forebrain development requires an understanding of enhancer activity and regulation. We generated stable transgenic mouse lines that express CreERT2 and GFP from ten different enhancer elements with activity in distinct domains within the embryonic basal ganglia. We used these unique tools to generate a comprehensive regional fate map of the mouse subpallium, including sources for specific subtypes of amygdala neurons. We then focused on deciphering transcriptional mechanisms that control enhancer activity. Using machine-learning computations, in vivo chromosomal occupancy of 13 transcription factors that regulate subpallial patterning and differentiation and analysis of enhancer activity in Dlx1/2 and Lhx6 mutants, we elucidated novel molecular mechanisms that regulate region-specific enhancer activity in the developing brain. Thus, these subpallial enhancer transgenic lines are data and tool resources to study transcriptional regulation of GABAergic cell fate.
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28
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Efficient and Fast Differentiation of Human Neural Stem Cells from Human Embryonic Stem Cells for Cell Therapy. Stem Cells Int 2017; 2017:9405204. [PMID: 29075299 PMCID: PMC5624175 DOI: 10.1155/2017/9405204] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/28/2017] [Accepted: 07/27/2017] [Indexed: 12/29/2022] Open
Abstract
Stem cell-based therapies have been used for repairing damaged brain tissue and helping functional recovery after brain injury. Aberrance neurogenesis is related with brain injury, and multipotential neural stem cells from human embryonic stem (hES) cells provide a great promise for cell replacement therapies. Optimized protocols for neural differentiation are necessary to produce functional human neural stem cells (hNSCs) for cell therapy. However, the qualified procedure is scarce and detailed features of hNSCs originated from hES cells are still unclear. In this study, we developed a method to obtain hNSCs from hES cells, by which we could harvest abundant hNSCs in a relatively short time. Then, we examined the expression of pluripotent and multipotent marker genes through immunostaining and confirmed differentiation potential of the differentiated hNSCs. Furthermore, we analyzed the mitotic activity of these hNSCs. In this report, we provided comprehensive features of hNSCs and delivered the knowledge about how to obtain more high-quality hNSCs from hES cells which may help to accelerate the NSC-based therapies in brain injury treatment.
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29
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Chang WL, Lai WW, Kuo IY, Lin CY, Lu PJ, Sheu BS, Wang YC. A six-CpG panel with DNA methylation biomarkers predicting treatment response of chemoradiation in esophageal squamous cell carcinoma. J Gastroenterol 2017; 52:705-714. [PMID: 27671002 DOI: 10.1007/s00535-016-1265-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/13/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND Prognosis of esophageal squamous cell carcinoma (ESCC) patients remains poor, and the chemoradiotherapy (CRT) applied to ESCC patients often failed. Therefore, development of biomarkers to predict CRT response is immensely important for choosing the best treatment strategy of an individual patient. METHODS The methylation array and pyrosequencing methylation assay were performed in pre-treatment endoscopic biopsies to identify probes with differential CpG methylation levels between good and poor CRT responders in a cohort of 12 ESCC patients. Receiver operating characteristic curves and multivariate logistic regressions were conducted to build the risk score equation of selected CpG probes in another cohort of 91 ESCC patients to predict CRT response. Kaplan-Meier analysis was used to estimate progression-free survival or time-to-progression of patients predicted with good and poor CRT responses. RESULTS Nine differentially methylated CpG probes were identified to be associated with CRT response. A risk score equation comprising six CpG probes located in IFNGR2, KCNK4, NOTCH4, NPY, PAX6, and SOX17 genes were built. The risk score was derived from the sum of each probe multiplied by its corresponding coefficient. Such a risk score has a good prediction performance in discriminating poor CRT responders from good responders (AUC: 0.930). Moreover, poor CRT responders predicted by risk score significantly had poorer prognosis in terms of shorter progression-free survival and time-to-progression (p = 0.004-0.008). CONCLUSION We established a proof-of-concept CRT response prediction panel consisting of six-CpG methylation biomarkers in identifying ESCC patients who are at high risk of CRT failure and need intensive care.
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Affiliation(s)
- Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wu-Wei Lai
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - I-Ying Kuo
- Department of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chien-Yu Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Pei-Jung Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan
| | - Bor-Shyang Sheu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan. .,Department of Internal Medicine, Tainan Hospital, Ministry of Health and Welfare, Tainan, 700, Taiwan.
| | - Yi-Ching Wang
- Department of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan. .,Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, 701, Taiwan.
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30
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Chen CA, Yin J, Lewis RA, Schaaf CP. Genetic causes of optic nerve hypoplasia. J Med Genet 2017; 54:441-449. [PMID: 28501829 DOI: 10.1136/jmedgenet-2017-104626] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 04/05/2017] [Indexed: 01/25/2023]
Abstract
Optic nerve hypoplasia (ONH) is the most common congenital optic nerve anomaly and a leading cause of blindness in the USA. Although most cases of ONH occur as isolated cases within their respective families, the advancement in molecular diagnostic technology has made us realise that a substantial fraction of cases has identifiable genetic causes, typically de novo mutations. An increasing number of genes has been reported, mutations of which can cause ONH. Many of the genes involved serve as transcription factors, participating in an intricate multistep process critical to eye development and neurogenesis in the neural retina. This review will discuss the respective genes and mutations, human phenotypes, and animal models that have been created to gain a deeper understanding of the disorders. The identification of the underlying gene and mutation provides an important step in diagnosis, medical care and counselling for the affected individuals and their families. We envision that future research will lead to further disease gene identification, but will also teach us about gene-gene and gene-environment interactions relevant to optic nerve development. How much of the functional impairment of the various forms of ONH is a reflection of altered morphogenesis versus neuronal homeostasis will determine the prospect of therapeutic intervention, with the ultimate goal of improving the quality of life of the individuals affected with ONH.
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Affiliation(s)
- Chun-An Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Jiani Yin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Richard Alan Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Department of Ophthalmology, Baylor College of Medicine, Houston, Texas, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
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31
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Wang X, Shan X, Gregory-Evans CY. A mouse model of aniridia reveals the in vivo downstream targets of Pax6 driving iris and ciliary body development in the eye. Biochim Biophys Acta Mol Basis Dis 2017; 1863:60-67. [DOI: 10.1016/j.bbadis.2016.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/13/2016] [Accepted: 10/18/2016] [Indexed: 11/28/2022]
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32
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Sun J, Zhao Y, McGreal R, Cohen-Tayar Y, Rockowitz S, Wilczek C, Ashery-Padan R, Shechter D, Zheng D, Cvekl A. Pax6 associates with H3K4-specific histone methyltransferases Mll1, Mll2, and Set1a and regulates H3K4 methylation at promoters and enhancers. Epigenetics Chromatin 2016; 9:37. [PMID: 27617035 PMCID: PMC5018195 DOI: 10.1186/s13072-016-0087-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 08/31/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Pax6 is a key regulator of the entire cascade of ocular lens formation through specific binding to promoters and enhancers of batteries of target genes. The promoters and enhancers communicate with each other through DNA looping mediated by multiple protein-DNA and protein-protein interactions and are marked by specific combinations of histone posttranslational modifications (PTMs). Enhancers are distinguished from bulk chromatin by specific modifications of core histone H3, including H3K4me1 and H3K27ac, while promoters show increased H3K4me3 PTM. Previous studies have shown the presence of Pax6 in as much as 1/8 of lens-specific enhancers but a much smaller fraction of tissue-specific promoters. Although Pax6 is known to interact with EP300/p300 histone acetyltransferase responsible for generation of H3K27ac, a potential link between Pax6 and histone H3K4 methylation remains to be established. RESULTS Here we show that Pax6 co-purifies with H3K4 methyltransferase activity in lens cell nuclear extracts. Proteomic studies show that Pax6 immunoprecipitates with Set1a, Mll1, and Mll2 enzymes, and their associated proteins, i.e., Wdr5, Rbbp5, Ash2l, and Dpy30. ChIP-seq studies using chromatin prepared from mouse lens and cultured lens cells demonstrate that Pax6-bound regions are mostly enriched with H3K4me2 and H3K4me1 in enhancers and promoters, though H3K4me3 marks only Pax6-containing promoters. The shRNA-mediated knockdown of Pax6 revealed down-regulation of a set of direct target genes, including Cap2, Farp1, Pax6, Plekha1, Prox1, Tshz2, and Zfp536. Pax6 knockdown was accompanied by reduced H3K4me1 at enhancers and H3K4me3 at promoters, with little or no changes of the H3K4me2 modifications. These changes were prominent in Plekha1, a gene regulated by Pax6 in both lens and retinal pigmented epithelium. CONCLUSIONS Our study supports a general model of Pax6-mediated recruitment of histone methyltransferases Mll1 and Mll2 to lens chromatin, especially at distal enhancers. Genome-wide data in lens show that Pax6 binding correlates with H3K4me2, consistent with the idea that H3K4me2 PTMs correlate with the binding of transcription factors. Importantly, partial reduction of Pax6 induces prominent changes in local H3K4me1 and H3K4me3 modification. Together, these data open the field to mechanistic studies of Pax6, Mll1, Mll2, and H3K4me1/2/3 dynamics at distal enhancers and promoters of developmentally controlled genes.
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Affiliation(s)
- Jian Sun
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Yilin Zhao
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Rebecca McGreal
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Yamit Cohen-Tayar
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol school of Neuroscience, Tel-Aviv University, Tel Aviv, 69978 Israel
| | - Shira Rockowitz
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Carola Wilczek
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Ruth Ashery-Padan
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine, Sagol school of Neuroscience, Tel-Aviv University, Tel Aviv, 69978 Israel
| | - David Shechter
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Ales Cvekl
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461 USA
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33
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Wilsch-Bräuninger M, Florio M, Huttner WB. Neocortex expansion in development and evolution — from cell biology to single genes. Curr Opin Neurobiol 2016; 39:122-32. [DOI: 10.1016/j.conb.2016.05.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/15/2016] [Indexed: 02/06/2023]
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Götz M, Nakafuku M, Petrik D. Neurogenesis in the Developing and Adult Brain-Similarities and Key Differences. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a018853. [PMID: 27235475 DOI: 10.1101/cshperspect.a018853] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Adult neurogenesis in the mammalian brain is often viewed as a continuation of neurogenesis at earlier, developmental stages. Here, we will critically review the extent to which this is the case highlighting similarities as well as key differences. Although many transcriptional regulators are shared in neurogenesis at embryonic and adult stages, recent findings on the molecular mechanisms by which these neuronal fate determinants control fate acquisition and maintenance have revealed profound differences between development and adulthood. Importantly, adult neurogenesis occurs in a gliogenic environment, hence requiring adult-specific additional and unique mechanisms of neuronal fate specification and maintenance. Thus, a better understanding of the molecular logic for continuous adult neurogenesis provides important clues to develop strategies to manipulate endogenous stem cells for the purpose of repair.
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Affiliation(s)
- Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Neuherberg, Munich, Germany Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University, 80336 Munich, Germany Synergy, Munich Cluster for Systems Neurology, 81377 Munich, Germany
| | - Masato Nakafuku
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio 45140 Departments of Pediatrics and Neurosurgery, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267
| | - David Petrik
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Neuherberg, Munich, Germany Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University, 80336 Munich, Germany
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35
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Cvekl A, Callaerts P. PAX6: 25th anniversary and more to learn. Exp Eye Res 2016; 156:10-21. [PMID: 27126352 DOI: 10.1016/j.exer.2016.04.017] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 04/12/2016] [Accepted: 04/22/2016] [Indexed: 01/29/2023]
Abstract
The DNA-binding transcription factor PAX6 was cloned 25 years ago by multiple teams pursuing identification of human and mouse eye disease causing genes, cloning vertebrate homologues of pattern-forming regulatory genes identified in Drosophila, or abundant eye-specific transcripts. Since its discovery in 1991, genetic, cellular, molecular and evolutionary studies on Pax6 mushroomed in the mid 1990s leading to the transformative thinking regarding the genetic program orchestrating both early and late stages of eye morphogenesis as well as the origin and evolution of diverse visual systems. Since Pax6 is also expressed outside of the eye, namely in the central nervous system and pancreas, a number of important insights into the development and function of these organs have been amassed. In most recent years, genome-wide technologies utilizing massively parallel DNA sequencing have begun to provide unbiased insights into the regulatory hierarchies of specification, determination and differentiation of ocular cells and neurogenesis in general. This review is focused on major advancements in studies on mammalian eye development driven by studies of Pax6 genes in model organisms and future challenges to harness the technology-driven opportunities to reconstruct, step-by-step, the transition from naïve ectoderm, neuroepithelium and periocular mesenchyme/neural crest cells into the three-dimensional architecture of the eye.
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Affiliation(s)
- Ales Cvekl
- The Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY, 10461, USA; The Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
| | - Patrick Callaerts
- Laboratory of Behavioral and Developmental Genetics, K.U. Leuven, VIB, 3000, Leuven, Belgium.
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36
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Bery A, Mérot Y, Rétaux S. Genes expressed in mouse cortical progenitors are enriched in Pax, Lhx, and Sox transcription factor putative binding sites. Brain Res 2015; 1633:37-51. [PMID: 26721689 DOI: 10.1016/j.brainres.2015.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/25/2015] [Accepted: 12/14/2015] [Indexed: 11/19/2022]
Abstract
Considerable progress has been made in the understanding of molecular and cellular mechanisms controlling the development of the mammalian cortex. The proliferative and neurogenic properties of cortical progenitors located in the ventricular germinal zone start being understood. Little is known however on the cis-regulatory control that finely tunes gene expression in these progenitors. Here, we undertook an in silico-based approach to address this question, followed by some functional validation. Using the Eurexpress database, we established a list of 30 genes specifically expressed in the cortical germinal zone, we selected mouse/human conserved non-coding elements (CNEs) around these genes and we performed motif-enrichment search in these CNEs. We found an over-representation of motifs corresponding to binding sites for Pax, Sox, and Lhx transcription factors, often found as pairs and located within 100bp windows. A small subset of CNEs (n=7) was tested for enhancer activity, by ex-vivo and in utero electroporation assays. Two showed strong enhancer activity in the germinal zone progenitors. Mutagenesis experiments on a selected CNE showed the functional importance of the Pax, Sox, and Lhx TFBS for conferring enhancer activity to the CNE. Overall, from a cis-regulatory viewpoint, our data suggest an input from Pax, Sox and Lhx transcription factors to orchestrate corticogenesis. These results are discussed with regards to the known functional roles of Pax6, Sox2 and Lhx2 in cortical development.
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Affiliation(s)
- Amandine Bery
- DECA Group, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, 91198 Gif-sur-Yvette, France.
| | - Yohann Mérot
- DECA Group, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, 91198 Gif-sur-Yvette, France
| | - Sylvie Rétaux
- DECA Group, Institut des Neurosciences Paris-Saclay, Université Paris-Saclay, Université Paris-Sud, CNRS, UMR 9197, 91198 Gif-sur-Yvette, France.
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37
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Madhu V, Dighe AS, Cui Q, Deal DN. Dual Inhibition of Activin/Nodal/TGF-β and BMP Signaling Pathways by SB431542 and Dorsomorphin Induces Neuronal Differentiation of Human Adipose Derived Stem Cells. Stem Cells Int 2015; 2016:1035374. [PMID: 26798350 PMCID: PMC4699250 DOI: 10.1155/2016/1035374] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/03/2015] [Indexed: 12/16/2022] Open
Abstract
Damage to the nervous system can cause devastating diseases or musculoskeletal dysfunctions and transplantation of progenitor stem cells can be an excellent treatment option in this regard. Preclinical studies demonstrate that untreated stem cells, unlike stem cells activated to differentiate into neuronal lineage, do not survive in the neuronal tissues. Conventional methods of inducing neuronal differentiation of stem cells are complex and expensive. We therefore sought to determine if a simple, one-step, and cost effective method, previously reported to induce neuronal differentiation of embryonic stem cells and induced-pluripotent stem cells, can be applied to adult stem cells. Indeed, dual inhibition of activin/nodal/TGF-β and BMP pathways using SB431542 and dorsomorphin, respectively, induced neuronal differentiation of human adipose derived stem cells (hADSCs) as evidenced by formation of neurite extensions, protein expression of neuron-specific gamma enolase, and mRNA expression of neuron-specific transcription factors Sox1 and Pax6 and matured neuronal marker NF200. This process correlated with enhanced phosphorylation of p38, Erk1/2, PI3K, and Akt1/3. Additionally, in vitro subcutaneous implants of SB431542 and dorsomorphin treated hADSCs displayed significantly higher expression of active-axonal-growth-specific marker GAP43. Our data offers novel insights into cell-based therapies for the nervous system repair.
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Affiliation(s)
- Vedavathi Madhu
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Virginia, Charlottesville, VA 22908, USA
| | - Abhijit S. Dighe
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Virginia, Charlottesville, VA 22908, USA
| | - Quanjun Cui
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Virginia, Charlottesville, VA 22908, USA
| | - D. Nicole Deal
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University of Virginia, Charlottesville, VA 22908, USA
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38
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Abstract
Age-related cataracts are frequently associated with degenerative changes in the ocular lens including the aggregation of proteins - mainly crystallins, but also other proteins including amyloids (Aβ) leading to the hypothesis that cataracts could be used as "biomarkers" for Alzheimer disease. Even if this hypothesis was rejected by David Beebe's last paper (Bei et al., Exp. Eye Res., 2015), it is a fascinating aspect to look for commonalities between eye diseases and neurological disorders. In this review, I discuss such commonalities between eye and brain mainly from a developmental point of view. The finding of the functional homology of the Drosophila eyeless gene with the mammalian Pax6 gene marks a first highlight in the developmental genetics of the eye - this result destroyed the "dogma" of the different evolutionary routes of eye development in flies and mammals. The second highlight was the finding that Pax6 is also involved in the development of the forebrain supporting the pleiotropic role of many genes. These findings opened a new avenue for research showing that a broad variety of transcription factors, but also structural proteins are involved both, in eye and brain development as well as into the maintenance of the functional integrity of the corresponding tissue(s). In this review recent findings are summarized demonstrating that genes whose mutations have been identified first to be causative for congenital or juvenile eye disorders are also involved in regenerative processes and neurogenesis (Pax6), but also in neurodegenerative diseases like Parkinson (e.g. Pitx3) or in neurological disorders like Schizophrenia (e.g. Crybb1, Crybb2).
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Affiliation(s)
- Jochen Graw
- Helmholtz Zentrum München, Institute of Developmental Genetics, Ingolstaedter Landstr, 1, D-85764 Neuherberg, Germany.
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39
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Ypsilanti AR, Rubenstein JLR. Transcriptional and epigenetic mechanisms of early cortical development: An examination of how Pax6 coordinates cortical development. J Comp Neurol 2015; 524:609-29. [PMID: 26304102 DOI: 10.1002/cne.23866] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/14/2015] [Accepted: 07/17/2015] [Indexed: 12/26/2022]
Abstract
The development of the cortex is an elaborate process that integrates a plethora of finely tuned molecular processes ranging from carefully regulated gradients of transcription factors, dynamic changes in the chromatin landscape, or formation of protein complexes to elicit and regulate transcription. Combined with cellular processes such as cell type specification, proliferation, differentiation, and migration, all of these developmental processes result in the establishment of an adult mammalian cortex with its typical lamination and regional patterning. By examining in-depth the role of one transcription factor, Pax6, on the regulation of cortical development, its integration in the regulation of chromatin state, and its regulation by cis-regulatory elements, we aim to demonstrate the importance of integrating each level of regulation in our understanding of cortical development.
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Affiliation(s)
- Athéna R Ypsilanti
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, California
| | - John L R Rubenstein
- Department of Psychiatry, Neuroscience Program, and the Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, California
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40
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Wong FK, Fei JF, Mora-Bermúdez F, Taverna E, Haffner C, Fu J, Anastassiadis K, Stewart AF, Huttner WB. Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex. PLoS Biol 2015; 13:e1002217. [PMID: 26252244 PMCID: PMC4529158 DOI: 10.1371/journal.pbio.1002217] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/30/2015] [Indexed: 11/21/2022] Open
Abstract
The evolutionary expansion of the neocortex in mammals has been linked to enlargement of the subventricular zone (SVZ) and increased proliferative capacity of basal progenitors (BPs), notably basal radial glia (bRG). The transcription factor Pax6 is known to be highly expressed in primate, but not mouse, BPs. Here, we demonstrate that sustaining Pax6 expression selectively in BP-genic apical radial glia (aRG) and their BP progeny of embryonic mouse neocortex suffices to induce primate-like progenitor behaviour. Specifically, we conditionally expressed Pax6 by in utero electroporation using a novel, Tis21–CreERT2 mouse line. This expression altered aRG cleavage plane orientation to promote bRG generation, increased cell-cycle re-entry of BPs, and ultimately increased upper-layer neuron production. Upper-layer neuron production was also increased in double-transgenic mouse embryos with sustained Pax6 expression in the neurogenic lineage. Strikingly, increased BPs existed not only in the SVZ but also in the intermediate zone of the neocortex of these double-transgenic mouse embryos. In mutant mouse embryos lacking functional Pax6, the proportion of bRG among BPs was reduced. Our data identify specific Pax6 effects in BPs and imply that sustaining this Pax6 function in BPs could be a key aspect of SVZ enlargement and, consequently, the evolutionary expansion of the neocortex. "Humanizing" the expression of the transcription factor Pax6 in cortical progenitors in the developing mouse brain is sufficient to endow these progenitors with a primate-like proliferative capacity. During development, neural progenitors generate all cells that make up the mammalian brain. Differences in brain size among the various mammalian species are attributed to differences in the abundance and proliferative capacity of a specific class of neural progenitors called basal progenitors. Among these, a specific progenitor type called basal radial glia is thought to have played an important role during evolution in the expansion of the neocortex, the part of the brain associated with higher cognitive functions like conscious thought and language. In the neocortex, the expression of the transcription factor Pax6 in basal progenitors is low in rodents, but high in primates, including humans. In this study, we aimed to mimic the elevated expression pattern of Pax6 seen in humans in basal progenitors of the embryonic mouse neocortex. To this end, we generated a novel, transgenic mouse line that allows sustained expression of the Pax6 gene in basal progenitors. This elevated expression resulted in an increase in the generation of basal radial glia, in the proliferative capacity of basal progenitors, and, ultimately, in the number of neurons produced. Our findings demonstrate that altering the expression of a single transcription factor from a mouse to a human-like pattern suffices to induce a primate-like proliferative behaviour in neural progenitors, which is thought to underlie the evolutionary expansion of the neocortex.
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Affiliation(s)
- Fong Kuan Wong
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ji-Feng Fei
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Elena Taverna
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christiane Haffner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jun Fu
- Biotechnology Center of the Technische Universität Dresden, Dresden, Germany
| | | | - A. Francis Stewart
- Biotechnology Center of the Technische Universität Dresden, Dresden, Germany
| | - Wieland B. Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- * E-mail:
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41
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Sirko S, Irmler M, Gascón S, Bek S, Schneider S, Dimou L, Obermann J, De Souza Paiva D, Poirier F, Beckers J, Hauck SM, Barde YA, Götz M. Astrocyte reactivity after brain injury-: The role of galectins 1 and 3. Glia 2015; 63:2340-61. [PMID: 26250529 PMCID: PMC5042059 DOI: 10.1002/glia.22898] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/14/2015] [Accepted: 07/22/2015] [Indexed: 01/18/2023]
Abstract
Astrocytes react to brain injury in a heterogeneous manner with only a subset resuming proliferation and acquiring stem cell properties in vitro. In order to identify novel regulators of this subset, we performed genomewide expression analysis of reactive astrocytes isolated 5 days after stab wound injury from the gray matter of adult mouse cerebral cortex. The expression pattern was compared with astrocytes from intact cortex and adult neural stem cells (NSCs) isolated from the subependymal zone (SEZ). These comparisons revealed a set of genes expressed at higher levels in both endogenous NSCs and reactive astrocytes, including two lectins-Galectins 1 and 3. These results and the pattern of Galectin expression in the lesioned brain led us to examine the functional significance of these lectins in brains of mice lacking Galectins 1 and 3. Following stab wound injury, astrocyte reactivity including glial fibrillary acidic protein expression, proliferation and neurosphere-forming capacity were found significantly reduced in mutant animals. This phenotype could be recapitulated in vitro and was fully rescued by addition of Galectin 3, but not of Galectin 1. Thus, Galectins 1 and 3 play key roles in regulating the proliferative and NSC potential of a subset of reactive astrocytes.
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Affiliation(s)
- Swetlana Sirko
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University Munich, Germany.,Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Sergio Gascón
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University Munich, Germany.,Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Sarah Bek
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University Munich, Germany
| | - Sarah Schneider
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University Munich, Germany.,Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Leda Dimou
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University Munich, Germany.,Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jara Obermann
- Research Unit Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Daisylea De Souza Paiva
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University Munich, Germany.,Department of Physiology, Federal University of Sao Paulo, Sao Paulo, Brazil
| | - Francoise Poirier
- Institut Jacques Monod, CNRS-University Paris Diderot, Paris, France
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,Chair of Experimental Genetics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Yves-Alain Barde
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Magdalena Götz
- Physiological Genomics, Biomedical Center, Ludwig-Maximilians-University Munich, Germany.,Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.,SYNERGY, Excellence Cluster of Systems Neurology, Ludwig-Maximilians-University Munich, Germany
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42
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Curto GG, Gard C, Ribes V. Structures and properties of PAX linked regulatory networks architecting and pacing the emergence of neuronal diversity. Semin Cell Dev Biol 2015; 44:75-86. [DOI: 10.1016/j.semcdb.2015.09.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 09/07/2015] [Accepted: 09/16/2015] [Indexed: 12/13/2022]
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43
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Mayran A, Pelletier A, Drouin J. Pax factors in transcription and epigenetic remodelling. Semin Cell Dev Biol 2015; 44:135-44. [PMID: 26234816 DOI: 10.1016/j.semcdb.2015.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 07/22/2015] [Accepted: 07/24/2015] [Indexed: 11/25/2022]
Abstract
The nine Pax transcription factors that constitute the mammalian family of paired domain (PD) factors play key roles in many developmental processes. As DNA binding transcription factors, they exhibit tremendous variability and complexity in their DNA recognition patterns. This is ascribed to the presence of multiple DNA binding structural domains, namely helix-turn-helix (HTH) domains. The PD contains two HTH subdomains and four of the nine Pax factors have an additional HTH domain, the homeodomain (HD). We now review these diverse DNA binding modalities together with their properties as transcriptional activators and repressors. The action of Pax factors on gene expression is also exerted through recruitment of chromatin remodelling complexes that introduce either activating or repressive chromatin marks. Interestingly, the recent demonstration that Pax7 has pioneer activity, the unique property to "open" chromatin, further underlines the mechanistic versatility and the developmental importance of these factors.
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Affiliation(s)
- Alexandre Mayran
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Audrey Pelletier
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada
| | - Jacques Drouin
- Laboratoire de Génétique Moléculaire, Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
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44
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Huettl RE, Eckstein S, Stahl T, Petricca S, Ninkovic J, Götz M, Huber AB. Functional dissection of the Pax6 paired domain: Roles in neural tube patterning and peripheral nervous system development. Dev Biol 2015; 413:86-103. [PMID: 26187199 DOI: 10.1016/j.ydbio.2015.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/21/2015] [Accepted: 07/11/2015] [Indexed: 10/23/2022]
Abstract
During development of the CNS, stem and progenitor cell proliferation, cell fate designation, and patterning decisions are tightly regulated by interdependent networks of key transcriptional regulators. In a genetic approach we analyzed divergent functionality of the PAI and RED sub-domains of the Pax6 Paired domain (PD) during progenitor zone formation, motor and interneuron development, and peripheral connectivity at distinct levels within the neural tube: within the hindbrain, mutation of the PAI sub-domain severely affected patterning of the p3 and pMN domains and establishment of the corresponding motor neurons. Exit point designation of hypoglossal axons was disturbed in embryos harboring either mutations in the PD sub-domains or containing a functional Pax6 Null allele. At brachial spinal levels, we propose a selective involvement of the PAI sub-domain during patterning of ventral p2 and pMN domains, critically disturbing generation of specific motor neuron subtypes and increasing V2 interneuron numbers. Our findings present a novel aspect of how Pax6 not only utilizes its modular structure to perform distinct functions via its paired and homeodomain. Individual sub-domains can exert distinct functions, generating a new level of complexity for transcriptional regulation by one single transcription factor not only in dorso-ventral, but also rostro-caudal neural tube patterning.
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Affiliation(s)
- Rosa-Eva Huettl
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Simone Eckstein
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Tessa Stahl
- Institute of Stem Cell Research, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Stefania Petricca
- Institute of Stem Cell Research, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Jovica Ninkovic
- Institute of Stem Cell Research, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Andrea B Huber
- Institute of Developmental Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health (GmbH), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany.
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45
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Sun J, Rockowitz S, Xie Q, Ashery-Padan R, Zheng D, Cvekl A. Identification of in vivo DNA-binding mechanisms of Pax6 and reconstruction of Pax6-dependent gene regulatory networks during forebrain and lens development. Nucleic Acids Res 2015; 43:6827-46. [PMID: 26138486 PMCID: PMC4538810 DOI: 10.1093/nar/gkv589] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/23/2015] [Indexed: 01/18/2023] Open
Abstract
The transcription factor Pax6 is comprised of the paired domain (PD) and homeodomain (HD). In the developing forebrain, Pax6 is expressed in ventricular zone precursor cells and in specific subpopulations of neurons; absence of Pax6 results in disrupted cell proliferation and cell fate specification. Pax6 also regulates the entire lens developmental program. To reconstruct Pax6-dependent gene regulatory networks (GRNs), ChIP-seq studies were performed using forebrain and lens chromatin from mice. A total of 3514 (forebrain) and 3723 (lens) Pax6-containing peaks were identified, with ∼70% of them found in both tissues and thereafter called 'common' peaks. Analysis of Pax6-bound peaks identified motifs that closely resemble Pax6-PD, Pax6-PD/HD and Pax6-HD established binding sequences. Mapping of H3K4me1, H3K4me3, H3K27ac, H3K27me3 and RNA polymerase II revealed distinct types of tissue-specific enhancers bound by Pax6. Pax6 directly regulates cortical neurogenesis through activation (e.g. Dmrta1 and Ngn2) and repression (e.g. Ascl1, Fezf2, and Gsx2) of transcription factors. In lens, Pax6 directly regulates cell cycle exit via components of FGF (Fgfr2, Prox1 and Ccnd1) and Wnt (Dkk3, Wnt7a, Lrp6, Bcl9l, and Ccnd1) signaling pathways. Collectively, these studies provide genome-wide analysis of Pax6-dependent GRNs in lens and forebrain and establish novel roles of Pax6 in organogenesis.
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Affiliation(s)
- Jian Sun
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Shira Rockowitz
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Qing Xie
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ruth Ashery-Padan
- Sackler School of Medicine and Sagol School of Neuroscience, Tel-Aviv University, 69978 Ramat Aviv, Tel Aviv, Israel
| | - Deyou Zheng
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Ales Cvekl
- The Departments of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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Javeed N, Tardi NJ, Maher M, Singari S, Edwards KA. Controlled expression of Drosophila homeobox loci using the Hostile takeover system. Dev Dyn 2015; 244:808-25. [PMID: 25820349 PMCID: PMC4449281 DOI: 10.1002/dvdy.24279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/12/2015] [Accepted: 03/16/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Hostile takeover (Hto) is a Drosophila protein trapping system that allows the investigator to both induce a gene and tag its product. The Hto transposon carries a GAL4-regulated promoter expressing an exon encoding a FLAG-mCherry tag. Upon expression, the Hto exon can splice to a downstream genomic exon, generating a fusion transcript and tagged protein. RESULTS Using rough-eye phenotypic screens, Hto inserts were recovered at eight homeobox or Pax loci: cut, Drgx/CG34340, Pox neuro, araucan, shaven/D-Pax2, Zn finger homeodomain 2, Sex combs reduced (Scr), and the abdominal-A region. The collection yields diverse misexpression phenotypes. Ectopic Drgx was found to alter the cytoskeleton and cell adhesion in ovary follicle cells. Hto expression of cut, araucan, or shaven gives phenotypes similar to those of the corresponding UAS-cDNA constructs. The cut and Pox neuro phenotypes are suppressed by the corresponding RNAi constructs. The Scr and abdominal-A inserts do not make fusion proteins, but may act by chromatin- or RNA-based mechanisms. CONCLUSIONS Hto can effectively express tagged homeodomain proteins from their endogenous loci; the Minos vector allows inserts to be obtained even in transposon cold-spots. Hto screens may recover homeobox genes at high rates because they are particularly sensitive to misexpression.
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Affiliation(s)
- Naureen Javeed
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Nicholas J. Tardi
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Maggie Maher
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Swetha Singari
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Kevin A. Edwards
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
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Bunt J, Lim JWC, Zhao L, Mason S, Richards LJ. PAX6 does not regulate Nfia and Nfib expression during neocortical development. Sci Rep 2015; 5:10668. [PMID: 26021864 PMCID: PMC4448127 DOI: 10.1038/srep10668] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 04/24/2015] [Indexed: 12/20/2022] Open
Abstract
The Nuclear factor I (NFI) family of transcription factors regulates proliferation and differentiation throughout the developing central nervous system. In the developing telencephalon of humans and mice, reduced Nfi expression is associated with agenesis of the corpus callosum and other neurodevelopmental defects. Currently, little is known about how Nfi expression is regulated during early telencephalic development. PAX6, a transcription factor important for telencephalic development, has been proposed as an upstream regulator of Nfi expression in the neocortex. Here we demonstrate that, in the developing neocortex of mice, NFIA and NFIB are endogenously expressed in gradients with high caudo-medial to low rostro-lateral expression and are most highly expressed in the cortical plate. We found that this expression pattern deviates from that of PAX6, suggesting that PAX6 does not drive Nfi expression. This is supported by in vitro reporter assays showing that PAX6 over-expression does not regulate Nfi promoter activity. Similarly, we also found that in the Pax6 Small Eye mutant, no changes in Nfi mRNA or protein expression are observed in the neocortical ventricular zone where PAX6 and the NFIs are expressed. Together these data demonstrate that in mice, PAX6 is not a transcriptional activator of Nfi expression during neocortical development.
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Affiliation(s)
- Jens Bunt
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia
| | - Jonathan W C Lim
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia
| | - Lu Zhao
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia
| | - Sharon Mason
- Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia
| | - Linda J Richards
- 1] Queensland Brain Institute, The University of Queensland, Brisbane, 4072, Australia [2] The School of Biomedical Sciences, The University of Queensland, Brisbane, 4072, Australia
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Manuel MN, Mi D, Mason JO, Price DJ. Regulation of cerebral cortical neurogenesis by the Pax6 transcription factor. Front Cell Neurosci 2015; 9:70. [PMID: 25805971 PMCID: PMC4354436 DOI: 10.3389/fncel.2015.00070] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Accepted: 02/18/2015] [Indexed: 12/19/2022] Open
Abstract
Understanding brain development remains a major challenge at the heart of understanding what makes us human. The neocortex, in evolutionary terms the newest part of the cerebral cortex, is the seat of higher cognitive functions. Its normal development requires the production, positioning, and appropriate interconnection of very large numbers of both excitatory and inhibitory neurons. Pax6 is one of a relatively small group of transcription factors that exert high-level control of cortical development, and whose mutation or deletion from developing embryos causes major brain defects and a wide range of neurodevelopmental disorders. Pax6 is very highly conserved between primate and non-primate species, is expressed in a gradient throughout the developing cortex and is essential for normal corticogenesis. Our understanding of Pax6’s functions and the cellular processes that it regulates during mammalian cortical development has significantly advanced in the last decade, owing to the combined application of genetic and biochemical analyses. Here, we review the functional importance of Pax6 in regulating cortical progenitor proliferation, neurogenesis, and formation of cortical layers and highlight important differences between rodents and primates. We also review the pathological effects of PAX6 mutations in human neurodevelopmental disorders. We discuss some aspects of Pax6’s molecular actions including its own complex transcriptional regulation, the distinct molecular functions of its splice variants and some of Pax6’s known direct targets which mediate its actions during cortical development.
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Affiliation(s)
- Martine N Manuel
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - Da Mi
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - John O Mason
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
| | - David J Price
- Centre for Integrative Physiology, The University of Edinburgh, Edinburgh UK
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Narasimhan K, Pillay S, Huang YH, Jayabal S, Udayasuryan B, Veerapandian V, Kolatkar P, Cojocaru V, Pervushin K, Jauch R. DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors. Nucleic Acids Res 2015; 43:1513-28. [PMID: 25578969 PMCID: PMC4330359 DOI: 10.1093/nar/gku1390] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Sox2 and Pax6 are transcription factors that direct cell fate decision during neurogenesis, yet the mechanism behind how they cooperate on enhancer DNA elements and regulate gene expression is unclear. By systematically interrogating Sox2 and Pax6 interaction on minimal enhancer elements, we found that cooperative DNA recognition relies on combinatorial nucleotide switches and precisely spaced, but cryptic composite DNA motifs. Surprisingly, all tested Sox and Pax paralogs have the capacity to cooperate on such enhancer elements. NMR and molecular modeling reveal very few direct protein-protein interactions between Sox2 and Pax6, suggesting that cooperative binding is mediated by allosteric interactions propagating through DNA structure. Furthermore, we detected and validated several novel sites in the human genome targeted cooperatively by Sox2 and Pax6. Collectively, we demonstrate that Sox-Pax partnerships have the potential to substantially alter DNA target specificities and likely enable the pleiotropic and context-specific action of these cell-lineage specifiers.
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Affiliation(s)
- Kamesh Narasimhan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Shubhadra Pillay
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Yong-Heng Huang
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Sriram Jayabal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3G 0B1, Canada
| | - Barath Udayasuryan
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Veeramohan Veerapandian
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore University of Chinese Academy of Sciences, No. 19A Yuquanlu, Beijing 100049, China
| | - Prasanna Kolatkar
- Qatar Biomedical Research Institute, Qatar Foundation, PO Box 5825, Doha, Qatar
| | - Vlad Cojocaru
- Computational Structural Biology Laboratory, Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
| | - Konstantin Pervushin
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences,190 Kai Yuan Avenue, Science Park, Guangzhou 510530, China
| | - Ralf Jauch
- Laboratory for Structural Biochemistry, Genome Institute of Singapore, Singapore 138672, Singapore
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Pettinato G, Vanden Berg-Foels WS, Zhang N, Wen X. ROCK inhibitor is not required for embryoid body formation from singularized human embryonic stem cells. PLoS One 2014; 9:e100742. [PMID: 25365581 PMCID: PMC4217711 DOI: 10.1371/journal.pone.0100742] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 05/30/2014] [Indexed: 12/18/2022] Open
Abstract
We report a technology to form human embryoid bodies (hEBs) from singularized human embryonic stem cells (hESCs) without the use of the p160 rho-associated coiled-coil kinase inhibitor (ROCKi) or centrifugation (spin). hEB formation was tested under four conditions: +ROCKi/+spin, +ROCKi/-spin, -ROCKi/+spin, and -ROCKi/-spin. Cell suspensions of BG01V/hOG and H9 hESC lines were pipetted into non-adherent hydrogel substrates containing defined microwell arrays. hEBs of consistent size and spherical geometry can be formed in each of the four conditions, including the -ROCKi/-spin condition. The hEBs formed under the -ROCKi/-spin condition differentiated to develop the three embryonic germ layers and tissues derived from each of the germ layers. This simplified hEB production technique offers homogeneity in hEB size and shape to support synchronous differentiation, elimination of the ROCKi xeno-factor and rate-limiting centrifugation treatment, and low-cost scalability, which will directly support automated, large-scale production of hEBs and hESC-derived cells needed for clinical, research, or therapeutic applications.
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Affiliation(s)
- Giuseppe Pettinato
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
| | - Wendy S. Vanden Berg-Foels
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
- Department of Craniofacial Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
| | - Ning Zhang
- Department of Biomedical Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
- * E-mail: (NZ); (XW)
| | - Xuejun Wen
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Department of Bioengineering, Clemson University, Clemson, South Carolina, United States of America
- Department of Craniofacial Biology, Medical University of South Carolina, Charleston, South Carolina, United States of America
- Institute for Biomedical Engineering and Nano Science (iNANO), Shanghai East Hospital, Tongji Medical School, Tongji University, Shanghai, People's Republic of China
- * E-mail: (NZ); (XW)
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