Patterning of the Mammalian Cochlea
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Core Transcriptional Regulatory Circuitries in Cancer
Oncogene (2020) 39:6633–6646 https://doi.org/10.1038/s41388-020-01459-w REVIEW ARTICLE Core transcriptional regulatory circuitries in cancer 1 1,2,3 1 2 1,4,5 Ye Chen ● Liang Xu ● Ruby Yu-Tong Lin ● Markus Müschen ● H. Phillip Koeffler Received: 14 June 2020 / Revised: 30 August 2020 / Accepted: 4 September 2020 / Published online: 17 September 2020 © The Author(s) 2020. This article is published with open access Abstract Transcription factors (TFs) coordinate the on-and-off states of gene expression typically in a combinatorial fashion. Studies from embryonic stem cells and other cell types have revealed that a clique of self-regulated core TFs control cell identity and cell state. These core TFs form interconnected feed-forward transcriptional loops to establish and reinforce the cell-type- specific gene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcriptional regulatory circuitry (CRC). Here, we summarize recent progress in computational reconstitution and biologic exploration of CRCs across various human malignancies, and consolidate the strategy and methodology for CRC discovery. We also discuss the genetic basis and therapeutic vulnerability of CRC, and highlight new frontiers and future efforts for the study of CRC in cancer. Knowledge of CRC in cancer is fundamental to understanding cancer-specific transcriptional addiction, and should provide important insight to both pathobiology and therapeutics. 1234567890();,: 1234567890();,: Introduction genes. Till now, one critical goal in biology remains to understand the composition and hierarchy of transcriptional Transcriptional regulation is one of the fundamental mole- regulatory network in each specified cell type/lineage. -
Glioblastoma Stem Cells Induce Quiescence in Surrounding Neural Stem Cells Via Notch Signalling
bioRxiv preprint doi: https://doi.org/10.1101/856062; this version posted November 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Glioblastoma stem cells induce quiescence in surrounding neural stem cells via Notch signalling. Katerina Lawlor1, Maria Angeles Marques-Torrejon2, Gopuraja Dharmalingham3, Yasmine El-Azhar1, Michael D. Schneider1, Steven M. Pollard2§ and Tristan A. Rodríguez1§ 1National Heart and Lung Institute, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, United Kingdom. 2 MRC Centre for Regenerative Medicine & Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK. 3MRC London Institute of Medical Sciences, Institute of Clinical Sciences, Imperial College London, UK §Authors for correspondence: [email protected] and [email protected] Running title: Glioblastoma stem cell competition Keyword: Neural stem cells, quiescence, glioblastoma, Notch, cell competition 1 bioRxiv preprint doi: https://doi.org/10.1101/856062; this version posted November 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Abstract 2 There is increasing evidence suggesting that adult neural stem cells (NSCs) are a cell of 3 origin of glioblastoma, the most aggressive form of malignant glioma. The earliest stages of 4 hyperplasia are not easy to explore, but likely involve a cross-talk between normal and 5 transformed NSCs. How normal cells respond to this cross-talk and if they expand or are 6 outcompeted is poorly understood. -
Supplemental Materials ZNF281 Enhances Cardiac Reprogramming
Supplemental Materials ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression Huanyu Zhou, Maria Gabriela Morales, Hisayuki Hashimoto, Matthew E. Dickson, Kunhua Song, Wenduo Ye, Min S. Kim, Hanspeter Niederstrasser, Zhaoning Wang, Beibei Chen, Bruce A. Posner, Rhonda Bassel-Duby and Eric N. Olson Supplemental Table 1; related to Figure 1. Supplemental Table 2; related to Figure 1. Supplemental Table 3; related to the “quantitative mRNA measurement” in Materials and Methods section. Supplemental Table 4; related to the “ChIP-seq, gene ontology and pathway analysis” and “RNA-seq” and gene ontology analysis” in Materials and Methods section. Supplemental Figure S1; related to Figure 1. Supplemental Figure S2; related to Figure 2. Supplemental Figure S3; related to Figure 3. Supplemental Figure S4; related to Figure 4. Supplemental Figure S5; related to Figure 6. Supplemental Table S1. Genes included in human retroviral ORF cDNA library. Gene Gene Gene Gene Gene Gene Gene Gene Symbol Symbol Symbol Symbol Symbol Symbol Symbol Symbol AATF BMP8A CEBPE CTNNB1 ESR2 GDF3 HOXA5 IL17D ADIPOQ BRPF1 CEBPG CUX1 ESRRA GDF6 HOXA6 IL17F ADNP BRPF3 CERS1 CX3CL1 ETS1 GIN1 HOXA7 IL18 AEBP1 BUD31 CERS2 CXCL10 ETS2 GLIS3 HOXB1 IL19 AFF4 C17ORF77 CERS4 CXCL11 ETV3 GMEB1 HOXB13 IL1A AHR C1QTNF4 CFL2 CXCL12 ETV7 GPBP1 HOXB5 IL1B AIMP1 C21ORF66 CHIA CXCL13 FAM3B GPER HOXB6 IL1F3 ALS2CR8 CBFA2T2 CIR1 CXCL14 FAM3D GPI HOXB7 IL1F5 ALX1 CBFA2T3 CITED1 CXCL16 FASLG GREM1 HOXB9 IL1F6 ARGFX CBFB CITED2 CXCL3 FBLN1 GREM2 HOXC4 IL1F7 -
Morphological and Functional Changes in a New Animal Model Of
Laboratory Investigation (2013) 93, 1001–1011 & 2013 USCAP, Inc All rights reserved 0023-6837/13 Morphological and functional changes in a new animal model of Me´nie`re’s disease Naoya Egami1, Akinobu Kakigi1, Takashi Sakamoto1, Taizo Takeda2, Masamitsu Hyodo2 and Tatsuya Yamasoba1 The purpose of this study was to clarify the underlying mechanism of vertiginous attacks in Me´nie`re’s disease (MD) while obtaining insight into water homeostasis in the inner ear using a new animal model. We conducted both histopatho- logical and functional assessment of the vestibular system in the guinea-pig. In the first experiment, all animals were maintained 1 or 4 weeks after electrocauterization of the endolymphatic sac of the left ear and were given either saline or desmopressin (vasopressin type 2 receptor agonist). The temporal bones from both ears were harvested and the extent of endolymphatic hydrops was quantitatively assessed. In the second experiment, either 1 or 4 weeks after surgery, animals were assessed for balance disorders and nystagmus after the administration of saline or desmopressin. In the first experiment, the proportion of endolymphatic space in the cochlea and the saccule was significantly greater in ears that survived for 4 weeks after surgery and were given desmopressin compared with other groups. In the second experiment, all animals that underwent surgery and were given desmopressin showed spontaneous nystagmus and balance disorder, whereas all animals that had surgery but without desmopressin administration were asymptomatic. Our animal model induced severe endolymphatic hydrops in the cochlea and the saccule, and showed episodes of balance disorder along with spontaneous nystagmus. -
UNIVERSITY of CALIFORNIA, IRVINE Combinatorial Regulation By
UNIVERSITY OF CALIFORNIA, IRVINE Combinatorial regulation by maternal transcription factors during activation of the endoderm gene regulatory network DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biological Sciences by Kitt D. Paraiso Dissertation Committee: Professor Ken W.Y. Cho, Chair Associate Professor Olivier Cinquin Professor Thomas Schilling 2018 Chapter 4 © 2017 Elsevier Ltd. © 2018 Kitt D. Paraiso DEDICATION To the incredibly intelligent and talented people, who in one way or another, helped complete this thesis. ii TABLE OF CONTENTS Page LIST OF FIGURES vii LIST OF TABLES ix LIST OF ABBREVIATIONS X ACKNOWLEDGEMENTS xi CURRICULUM VITAE xii ABSTRACT OF THE DISSERTATION xiv CHAPTER 1: Maternal transcription factors during early endoderm formation in 1 Xenopus Transcription factors co-regulate in a cell type-specific manner 2 Otx1 is expressed in a variety of cell lineages 4 Maternal otx1 in the endodermal conteXt 5 Establishment of enhancers by maternal transcription factors 9 Uncovering the endodermal gene regulatory network 12 Zygotic genome activation and temporal control of gene eXpression 14 The role of maternal transcription factors in early development 18 References 19 CHAPTER 2: Assembly of maternal transcription factors initiates the emergence 26 of tissue-specific zygotic cis-regulatory regions Introduction 28 Identification of maternal vegetally-localized transcription factors 31 Vegt and OtX1 combinatorially regulate the endodermal 33 transcriptome iii -
SUPPLEMENTARY MATERIAL Bone Morphogenetic Protein 4 Promotes
www.intjdevbiol.com doi: 10.1387/ijdb.160040mk SUPPLEMENTARY MATERIAL corresponding to: Bone morphogenetic protein 4 promotes craniofacial neural crest induction from human pluripotent stem cells SUMIYO MIMURA, MIKA SUGA, KAORI OKADA, MASAKI KINEHARA, HIROKI NIKAWA and MIHO K. FURUE* *Address correspondence to: Miho Kusuda Furue. Laboratory of Stem Cell Cultures, National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8, Saito-Asagi, Ibaraki, Osaka 567-0085, Japan. Tel: 81-72-641-9819. Fax: 81-72-641-9812. E-mail: [email protected] Full text for this paper is available at: http://dx.doi.org/10.1387/ijdb.160040mk TABLE S1 PRIMER LIST FOR QRT-PCR Gene forward reverse AP2α AATTTCTCAACCGACAACATT ATCTGTTTTGTAGCCAGGAGC CDX2 CTGGAGCTGGAGAAGGAGTTTC ATTTTAACCTGCCTCTCAGAGAGC DLX1 AGTTTGCAGTTGCAGGCTTT CCCTGCTTCATCAGCTTCTT FOXD3 CAGCGGTTCGGCGGGAGG TGAGTGAGAGGTTGTGGCGGATG GAPDH CAAAGTTGTCATGGATGACC CCATGGAGAAGGCTGGGG MSX1 GGATCAGACTTCGGAGAGTGAACT GCCTTCCCTTTAACCCTCACA NANOG TGAACCTCAGCTACAAACAG TGGTGGTAGGAAGAGTAAAG OCT4 GACAGGGGGAGGGGAGGAGCTAGG CTTCCCTCCAACCAGTTGCCCCAAA PAX3 TTGCAATGGCCTCTCAC AGGGGAGAGCGCGTAATC PAX6 GTCCATCTTTGCTTGGGAAA TAGCCAGGTTGCGAAGAACT p75 TCATCCCTGTCTATTGCTCCA TGTTCTGCTTGCAGCTGTTC SOX9 AATGGAGCAGCGAAATCAAC CAGAGAGATTTAGCACACTGATC SOX10 GACCAGTACCCGCACCTG CGCTTGTCACTTTCGTTCAG Suppl. Fig. S1. Comparison of the gene expression profiles of the ES cells and the cells induced by NC and NC-B condition. Scatter plots compares the normalized expression of every gene on the array (refer to Table S3). The central line -
The Camp Signaling System Regulates Lhβ Gene Expression: Roles of Early
291 The cAMP signaling system regulates LH gene expression: roles of early growth response protein-1, SP1 and steroidogenic factor-1 C D Horton and L M Halvorson Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9032, USA (Requests for offprints should be addressed to L M Halvorson; Email: [email protected]) Abstract Expression of the gonadotropin genes has been shown to be modulated by pharmacological or physiological activators of both the protein kinase C (PKC) and the cAMP second messenger signaling pathways. Over the past few years, a substantial amount of progress has been made in the identification and characterization of the transcription factors and cognate cis-elements which mediate the PKC response in the LH -subunit (LH) gene. In contrast, little is known regarding the molecular mechanisms which mediate cAMP-mediated regulation of this gene. Using pituitary cell lines, we now demonstrate that rat LH gene promoter activity is stimulated following activation of the cAMP system by the adenylate cyclase activating agent, forskolin, or by the peptide, pituitary adenylate cyclase-activating peptide. The forskolin response was eliminated with mutation of a previously identified 3′ cis-acting element for the early growth response protein-1 (Egr-1) when evaluated in the context of region −207/+5 of the LH gene. Activation of the cAMP system increased Egr-1 gene promoter activity, Egr-1 protein levels and Egr-1 binding to the LH gene promoter, supporting the role of this transcription factor in mediating the cAMP response. Analysis of a longer LH promoter construct (−797/+5) revealed additional contribution by upstream Sp1 DNA-regulatory regions. -
Otx1 and Otx2 in Inner Ear Development 2337 by BMP4 Expression (Lc in Fig
Development 126, 2335-2343 (1999) 2335 Printed in Great Britain © The Company of Biologists Limited 1999 DEV1416 Otx1 and Otx2 activities are required for the normal development of the mouse inner ear Hakim Morsli1, Francesca Tuorto2, Daniel Choo1,*, Maria Pia Postiglione2, Antonio Simeone2 and Doris K. Wu1,‡ 1National Institute on Deafness and Other Communication Disorders, 5 Research Ct., Rockville, MD 20850, USA 2International Institute of Genetics and Biophysics, CNR, Via G. Marconi, 12, 80125 Naples, Italy *Present address: Children’s Hospital Medical Center of Cincinnati, Department of Otolaryngology, 3333 Burnet Ave., Cincinnati, OH 45229, USA ‡Author for correspondence (e-mail: [email protected]) Accepted 12 March; published on WWW 4 May 1999 SUMMARY The Otx1 and Otx2 genes are two murine orthologues of variable in Otx1−/− mice and were much more severe the Orthodenticle (Otd) gene in Drosophila. In the in an Otx1−/−;Otx2+/− background. Histological and in developing mouse embryo, both Otx genes are expressed situ hybridization experiments of both Otx1−/− and in the rostral head region and in certain sense organs such Otx1−/−;Otx2+/− mutants revealed that the lateral crista as the inner ear. Previous studies have shown that mice was absent. In addition, the maculae of the utricle and lacking Otx1 display abnormal patterning of the brain, saccule were partially fused. In mutant mice in which whereas embryos lacking Otx2 develop without heads. In both copies of the Otx1 gene were replaced with a human this study, we examined, at different developmental Otx2 cDNA (hOtx21/ hOtx21), most of the defects stages, the inner ears of mice lacking both Otx1 and Otx2 associated with Otx1−/− mutants were rescued. -
CONGENITAL MALFORMATIONS of the INNER EAR Malformaciones Congénitas Del Oído Interno
topic review CONGENITAL MALFORMATIONS OF THE INNER EAR Malformaciones congénitas del oído interno. Revisión de tema Laura Vanessa Ramírez Pedroza1 Hernán Darío Cano Riaño2 Federico Guillermo Lubinus Badillo2 Summary Key words (MeSH) There are a great variety of congenital malformations that can affect the inner ear, Ear with a diversity of physiopathologies, involved altered structures and age of symptom Ear, inner onset. Therefore, it is important to know and identify these alterations opportunely Hearing loss Vestibule, labyrinth to lower the risks of all the complications, being of great importance, among others, Cochlea the alterations in language development and social interactions. Magnetic resonance imaging Resumen Existe una gran variedad de malformaciones congénitas que pueden afectar al Palabras clave (DeCS) oído interno, con distintas fisiopatologías, diferentes estructuras alteradas y edad Oído de aparición de los síntomas. Por lo anterior, es necesario conocer e identificar Oído interno dichas alteraciones, con el fin de actuar oportunamente y reducir el riesgo de las Pérdida auditiva Vestíbulo del laberinto complicaciones, entre otras —de gran importancia— las alteraciones en el área del Cóclea lenguaje y en el ámbito social. Imagen por resonancia magnética 1. Epidemiology • Hyperbilirubinemia Ear malformations occur in 1 in 10,000 or 20,000 • Respiratory distress from meconium aspiration cases (1). One in every 1,000 children has some degree • Craniofacial alterations (3) of sensorineural hearing impairment, with an average • Mechanical ventilation for more than five days age at diagnosis of 4.9 years. The prevalence of hearing • TORCH Syndrome (4) impairment in newborns with risk factors has been determined to be 9.52% (2). -
Supplement-Molecular Sys Biology
Supplementary Material for: Iwona Stelniec-Klotz, Stefan Legewie, Oleg Tchernitsa, Franziska Witzel, Bertram Klinger, Christine Sers, Hanspeter Herzel, Nils Blüthgen and Reinhold Schäfer: Reverse-engineering a hierarchical regulatory network downstream of oncogenic KRAS Content (9 Figures, 3 Tables, 1 Text, 1 List of References) Supplementary Figures S1: Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells. S2: Impact of transcription factor knock-down on the KRAS pathway-mediated mRNA expression profile S3: RNA expression of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS- transformed RAS-ROSE cells S4: Effects of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA knock-down in RAS-ROSE cells on the activity of cytoplasmic signaling downstream of RAS S5: Effect of Fosl1 overepxression and Otx1 knockdown on Fosl1mRNA and phospho-Erk. S6: Effects on growth characteristics of RAS-ROSE cells after silencing Fosl1, Hmga2, Klf6, JunB S7: Effects on growth characteristics of RAS-ROSE cells after silencing Otx1, Gfi1, RelA S8: Effects on distribution of cell cycle phases in KRAS-transformed RAS-ROSE cells after silencing of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA S9: Effect of perturbation strength and noise on algorithm performance. Supplementary Tables S1: Rules for finding transcription factor-related patterns in genome-wide expression data (related to Fig. 3B and C). S2: Known interaction (related to Fig. 4) S3: Quantification of the network. Supplementary Texts Generation of artificial data sets Supplementary References Supplementary Fig. 1 Nuclear protein levels of Fosl1, Hmga2, Klf6, JunB, Otx1, Gfi1, RelA after silencing in KRAS-transformed RAS-ROSE cells. -
Downloaded from UCSC Genome Browser Was Performed Using Rna-Star/2.4.2A (Dobin Et Al., 2013)
Neuromesodermal progenitor origin of trunk neural crest in vivo Martyna Lukoseviciute1,2, Sarah Mayes1, Tatjana Sauka-Spengler1,∗ Abstract Neural crest (NC) is a vertebrate-specific population of multipotent embryonic cells predisposed to diverse derivatives along the anteroposterior (A-P) axis. Only cranial NC progenitors give rise to ectomesenchymal cell types, whereas trunk NC is biased for neuronal cell fates. By integrating multimodal single-cell analysis, we provide evidence for divergent embryonic origins of cranial vs. trunk NC that explain this dichotomy. We show that the NC regulator foxd3 is heterogeneously expressed across the A-P axis and identify its specific cranial and trunk autoregulatory enhancers. Whereas cranial-specific enhancer is active in the bona fide NC, the trunk foxd3 autoregulatory element surprisingly marked bipotent tailbud neuromesodermal progenitors (NMps). We integrated NMp single cell epigemomics and trasncriptomics data and for the first time reconstructed anamniote NMp gene regulatory network. Moreover, using pseudotime and developmental trajectory analyses of NMps and NC during normal development and in foxd3 mutants, we demonstrate an active role for foxd3 in balancing non-cranial NC and NMp fates during early embryonic devel- opment. Strikingly, we show that a portion of posterior NC in the developing zebrafish embryo is derived from the pro-neural NMps. This suggests a common embryonic origin of trunk NC and NM progenitors that is distinct from cranial NC anlage, and elucidates pro-neural bias of trunk NC. Keywords: neural crest, neuromesodermal progenitors, gene regulatory network, axial progenitors, embryo patterning Introduction The neural crest (NC) is a unique multipotent cell population that gives rise to an extraordinary diversity of tissues in vertebrate embryos, including chondrocytes and osteocytes of the craniofacial skeleton, neurons and glia of the peripheral nervous system, and all skin pigment cells in the body. -
The Viral Oncoproteins Tax and HBZ Reprogram the Cellular Mrna Splicing Landscape
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The viral oncoproteins Tax and HBZ reprogram the cellular mRNA splicing landscape Charlotte Vandermeulen1,2,3, Tina O’Grady3, Bartimee Galvan3, Majid Cherkaoui1, Alice Desbuleux1,2,4,5, Georges Coppin1,2,4,5, Julien Olivet1,2,4,5, Lamya Ben Ameur6, Keisuke Kataoka7, Seishi Ogawa7, Marc Thiry8, Franck Mortreux6, Michael A. Calderwood2,4,5, David E. Hill2,4,5, Johan Van Weyenbergh9, Benoit Charloteaux2,4,5,10, Marc Vidal2,4*, Franck Dequiedt3*, and Jean-Claude Twizere1,2,11* 1Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium.2Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA.3Laboratory of Gene Expression and Cancer, GIGA Institute, University of Liege, Liege, Belgium.4Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. 5Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.6Laboratory of Biology and Modeling of the Cell, CNRS UMR 5239, INSERM U1210, University of Lyon, Lyon, France.7Department of Pathology and Tumor Biology, Kyoto University, Japan.8Unit of Cell and Tissue Biology, GIGA Institute, University of Liege, Liege, Belgium.9Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven, Leuven, Belgium.10Department of Human Genetics, CHU of Liege, University of Liege, Liege, Belgium.11Lead Contact. *Correspondence: [email protected]; [email protected]; [email protected] bioRxiv preprint doi: https://doi.org/10.1101/2021.01.18.427104; this version posted January 18, 2021.