Differentiation of Human Embryonic Stem Cells Into Cone Photoreceptors
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The Title of the Dissertation
UNIVERSITY OF CALIFORNIA SAN DIEGO Novel network-based integrated analyses of multi-omics data reveal new insights into CD8+ T cell differentiation and mouse embryogenesis A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioinformatics and Systems Biology by Kai Zhang Committee in charge: Professor Wei Wang, Chair Professor Pavel Arkadjevich Pevzner, Co-Chair Professor Vineet Bafna Professor Cornelis Murre Professor Bing Ren 2018 Copyright Kai Zhang, 2018 All rights reserved. The dissertation of Kai Zhang is approved, and it is accept- able in quality and form for publication on microfilm and electronically: Co-Chair Chair University of California San Diego 2018 iii EPIGRAPH The only true wisdom is in knowing you know nothing. —Socrates iv TABLE OF CONTENTS Signature Page ....................................... iii Epigraph ........................................... iv Table of Contents ...................................... v List of Figures ........................................ viii List of Tables ........................................ ix Acknowledgements ..................................... x Vita ............................................. xi Abstract of the Dissertation ................................. xii Chapter 1 General introduction ............................ 1 1.1 The applications of graph theory in bioinformatics ......... 1 1.2 Leveraging graphs to conduct integrated analyses .......... 4 1.3 References .............................. 6 Chapter 2 Systematic -
VSX1 Mutational Analysis in a Series of Italian Patients Affected by Keratoconus: Detection of a Novel Mutation
VSX1 Mutational Analysis in a Series of Italian Patients Affected by Keratoconus: Detection of a Novel Mutation Luigi Bisceglia,1 Marilena Ciaschetti,2 Patrizia De Bonis,1 Pablo Alberto Perafan Campo,2 Costantina Pizzicoli,3 Costanza Scala,1 Michele Grifa,1 Pio Ciavarella,1 Nicola Delle Noci,3 Filippo Vaira,4 Claudio Macaluso,5 and Leopoldo Zelante1 PURPOSE. Keratoconus is a noninflammatory corneal disorder Most cases of keratoconus appear to be sporadic, but a that is clinically and genetically heterogeneous. Mutations in positive family history has been documented in 6% to 10% of the VSX1 (visual system homeobox 1) gene have been identi- patients.5 Both recessive and dominant patterns of inheritance fied for two distinct, inherited corneal dystrophies: posterior have been described.6–8 Autosomal dominant inheritance has polymorphous corneal dystrophy and keratoconus. To evalu- more frequently been reported in families, showing incom- ate the possible role of the VSX1 gene in a series of Italian plete penetrance and variable expressivity. Subtle videokerato- patients, 80 keratoconus-affected subjects were screened for graphic anomalies have been reported among relatives of pa- mutations. tients with keratoconus, allowing the detection of low- ETHODS expressivity forms of keratoconus, usually referred to as M . The diagnosis of keratoconus was made on the basis 9–11 of clinical examination and corneal topography. The whole subclinical or forme fruste keratoconus. Multifactorial in- heritance and a major gene model have also been pro- coding region and the exon–intron junctions of the VSX1 gene 12,13 were analyzed by direct sequencing. posed. In some cases nongenetic causes have been postu- lated, such as eye rubbing or rigid contact lens wear, which RESULTS. -
Whole Exome Sequencing in Families at High Risk for Hodgkin Lymphoma: Identification of a Predisposing Mutation in the KDR Gene
Hodgkin Lymphoma SUPPLEMENTARY APPENDIX Whole exome sequencing in families at high risk for Hodgkin lymphoma: identification of a predisposing mutation in the KDR gene Melissa Rotunno, 1 Mary L. McMaster, 1 Joseph Boland, 2 Sara Bass, 2 Xijun Zhang, 2 Laurie Burdett, 2 Belynda Hicks, 2 Sarangan Ravichandran, 3 Brian T. Luke, 3 Meredith Yeager, 2 Laura Fontaine, 4 Paula L. Hyland, 1 Alisa M. Goldstein, 1 NCI DCEG Cancer Sequencing Working Group, NCI DCEG Cancer Genomics Research Laboratory, Stephen J. Chanock, 5 Neil E. Caporaso, 1 Margaret A. Tucker, 6 and Lynn R. Goldin 1 1Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 2Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; 3Ad - vanced Biomedical Computing Center, Leidos Biomedical Research Inc.; Frederick National Laboratory for Cancer Research, Frederick, MD; 4Westat, Inc., Rockville MD; 5Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD; and 6Human Genetics Program, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, MD, USA ©2016 Ferrata Storti Foundation. This is an open-access paper. doi:10.3324/haematol.2015.135475 Received: August 19, 2015. Accepted: January 7, 2016. Pre-published: June 13, 2016. Correspondence: [email protected] Supplemental Author Information: NCI DCEG Cancer Sequencing Working Group: Mark H. Greene, Allan Hildesheim, Nan Hu, Maria Theresa Landi, Jennifer Loud, Phuong Mai, Lisa Mirabello, Lindsay Morton, Dilys Parry, Anand Pathak, Douglas R. Stewart, Philip R. Taylor, Geoffrey S. Tobias, Xiaohong R. Yang, Guoqin Yu NCI DCEG Cancer Genomics Research Laboratory: Salma Chowdhury, Michael Cullen, Casey Dagnall, Herbert Higson, Amy A. -
Structure of Cone Photoreceptors
Progress in Retinal and Eye Research 28 (2009) 289–302 Contents lists available at ScienceDirect Progress in Retinal and Eye Research journal homepage: www.elsevier.com/locate/prer Structure of cone photoreceptors Debarshi Mustafi a, Andreas H. Engel a,b, Krzysztof Palczewski a,* a Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106-4965, USA b Center for Cellular Imaging and Nanoanalytics, M.E. Mu¨ller Institute, Biozentrum, WRO-1058, Mattenstrasse 26, CH 4058 Basel, Switzerland abstract Keywords: Although outnumbered more than 20:1 by rod photoreceptors, cone cells in the human retina mediate Cone photoreceptors daylight vision and are critical for visual acuity and color discrimination. A variety of human diseases are Rod photoreceptors characterized by a progressive loss of cone photoreceptors but the low abundance of cones and the Retinoids absence of a macula in non-primate mammalian retinas have made it difficult to investigate cones Retinoid cycle directly. Conventional rodents (laboratory mice and rats) are nocturnal rod-dominated species with few Chromophore Opsins cones in the retina, and studying other animals with cone-rich retinas presents various logistic and Retina technical difficulties. Originating in the early 1900s, past research has begun to provide insights into cone Vision ultrastructure but has yet to afford an overall perspective of cone cell organization. This review Rhodopsin summarizes our past progress and focuses on the recent introduction of special mammalian models Cone pigments (transgenic mice and diurnal rats rich in cones) that together with new investigative techniques such as Enhanced S-cone syndrome atomic force microscopy and cryo-electron tomography promise to reveal a more unified concept of cone Retinitis pigmentosa photoreceptor organization and its role in retinal diseases. -
Mouse Mutants As Models for Congenital Retinal Disorders
Experimental Eye Research 81 (2005) 503–512 www.elsevier.com/locate/yexer Review Mouse mutants as models for congenital retinal disorders Claudia Dalke*, Jochen Graw GSF-National Research Center for Environment and Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany Received 1 February 2005; accepted in revised form 1 June 2005 Available online 18 July 2005 Abstract Animal models provide a valuable tool for investigating the genetic basis and the pathophysiology of human diseases, and to evaluate therapeutic treatments. To study congenital retinal disorders, mouse mutants have become the most important model organism. Here we review some mouse models, which are related to hereditary disorders (mostly congenital) including retinitis pigmentosa, Leber’s congenital amaurosis, macular disorders and optic atrophy. q 2005 Elsevier Ltd. All rights reserved. Keywords: animal model; retina; mouse; gene mutation; retinal degeneration 1. Introduction Although mouse models are a good tool to investigate retinal disorders, one should keep in mind that the mouse Mice suffering from hereditary eye defects (and in retina is somehow different from a human retina, particular from retinal degenerations) have been collected particularly with respect to the number and distribution of since decades (Keeler, 1924). They allow the study of the photoreceptor cells. The mouse as a nocturnal animal molecular and histological development of retinal degener- has a retina dominated by rods; in contrast, cones are small ations and to characterize the genetic basis underlying in size and represent only 3–5% of the photoreceptors. Mice retinal dysfunction and degeneration. The recent progress of do not form cone-rich areas like the human fovea. -
How Photons Start Vision DENIS BAYLOR Department of Neurobiology, Sherman Fairchild Science Building, Stanford University School of Medicine, Stanford, CA 94305
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 560-565, January 1996 Colloquium Paper This paper was presented at a coUoquium entitled "Vision: From Photon to Perception," organized by John Dowling, Lubert Stryer (chair), and Torsten Wiesel, held May 20-22, 1995, at the National Academy of Sciences in Irvine, CA. How photons start vision DENIS BAYLOR Department of Neurobiology, Sherman Fairchild Science Building, Stanford University School of Medicine, Stanford, CA 94305 ABSTRACT Recent studies have elucidated how the ab- bipolar and horizontal cells. Light absorbed in the pigment acts sorption of a photon in a rod or cone cell leads to the to close cationic channels in the outer segment, causing the generation of the amplified neural signal that is transmitted surface membrane of the entire cell to hyperpolarize. The to higher-order visual neurons. Photoexcited visual pigment hyperpolarization relays visual information to the synaptic activates the GTP-binding protein transducin, which in turn terminal, where it slows ongoing transmitter release. The stimulates cGMP phosphodiesterase. This enzyme hydrolyzes cationic channels in the outer segment are controlled by the cGMP, allowing cGMP-gated cationic channels in the surface diffusible cytoplasmic ligand cGMP, which binds to channels membrane to close, hyperpolarize the cell, and modulate in darkness to hold them open. Light closes channels by transmitter release at the synaptic terminal. The kinetics of lowering the cytoplasmic concentration of cGMP. The steps reactions in the cGMP cascade limit the temporal resolution that link light absorption to channel closure in a rod are of the visual system as a whole, while statistical fluctuations illustrated schematically in Fig. -
Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in -
A Three-Dimensional Organoid Model Recapitulates Tumorigenic Aspects
www.nature.com/scientificreports OPEN A three-dimensional organoid model recapitulates tumorigenic aspects and drug responses of Received: 22 June 2018 Accepted: 10 October 2018 advanced human retinoblastoma Published: xx xx xxxx Duangporn Saengwimol1, Duangnate Rojanaporn2, Vijender Chaitankar3, Pamorn Chittavanich4, Rangsima Aroonroch5, Tatpong Boontawon4, Weerin Thammachote4, Natini Jinawath4, Suradej Hongeng6 & Rossukon Kaewkhaw4 Persistent or recurrent retinoblastoma (RB) is associated with the presence of vitreous or/and subretinal seeds in advanced RB and represents a major cause of therapeutic failure. This necessitates the development of novel therapies and thus requires a model of advanced RB for testing candidate therapeutics. To this aim, we established and characterized a three-dimensional, self-organizing organoid model derived from chemotherapy-naïve tumors. The responses of organoids to drugs were determined and compared to relate organoid model to advanced RB, in terms of drug sensitivities. We found that organoids had histological features resembling retinal tumors and seeds and retained DNA copy-number alterations as well as gene and protein expression of the parental tissue. Cone signal circuitry (M/L+ cells) and glial tumor microenvironment (GFAP+ cells) were primarily present in organoids. Topotecan alone or the combined drug regimen of topotecan and melphalan efectively targeted proliferative tumor cones (RXRγ+ Ki67+) in organoids after 24-h drug exposure, blocking mitotic entry. In contrast, methotrexate showed the least efcacy against tumor cells. The drug responses of organoids were consistent with those of tumor cells in advanced disease. Patient-derived organoids enable the creation of a faithful model to use in examining novel therapeutics for RB. Retinoblastoma (RB) is a serious childhood retinal tumor that, if lef untreated, can cause death within 1–2 years. -
Antioxidants Reduce Cone Cell Death in a Model of Retinitis Pigmentosa
Antioxidants reduce cone cell death in a model of retinitis pigmentosa Keiichi Komeima, Brian S. Rogers, Lili Lu, and Peter A. Campochiaro* Departments of Ophthalmology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21287-9277 Edited by Jeremy Nathans, Johns Hopkins University School of Medicine, and approved June 9, 2006 (received for review May 16, 2006) Retinitis pigmentosa (RP) is a label for a group of diseases caused to release a chemoattractant for RPE cells stimulating their tran- by a large number of mutations that result in rod photoreceptor sretinal migration. It is remarkable that the death of rods can have cell death followed by gradual death of cones. The mechanism of these remote effects long after they have departed. cone cell death is uncertain. Rods are a major source of oxygen The loss of rods has delayed effects on other cells in addition to utilization in the retina and, after rods die, the level of oxygen in vascular and RPE cells. After the death of rods, cone photorecep- the outer retina is increased. In this study, we used the rd1 mouse tors begin to die. Depletion of rods is responsible for night model of RP to test the hypothesis that cones die from oxidative blindness, the first symptom of RP, but it is the death of cones that damage. A mixture of antioxidants was selected to try to maximize is responsible for the gradual constriction of the visual fields and protection against oxidative damage achievable by exogenous eventual blindness. The mechanism of the gradual death of cones supplements; ␣-tocopherol (200 mg͞kg), ascorbic acid (250 mg͞kg), is one of the key unsolved mysteries of RP. -
Analysis of the VSX1 Gene in Sporadic Keratoconus Patients from China Tao Guan1†, Xue Wang2†, Li-Bin Zheng3, Hai-Jian Wu1 and Yu-Feng Yao3*
Guan et al. BMC Ophthalmology (2017) 17:173 DOI 10.1186/s12886-017-0567-3 RESEARCH ARTICLE Open Access Analysis of the VSX1 gene in sporadic keratoconus patients from China Tao Guan1†, Xue Wang2†, Li-Bin Zheng3, Hai-Jian Wu1 and Yu-Feng Yao3* Abstract Background: Keratoconus normally presents as a sporadic disease. Although different studies have found sequence variants of the visual system homeobox 1 (VSX1) gene associated with keratoconus in humans, no research has detected such variants in sporadic keratoconus patients from China. To investigate the possibility of VSX1 being a candidate susceptibility gene for Chinese patients with sporadic keratoconus, we performed sequence screening of this gene in such patients. Methods: Whole DNA was obtained from the leukocytes in the peripheral venous blood of 50 patients with sporadic keratoconus and 50 control subjects without this ocular disorder. Polymerase chain reaction single-strand conformation polymorphism analysis and direct DNA sequencing technology were used to detect sequence variation in the five exons and splicing regions of the introns of the VSX1 gene. The sequencing results were analyzed using DNAstar software. Results: One novel missense heterozygous sequence variant (p.Arg131Pro) was found in the first exon of the VSX1 gene in one keratoconus patient. Another heterozygous sequence variant (p.Gly160Val) in the second exon was found in two keratoconus patients. These variants were not detected in the control subjects. In the third intron of the VSX1 gene, c.8326G > A nucleotide substitution (including heterozygous and homozygous change) was also discovered. The frequency of this variation did not differ significantly between patients and controls, it should belong to single-nucleotide polymorphism of the VSX1 gene. -
Viewpoints, Specific- Ally the Relative Growth of the Eye, Directional Sensitivity of Ommatidia, and Sensitivity to Polarized Light
N. SHUSTER.~JR..PH.D.. Zeitschrift fur Zellforschung 87, 278-291 (1968) The Morphology of the Eyes of Limulus I. Cornea and Epidermis of the Compound Eye * WOLFH. FAHRENBACH OregonRegional Primate ResearchCenter, Beaverton, Oregon (U.S.A. ReceivedDecember 11, 1967 * This study constitutes publication No. 288 from the Oregon Regional Primate Research Center, supported in part by Grants FR 00163 and NBO77l7-01 from the National Institutes of Health and in part by a Bob Hope Fight For Sight Grant-in-Aid of the National Council to Combat Blindness, Inc. The author wishes to thank Mrs. AUDREY GRIFFIN for patient and excellent technical assistance. '.. c. Summary. The dioptric apparatus of the Limulu8 compound eye is composed of the corneal cuticle with its internally projecting cuticular cones and the specialized underlying epidermis. The latter is composed of three distinct cell types. The guanophores, located between cuticular cones, contain guanine as a reflecting pigment. The distal pigment cells, which clothe the sides of the cuticular cones and form a sheath around the underlying ommatidium, contain massive bundles of microtubules, abundant pigment droplets and a large Golgi system. The cone cells are positioned between the flattened tip of the cuticular cone and the apex of the ommatidium. They serve to anchor the retinula cells to the cuticle and, by virtue of long processesalong the periphery of the rhabdome, perform a glial function with respect to the interaction of adjacent retinula cells. The geometry and fine structure of the dioptric apparatus provide supporting evidence for the wide angle of acceptance and lack of polarized light perception by the ommatidia. -
Shedding New Light on the Generation of the Visual Chromophore PERSPECTIVE Krzysztof Palczewskia,B,C,1 and Philip D
PERSPECTIVE Shedding new light on the generation of the visual chromophore PERSPECTIVE Krzysztof Palczewskia,b,c,1 and Philip D. Kiserb,d Edited by Jeremy Nathans, Johns Hopkins University School of Medicine, Baltimore, MD, and approved July 9, 2020 (received for review May 16, 2020) The visual phototransduction cascade begins with a cis–trans photoisomerization of a retinylidene chro- mophore associated with the visual pigments of rod and cone photoreceptors. Visual opsins release their all-trans-retinal chromophore following photoactivation, which necessitates the existence of pathways that produce 11-cis-retinal for continued formation of visual pigments and sustained vision. Proteins in the retinal pigment epithelium (RPE), a cell layer adjacent to the photoreceptor outer segments, form the well- established “dark” regeneration pathway known as the classical visual cycle. This pathway is sufficient to maintain continuous rod function and support cone photoreceptors as well although its throughput has to be augmented by additional mechanism(s) to maintain pigment levels in the face of high rates of photon capture. Recent studies indicate that the classical visual cycle works together with light-dependent pro- cesses in both the RPE and neural retina to ensure adequate 11-cis-retinal production under natural illu- minances that can span ten orders of magnitude. Further elucidation of the interplay between these complementary systems is fundamental to understanding how cone-mediated vision is sustained in vivo. Here, we describe recent