DOCSLIB.ORG

The Identification of Effectors of Retinal Cell Fate Determination Through Single Cell Transcriptomics Jillian Joanne Goetz Iowa State University

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
The Identification of Effectors of Retinal Cell Fate Determination Through Single Cell Transcriptomics Jillian Joanne Goetz Iowa State University Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2015 The identification of effectors of retinal cell fate determination through single cell transcriptomics Jillian JoAnne Goetz Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Developmental Biology Commons, Molecular Biology Commons, and the Neuroscience and Neurobiology Commons Recommended Citation Goetz, Jillian JoAnne, "The identification of effectors of retinal cell fate determination through single cell transcriptomics" (2015). Graduate Theses and Dissertations. 14585. https://lib.dr.iastate.edu/etd/14585 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. The identification of effectors of retinal cell fate determination through single cell transcriptomics by Jillian JoAnne Goetz A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Neuroscience Program of Study Committee: Jeffrey Trimarchi, Major Professor Drena Dobbs M. Heather Greenlee Don Sakaguchi Jeanne Serb Iowa State University Ames, Iowa 2015 Copyright © Jillian JoAnne Goetz, 2015. All rights reserved. ii DEDICATION This dissertation is dedicated to my grandpa, the first Doc Goetz. Grandpa Doc is the total package: not only is he resilient and tough, but also quick with a joke or an offering of his own eye if it could help my research. The past few years have been so hard for our entire family, Grandpa Doc especially, and I regret not being there for him more. Hopefully this offering makes up for a bit of it. iii TABLE OF CONTENTS DEDICATION ............................................................................................................................... ii ACKNOWLEDGEMENTS............................................................................................................ v CHAPTER 1. GENERAL INTRODUCTION ............................................................................. 1 1. Background information ............................................................................................................. 1 1.1 Introduction to the retina...................................................................................... 1 1.2 Cell types that comprise the retina .................................................................... 2 2. Retinal cell fate specification ..................................................................................................... 9 2.1 Retinal progenitor cells are multipotent .......................................................11 2.2 Competence in retinal cell fate determination ...........................................13 2.3 Models of retinal cell fate determination ......................................................15 3. “Omics” approaches to understanding retinal cell fate decisions.............................18 3.1 Whole retina studies .............................................................................................18 3.2 Single cell studies ...................................................................................................20 4. Intrinsic signals and retinal development .........................................................................22 4.1 Basic helix-loop-helix factors .............................................................................23 4.2 Homeodomain-containing transcription factors .......................................31 4.3 Other transcription factors and their effects on retinal cell fate .........36 5. Other influences on cell fate determination ......................................................................37 5.1 Asymmetric versus symmetric cell divisions ..............................................37 5.2 The cell cycle’s influence on cell fate ..............................................................39 6. Conclusions ....................................................................................................................................40 7. References ......................................................................................................................................42 8. Figures and legends ....................................................................................................................54 CHAPTER 2. ONECUT1 AND ONECUT2 PLAY CRITICAL ROLES IN THE DEVELOPMENT OF THE MOUSE RETINA ........................................................................ 56 1. Abstract ...........................................................................................................................................57 2. Introduction ...................................................................................................................................58 3. Materials and methods ..............................................................................................................62 4. Results ..............................................................................................................................................69 5. Discussion .......................................................................................................................................79 6. Acknowledgements .....................................................................................................................84 7. References ......................................................................................................................................84 8. Figures and legends ....................................................................................................................89 CHAPTER 3. THE EXPRESSION OF POLO-LIKE KINASE 3 AND ITS ROLE IN RETINAL DEVELOPMENT .................................................................................................. 102 1. Abstract ........................................................................................................................................ 102 2. Introduction ................................................................................................................................ 103 3. Materials and methods ........................................................................................................... 107 iv 4. Results ........................................................................................................................................... 112 5. Discussion .................................................................................................................................... 121 6. Acknowledgements .................................................................................................................. 123 7. References ................................................................................................................................... 123 8. Figures and legends ................................................................................................................. 127 CHAPTER 4. SINGLE CELL TRANSCRIPTOME PROFILING OF DEVELOPING CHICK RETINAL NEURONS ............................................................................................... 138 1. Abstract ........................................................................................................................................ 138 2. Introduction ................................................................................................................................ 139 3. Materials and methods ........................................................................................................... 141 4. Results and discussion ............................................................................................................ 146 5. Conclusions ................................................................................................................................. 156 6. References ................................................................................................................................... 157 7. Figures and legends ................................................................................................................. 160 CHAPTER 5. GENERAL DISCUSSION............................................................................... 166 1. Introduction ................................................................................................................................ 166 2. Retinal transcriptomes reveal subsets of transcription factors present in Math5+ cells ..................................................................................................................................... 168 3. Explorations of genes expressed during retinogenesis with roles outside of direct transcription regulation................................................................................................. 173 4. The future of single-cell isolation in the retina ............................................................. 178 5. Conclusions ................................................................................................................................. 182 7. References ..................................................................................................................................
Load more

Recommended publications
  • Theory and Practice of Lineage Tracing
    REGENERATIVE MEDICINE Theory and Practice of Lineage Tracing a,b YA-CHIEH HSU Key Words. Cell surface markers • Stem cell-microenvironment interactions • Cell cycle • Cell biology • Adult stem cells aDepartment of Stem Cell ABSTRACT and Regenerative Biology, Lineage tracing is a method that delineates all progeny produced by a single cell or a group of Harvard University, cells. The possibility of performing lineage tracing initiated the field of Developmental Biology Cambridge, Massachusetts, and continues to revolutionize Stem Cell Biology. Here, I introduce the principles behind a suc- USA; bHarvard Stem Cell cessful lineage-tracing experiment. In addition, I summarize and compare different methods for Institute, Cambridge, conducting lineage tracing and provide examples of how these strategies can be implemented Massachusetts, USA to answer fundamental questions in development and regeneration. The advantages and limita- Correspondence: Ya-Chieh Hsu, tions of each method are also discussed. STEM CELLS 2015;33:3197–3204 Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Ave., SIGNIFICANCE STATEMENT Cambridge, Massachusetts 02138, USA. Telephone: Lineage relationships allow one to understand the cellular hierarchy of a tissue or organ, which (617) 496-3757; Fax: (617) 496- is central to both Developmental Biology and Stem Cell Biology. Different approaches have 3763; e-mail: yachiehhsu@fas. been developed to conduct lineage tracing. Understanding the underlying basis of these harvard.edu approaches, as well as their advantages and limitations, will allow one to choose the most Received March 26, 2015; appropriate method for a given question. accepted for publication June 23, 2015; first published online STEM CELLS in EXPRESS August 3, cells that are marked at the initial time point, 2015.
    [Show full text]
  • Delta-Notch Signaling: the Long and the Short of a Neuron’S Influence on Progenitor Fates
    Journal of Developmental Biology Review Delta-Notch Signaling: The Long and the Short of a Neuron’s Influence on Progenitor Fates Rachel Moore 1,* and Paula Alexandre 2,* 1 Centre for Developmental Neurobiology, King’s College London, London SE1 1UL, UK 2 Developmental Biology and Cancer, University College London Great Ormond Street Institute of Child Health, London WC1N 1EH, UK * Correspondence: [email protected] (R.M.); [email protected] (P.A.) Received: 18 February 2020; Accepted: 24 March 2020; Published: 26 March 2020 Abstract: Maintenance of the neural progenitor pool during embryonic development is essential to promote growth of the central nervous system (CNS). The CNS is initially formed by tightly compacted proliferative neuroepithelial cells that later acquire radial glial characteristics and continue to divide at the ventricular (apical) and pial (basal) surface of the neuroepithelium to generate neurons. While neural progenitors such as neuroepithelial cells and apical radial glia form strong connections with their neighbours at the apical and basal surfaces of the neuroepithelium, neurons usually form the mantle layer at the basal surface. This review will discuss the existing evidence that supports a role for neurons, from early stages of differentiation, in promoting progenitor cell fates in the vertebrates CNS, maintaining tissue homeostasis and regulating spatiotemporal patterning of neuronal differentiation through Delta-Notch signalling. Keywords: neuron; neurogenesis; neuronal apical detachment; asymmetric division; notch; delta; long and short range lateral inhibition 1. Introduction During the development of the central nervous system (CNS), neurons derive from neural progenitors and the Delta-Notch signaling pathway plays a major role in these cell fate decisions [1–4].
    [Show full text]
  • Molecular Cell and Developmental Biology Graduate Program 2018-2019
    Molecular Cell and Developmental Biology Graduate Program 2018-2019 The Ph.D. track in Molecular Cell and Developmental Biology (MCD) is designed to prepare students for productive careers in biological research and teaching. This training program emphasizes applying diverse approaches, including biochemistry, genetics, genomics, and imaging, to addressing critical questions in molecular, cellular, and developmental biology. Interdisciplinary research is encouraged and supported by a diverse group of faculty from the Departments of Molecular Cell & Developmental Biology (MCD), Chemistry & Biochemistry (Chem), Microbiology & Environmental Toxicology (METX), Biomolecular Engineering (BME), the Santa Cruz Institute for Particle Physics (Physics), and Ecology & Evolutionary Biology (EEB). MCD Faculty James Ackman Visualizing structured activity throughout the developing vertebrate brain Manny Ares Mechanisms and regulation of splicing machinery; structure and function of small RNAs Joshua Arribere Analyzing RNA quality control in C. elegans Needhi Bhalla Meiotic chromosome dynamics Hinrich Boeger Chromatin structure and gene regulation Barry Bowman Membrane biochemistry, genetics, and molecular biology Susan Carpenter Long non-coding RNAs in innate immunity Bin Chen Molecular control of neuronal identity and connectivity in mammalian brains David Feldheim Topographic mapping in vertebrates/CNS Grant Hartzog Chromatin and transcription Lindsay Hinck Molecular basis of neuronal chemotropism Melissa Jurica Structural approaches to large macromolecular
    [Show full text]
  • Cell Fate and Cell Morphogenesis in Higher Plants
    Cell fate and cell morphogenesis in higher plants John W Schiefelbein University of Michigan, Ann Arbor, USA The differentiation of plant cells depends on the regulation of cell fate and cell morphogenesis. Recent studies have led to the identification of mutants and the cloning of genes that influence these processes. In several instances, the genes encode products with homeodomains or Myb or Myc DNA-binding domains. Current Opinion in Genetics and Development 1994, 4:647451 Introduction mutants led eo the early notion that iUVl influences the Gte of leaf cells. Recent studies have shed light on the In higher plants, the formation and differentiation of normaI role of KNY. In localization experiments, KNl cells occurs in an orderly manner, ofien near meristems, is undetectable in leaves, but it is abundant in the api- which are groups of dividing cells chat act like permanent cal meristem and the immature axes of vegetative and stem cell populations. Cell differentiation in plants dif- floral shoots [7]. Also, the dominant Knl-N2 mutation fers horn that in animals because, for the most part, of a has been found to cause ectopic expression, such that lack of the relative cell movements that are characteristic KZVZ transcripts and KNl protein are detected in lateral of animal development. Also, the rigid plant cell wall veins of developing leaves (in addition to the normal makes the control of cell shape a critical aspect of cell accumulation in the meristem), which correlates well differentiation in plants. with the alterations in leaf cell fite and knot forma- The fate of undifferentiated plant cells is influenced pri- tion associated with Krzl mutants [7].
    [Show full text]
  • Of 10 Kai Zhang, Ph.D. Department of Biochemistry Office
    Kai Zhang, PhD University of Illinois at Urbana-Champaign Kai Zhang, Ph.D. Department of Biochemistry Office: (217) 300-0582 School of Molecular and Cellular Biology Fax: (217) 244-5858 600 South Mathews Avenue Email: [email protected] Urbana, Illinois 61801 http://publish.illinois.edu/kaizhanglab/ APPOINTMENT Assistant Professor, University of Illinois at Urbana-Champaign 2014-present Assistant Professor, Department of Biochemistry http://mcb.illinois.edu/faculty/profile/kaizkaiz/ Affiliated Faculty, Neuroscience Program https://neuroscience.illinois.edu/directory/faculty Affiliated Faculty, Center for Biophysical and Computational Biology http://biophysics.illinois.edu/people/faculty Affiliated Faculty, Beckman Institute https://beckman.illinois.edu/ Affiliated Faculty, Chemistry-Biology Interface Training Program https://www.cbitrainingprogramuiuc.com/faculty PROFESSIONAL PREPARATION Stanford University, Stanford, California 2009-2014 Postdoctoral Scholar Single-molecule imaging of axonal transport nerve growth factor in living neuronal cells Optogenetic activation of growth factor-mediated signaling in live cells Research Advisor: Dr. Bianxiao Cui (Chemistry) University of California, Berkeley, Berkeley, California 2002-2008 Ph.D. Chemistry Research Advisor: Dr. Haw Yang (Chemistry) Dissertation title: Methodology Development for Single Molecule/Particle Optical Study of Biological Systems University of Science and Technology of China (USTC) 1997-2002 B.S. Chemical Physics HONORS AND AWARDS Innovative Teaching and Learning Grant
    [Show full text]
  • Developmental Mechanisms Controlling Cell Fate, Evolution Of
    Developmental Mechanisms Controlling Cell Fate, Evolution of DC Lyons, Duke University, Durham, NC, USA M Srivastava, Harvard University, Cambridge, MA, USA DQ Matus, Stony Brook University, Stony Brook, NY, USA r 2016 Elsevier Inc. All rights reserved. Glossary Gene regulatory networks (GRNs) Set of genes and the Epidermal growth factor (EGF) Secreted growth factor control elements (cis-regulatory elements) that control a that binds to an EGF receptor. specific cell biological process. Epithelial to mesenchymal transition (EMT) Cellular Metazoa It is another name for the animal kingdom. behavior where individual cells lose epithelial characteristics Primary mesenchyme cells (PMCs) Embryonic such as adhesion and cell–cell polarity and adopt a echinoderm cells located in the vegetal plate that will mesenchymal phenotype. undergo EMT and ingress giving rise to mesoderm. Equivalence group Set of cells arising from the same Vulval precursor cells (VPCs) Set of ectodermally derived lineage that have equal potential to respond to neighboring cells that can give rise to the adult nematode vulva, or egg- inductive cues. laying organ. Introduction to problems of the cell” (Wilson, 1911). Today, we are able to be more reductionist, thanks to both our ability to rapidly The field of evolutionary developmental biology has matured generate transcriptome data and the increasing ease of func- substantially from its earliest days in the pre-genomic era. We tional studies. This allows researchers to characterize the have begun to generate answers to many important outstanding underlying GRNs that, in combination with inductive signal- evo-devo questions, and today there are few limits on the ing pathways, specify cell fate.
    [Show full text]
  • The Cell Cycle and Development: Lessons from C. Elegans David S
    Seminars in Cell & Developmental Biology 16 (2005) 397–406 Review The cell cycle and development: Lessons from C. elegans David S. Fay ∗ University of Wyoming, College of Agriculture, Department of Molecular Biology, Dept 3944, 1000 E. University Avenue, Laramie, WY 82071, USA Available online 14 March 2005 Abstract The invariant developmental cell lineage of Caenorhabditis elegans (and other similar nematodes) provides one of the best examples of how cell division patterns can be precisely coordinated with cell fates. Although the field has made substantial progress towards elucidating the many factors that control the acquisition of individual cell or tissue-specific identities, the interplay between these determinants and core regulators of the cell cycle is just beginning to be understood. This review provides an overview of the known mechanisms that govern somatic cell growth, proliferation, and differentiation in C. elegans. In particular, I will focus on those studies that have uncovered novel genes or mechanisms, and which may enhance our understanding of corresponding processes in other organisms. © 2005 Elsevier Ltd. All rights reserved. Keywords: Cell cycle; Caenorhabditis elegans; Development; Review Contents 1. Introduction to C. elegans development............................................................................. 397 2. Control of embryonic cell fates and divisions........................................................................ 398 3. Core regulators of the cell cycle in C. elegans ......................................................................
    [Show full text]
  • Jagged–Delta Asymmetry in Notch Signaling Can Give Rise to a Sender/Receiver Hybrid Phenotype
    Jagged–Delta asymmetry in Notch signaling can give rise to a Sender/Receiver hybrid phenotype Marcelo Boaretoa,b, Mohit Kumar Jollya,c, Mingyang Lua, José N. Onuchica,1, Cecilia Clementia,d, and Eshel Ben-Jacoba,e,1 aCenter for Theoretical Biological Physics, Rice University, Houston TX 77005; bInstitute of Physics, University of Sao Paulo, Sao Paulo 05508, Brazil; Departments of cBioengineering and dChemistry, Rice University, Houston, TX 77005; and eSchool of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel Edited by William Bialek, Princeton University, Princeton, NJ, and approved December 12, 2014 (received for review August 22, 2014) Notch signaling pathway mediates cell-fate determination during between two cells behaves as a two-way switch: one cell has [high embryonic development, wound healing, and tumorigenesis. This Delta (ligand), low Notch (receptor)] expression on its surface, pathway is activated when the ligand Delta or the ligand Jagged of whereas the other cell has [high Notch (receptor), low Delta one cell interacts with the Notch receptor of its neighboring cell, (ligand)] on its surface. According to common terminology, the releasing the Notch Intracellular Domain (NICD) that activates many first cell behaves as a Sender (S) and the second one as a Re- downstream target genes. NICD affects ligand production asym- ceiver (R). In other words, the Notch–Delta signaling standalone metrically––it represses Delta, but activates Jagged. Although the causes the two neighboring cells to acquire opposite fates. This dynamical role of Notch–Jagged signaling remains elusive, it is mechanism, known as lateral inhibition, is implicated, for ex- widely recognized that Notch–Delta signaling behaves as an inter- ample, in control of neurogenesis in Drosophila and vertebrates cellular toggle switch, giving rise to two distinct fates that neigh- (7), and in salt-and-pepper patterns observed during wing vein boring cells adopt––Sender (high ligand, low receptor) and Receiver formation (6).
    [Show full text]
  • Reversal of Cell Fate Determination in Caenorhabditis Elegans Vulval Development
    Dartmouth College Dartmouth Digital Commons Open Dartmouth: Peer-reviewed articles by Dartmouth faculty Faculty Work 4-28-1996 Reversal of Cell Fate Determination in Caenorhabditis Elegans Vulval Development Susan Euling University of Minnesota - Twin Cities Victor Ambros Dartmouth College Follow this and additional works at: https://digitalcommons.dartmouth.edu/facoa Part of the Biology Commons, and the Cell Biology Commons Dartmouth Digital Commons Citation Euling, Susan and Ambros, Victor, "Reversal of Cell Fate Determination in Caenorhabditis Elegans Vulval Development" (1996). Open Dartmouth: Peer-reviewed articles by Dartmouth faculty. 741. https://digitalcommons.dartmouth.edu/facoa/741 This Article is brought to you for free and open access by the Faculty Work at Dartmouth Digital Commons. It has been accepted for inclusion in Open Dartmouth: Peer-reviewed articles by Dartmouth faculty by an authorized administrator of Dartmouth Digital Commons. For more information, please contact [email protected]. Development 122, 2507-2515 (1996) 2507 Printed in Great Britain © The Company of Biologists Limited 1996 DEV9460 Reversal of cell fate determination in Caenorhabditis elegans vulval development Susan Euling† and Victor Ambros* Biological Sciences, Dartmouth College, Hanover, NH 03755, USA and Department of Cellular and Developmental Biology, Harvard University, Cambridge, MA 01238, USA *Author for correspondence at present address: Biological Sciences, Dartmouth College, Hanover, NH 03755, USA †Present address: Genetics and Cell Biology, University of Minnesota, St. Paul, MN 55108, USA SUMMARY In Caenorhabditis elegans, the fates of the multipotent vulvae consisting of VPC progeny. During post-dauer vulval precursor cells (VPCs) are specified by intercellular development, these otherwise determined VPC progeny signals. The VPCs divide in the third larval stage (L3) of become reprogrammed back to the multipotent, signal- the wild type, producing progeny of determined cell types.
    [Show full text]
  • Evolution of the Mechanisms That Establish the Embryonic Axes Claudio D Stern
    Evolution of the mechanisms that establish the embryonic axes Claudio D Stern A long-standing debate in developmental biology concerns the ‘higher’ vertebrates (i.e. amniotes) are largely regulative, extent to which embryos are largely ‘mosaic’ (cell fates are whereas ‘lower’ vertebrates and probably most inverte- allocated by localization of maternal determinants that are brates rely much more on maternal determinants. inherited differentially) or ‘regulative’ (cell interactions determine cell fates). Generally, it has been thought that The chick embryo has also long been thought of as an amniotes, especially birds and mammals, are at the extreme example of extreme regulative development, ever since regulative end of the spectrum, whereas most invertebrates, the experiments of Lutz [5] and Spratt [6] demonstrated lower chordates and anamnia are more mosaic. Various studies that when an embryo possessing as many as 20 000 cells have identified additional differences, including egg size, the (i.e. at the mid-blastula stage) is cut into several frag- timing of zygotic transcription and the speed of development. ments, each fragment can spontaneously initiate forma- However, new research is starting to reveal among the tion of a complete embryonic axis. However this too has vertebrate classes an astonishing degree of conservation in the been challenged recently by the finding that unknown intercellular signalling mechanisms that regulate cell fate and molecular components (within the so-called g- and d- embryonic polarity before gastrulation. ooplasm, of which the first is peripheral and the second more centrally located) within the acellular yolky material Addresses underlying the cleaving embryo can influence cell fate Department of Anatomy & Developmental Biology, University College decisions in the early blastoderm, and might bias embryo- London, Gower Street, London WC1E 6BT, UK nic polarity [7].
    [Show full text]
  • Tet Proteins Influence the Balance Between PNAS PLUS Neuroectodermal and Mesodermal Fate Choice by Inhibiting Wnt Signaling
    Tet proteins influence the balance between PNAS PLUS neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling Xiang Lia,b, Xiaojing Yuea, William A. Pastora,1, Lizhu Linc, Romain Georgesa, Lukas Chaveza,2, Sylvia M. Evansc,d,3, and Anjana Raoa,b,e,f,3 aDivision of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037; bSanford Consortium for Regenerative Medicine, La Jolla, CA 92037; cSkaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA 92093; dDepartment of Medicine, University of California at San Diego, La Jolla, CA 92093; eDepartment of Pharmacology, University of California at San Diego, La Jolla, CA 92093; and fMoores Cancer Center, University of California at San Diego, La Jolla, CA 92093 Contributed by Anjana Rao, November 2, 2016 (sent for review October 14, 2016; reviewed by Kristin K. Baldwin and Scott J. Bultman) TET-family dioxygenases catalyze conversion of 5-methylcytosine birth (17). Embryos lacking Tet1 and Tet3 only survive to embry- (5mC) to 5-hydroxymethylcytosine (5hmC) and oxidized methyl- onic day 10.5 (E10.5) and display poor forebrain formation and cytosines in DNA. Here, we show that mouse embryonic stem cells abnormal facial structures (18). The 5hmC generated by Tet family (mESCs), either lacking Tet3 alone or with triple deficiency of Tet1/2/3, dioxygenases is abundant in neurons (19) and may be critical for displayed impaired adoption of neural cell fate and concomitantly neural development (20). In Xenopus, Tet3 plays a vital function skewed toward cardiac mesodermal fate. Conversely, ectopic expres- in early eye and neural development by directly targeting several sion of Tet3 enhanced neural differentiation and limited cardiac key developmental genes (21).
    [Show full text]
  • Cell Population Structure Prior to Bifurcation Predicts Efficiency of Directed Differentiation in Human Induced Pluripotent Cells
    Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells Rhishikesh Bargajea,1, Kalliopi Trachanaa,1, Martin N. Sheltona, Christopher S. McGinnisa, Joseph X. Zhoua, Cora Chadicka, Savannah Cookb, Christopher Cavanaughb, Sui Huanga,2, and Leroy Hooda,2 aInstitute for Systems Biology, Seattle, WA 98109; and bInstitute for Stem Cell & Regenerative Medicine, University of Washington Medicine Research, Seattle, WA 98109 Contributed by Leroy Hood, December 29, 2016 (sent for review December 7, 2016; reviewed by Alfonso E. Martinez Arias and Irving L. Weissman) Steering the differentiation of induced pluripotent stem cells lineage trajectories at single-cell resolution captures cell fate (iPSCs) toward specific cell types is crucial for patient-specific transitions in a large statistical ensemble of identical systems as disease modeling and drug testing. This effort requires the capac- each individual progenitor cell in a differentiating population, ity to predict and control when and how multipotent progenitor allowing us to dissect molecular and cellular patterns driving cells commit to the desired cell fate. Cell fate commitment repre- lineage commitment. For instance, single-cell resolution analyses sents a critical state transition or “tipping point” at which complex have shown that cell types form discrete clusters when gene ex- systems undergo a sudden qualitative shift. To characterize such pression patterns are visualized in a low-dimensional space using, transitions during iPSC to cardiomyocyte differentiation, we ana- for example, principle component analysis or t-distributed sto- lyzed the gene expression patterns of 96 developmental genes at chastic neighbor-embedding plots (3, 6) (Fig. 1 A and B).
    [Show full text]