Essentials of stem cell biology 2nd ed r lanza (AP, 2009)

Academic Press is an imprint of Elsevier 525 B Street, Suite 1900, San Diego, CA 92101-4495, USA 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 32 Jamestown Road, London NW1 7BY, UK First edition 2006 Second edition 2009 Copyright © 2009 Elsevier Inc Apart from Chapter 68 which is in the public domain All rights reserved No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means electronic, mechanical, photocopying, recording, or otherwise without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science & Technology Rights Department in Oxford, UK: phone: (144) (0)1865 843830; fax: (144) (0) 1865 853333; e-mail: permissions@elsevier.com Alternatively visit the Science and Technology Books website at www.elsevierdirect.com/rights for further information Notice No responsibility is assumed by the publisher for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein Because of rapid advances in the medical sciences, in particular, independent verification of diagnoses and drug dosages should be made Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress British Library Cataloging in Publication Data A catalog record for this book is available from the British Library ISBN: 978-0-12-374729-7 For information on all Academic Press publications visit our website at www.elsevierdirect.com Typeset by Macmillan Publishing Solutions (www.macmillansolutions.com) Printed in Canada 09  10  11  12  13   10  9  8  7  6  5  4  3  2  Contributors Numbers in parentheses indicate the chapter number of the authors’ contribution Russell C Addis (42) John Hopkins University, School of Medicine, Baltimore, MD Michal Amit (40) Department of Obstetrics and Gynecology, Rambam Medical Center, and The Bruce Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel Peter W Andrews (11, 47) Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, UK Piero Anversa (59) Departments of Anesthesia and Medicine, and Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA Anthony Atala (16) Wake Forest Institute for Regenerative Medicine, Wake University School of Medicine, Winston-Salem, NC Susan Bonner-Weir (57) Section on Islet Transplantation and Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA Mairi Brittan (36) Centre for Gastroenterology, Institute of Cell and Molecular Sciences, Barts and the London School of Medicine and Dentistry, London, UK Hal E Broxmeyer (17) Walther Oncology Center and Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN Scott Bultman (10) Department of Genetics, University of North Carolina at Chapel Hill, NC Arnold I Caplan (29) Skeletal Research Center, Case Western Reserve University, Cleveland, OH Melissa K Carpenter (38, 44) Carpenter Group, 10330 Wateridge Circle #290, San Diego, CA Joyce Axelman (42) John Hopkins University, School of Medicine, Baltimore, MD Fatima Cavaleri (6) Max Planck Institute for Molecular Biomedicine, Muenster, Germany Anne G Bang (38) Novocell, Inc., 3500 General Atomics Ct, San Diego, CA Connie Cepko (21) Department of Genetics, Howard Hughes Medical Institute, Harvard Medical School, Boston, MA Yann Barrandon (61) Laboratory of Stem Cell Dynamics, School of Life Sciences, Swiss Federal Institute of Technology Lausanne and Department of Experimental Surgery, Lausanne University Hospital 1015, Lausanne, Switzerland Steven R Bauer (68) Laboratory of Stem Cell Biology, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Rockville, MD Daniel Becker (55) Department of Neurology, Johns Hopkins School of Medicine and Kennedy Krieger Institute, 707 North Broadway, Suite 518, Baltimore, MD Nissim Benvenisty (45) Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, 91904 Jerusalem, Israel Paolo Bianco (64) Dipartimento di Medicina Sperimentale, Sapienza, Universita di Roma, Rome, Italy; Parco Scientifico Biomedico San Raffaele, Rome, Italy Helen M Blau (30) Baxter Laboratory in Genetic Pharmacology, Dept of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA Howard Y Chang (51) Department of Dermatology and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA Xin Chen (51) Department of Biopharmaceutical Sciences, University of California, San Francisco, CA, USA Tao Cheng (9) Massachusetts General Hospital, Harvard Medical School, Boston, MA Susana M Chuva de Sousa Lopes (13, 14) Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands Gregory O Clark (42) Division of Endocrinology, John Hopkins University, School of Medicine, Baltimore, MD Michael F Clarke (53) Stanford Institute for Stem Cell and Regenerative Medicine; Department of Medicine, Division of Oncology, Stanford University School of Medicine, Stanford, CA Giulio Cossu (60) Stem Cell Research Institute, Dibit, H.S Raffaele, Milan, Italy Annelies Crabbe (28) Interdepartementeel Stamcelinstituut, Katholieke Universiteit Leuven, Belgium ix  George Q Daley (24) Children’s Hospital Boston, MA Ayelet Dar (27) Stem Cell Center, Bruce, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel Brian R Davis (65) Centre for Stem Cell Research, Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center, Houston, TX Natalie C Direkze (36) Centre for Gastroenterology, Institute of Cell and Molecular Sciences, Barts and the London School of Medicine and Dentistry, London, UK Histopathology Unit, London Research Institute, Cancer Research UK, London, UK Contributors John D Gearhart (42) Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA Pamela Gehron Robey (64) Craniofacial and Skeletal Diseases Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Department of Health and Human Services, Bethesda, MD Sharon Gerecht-Nir (27) Stem Cell Center, Bruce Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel Penney M Gilbert (30) Baxter Laboratory in Genetic Pharmacology, Dept of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA Yuval Dor (35) Department of Cellular Biochemistry and Human Genetics, The Hebrew University-Hadassah Medical School, Jerusalem, Israel Victor M Goldberg (62) Department of Orthopaedics, Case Western Reserve University/University Hospitals of Cleveland, Cleveland, OH Jonathan S Draper (47) Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, UK Rodolfo Gonzalez (54) Program in Stem Cell Biology (Developmental & Regeneration Cell Biology), The Burnham Institue, La Jolla, CA Gregory R Dressler (33) Department of Pathology, University of Michigan, Ann Arbor, MI Martin Evans (39) Cardiff School of Biosciences, Cardiff University, Cardiff, UK Elizabeth Gould (20) Department of Psychology, Princeton University, Princeton, NJ Margaret A Farley (67) Yale University Divinity School, New Haven, CT Trevor A Graham (36) Centre for Gastroenterology, Institute of Cell and Molecular Sciences, Barts and the London School of Medicine and Dentistry, London, UK Donna Fekete (21) Department of Biological Sciences, Purdue University, West Lafayette, IN Ronald M Green (66) Ethics Institute, Dartmouth College, Hanover, NH Qiang Feng (25) Stem Cell and Regenerative Medicine International, 381 Plantation Street, Worcester, MA Markus Grompe (34) Papé Family Pediatric Research Institute, Oregon Stem Cell Center, Oregon Health & Science University, Portland, OR Loren J Field (56) The Riley Heart Research Center, Herman B Wells Center for Pediatric Research; the Krannert Institute of Cardiology, Indiana University School of Medicine, Indianapolis, IN Donald W Fink (68) Cell Therapy Branch, Division of Cellular and Gene Therapies, Office of Cellular, Tissue and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration, Rockville, MD Dirk Hockemeyer (4) The Whitehead Institute, Cambridge Center, Cambridge, MA Marko E Horb (12) Centre for Regenerative Medicine, Department of Biology & Biochemistry, University of Bath, Bath, UK Jerry I Huang (62) University Hospitals Research Institute, Cleveland, OH K Rose Finley (52) Howard Hughes Medical Institute, Children’s Hospital, Boston, MA Adam Humphries (36) Centre for Gastroenterology, Institute of Cell and Molecular Sciences, Barts and the London School of Medicine and Dentistry, London, UK Elaine Fuchs (22) Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY Joseph Itskovitz-Eldor (27, 40) Department of Obstetrics and Gynecology, Rambam Medical Center, and The Bruce Rappaport Faculty of Medicine, Technion–Israel Institute of Technology, Haifa, Israel Margaret T Fuller (7) Stanford University School of Medicine, Department of Developmental Biology, Stanford, CA Rudolf Jaenisch (4) The Whitehead Institute, Cambridge, MA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA Richard L Gardner (1) University of Oxford, Dept of Zoology, Oxford, UK Penny Johnson (11) Department Biomedical Science, University of Sheffield, Western Bank, Sheffield, UK xi Contributors D Leanne Jones (7) Stanford University School of Medicine, Department of Developmental Biology, Stanford, CA John W Littlefield (42) Johns Hopkins University, School of Medicine, Baltimore, MD Jan Kajstura (59) Departments of Anesthesia and Medicine, and Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA Shi-Jiang Lu (25) Advanced Cell Technology, and Stem Cell and Regenerative Medicine International, 381 Plantation Street, Worcester, MA Gerard Karsenty (26) Baylor College of Medicine, Houston, TX Terry Magnuson (10) Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC Pritinder Kaur (58) The University of Melbourne, Epithelial Stem Cell Biology Laboratory, Peter MacCallum Cancer Institute, East Melbourne, Victoria, Australia Yoav Mayshar (45) Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem, Israel Kathleen C Kent (42) Johns Hopkins University, School of Medicine, Baltimore, MD John W McDonald (55) Department of Neurology, Johns Hopkins School of Medicine and Kennedy Krieger Institute, 707 North Broadway, Suite 518, Baltimore, MD Candace L Kerr (42) Department of Gynecology and Obstetrics, John Hopkins University, School of Medicine, Baltimore, MD Ali Khademhosseini (63) Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA Chris Kintner (18) The Salk Institute for Biological Studies, San Diego, CA Irina Klimanskaya (41) Advanced Cell Technology, 381 Plantation Street, Worcester, MA Naoko Koyano-Nakagawa (18) Stem Cell Institute, Department of Neuroscience, University of Minnesota, Minneapolis MN, USA Jennifer N Kraszewski (42) Johns Hopkins University, School of Medicine, Baltimore, MD Tilo Kunath (15) Mount Sinai Hospital, Toronto, Ontario, Canada Robert Langer (63) Langer Lab, Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA Robert Lanza (25) Advanced Cell Technology, and Stem Cell and Regenerative Medicine International, 381 Plantation Street, Worcester, MA Annarosa Leri (59) Departments of Anesthesia and Medicine, and Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA Shulamit Levenberg (63) Faculty Engineering Techion, Haifa, Israel of Stuart A C McDonald (36) Centre for Gastroenterology, Institute of Cell and Molecular Sciences, Barts and the London School of Medicine and Dentistry, London, UK; Histopathology Unit, London Research Institute, Cancer Research UK, London, UK Anne McLaren (14) The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK Tragically died on 7th of July 2007 Jill McMahon (41) Harvard University, 16 Divinity Ave, Cambridge, MA Douglas A Melton (35) Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, Harvard University, Cambridge, MA Christian Mirescu (20) Department of Psychology, Princeton University, Princeton, NJ Nathan Montgomery (10) Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC Malcolm A S Moore (23) Developmental Hematology, Memorial Sloan-Kettering Cancer Center, New York, NY Mary Tyler Moore (69) International Chairwoman, Juvenile Diabetes Research Foundation Christine L Mummery (13) Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, The Netherlands Biomedical Andras Nagy (48) Mount Sinai Hospital, Samuel Lunenfeld Research Institute, Toronto, Canada S Robert Levine (69) Research Portfolio Committee, Juvenile Diabetes Research Foundation Satomi Nishikawa (32) Stem Cell Research Group, Riken Center for Developmental Biology, Kobe, Japan Olle Lindvall (5) Laboratory of Neurogenesis and Cell Therapy, Section of Restorative Neurology, Wallenberg Neuroscience Center, University Hospital, Lund, Sweden; Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund, Sweden Shin-Ichi Nishikawa (32) Stem Cell Research Group, Riken Center for Developmental Biology, Kobe, Japan Hitoshi Niwa (8) Lab for Pluripotent Cell Studies, RIKEN Ctr for Developmental Biology, Chu-o-ku, Kobe C, Japan xii Jennifer S Park (25) Advanced Cell Technology, 381 Plantation Street, Worcester, MA Ethan S Patterson (42) Johns Hopkins University, School of Medicine, Baltimore, MD Alice Pébay (43) Centre for Neuroscience and Department of Pharmacology, The University of Melbourne, Parkville, Victoria, Australia Contributors Alessandra Sacco (30) Baxter Laboratory in Genetic Pharmacology, Dept of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA Maurilio Sampaolesi (60) Stem Cell Research Institute, Dibit, H.S Raffaele, Milan, Italy Maria Paola Santini (31) Heart Science Centre, NHLI Division, Imperial College London, UK Martin F Pera (43) Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA David T Scadden (9) Massachusetts General Hospital, Harvard Medical School, Boston, MA Christopher S Potten (3) EpiStem Limited, Incubator Building, Manchester, UK Tom Schulz (44) Novocell, Inc., 111 Riverbend Rd, Athens, GA Bhawana Poudel (31) Heart Science Centre, NHLI Division, Imperial College London, UK Michael J Shamblott (42) Institute for Cell Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD Sean L Preston (36) Centre for Gastroenterology, Institute of Cell and Molecular Sciences, Barts and the London School of Medicine and Dentistry, London, UK; Histopathology Unit, London Research Institute, Cancer Research UK, London, UK Hans Schöler (6) Max Planck Institute for Molecular Biomedicine, Muenster, Germany William B Slayton (50) University of Florida College of Medicine, Pediatric Hematology/Oncology, Gainesville, FL Nicole L Prokopishyn (65) Calgary Laboratory Services, Foothills Medical Centre, Calgary, Alberta, Canada Evan Y Snyder (54) Program in Stem Cell Biology (Developmental & Regeneration Cell Biology) The Burnham Institue, La Jolla, CA Emily K Pugach (52) Howard Hughes Medical Institute, Children’s Hospital, Boston, MA Frank Soldner (4) The Whitehead Institute, Cambridge Center, Cambridge, MA Jean Pyo Lee (54) Program in Stem Cell Biology (Developmental & Regeneration Cell Biology) The Burnham Institue, La Jolla, CA Gerald J Spangrude (50) University of Utah, Division of Hematology, Salt Lake City, UT Ariane Rochat (61) Laboratory of Stem Cell Dynamics, School of Life Sciences, Swiss Federal Institute of Technology Lausanne and Department of Experimental Surgery, Lausanne University Hospital 1015, Lausanne, Switzerland Lorenz Studer (19) Laboratory of Stem Cell & Tumor Biology, Neurosurgery and Developmental Biology, Memorial Sloan Kettering Cancer Center, New York, NY M Azim Surani (49) Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK Nadia Rosenthal (31) Heart Science Centre, NHLI Division, Imperial College London, UK; Mouse Biology Unit European Molecular Biology Laboratory, Monterotondo (Rome) Italy; Australian Regenerative Medicine Institute, Monash University, Melbourne, Australia James A Thomson (37, 46) Morgridge Institute for Research in Madison, Wisconsin; the University of Wisconsin School of Medicine and Public Health; Molecular, Cellular, and Developmental Biology (MCDB) Department at the University of California, Santa Barbara Janet Rossant (2, 15) Mount Sinai Hospital, Toronto, Ontario, Canada David Tosh (12) Centre for Regenerative Medicine, Department of Biology & Biochemistry, University of Bath, Bath, UK Michael Rothenberg (53) Stanford Institute for Stem Cell and Regenerative Medicine; Department of Medicine, Stanford University School of Medicine; Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA Michael Rubart (56) The Riley Heart Research Center, Herman B Wells Center for Pediatric Research, Indianapolis, IN Tudorita Tumbar (22) Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY Edward Upjohn (58) The University of Melbourne, Epithelial Stem Cell Biology Laboratory, Peter MacCallum Cancer Institute, East Melbourne, Victoria, Australia Contributors George Varigos (58) The University of Melbourne, Epithelial Stem Cell Biology Laboratory, Peter MacCallum Cancer Institute, East Melbourne, Victoria, Australia Catherine M Verfaillie (28) Interdepartementeel Stamcelinstituut, Katholieke Universiteit Leuven, Belgium Gordon C Weir (57) Section on Islet Transplantation and Cell Biology, Joslin Diabetes Center, Harvard Medical School, Boston, MA xiii Jun K Yamashita (32) Laboratory of Stem Cell Differentiation, Institute for Frontier Medical Sciences, Kyoto University; Center for iPS Cell Research and Application, Institute for Integrated Cell-Material Sciences, Kyoto University, Kyoto, Japan Holly Young (44) Novocell, Inc., 3500 General Atomics Ct, San Diego, CA Junying Yu (37) University of Wisconsin School of Medicine and Public Health, WI J W Wilson (3) EpiStem Limited, Incubator Building, Manchester, UK Leonard I Zon (52) Howard Hughes Medical Institute, Children’s Hospital, Boston, MA Nicholas A Wright (36) Centre for Gastroenterology, Institute of Cell and Molecular Sciences, Barts and the London School of Medicine and Dentistry, London, UK; Histopathology Unit, London Research Institute, Cancer Research UK, London, UK Thomas P Zwaka (46) Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX Preface Preface to the Second Edition The second edition of Essentials of Stem Cell Biology incorporates the latest advances in the field of stem cells, with new chapters on clinical translation, cancer stem cells, and direct reprogramming—including chapters by the scientists whose groundbreaking research ushered in the era of induced pluripotent stem (iPS) cells While the second edition offers a comprehensive—and much needed— update of the rapid progress that has been achieved in the field in the last half decade, we have retained those facts and subject matter which, while not new, is pertinent to the understanding of this exciting area of biology Like the original volume, the second edition of Essentials of Stem Cell Biology is presented in an accessible format, suitable for students and general readers interested in following the latest advances in stem cells The organization of the book remains largely unchanged, combining the prerequisites for a general understanding of embryonic, fetal, and adult stem cells; the tools, methods, and experimental protocols needed to study and characterize stem cells and progenitor populations; as well as a presentation by the world’s leading scientists of what is currently known about each specific organ system No topic in the field of stem cells is left uncovered, including basic biology/mechanisms, early development, ectoderm, mesoderm, endoderm, methods (such as detailed descriptions of how to generate both iPS and embryonic stem cells), application of stem cells to specific human diseases, regulation and ethics, and a patient perspective by Mary Tyler Moore The second edition also includes a Foreword by 2007 Nobel laureate Sir Martin Evans (who is credited with discovering embryonic stem cells) The result is a comprehensive reference that we believe will be useful to students and experts alike, and that represents the combined effort of eight editors and more than 200 scholars and scientists whose pioneering work has defined our understanding of stem cells Robert Lanza, M.D Boston, Massachusetts xv Foreword It is with great pleasure that I pen this foreword to the second edition of the Essentials of Stem Cell Biology The field of stem cell biology is moving extremely rapidly as the concept and potential practical applications have entered the mainstream Despite this worldwide intensity and diversity of endeavor, there remain a smaller number of definable leaders in the field, and this volume brings most of them together Although the concept of stem and progenitor cells has been known for a long time, it was the progress towards embryonic stem cells which lit the field Mouse embryonic stem (ES) cells originally came from work aimed at understanding the control and progress of embryonic differentiation, but their in vitro differentiation, despite being magnificent, was overshadowed experimentally by their use as a vector to the germline, and hence as a vehicle for experimental mammalian genetics This now has led to studies of targeted mutation in up to one third of gene loci, and an ongoing international program to provide mutation in every locus of the mouse These studies greatly illuminate our understanding of human genetics Jamie Thomson, reporting the advent of the equivalent human embryonic stem cells, very clearly signaled that their utility would be neither in genetic studies (impractical and unethical in man), nor in fundamental studies of embryonic development (already catered for by mouse ES cells), but, by providing a universal source of a diversity of tissue-specific precursors, as a resource for tissue repair and regenerative medicine Progress towards the understanding of pluripotentiality and the control of cellular differentiation, that is basic fundamental developmental biology at the cell and molecular level, now stands as a gateway to major future clinical applications This volume provides a timely, up-to-date state-of-the-art reference The ideas behind regenerative medicine, powered by the products of embryonic stem cells, reinvigorated study of committed stem and precursor cells within the adult body The use of such stem cells in regenerative medicine already has a long history, for example in bone marrow transplantation and skin grafting In both of these examples not only gross tissue transplantation, but also purified or cultured stem cells may be used They have been extensively applied in clinical treatment, and have most clearly demonstrated the problems which arise with histoincompatibility Ideally, in most cases, a patient is better treated with his own—autologous—cells than with partially matching allogeneic cells An ideal future would be isolation, manipulation, or generation of suitable committed stem or precursor cell populations from the patient for the patient The amazing advances of induced pluripotential stem cells point to the possibilities of patient-specific ad hominem treatment This personalized medicine would be an ideal scenario, but as yet the costs of the technologies may not allow it to be a commercial way forward The timelines are, however, likely to be long before the full promise of these technologies is realized, and there is every possibility that such hurdles will be circumvented Quite properly, much of this book concentrates on the fundamental developmental and cell biology from which the solid applications will arise This is a knowledge-based field in which we have come a long way, but are still relatively ignorant We know many of the major principles of cell differentiation, but as yet need to understand more in detail, more about developmental niches, more about the details of cell–cell and cell growth-factor interaction, and more about the epigenetic programming which maintains the stability of the differentiated state Professor Sir Martin Evans Sir Martin Evans, PhD, FRS Nobel Prize for Medicine 2007 Sir Martin is credited with discovering embryonic stem cells, and is considered one of the chief architects of the field of stem cell research His ground-breaking discoveries have enabled gene targeting in mice, a technology that has revolutionized genetics and developmental biology, and have been applied in virtually all areas of biomedicine—from basic research to the development of new medical therapies Among other things, his research inspired the effort of Ian Wilmut and his team to create Dolly the cloned sheep, and Jamie Thomson’s efforts to isolate embryonic stem cells from human embryos, another of the great medical milestones in the field of stem cell research Professor Evans was knighted in 2004 by Queen Elizabeth for his services to medical science He studied at Cambridge University and University College London before leaving to become director of bioscience at Cardiff University xvii Why Stem Cell Research Medical research is endlessly exciting, by its very nature continuously uncovering new facts and principles that build upon existing knowledge to modify the way we think about biological processes In the history of science, certain discoveries have indeed transformed our thinking and created opportunities for major advancement, and so it is with the discovery and isolation of pluripotential stem cells Although appearing only briefly in mammalian development, they are a source of an organism’s complete array of cell types at every stage of development, from embryogenesis through senescence, in health and in disease Scientists recognizing the remarkable opportunities pluripotential stem cells provide have, in a less than a decade, progressed from being able to isolate pluripotential stem cells from early embryos and grow the cells in the laboratory (Thomson et al., 1998; Reubinoff et al., 2000), to being able to generate them by reprogramming somatic cells using viral insertion of key transcription factors (Okita et al., 2007; Takahashi et al., 2007) These advances now make it possible, in principle, to use stem cells for cell therapy—to identify new molecular targets for disease treatment, to contain oncogenesis, to reconstruct or replace diseased tissues—and for gene therapy New opportunities for expanding effective hematopoietic and other adult stem cell therapies appear in the literature almost daily, and increasing numbers of scientists, clinicians, and patient advocates are becoming excited about an impending revolution in non-hematopoietic cell-based medicine Embryonic stem (ES) cells will remain the gold standard for pluripotentiality research, but induced pluripotential stem (iPS) cells hold the promise of making personalized medicine a reality By using them we can analyze the heterogeneity of complex human diseases, including the diverse causes of cell degeneration and cell death—information certain to help us develop new drugs IPs cells will also help us understand adverse responses to new drugs by those small cohorts within larger patient populations who can stall or collapse otherwise successful clinical trials Central to these studies will be the need to precisely manipulate cell fate and commitment decisions to create the tissues that are needed, but doing so will require much more information about the cocktails of transcription factors necessary to regulate cell differentiation (Zhou et al., 2008) Stem cell technology will also become invaluable in animal science, and perhaps even animal conservation (Trounson, 2008) One exciting new direction currently underway is to generate iPS cells in endangered species, and to re-establish these populations through chimerism in closely-related species The stem cell revolution was initially delayed by funding restrictions, arising from those with ethical concerns about using human embryos for research The tide is turning, however, not only because of wider acceptance of the technology and appreciation for its potential importance, but also because of iPS cell technology, which obviates the use of human embryos As a result, many agencies around the world are now funding stem cell research, and growing numbers of scientists and their students are entering the field The result should be a global collaboration focused on delivering clinical outcomes of immense benefit to the world’s population We are just at the beginning of a very long road of work and discovery, but one thing is certain: stem cell research is vital and must go forward Alan Trounson California Institute for Regenerative Medicine San Francisco, CA, USA FURTHER READING Okita, K., Ichisaka, T., & Yamanaka, S (2007) Generation of germlinecompetent induced pluripotent stem cells Nature, 448(7151), 313–317 Reubinoff, B E., Pera, M F., Fong, C-Y., Trounson, A., & Bongso, A (2000) Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro Nat Biotech., 18(4), 399–404 Takahashi, K., Tanabe, K., Ohnuki, M., Narita, M., Ichisaka, T., Tomoda, K., & Yamanaka, S (2007) Induction of pluripotent stem cells from adult human fibroblasts by defined factors Cell, 131(5), 861–872 Thomson, J A., Itskovitz-Eldor, J., Shapiro, S S., Waknitz, M A., Swiergiel, J J., Marshall, V S., et al (1998) Embryonic stem cell lines derived from human blastocysts Science, 282(5391), 1145–1147 Trounson, A (2009) Rats, cats, and elephants, but still no unicorn: Induced pluripotent stem cells from new species Cell Stem Cell, 4(1), 3–4 doi:10.1016/j.stem.2008.12.002 Zhou, Q., Brown, J., Kanarek, A., Rajagopal, J., & Melton, D A (2008) In vivo reprogramming of adult pancreatic exocrine cells to b-cells Nature, 455(7213), 627–632 xix 636 PART  |  VI  Regulation and Ethics is the greatest opportunity for JDRF investment to make a difference The experience at JDRF infers that decisions regarding embryonic stem cell research are best made in the open, with the full engagement of the public, and with particular attention to presentation of the broadest breadth of available information and opinion We can be confident that the powers of society (in overseeing the conduct of science) can be safely ceded to the discretion of a well-informed populace BETTER HEALTH FOR ALL William Bradford, speaking in 1630 of the founding of the Plymouth Bay Colony, said that all great and honorable actions are accompanied with great difficulties, and both must be enterprised and overcome with answerable courage If … our progress teaches us anything, it is that man, in his quest for knowledge and progress, is determined and cannot be deterred President John F Kennedy, speech at Rice University September 12, 1962 People like me who struggle daily with disease or disability, and the people who love us, recognize the difficulties of scientific advancement, accept the challenges, and every day answer with courage—if not for our own sake, for our children and our children’s children We are motivated not by curiosity, but by our dedication to finding cures New therapies derived from embryonic stem cell research, conducted with public support by scientists from all areas of the globe, and made available to all who might benefit, are part of our broader vision of better health for all Index 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), 492 A AAV (adeno-associated virus) vectors, 592, 593–594, 595 aberrant crypt foci (ACF), 324 Achilles tendon injuries, 567, 568 acinar cells, 302, 316 acini, 302–303 ACL (anterior cruciate ligament) injuries, 566, 567, 568 active exogenous genetic markers, 431–433 activin, 46, 394 actual stem cells, 19 acute myelogenous leukemia (AML), 473–474, 477 adeno-associated virus (AAV) vectors, 592, 593, 594, 595 adenoma morphogenesis, 322–326 adenomatous polyposis coli (APC) gene, 69, 319–320, 322, 323, 476 adenosine deaminase deficiency (ADA), 593 adipocytes, 146 adrenal steroids, 182 adult brain, neuronal progenitors in, 179–187 adult keratinocyte stem cells, see keratinocyte stem cells (KSCs) adult mammalian liver, organization and functions of, 285 adult neurogenesis in vivo, 180–182 adult pancreas, progenitor cells in, 301–303 adult stem cells, 237 vs embryonic cells, 10 immortal liver progenitor cell lines, 292–298 liver stem cells, 285–292 source of insulin-producing cells, 516–519 African green monkeys, 389 aggregation chimeras, 434 AGM (aorta–gonad–mesonephros) region, 202–205, 459, 460, 464 AKN-1, 292 alkaline phosphatase (AP), 387 detection of, 405 positive cells, 381–382 allelic exclusion, 101–102 allografts, burns, 525–526 ALS (amyotrophic lateral sclerosis), 173, 490, 492, 497 Alzheimer’s disease, 177, 485, 490 amniocentesis, 145–146 amniotic fluid-derived pluripotential cells, 145–149 amniotic fluid and amniocentesis, 145–146 in vivo behavior of amniotic fluid stem cells, 149 progenitor cells differentiation potential of, 146–149 isolation and characterization of, 146 amniotic fluid stem cells (AFSCs), 145 amniotic stem cells, 291–292 amyotrophic lateral sclerosis (ALS), 173, 490, 492, 497 analysis of variance (ANOVA), 452 angiogenesis, 229 animal models, preclinical studies with stem cells in, 34 ANOVA (analysis of variance), 452 anterior cruciate ligament (ACL) injuries, 566, 567, 568 antibodies, 387, 423 antigen markers, surface, 423–428 anti-rat immunoglobulin, 445 aorta–gonad–mesonephros (AGM) region, 202–205, 459, 460, 464 AP (alkaline phosphatase), 387 detection of, 405 positive cells, 381–382 array-based comparative genomic hybridization (aCGH), 454 astrocytes, 70, 174 astroglia, 180 ATPase chromatin-remodeling complexes, 94–95 autografts, burns, 524–525 avian bursa of Fabricius, 208 avian intra-aortic and para-aortic hematopoiesis, 202–205 B bacterial artificial chromosome (BAC), 412 Barrett’s metaplasia, 113–114 basal ganglia, 489 basic fibroblast growth factor (bFGF), 40, 46, 357, 367, 382, 386, 397 B-cell progenitors, 299, 301 BCR/ABL, transformation of an EB-derived HSC by, 212 BDNF (brain-derived neurotrophic factor), 181, 486, 489 b-cells, 519 adult stem/progenitor cells, source of insulin-producing cells, 516–517 defining, 513 replacement therapy, 513 bFGF (basic fibroblast growth factor), 40, 46, 357, 367, 382, 386, 397 bile duct epithelial phenotypes in vitro, 290–291 biodegradable polymer scaffolds, 573 bioreactors, 511, 587–588 blast colony forming cell (BL-CFC), 212 blastocyst, 3, formation, 119–121 blastocyst stage, 351 blastomeres, 119, 429 BL-CFC (blast colony forming cell), 212 blood in embryoid bodies, 212 islands, 200, 227 promoting in vitro with embryonic morphogens, 214 transfusion, 572 in zebrafish, 459–461 B lymphocytes, ontogeny of, 208–209 BMP (bone morphogenic pathway), 191, 195, 196, 322 BMPs (bone morphogenetic proteins), 243, 247, 266, 392, 393, 563 protein (BMP4), 46, 455 signaling, 462 bone marrow, 243–245, 584–585 derived cells (BMDCs), 315 ontogeny of, 206 stem cells contribution to gut repopulation after damage, 314–316 stem cells, 114 transplantation, 544, 572 bone marrow-derived hepatocytes, 296–298 bone marrow stromal cells (BMSCs), 584, 586 bone morphogenetic proteins (BMPs), 63, 243, 247, 266, 392, 393, 563 protein (BMP4), 455 signaling, 462 bone morphogenic pathway (BMP), 191, 195, 196, 322 bone regeneration, 246–247 bone repair, 246–247 bottom-up proliferation, 307–308, 324 bottom-up theory, 323 bovine spongiform encephalopathy (BSE), 624 brain, neuronal progenitors in, 179–187 brain-derived neurotrophic factor (BDNF), 181, 486, 489 BrdU (Bromodeoxyuridine) label-retaining cells, 523 British Human Fertilisation and Embryology Authority, 604 Bromodeoxyuridine (BrdU) label-retaining cells, 523 BSE (bovine spongiform encephalopathy), 624 Buddhism, religious considerations for stem cell research, 611 bulge activation hypothesis, 193–194 bulge cells, 189, 191, 192, 193, 194 637 638 burns ulcers, 523 burst-forming units-erythroid (BFU-E), 217 C Caenorhabditis elegans, 253, 318, 381, 435, 438, 461, 464 Canal of Hering (CH), 285, 286 cancer stem cells (CSCs), 469 clinical implications of, 478–479 functional definition, 470–471 future directions, 479 models, 470–471 nonmalignancy, 473 non-tumorigenic cancer cells, 472–473 plasticity of self-renewal, 476–477 prospective isolation, 473–476 signaling pathways in, 477–478 tumors, clonality and heterogeneity in, 469–470 carcinogenesis, 596 carcinogens, 307 cardiac alpha actin promoter, 412 cardiac homeostasis, 529, 530 cardiac ischemia, 236 cardiac progenitor cells, 259, 260, 534–535 cardiac regeneration, 259–263 cardiac stem cell, elusive, 259–260 cardiomyocytes, 259, 315, 362, 421, 507–512, 530, 533, 534, 572, 576 cardiomyocyte transplantation, 507–508, 509 cardiomyogenic differentiation, of ES cells in vitro, 508–509 cartilage injuries, 563 orthopedic applications of stem cells, 563–565 repair of, 247 stimulation techniques, 564 cavitation formation, 119–121 CCD (Cleidocranial dysplasia), 225 CD26, 154–155 CD34, 446–447 CDK inhibitors (CKIs), 83, 86, 87 cDNA microarrays, 449–450, 451 cDNA probe, 449, 451 CEAs (cultured epidermal autografts), 558–559 cell cycle checkpoints, 153–154 cell cycle regulators in adult stem cells, 81 cell cycle kinetics of stem cells in vivo, 81–82 cyclin-dependent kinase inhibitors in stem cell regulation, roles of, 83 CKIs and notch, 86 p21 in stem cell regulation, roles of, 83–84 p27 in stem cell regulation, roles of, 84 and retinoblastoma pathway, 85 TGFb-1 and cyclin-dependent kinase inhibitors, relation between, 85–86 mammalian cell cycle regulation and cyclindependent kinase inhibitors, 82–83 overview, 81 stem cell expansion ex vivo, 82 cell death, 497, 498, 499 cell differentiation in skeleton, 223–226 Index cell fate determination, 438 dominant effectors of, 412 cell fusion and differentiated state hybrid cells and differentiated phenotypes, 105–106 pluripotent cells, hybrids of, 106–107 somatic cell reprogramming, 107–108 stem cell plasticity, 108–109 cell grafting, 433–434 cell lineages, and stem cells in embryonic kidney, 273–282 anatomy of kidney development, 273–276 constituting renal stem cell, 281–282 establishment of additional cell lineages, 279–281 genes that control early kidney development, 276–279 overview, 273 cell migration to primary lymphoid organs, 206–209 cell patterning techniques, 577 cell polarization, 119 cell replacement, using neural stem cells, 490 cell signaling, in hair follicle stem cells, 195–196 cell sorting prospective isolation of hepatocyte progenitors by, 290–291 zebrafish, 463–464 cells responsible for progenitor-dependent regeneration, 287–290 cell substitutes, as cellular replacement parts, 572 cell-surface antigen expression, fluorescenceactivated cell sorting selection, 445 cell-surface embryonic antigens, of laboratory mouse, 423–424 cell therapy, 558 cell type specific “markers”, 430 cell typing via antigens, 423 cellular behavior of endothelial cells, 269 cellular differentiation pathways, 622 cellular memory, epigenetic mechanisms of allelic exclusion, 101–102 ATPase chromatin-remodeling complexes, 94–95 chromatin and transcriptional regulation during development, 89 chromatin-modifying factors, 92–94 and transcriptional factors, to improve nuclear reprogramming for regenerative medicine, 90–92 epigenetic processes, 95–96 genomic imprinting, 100–101 importance of chromatin in heredity, 89–90 overview, 89–90 polycomb and trithorax groups, 98–100 trithrax group (trxG) activation, 100 X-chromosome inactivation, 97 escape from, 97–98 reactivation and imprinted XCI, 98 Xist and heterochromatin assembly, 97 cellular models, of pluripotency, 39 EG cells, 40 embryonal carcinoma (EC) cells, 39 ES cells, 39 human ES and EG cells, 40 cellular replacement parts, 572 central nervous system (CNS), 179, 253 central nervous system (CNS) parenchyma, 485 CFRS (code of federal regulations), 620 CFU-S (colony-forming unit-spleen) assay, 443 cGMPs (current good manufacturing practices), 626 chimera, 433 chondrocytes, 223–226 chondrogenesis, 224, 564 chondrogenic differentiation, 565 chondrogenic stimulating activity (CSA), 243 Christianity, religious considerations for stem cell research, 612–614 chromatin in heredity, 89–90 and molecular basis of, 95 and transcriptional regulation during development, 89 chromatin immunoprecipitation followed by microarray analysis (ChIP-chIP), 454 chromatin-modifying factors, 92–94 coordinate action of, 91–92 DNA methylation, 92–93 histone code, 93–94 and transcriptional factors to improve nuclear reprogramming for regenerative medicine, 90–92 chronic myelogenous leukemia, 476–477 chronic myeloid leukemia, 212 chronic neurodegenerative diseases, 486 CKIs (CDK inhibitors), 83, 85, 86 c-kit ligand (KL), 382, 386 c-kit-positive CPCs, 529, 530 claudin, 149 cleavage cells, 429 Cleidocranial dysplasia (CCD), 225 clonal analysis, 552–553 clonal conversion, 553–554 clonal populations, 309–310 clonal stabilization time, 313 clonal succession, 310–312 clonal types, 553 cloned animals, developmental defects in, 89–90 cloning single-cell clones, 357 clonogenic assay of endothelial cells, 267–268 closed systems, 575 CLP (common lymphoid progenitor), 207–208 CM (conditioned medium), 397, 399–400 CMP (common myeloid progenitor), 207 c-MYC, 29, 30, 196 CNS (central nervous system), 179, 253 CNS (central nervous system) parenchyma, 485 CNS repair, 485–496 Coalition for the Advancement of Medical Research (CAMR), 633 code of federal regulations (CFRs), 620 colonocytes, 308 colony-forming assay, for testing culture conditions, 346–347 colony-forming units-erythroid (CFU-E), 217 colony-forming unit-spleen (CFU-S) assay, 443 colorectal carcinoma, 322, 475 639 Index committed epithelial progenitor cells, 310 common lymphoid progenitor (CLP), 207–208 common myeloid progenitor (CMP), 207 components manufacturing, 624 computer modeling, 324 conception, 601 conditional Genetic Modification, 414 conditioned medium (CM), 397, 399–400 feeder-free culture, 400–401 connective tissue growth factor (CTGF), 225 cord blood (CB), 217 cord blood hematopoietic stem, and progenitor cells, 151–155 characteristics and cryopreservation of, 151 cryopreservation of cord blood, 152 cycling status and responses to growth factors, 151–152 number of cord blood cells required for durable engraftment, 152 cord blood transplantation and banking, 151 advantages and disadvantages of, 151 problems and possible countermeasures, 152–154 homing of stem and progenitor cells, 154 homing, importance of, 154 Sdf1/Cxcl12–Cxcr4 and CD26, in homing of stem cells, 154–155 Cre recombinase, 434 Crohn’s disease, 307, 316 cryopreservation of cord blood, 152 hES cells, 403 of MEFs, 399 crypt-base columnar cells (CBCs), 69 crypt cycle, 312 crypt fission index, 324 crypts, single intestinal stem cells regenerating, 309 CSA (chondrogenic stimulating activity), 243 CTGF (connective tissue growth factor), 225 C-treated PMEF plates, mitomycin, 369 cultivated human islet buds (CHIBs), 517 culture conditions colony-forming assay for testing, 346–347 culture, condition of, 8–9 cultured epidermal autografts (CEAs), 525, 558–559 culture systems, critical components of original, 392–393 Cuono’s procedure, 556 current good manufacturing practices (cGMPs), 626 cyclin-dependent kinase inhibitors (CDK inhibitors), 82–83 in stem cell regulation, 83–85 and transforming growth factor b-1, relation between, 85–86 cycling status, of cord blood hematopoietic stem, 151–152 cyst progenitor cells, 62 cytochrome c oxidase (COX), 314 cytokeratins, 316 cytokine-receptor binding, on ES cells, 41 cytokine receptor function in vivo, 41 dimerization, 41 expression of, 41 Gp130 and LIFR function, in diapause and ES cells, 41–42 structure, 41 cytokines, 40–41, 153, 526, 537, 540 D DA (dopamine) neurons, 492 Danio rerio, 459 see also zebrafish data analysis, 452 defined media, 401–405 delayed blastocysts, 348–349 delivery of stem cells, 586–588 ex vivo reconstructions, 587–588 reconstruction of the skeletal tissues, 586–587 skeletal and cardiac muscle, regeneration of, 587 demyelination, 177 dental pulp stem cells (DPSCs), 587 derivation of stem cell lines, 624–625 dermal papilla (DP), 190, 191, 193–194 developmental view of life’s beginnings, 601 DGCR8, 56 diabetes, 520, 523 Diabetes Research and Education Act, 632 diabetogenic insult, 303 Dicer (endonuclease) processing, 414 Dicer, 55 differentiation, 189 in early development, 119–129 from implantation to gastrulation, 125–129 overview, 119 preimplantation development, 119–125 of ES cells, 575 of human embryonic stem cells, 392–394 and microarray analysis of stem cells, 449–456 prevention of, 78 differentiation antigen, 423 differentiation inhibiting activity (DIA), 40 differentiation systems, primate ES cells, 362 dimethyl sulfoxide (DMSO) cryopreservation, 384 disease models in zebrafish, 464 diseases, 177 distant stem cells, mobilization and recruitment of, 589 DMD (Duchenne’s muscular dystrophy), 250, 543, 544 DMSO (dimethyl sulfoxide) cryopreservation, 384 DNA demethylation, 440 DNA methylation, 92–93, 339–340 donor eligibility, 622–624 donor issues, 605–606 dopamine (DA) neurons, 492 dopaminergic neurons, midbrain, 172 DP (dermal papilla), 190, 191, 193–194 Drosophila, 225, 253, 278, 317, 438, 461, 464 germline, 61 coordinate control of germline stem cell and somatic stem cell, 64 germline stem cell niche in Drosophila ovary, 62–63 germline stem cell niche in Drosophila testis, 63–64 overview, 61 structural components of niche, 64–65 Drosophila melanogaster, 63, 255, 477 Duchenne’s muscular dystrophy (DMD), 250, 543, 544 duct cells, 517–518 ducts, 301–302 dyes, 430 dysfunctional neurons, 492–494 dystrophic muscle, 547–548 dystrophin, 250, 544, 546 E EBD (human embryonic body-derived) cells, 381, 387–390 Eberwine’s protocol, 449 EBs, see embryoid bodies (EBs) EC cells, see embryonal carcinoma (EC) cells EC–ES phenotype, 424 ECFC (epithelial colony forming cells), 290, 291 ectoderm, 157 ectopic transplantation, 348 edging effect, 526 EDL (extensor digitorum longus) muscle, 250 EG cells, see embryonic germ (EG) cells EGF (epidermal growth factor), 128, 187, 291, 388 EGFP (enhanced green fluorescent protein), 303, 419–420, 434, 507, 508 EKLF (Erythroid Kruppel-like Factor), 200 electroporation, 410, 419 embryogenesis, 190, 304 embryoid bodies (EBs), 212–214, 218, 265, 351, 362, 409, 500, 505, 508, 576 analysis, 387 blood formation in, 212 EB-derived HSC, transformation of, 212 embedding, 387 formation, 387, 508–509 immunohistochemistry, 387 embryoid-body based protocols, 170–171 embryonal carcinoma (EC) cell, 3, 13, 39, 347, 351, 392, 424–425, 439 human, 392, 404 mouse, 423–424 reprogramming somatic cell nuclei with, 107–108 embryonic antigens, cell-surface, 423–424 embryonic bodies (EBs), 381, 384, 387, 388 embryonic carcinoma (EC) cells, 339 embryonic cells, vasculogenic, 227–228 embryonic erythropoiesis, 211 embryonic germ (EG) cells, 6–7, 107–108, 340, 438 derivation, 135 EG cell cultures evaluation of, 386–387 subsequent passage of, 383–385 human, derivation and differentiation of, 381–395 comparison to ES cells, 382 EBD cells, 387–390 human EG cell derivation, 382–387 overview, 381–382 primordial germ cells, 381–382 human EG cell derivation, 382–387 640 embryonic hematopoiesis, 211–212 embryonic induction, 157 embryonic kidney, see cell lineages and stem cells in embryonic kidney embryonic morphogenesis, 302 embryonic stem cell-derived glia, 174 embryonic stem cell-derived neurons, derivation of, 172–174 embryonic stem cells (ESCs), 4, 29, 30, 39, 107–108, 204, 211–214, 224, 265, 292, 339–340, 345, 351, 424–425, 507 vs adult stem cells, 10 comparison to, 382 conclusions about, 516 conditions of culture, 8–9 cytokine-receptor binding on, 6–7 differentiation, 265–266 effector molecules to retain self-renewal, 78 environment, 40–41 ES cell transgenesis, extracellular signals for, 74–76 germline competence, human, 382–394 derivation of stem cell lines, 624–625 homologous recombination in, 417–421 identity, 55 immunological barriers faced by transplanted insulin-producing cells derived from, 516 insulin producing cells derived from, 515 isolation, 347–348 line, 213 line derivation from mouse blastocysts, 355 with low and high levels, 49–50 maintenance, 345–346 method for derivation of, 348–349 monkey, 391 mouse, 391–392 origin and properties of, 7–8 in other species, 2–4 passage culture, 347 in perspective, 13 pluripotency, potential of, as source of insulin-producing cells, 514–516 renewal, 43–44 renewal, new paradigm of, 47 as source of retinal neurons, 186–187 spinal cord injury, 500 susceptibility versus resistance to derivation, testing culture conditions, colony-forming assay for, 346–347 therapies based on, 575–576 in tissue engineering, 571–577 limitations and hurdles, 575–577 principles and perspectives, 571–575 transcriptional regulation for self-renewal, 76–77 transplantation, for spinal cord injury, 500–504 transplanted insulin-producing cells derived from, 516 use of, to treat heart disease, 507–512 Index embryos human, 127–128 benefiting from others’ destruction of, 602–603 cloning, 603–604 creating to destroy, 603 destroying human, 601–602 frozen, 366 late-stage, 355–356 mouse, developmental potency of, 122 preimplantation tetraploid, 433 with no Oct4, 49 encephalomyocarditis, 419 endocytosis, 410 endoderm cells, primitive, 126 endogenous defective gene product, 596 endogenous identifiers, 430–435 endonuclease (Dicer) processing, 414 endothelial cells (EC), 146, 148, 234, 265 cellular behavior of, 269 differentiation, markers for defining intermediate stages during, 266–267 diversification, 268–269 vascular structure formation, 269–270 endothelial-hematopoietic common progenitor cells, 227–228 endothelial progenitor cells (EPCs), 545, 547 endothelial-smooth muscle cell common progenitors, 228 engraftment, 152 enhanced green fluorescent protein (eGFP), 303, 419–420, 434, 507, 508 enterocytes, 308, 321 ENU (ethylnitrosourea), 461 enucleation of erythroid cells, 221–222 enzyme activity-based reporters, 431–432 enzymes, marking with, 430 EPCs (endothelial progenitor cells), 545, 547 epiblast, development of murine inner cell mass to, 126–127 epiblast cells, 340–341 epiblast-like (EPL) cells, epiblast stem cells (EpiSc), epidermal basal cells, 195 epidermal growth factor (EGF), 187, 388 epidermal proliferative unit (EPU), 20, 21 epidermal stem cells, 523–524, 527 epidermal T-cells, 551 epidermis, 189–191 interfollicular, 69 mammalian, 67–69 regeneration of, from adult keratinocyte stem cells, 551–559 indications of CEAs, 558 keratinocyte cultivation, 554–555 keratinocyte stem cell, 552–555 overview, 551 regeneration of epidermis, 556–558 transplantable matrices, 555–556 transplantation of keratinocyte stem cells, 556–558 epigenesis, 437 epigenetic asymmetry, 440 epigenetic changes, 134–135 epigenetic landscape, 437 epigenetic processes, 95–96 epigenetic reprogramming, 441 in germ cells, 439–440 epithelial colony forming cells (ECFC), 290, 291 epithelial hair follicle stem cells, see hair follicle stem cells (HFSCs) epithelial lineages, 309 epithelial stem cell, development of concepts of, 17–25 definition of stem cells, 18–19 generalized scheme, 24–25 hierarchically organized stem cell populations, 19–20 intestinal stem cell system, 22–23 overview, 17 skin stem cells, 20–22 stem cell organization on tongue, 23–24 epithelial tissue, 206–207 epithelia vs stroma, 279–280 ERK, 45 erythrocytes from adult stem cells in vitro, 217–218 from human embryonic stem cells, 218–221 from mouse embryonic stem cells, 218 erythroid cells, enucleation of, 221–222 Erythroid Kruppel-like Factor (EKLF), 200 erythropoiesis, 217 erythropoietin (Epo), 152, 217 ES cell-derived cardiomyocytes, 261 and cardiomyogenic differentiation, 508–509 transplantation and challenges for clinical implementation, 509 donor cell immune rejection, 511–512 donor cell production, overcoming limitations in, 511 graft size, overcoming limitations in, 510–511 ES cell lines, isolation of, 347–348 ES cell niche, 40 ES cell renewal factor (ESRF), 44 ES cells, see embryonic stem cells (ESCs) ES cell self-renewal, 74 effector molecules to retain differentiation, prevention of, 78 stem cell proliferation, maintenance of, 78 extracellular signals for, 74–76 inner cell mass outgrowth, transcription factors involving, 77–78 transcriptional regulation of, 76–77 Escherichia coli, 431 Escort stem cells, 64 Escro Review, 605 ESCs, see embryonic stem cells (ESCs) ES/EG-somatic cell hybrids, reprogramming in, 441 ES-like (ESL) cells, conditions of culture, 8–9 ES cell transgenesis, germline competence, human ESL cell, mouse epiblast cells, origin and properties of, 7–8 pluripotency, susceptibility versus resistance to derivation, 641 Index ethylnitrosourea (ENU), 461 exogenous gene expression, 410–412 exogenous genetic identifiers, marking with, 430–435 exogenous recombinases, 414 expressor transgenic mouse lines, 433 extensor digitorum longus (EDL) muscle, 250 extracellular matrix (ECM), 588 extracellular matrix components, 394 extracellular signals, 74–76 extraembryonic ectoderm (ExE), 137, 141 extraembryonic endoderm development, 143 extraembryonic endoderm lineage, 143–144 extraembryonic endoderm progenitors, 143 extraembryonic lineages, stem cells in, 137–144 extraembryonic endoderm lineage, 143–144 overview, 137 trophoblast lineage, 137–141 TS cell lines, 141–143 extraembryonic tissues, in patterning mouse embryo, 128–129 extrahepatic liver cell progenitors, 291 ex vivo expansion cell cycle checkpoints, asymmetry of division, and self-renewal, 153–154 current knowledge, 153 cytokines and intracellular molecules, implicated in self-renewal of stem cells, 153 self-renewal, implications of, 154 ex vivo gene therapy, 558–559, 591 ex vivo skin cell therapy, 556 ex vivo stem cell expansion, 82 eye and ear, sensory epithelium of, 185 embryonic stem cells, as source of retinal neurons, 186–187 mueller glia, as source of new retinal neurons, 185–186 F F9 antigen, 423, 424 FACS (fluorescence-activated cell sorting), 251, 252, 411, 427, 444–445, 508, 524 facultative liver stem cell, 287 false discovery rate (FDR), 452, 453 familial adenomatous polyposis (FAP), 313, 322, 323–324 FAP (familial adenomatous polyposis), 313, 322, 323–324 fate mapping, 433, 460 FBS, screening of, 368 FDA product, 619–629 control of manufacturing process, general expectations for, 626 critical elements for developing safe stem cell-based therapy, 621–626 manufacturing and characterization issues, pertaining to stem cell products, 622–624 stem cell lines, derivation of, 624–625 stem cell products, testing of, 625–626 overview, 619–620 proof-of-concept, demonstrating, 627 resources to develop recommendations for manufacture and characterization of stem cell-based products, 620–621 code of federal regulations (CFRs), 620 guidance documents, 620 scientific interactions, 620–621 toxicological assessment, 627–628 FDR (false discovery rate), 452, 453 feeder-free culture, 397–406 of HES cells, 359–360 materials for feeder-free hES cell culture, 405–406 using conditioned medium and Matrigel, 397, 399–400 using conditioned medium and Matrigel or Laminin, 400–401 using defined media and Matrigel, 401–405 fertilization, 615 fetal bovine serum, screening of, 368–369 fetal calf serum (FCS), 46 fetal donor cells, 508 fetal hepatoblasts, 294 FGF (fibroblast growth factor), 68, 138–141, 158, 181, 439, 499, 566, 567, 568 FGF-2 (fibroblast growth factor-2), 45, 70, 393–394, 565 FGF-4 (Fibroblast growth factor-4), 45, 235 fibroblast growth factor (FGF), 68, 138–141, 158, 181, 439, 499, 566, 567, 568 fibroblast growth factor-2 (FGF-2), 393–394 fibroblast growth factor-4 (FGF-4), 45, 235 fibroblast growth factor receptor (FGFR2), 45 fibroblasts, 345 fibrochondrocytes, 566 fibrosis, murine models of, 317 first-degree burns, 552, 555 FISH (fluorescence in situ hybridization), 357 fish, zebra, 459–465 flame-pulled thin capillaries, 369 flow cytometry, 426–427, 471 analysis, of surface markers, 404 in cell sorting, 463 Flt3-ligand (FL), 152 fluorescence-activated cell sorting (FACS), 141, 185, 251, 252, 357, 411, 427, 444–445, 471, 508, 524 fluorescent proteins, 432–433 follicle stem cells (FSCs), 64 Forssman antigen, 424 FoxD3, 55 Friedenstein, A.J., 243 F statistic, 452 fusion model of liver cell maintenance, 297 G GABA neurons, 173 Ganglioside antigen, 425 gastrointestinal tract, stem cells in, 307–327 bone marrow stem cells, 314–316 bone morphogenic pathway signaling, 322 epithelial cell lineages originating from common precursor cell, 308–309 gastrointestinal mucosa contains multiple lineages, 308 gastrointestinal neoplasms originate in stem cell populations, 322–326 hedgehog signaling, 322 HOX genes, 322 mouse aggregation chimaeras, 309–310 multiple epithelial cell lineages derived from a single stem cell, 313–314 multiple signaling pathways regulating gastrointestinal development, proliferation, and differentiation, 319 niche maintained by intestinal subepithelial myofibroblasts in the lamina propria, 317–319 Notch signaling, 321–322 overview, 307–308 single intestinal stem cells regenerating whole crypts, 309 somatic mutations in stem cells, 310–312 Wnt/b-catenin signaling pathway maintains the proliferative compartment of intestinal crypts, 319–320 Wnt targets, 320–321 gastrulation, 125, 200, 273, 274 G-CSF (granulocyte colony-stimulating factor), 152, 446, 537 gene addition, 592–593 absence of adverse effects, 596 absence of interference from endogenous defective gene product, 596 genetically corrected stem cells, 594 genetic modification directly in stem cells, 593–594 nonviral integration strategies, 593 physiologically appropriate expression levels, 595–596 synthetic microchromosomes, 593 viral vectors, 592–593 GeneChip, 450, 451 gene expression, 133 exogenous, 410–412 profile, 430 gene ontology, 453 genes importance of during preimplantation mouse development, 123–125 that control early kidney development, 276–279 that determine nephrogenic field, 276–278 that function at time of metanephric induction, 278–279 gene silencing, 412–413 gene targeting, 412–413 advanced methods of, 413–414 in human embryonic stem cells, 412–413 gene therapy, 247, 447, 543, 563, 567, 568, 569 approaches in wound healing, 526–527 ex vivo, 562, 565 in vivo, 562 using neural stem cells, 489 genetically corrected stem cells, 594–595 genetic correction, 544, 548 genetic defects, 592 genetic disease, 593 genetic engineering of human embryonic stem cells, 409–410 of skin grafts, 526 see also tissue engineering genetic labeling, 411–412 642 genetic manipulation in vitro, 409 of human embryonic stem cells, 409–414 genetic modification approaches, 410–414 methods of genetic manipulation, 409–410 overview, 409 methods of, 409–410 genetic modification, 509, 511 approaches, 410–414 in stem cells, 593–594 genetic screens, in zebrafish, 461–462 genetic switches, 434–435 gene trap, 412 genital ridge, germ cells in, 133 epigenetic changes, 134–135 phenotype, 133–134 sex determination, 134 X-chromosome reactivation, 134 genome editing, 593 absence of adverse effects, 596 absence of interference from endogenous defective gene product, 596 genetically corrected stem cells, 594–595 genetic modification directly in stem cells, 594 physiologically appropriate expression levels, 596 genomic imprinting, 100–101 genomic reprogramming, 437–442 germ cells competence, 438 in genital ridge, 133–135 genomic reprogramming in, 437–441 lineage, 131–133 early studies, 131–132 gene expression, 133 lineage determination, time and place of, 132 PGCs, identification of, 131 signaling factors, 132–133 germline competence, germline potential, 349 germline stem cell niche in Drosophila ovary, 62–63 in Drosophila testis, 63–64 germline stem cells (GSCs), 62 GFP (green fluorescent protein), 180, 191, 213, 411, 432–433, 463, 464 glial cell line-derived neurotrophic factor, 66 glial cells, 498 glial characteristics of neural stem cells, 179–180 glial derived neurotrophic factor, 149, 274–275, 278, 486 global cell replacement, using neural stem cells, 490–492 global gene expression patterns, 453, 456 glomerular tuft, cells of, 280–281 glomerulus, 280 glucagon, 515 glucose stimulated insulin secretion (GSIS), 515 glutamate, 181 glutamate neurons, 173 Index Glycogen Synthase Kinase (GSK-3), 45 glycosphingolipid, 424 Gp130 and LIFR function in diapause and ES cells, 41–42 gradualist view of life’s beginnings, 601 grafting, cell and tissue, 433–434 granulocyte colony-stimulating factor (G-CSF), 152, 446, 537 granulocyte colony-stimulating factor receptor (G-CSF-R), 43 granulocyte–macrophage colony-stimulating factor (GM-CSF), 152 granulopoiesis, 206 gray matter, 497 Grb2 functional ablation of, 45 and Gab1 adaptor proteins, 44–45 green fluorescent protein (GFP), 149, 180, 191, 213, 411, 432–433, 463, 464 growth factors b-1, transforming, 85–86 GSIS (glucose stimulated insulin secretion), 515 guidance documents, 620 guidance mechanisms, 133 gut epithelium, 69–70 gynogenetic diploid embryos, 462 H HA (hyaluronan) scaffolds, 247 haematopoietic bone marrow transplantation, 316 hair follicle, 67–69 hair follicle stem cells (HFSCs), 189–196 bulge as residence of, 191–193 cell signaling in, 195–196 models of HFSC activation, 193–194 molecular fingerprint of bulge putative stem cell markers, 194–195 mouse skin organization, 189–191 overview, 189 hair predetermination hypothesis, 194 hanging drop technique, 576 harvesting MEFs, 397, 399 Harvey, William, 437 HBC-3 cells, 292 hCPC (human cardiac progenitor cell), 530–534 heart disease and stem cells, 529–542 use of embryonic stem cells to treat, 507–512 hEBs (human embryoid bodies), 229 hedgehog (Hh) signaling, 322 Hedgehog signaling, 200, 478 hemangioblasts, 203, 204, 205, 206, 209, 218 hemangioblasts, 459 Hemangioblasts/angiohematopoietic cells, 227–228 hematopoiesis, 199–205, 211–214, 246, 443 hematopoietic cell (HPC), 266 hematopoietic stem cells (HSCs), 66, 81, 217, 288–289, 296, 297, 471, 519, 529, 545, 584, 591, 592, 593, 594, 595 blood formation in embryoid bodies, 212 embryonic stem cells and embryonic hematopoiesis, 211–212 isolation and characterization of, 443–447 overview, 211 promoting blood formation in vitro with embryonic morphogens, 214 promoting hematopoietic engraftment with STAT5 and HoxB4, 212–214 transformation of an EB-derived HSC by BCR/ABL, 212 hematopoietic system, 66–67 ontogeny of, 199–209 cell migration to primary lymphoid organs, 206–209 historic perspective, 199 overview, 199 sites of initiation of primitive and definitive hematopoiesis and vasculogenesis, 199–205 stem cell migration to later sites of hematopoiesis, 205–206 hepatectomy, 287 hepatic hematopoiesis, human, 206 hepatic lobule, 285, 286 hepatocarcinoma cell line (HepG2), 171 hepatocyte growth factor (HGF), 235, 287, 291, 308, 566 “hepatocyte-like” cells, 291, 292 hepatocytes, 148, 285–292 cells that produce in, 290–291 as liver repopulating cells, 294 progenitors, prospective isolation of by cell sorting, 290–291 heregulin, 393–394 hESCs, see human embryonic stem cells (hESCs) heterochromatin, 430 HGF (hepatocyte growth factor), 235, 287, 291, 308, 566 hierarchically organized stem cell populations, 19–20 high-mobility-group (HMG) family, 224 high-proliferative potential progenitors (HPPs), 200 Hinduism, religious considerations for stem cell research, 611 histone code, 93–94 hit and run methods, 414 HLA (human leukocyte antigen), 563 HMG (high-mobility-group) family, 224 holoclones, 524, 553–554 homing of stem and progenitor cells, 154–155 homologous recombination, 413, 417–421 homozygosity in mutant alleles, 413 hopscotch (hop) gene, 63 HoxB4, 212–213 HOX genes, 322 HPC (hematopoietic cell), 266 hPLAP (human placental alkaline phosphatase), 432, 434 HPPs (high-proliferative potential progenitors), 200 HPRT (hypoxanthine guanine phosphorybosyl transferase gene), 413, 417–419 hrbFGF (human recombinant basic fibroblast growth factor), 386 643 Index HSCs, see hematopoietic stem cells human cardiac progenitor cell (hCPC), 530–534 human chorionic gonadropin (hCG), 51 human embryoid bodies (hEBs), 229 human embryonal carcinoma (EC) cells, 392, 404, 424–425 human embryonic body-derived (EBD) cells, 381, 387–390 human embryonic germ cells, derivation and differentiation of, 381–395 comparison to ES cells, 382 EBD cells, 387–390 human EG cell derivation, 382–387 overview, 381–382 primordial germ cells, 381–382 human embryonic stem cell lines, 353–360, 365–366 human embryonic stem cells (hESCs), 157, 351, 392–394, 514, 571 adaptation of to trypsin, 373–376 approaches for derivation and maintenance of, 365–373 derivation of hES cells, 371 freezing hES cells, 376–377 hES cell quality control, 378 maintenance of established hES cell cultures, 372–373 mechanical passaging of hES cell colonies, 369–378 overview, 365 preparing and screening reagents, 366–369 preparing PMEF feeders, 369 setting up lab, 365–366 thawing hES cells, 377–378 cell basal medium, 367 cell culture feeder-free, 400–401, 405–406 methods for, 358–360 cell derivation medium, 367 cell growth medium, 367 cell lines, techniques for derivation of, 353, 355–357 cell research, postponing, 602 cell subclones, derivation of, 357–358 characterization of feeder-free hESCs, 404 cryopreserving, 403 culture of, 400–401 cultures, maintenance of established, 372–373 derivation of, 371 derivation of stem cell lines, 624–625 differentiation of, 405 erythrocytes generated from, 218–221 ethical guidelines for research, 605–606 feeder-free culture of, 359–360, 400–401 freezing, 376–377 homologous recombination in, 417–421 and induced pluripotent stem cells, 270 on Matrigel or Laminin, 400–401 mechanical passaging of hES cell colonies, 369–378 neural differentiation of, 175 propagation methodology of, 393 quality control, 378 self-renewal of, 79 as source for vascular progenitors, 229–231 thawing, 377–378, 403–404 human embryos benefiting from others’ destruction of, 602–603 cloning, 603–604 creating to destroy, 603 destroying, 601–602 frozen, 366 induced pluripotent stem cell research, 604–605 human ESL cell, human feeders, 358–359 human hepatic hematopoiesis, 206 human intestinal crypts, 313–314 human leukocyte antigen (HLA), 563 human placental alkaline phosphatase (hPLAP), 432, 434 human pluripotent stem cells, 391–395 characterization cytogenetic analysis, 342 differentiation, 342 markers, 341–342 embryonic cell sources, 339–341 reprogramming, 341 see also pluripotent stem cells human recombinant basic fibroblast growth factor (hrbFGF), 386 humans isolation of hematopoietic stem cells from, 466–467 myocardial regeneration in, 541–542 Oct4 expression in, 49 human vascular progenitor cells, 227–231 Huntington’s disease (HD), 176–177, 485, 489 hyaluronan (HA) scaffolds, 247 hybrid cells, 105–106 hypertrophic chondrocytes, 206 hypoxanthine guanine phosphorybosyl transferase gene (HPRT), 413, 417–419 hypoxia–ischemia, 492, 573 I ICH (International Conference on Harmonization), 620 ICM (inner cell mass), see inner cell mass (ICM) Ihh (Indian hedgehog) signaling, 214, 224 immunocytochemical staining, 387 immunocytochemistry, of surface markers, 404–405 imprinted gene clusters, similarities and differences among, 101 IND (Investigational New Drug application), 620, 621, 623, 624 Indian hedgehog (Ihh) signaling, 214, 224 indirect immunofluorescence, 426–427 induced pluripotent stem (iPS) cells, 10, 29, 14, 270, 341, 351–352, 500, 514, 516 derivation, 331 human foreskin fibroblasts, reprogramming, 335–337 materials, 331–332 transgene-expressing lentivirus preparation, 332–335 see also pluripotent stem cells vs ES cells, 57–58 infection, genetic manipulation of human embryonic stem cells, 410 INL (inner nuclear layer), 186, 187 inner cell mass (ICM), 39, 137, 352, 355–356, 357, 423, 459, 460 dispersion, 371–372 outgrowth, 367, 370 transcription factors involving, 77–78 inner nuclear layer (INL), 186, 187 in silico analysis, 454 in situ hybridization, 430, 454, 501 in situ immunofluorescence, for surface antigens, 427 insulin, 513–520 insulin-like growth factor (IGF), 181, 388, 393–394, 539 insulin-like growth factor (IGF-1), 187 insulin-producing cells, derived from stem cells for diabetes conclusion on adult sources of new islet cells, 520 defining b-cells, stem cells, and progenitor cells, 513–514 need for insulin-producing cells, 513 potential of adult stem/progenitor cells as source of insulin-producing cells, 516–519 potential of embryonic stem cells as source of insulin-producing cells, 514–516 transdifferentiation of non-islet cells to islet cells, 519–520 integration strategies, nonviral, 593 interfollicular epidermis, 69 interleukin (IL)-3, 152 intermediate mesoderm, 273–282 internal ribosomal entry site (IRES), 419 International Conference on Harmonization (ICH), 620 International Society for Stem Cell Research (ISSCR), 33, 35 interstitial cells of Cajal, 308 intestinal crypts, 20, 308, 309–310, 313–314, 317, 319–320, 321–322 intestinal stem cell community, 307 intestinal stem cells, 22–23 regenerate whole crypts containing all epithelial lineages, 309 transcription factors defining, 321 intestinal subepithelial myofibroblasts (ISEMFs), 308, 315, 317–319 intraembryonic hematopoiesis, 199, 201, 202 intrinsic determinants, of pluripotency, 48 investigational New Drug application (IND), 620, 623, 624 in vitro colony-forming assays, 446 in vitro differentiation, 435 assays, 433 of embryonic stem cells, 573 in vitro fertilization (IVF), 357, 500, 610, 613, 602, 603, 605 in vitro mobilization, 539 in vitro oocyte generation, 506 644 in vitro regeneration of keratinocytes, 524 in vivo, adult neurogenesis, 180–182 in vivo, cytokine receptor function, 41 in vivo, stem cells, 81–82 in vivo B–A–D relationship, 515, 516 in vivo transduction of hepatocytes, 520 iPS cell, see induced pluripotent stem (iPS) cells IRES (internal ribosomal entry site), 419 ISEMFs (intestinal subepithelial myofibroblasts), 308, 315, 317 Islam, religious considerations for stem cell research, 611–612 islet cells adult sources of new, 520 of Langerhans, 300 non-b-cells, 515, 520 precursor, 518–519 transdifferentiation of non-islet cells to isogenic DNA, 421 IVF (in vitro fertilization), 357, 500, 602, 603, 605, 610, 613 J Janus Kinase-Signal Transducer and Activator of Transcription (JAK-STAT) pathway, 63 JDRF (Juvenile Diabetes Research Foundation), 632, 635, 636 JEB (junctional epidermolysis bullosa), 558 Judaism, religious considerations for stem cell research, 612 junctional epidermolysis bullosa (JEB), 558 Juvenile Diabetes Research Foundation (JDRF), 632, 635, 636 K K cells, 520 keratinocyte growth factor (KGF), 295, 308 keratinocyte lifespan, 555 keratinocytes, 189, 192, 195, 196, 524, 527 keratinocyte stem cells (KSCs), 524, 552–555 adult, regeneration of epidermis from, 551–559 indications of cultured epidermal autografts (CEAs), 558 keratinocyte cultivation, 554–555 keratinocyte stem cell, 552–555 overview, 551 regeneration of epidermis, 556–558 transplantable matrices, 555–556 transplantation of keratinocyte stem cells, 556–558 KGF (keratinocyte growth factor), 295, 308 kidney development anatomy of, 273–276 genes that control early, 276–279 kinase inhibitors, cyclin-dependent, 82–83 in stem cell regulation, 83–85 and transforming growth factor b-1, relation between, 85–86 Kit ligand (KL), 439 KL (c-kit ligand), 382, 386, 439 KL (Kit ligand), 439 Klf4, 29, 30, 77 Index knockout serum replacement, screening of, 368–369 Knockout Serum Replacer, 393, 394 KSCs, see keratinocyte stem cells (KSCs) Kupffer cells, 285 L labeling, genetic, 411–412 label-retaining cells (LRCs), 191–193, 194, 195 lacZ gene, 431–433, 438, 568 Lamina Propria, 317–319 laminin feeder-free culture, 400–401 passage of hES cells on, 400–401 preparation of laminin-coated plates, 400 Langendorff apparatus, 507 Langerhans cells, 551, 557 “late stage” embryos, 355–356 left anterior descendant (LAD), 236 lentiviral vectors, 388, 409 Lesch-Nyhan syndrome, 413, 421 leukemia inhibitory factor (LIF), 345, 358, 361, 514, 265, 367, 382, 386, 391–392, 439 leukemia-initiating cells, prospective isolation of, 473–474 LHX2, 190, 195, 196 LIF (leukemia inhibitory factor), 40, 43, 45, 265, 345, 358, 361, 367, 382, 386, 391–392, 514 LIFR function and gp130, in diapause and ES cells, 41–42 Lin28, 30, 331, 334 lineage determination, time and place of, 132 lineage marking, 429–435 lineage selection, 174–175 lineage-tracing, 69, 192, 200, 205, 300, 517 liver adult mammalian liver, organization and functions of, 285 hematopoiesis, ontogeny of, 205–206 immortal liver progenitor cell lines, 292–298 to pancreas, 112–113 regeneration, 287 repopulation by non-hepatocytes, 294–295 repopulation with bone marrow-derived progenitors, 295–298 source of insulin-producing cells, 519–520 stem cells, 286–292 transplantable liver repopulating cells, 293–294 lobular zonation, 286 local and distant endogenous stem cells, activation of, 589 distant stem cells, mobilization and recruitment of, 589 local cells, 589 local cells, 589 Lou Gehrig’s disease, 497 LRCs (label-retaining cells), 191–193, 194, 195 L-type pyruvate kinase promoter, 520 lymphocytes, 423 lymphoid organs, 199, 206–209 lymphopoiesis, 206 M macrophage, 201–202 macrophage colony stimulating factor (MCSF), 218, 266 macrophage inhibitory protein-1a (MIP-1a), 82 magnetic selection techniques, 444–445 major histocompatibility complex (MHC), 107, 623, 625 mammalian B cell ontogeny, 208–209 mammalian cell cycle regulation, 82–83 mammalian epidermis, 67–69 mammalian liver, 285 mammalian PcG complexes in development and disease, 99–100 mammalian testis, 65–66 mammalian tissues, 65 gut epithelium, 69–70 hematopoietic system, 66–67 mammalian epidermis, 67–69 mammalian testis, 65–66 neural stem cells, 70 overview, 65 mammals stem cell model for specification of germ cells in, 438–439 MAPCs, see multipotent adult progenitor cell (MAPC) markers, 430–431 marrow hematopoiesis, 206 regeneration, 247 stem cells, 237 Marshall R Urist, 243 maternal vs embryonic factors, 128 Math1 signaling pathway, 321 Matrigel, 401–405 culture of hESCs on, 400–401 passage of hES cells on, 400–401 preparation of, 400 MBP (myelin basic protein), 489 MCL (medial collateral ligament) injuries, 567 medial collateral ligament (MCL) injuries, 567 media recipes, preparing and screening reagents, 367 MEF, see mice, mouse embryonic fibroblasts (MEF) meniscal allograft transplantation, 566 meniscus, orthopedic applications of stem cells, 565–566 Merkel cells, 551, 557 meroclone, 553, 554 mesangial cell, 276 mESCs, see mice, mouse embryonic stem cells (mESCs) mesencephalon, 493 mesenchymal stem cells (MSCs), 233, 243–248, 291, 295–296, 297, 545, 561–569, 584, 591, 594 mesenchymal tissue, 206–207 mesengenesis, 246 mesengenic process, 244–245 mesoan-gioblasts, 252 mesoangioblasts, 546 mesoderm, 200, 201, 202, 203 metabolic zonation, 285 645 Index metanephric induction, genes that function at time of, 278–279 metaplasia, 111 MHC (major histocompatibility complex), 623, 625 mice aggregation chimeras axis specification during pre-implantation in, 121–122 cell-surface embryonic antigens of, 423–424 embryo developmental potency of, 122 extraembryonic tissues in patterning, 128–129 genes important during preimplantation development, 123–125 genome, 417 hematopoietic stem cells, methods for enrichment, 444–446 isolation of hematopoietic stem cells from, 443–446 models of human disease, 417 mouse aggregation chimaeras, 309–310 mouse embryonic fibroblasts (MEF) conditioned medium (CM) from, 397, 399 cryopreserving, 399 harvesting, 397, 399 irradiating and plating, 399–400 thawing and maintaining, 399 use of, for preparing conditioned media, 397 mouse embryonic stem cells (mESCs), 368, 386, 389, 391–392 neural differentiation of, 170–175 potential of embryonic stem cells as source of insulin-producing cells, 514–516 mouse skin organization, HFSCs, 189–191 Oct4 expression in, 48–49 primordial germ cells in, 131–135 skin organization, HFSCs, 189–191 transgenic mouse model, 466 microarray analysis of stem cells and differentiation, 449–456 array-based comparative genomic hybridization (aCGH), 454 chromatin immunoprecipitation followed by microarray analysis (ChIP-chIP), 454 data analysis, 452 differentiation, 455 experimental design, 451–452 gene module analysis, 453 identification of stemness, 454–455 microarray experiments, 454 microarray technology, 449–451 MicroRNA arrays, 454 overview, 449 post data analysis, 453 regulatory networks, 453–454 stem cell niches, 455–456 microarray technology, 449–451 microchromosomes, synthetic, 593 microglial ontogeny, 201–202 Micro-RNAs, role of, 55–56, 454 DGCR8, 56 dicer, 55 REST and miR-21, 56 midbrain dopaminergic neurons, 172 migration, primordial germ cells, 133 mitomycin C, 367, 369 mitotic spindle assembly checkpoint (MSAC), 154 MNs (motor neurons), 173, 497 models of human disease cellular, 409–414 in vitro, 421 mouse, 417 modification approaches, genetic, 410–414 molecular basis, 95 molecular mechanisms for retention of embryonic stem cell selfrenewal, 74–79 effector molecules, 78 extracellular signals for embryonic stem cell self-renewal, 74–76 overview, 73 transcriptional regulation of, 76–77 transcription factors involving inner cell mass outgrowth, 77–78 monkey embryonic stem cells, 391 monoclonal antibodies, 244 monoclonal conversion, 309, 314 monocyte chemoattractant protein-1 (MCP)-1, 236 “monophenotypic” crypts, 311 moral realism, 611, 614 motoneuron disorders, 177 motor neurons (MNs), 173, 497, 499, 501 mouse, see mice mouse embryonic stem cells (mESCs), 217, 345, 351, 358, 360–362, 410, 417 erythrocytes generated from, 218 potential of embryonic stem cells as source of insulin-producing cells, 516–519 mouse epiblast cells, mouth-controlled suction device, 369 MPTP (1-methyl-4-phenyl-1,2,3,6tetrahydropyridine), 492 MRFs (muscle regulatory factors), 254 MSCs (mesenchymal stem cells), 243–248, 285–286, 297, 545, 561–569, 591, 594 mTesf1, 394 mucosa, gastrointestinal, 308 mueller glia (MG) as source of new retinal neurons, 185–186 multiple sclerosis, 494 multipotency, 246, 259, 351, 552, 558 multipotent adult progenitor cell (MAPC), 49, 233, 291–292, 545–546, 584 with greater differentiation potential, 237, 238 in ischemia models, 235 cardiac ischemia, 236 peripheral vascular disease, 235–236 stroke, 236 in vitro differentiation potential of, 234–235 in vivo engraftment, 235 isolation, 233–234 phenotypic characterization, 233–234 possible mechanisms, 237, 239 systemic transplantation of, 236–237 chimera formation, 237 multipotent stem cells neural, 488 murine embryonic stem cells, 345–349, 500 murine inner cell mass, 126–127 murine models of fibrosis, 317 murine trophectoderm, 126 muscle-derived stem cells (MDSC), 252 muscle fiber degeneration, 543 muscle regeneration, 247 muscle regulatory factors (MRFs), 254 muscle stem cell (MuSC), 249, 250 muscular dystrophy stem cells for treatment of, 543–548 cellular environment of dystrophic muscle, 547–548 myoblast transplantation, reasons for failure and new perspectives, 544 myogenic stem cells in bone marrow and bone marrow transplantation, 544–547 overview, 543 musculoskeletal injuries, 561 mutant alleles, homozygosity in, 413 Myc (myelocytomatosis oncogene), 77 myelin, 499 myelin basic protein (MBP), 489 myelocytomatosis oncogene (Myc), 77 myoblasts, 251 myoblast transplantation, 544 myocardial damage, repair of by nonresident primitive cells, 535–537 by resident primitive cells, 537–541 myocardial hypertrophy, 529 myocardial regeneration, 541–542 myocardium, 259, 260, 530, 533, 537, 540 myocyte death, 529, 541 myocytes, 148 myofibers, 249, 259 myofiber sarcolemma, 249 myogenic cells, 544 myogenic markers, 547 myogenic progenitors, 543 myogenic stem cells in bone marrow and bone marrow transplantation, 544–547 from embryonic stem cells and inducible pluripotent stem cells, 546 N Nanog, 14, 30, 53–55, 77 National Bioethics Advisory Committee, 611 National Research Council, 602, 605 Natural Institutes of Health (NIH), 179 neoangiogenesis, 265 neocartilage, 564 neocortex, 495 neogenesis, 301 neovascularization, 505 nephrogenic field, genes that determine, 276–278 nephropathy, 513 nerve growth factor (NGF), 486 646 nervous system, 169–177 developmental perspective, 176 human and nonhuman primate ES cells, neural differentiation of, 175 mouse embryonic stem cells, neural differentiation of, 170 embryonic stem cell-derived glia, 174 embryonic stem cell-derived neurons, derivation of, 172–174 lineage selection, 174–175 neural induction, 170–172 neural development, 169–170 neural stem cells, 170 overview, 169 therapeutic perspectives, 176 demyelination, 177 Huntington’s disease, 176–177 Parkinson’s disease, 176 spinal cord injury and motoneuron disorders, 177 stroke, 177 neural crest differentiation, 174 neural development, 169–170 neural differentiation, 501 by default, 172 of human and nonhuman primate ES cells, 175 of mouse embryonic stem cells, 170 embryonic stem cell-derived glia, 174 embryonic stem cell-derived neurons, derivation of, 172–174 lineage selection, 174–175 neural induction, 170–172 neural induction, 157–159, 170–172 neural patterning, 160–164 and neurogenesis control, potential links between, 164 neural stem cells (NSCs), 58, 70, 170, 235, 494–496 for CNS repair cell replacement using, 490 displaying inherent mechanism for rescuing dysfunctional neurons, 492–494 gene therapy using, 489 global cell replacement using, 490–492 as glue that holding multiple therapies together, 494 therapeutic potential of, 485–489 glial characteristics of, 179–180 transplantation, 491 neural subtypes, 173–174 neural tissue, and embryonic induction, 157 neural transplantation, 505 neuroepithelial cells (NECs), 157 neurofilament (NF) expression, 502, 503 neurogenesis, 505 adult neurogenesis in vivo, 180–182 control, 164 in vertebrate embryo, 157–166 embryonic induction and establishment of neural tissue, 157 negative regulators of proneural activity, 164–166 neural induction, molecular bases of, 157–159 neural patterning, 160–164 Index neurogenesis to gliogenesis, switch from, 166 neuronal differentiation by sox proteins, regulation of, 166 overview, 157 potential links between neural patterning and neurogenesis control, 164 proneural cascade, 164 proneural gene cascade, 161–164 proneural gene expression, 164 proneural target genes during neuronal differentiation, divergence of, 166 regulation of neuronal differentiation by REST/NRSF, 166 neurogenin3, 300, 304 neuronal, 173–174 neuronal cells, 148 neuronal degeneration, 488 neuronal differentiation by Sox proteins, regulation of, 166 neuronal progenitors, in adult brain, 179–187 adult central nervous system, stem cells in, 179 in vivo, adult neurogenesis, 180–182 adrenal steroids, 182 fibroblast growth factor, 181 glutamate, 181 insulin-like growth factor (IGF), 181 neurotrophins, 181 ovarian steroids, 182 serotonin, 181–182 neural stem cells, glial characteristics of, 179–180 astroglia, 180 radial glia, 179–180 neuropathy, 513 neurotrophin-3 (NT-3), 181 neurotrophins, 181, 505 NF (neurofilament) expression, 502, 503 NFATc1, 196 NGF (nerve growth factor), 486 “niche succession”, 314 Nodal, 394 NOD–SCID (non-obese diabetic–severe combined immunodeficiency), 152, 154, 446 non-duct cells, 518 non-hepatocytes, liver repopulation by, 294–295 nonhuman primate ES cells, neural differentiation of, 175 non-islet cells, 519–520 non-obese diabetic (NOD) strain, 4, non-obese diabetic–severe combined immunodeficiency (NOD–SCID), 152, 154, 446 non-tumorigenic cancer cells, 472–473, 479 nonviral integration strategies, 593 non-b-cells, engineering to produce insulin, 520 notch, 86 Notch-Delta signaling pathway, 307 Notch pathway, 300 Notch signaling, 165, 207, 321–322 Novocell Inc., 514–515 nuclear reprogramming for regenerative medicine chromatin-modifying factors and and transcriptional factors to improve, 90–92 nuclear transplantation, 441 nucleus-to-cytoplasm ratio, 353 Nurr transcription factor, 575 O Oct3/4, 76 Oct4, 14, 29, 30, 48, 341, 455 activity in assays, 49–50 expression, 48–49 regulation of, 50–51 intranuclear transcription factor, 404 and Sox2, 52 target genes, 51 Oct4 EGFP/neo knockin, 419–420 Oct4 FoxD3 Nanog regulatory loop, 55 Oct4-GFP reporter gene, 441 oligodendrocytes, 486, 490, 494, 497–506 oligonucleotide arrays, 450–451 oligonucleotides, 450–451 oliodendrocyte precursors (OPCs), 166 oliogodendrocytes, 174 Oncostatin M, 205 ONL (outer nuclear layer), 186, 187 oocytes, genomic reprogramming in, 339–440 open systems, 572–575 organ donation, 571 ORS (outer root sheath) of epidermis, 189, 190, 191, 192, 194, 195 orthopedic applications of stem cells, 561–569 bone, 562–563 cartilage, 563–565 ligaments and tendons, 566–568 meniscus, 565–566 overview, 561–562 spine, 568–569 Osiris Therapeutics Inc (OTI), 246 ossification, 223–224 osteoarthritis, 563–564 osteoblast differentiation, 225–226 osteoblasts, 223–226, 243, 244 osteocytes, 148 OTI (Osiris Therapeutics Inc), 246 outer nuclear layer (ONL), 186, 187 outer root sheath (ORS) of the epidermis, 190, 191, 192, 194, 195 OV6, 288 oval cells, 287–290, 294–295 ovarian steroids, 182 ovulation induction, 606 Owen, Maureen, 243 P p21, in stem cell regulation, 83–84 p27, in stem cell regulation, 84 p53 and Nanog, 54 pancreas embryonic development of, 300–301 to liver, 112 non-duct cell, 518 transplants, 513 pancreatectomy, 303 pancreatic acinar cell transdifferentiation, 519 pancreatic and islet differentiation, 514 pancreatic development, 514 pancreatic liver stem cell, 295 pancreatic phenotype, 303–304 647 Index pancreatic progenitors, 295, 299–305 pancreatic stem cells, 299–305 definition of stem cells and of progenitor cells, 299c forcing other tissues to adopt pancreatic phenotype, 303–304 in vitro studies, 304–305 overview, 299 progenitor cells in adult pancreas, 301–303 self-renewing, 299 pancreatic transcription factors Paneth cells, 23, 70, 318, 321 paraclone, 553–554 parathyroid hormone-related protein (PTHrP), 143 parental genomes, maternal inheritance and reprogramming of, 440 parietal endoderm (PE), 143 Parkinson’s disease (PD), 176, 485, 489, 492, 606, 623 parthenogenic activation, 500 partial hepatectomy, cells giving rise to regeneration after, 287 passive exogenous genetic markers, 430–431 Pax3, 253–254 Pax7, 253–254 Pax genes, 253–254 PcG complexes, 98–99 PCR, see polymerase chain reaction (PCR) PDGF (platelet-derived growth factor), 392, 394, 577 PDGF-BB (platelet-derived growth factor BB), 231 PDGFR (platelet-derived growth factor receptor), 281 PdXl, 304 Pdxl-VP16, 304 peripheral blood (PB), 217 peripheral vascular disease, 235–236 PEV (position-effect variegation), 95–97 PGCs, see primordial germ cells (PGCs) phenotypes, 133–134 differentiated, 105–106 how cells change, 111–116 Barrett’s metaplasia, 113–114 bone marrow-derived stem cells, 114 changing cell’s phenotype experimentally, 115–116 de-differentiation as prerequisite for transdifferentiation, 114–115 liver to pancreas, 112–113 metaplasia and transdifferentiation, definitions and theoretical implications, 111 overview, 111 pancreas to liver, 112 regeneration, 114 transdifferentiation why study, 111 pancreatic, 303–304 phosphoinositide 3-kinases (PI3K), 46, 54 phosphorylate phosphatidylinositol-3, 4diphosphate (PIP2), 46 photoreceptor (PR) cells, 185 PHS Act (Public Health Service Act), 620 PI3K/AKT signaling pathway, 46–47 PICM-19 cells, 292 plasmanate, screening of, 368–369 plasticity, 245, 584 platelet-derived growth factor (PDGF), 392, 394, 577 platelet-derived growth factor BB (PDGF-BB), 231, 236 platelet-derived growth factor receptor (PDGFR), 281 platelet-derived growth factor a receptor (PDGFaR), 51 pluripotency, 8, 347–348, 378, 382, 391, 395, 438, 441, 514, 561 molecular bases of, 39 BMP4, 46 cellular models, 39–40 cytokine-receptor binding on ES cells, 41–42 cytokines and pluripotency, 40–41 embryonic stem cell renewal, new paradigm of, 47 ES cell identity, core transcriptional regulatory circuitry controlling, 55 FoxD3, 53 intrinsic determinants of, 48 Micro-RNAs, role of, 55–56 Nanog, 53–55 Oct4 activity in assays, 49–50 Oct4 expression, 48–49, 50–51 Oct4 key transcription in, 48 Oct4 target genes, 51 PI3K/AKT signaling pathway, 46–47 signal transduction, 42 somatic cells to pluripotent state, reprogramming of, 57–58 Sox2, 51–53 STATs, 42–45 stem cell identity, chromatin status defining, 56–57 TGFb signaling pathway, 45–46 Wnt signaling, 45 pluripotent stem cells, 3, 270, 339, 391–395 embryonic germ (EG) cells, 6–7 ES and ES-like cells, biology of conditions of culture, 8–9 ES cell transgenesis, germline competence, human ES-like cell, origin and properties of, 7–8 pluripotency, susceptibility vs resistance to derivation, ES-like (ESL) cells in other species, mouse epiblast cells, recent findings on, future challenges, human characteristics, 339–341 characterization, 341–342 hybrids of, 106–107 self-renewal of, 73–74 stem cell therapy embryonic vs adult stem cells, 10 potential hurdles, 9–10 therapeutic cloning, 10 terminology, see also induced pluripotent stem (iPS) cells PMEF, see primary mouse embryo fibroblast (PMEF) polycomb and trithorax groups, 98–100 mammalian PcG complexes in development and disease, 99–100 PcG complexes, 98–99 polycomb group (PcG)-mediated cellular memory, genetics of, 98 polycomb group (PcG)-mediated cellular memory, genetics of, 98 polymerase chain reaction (PCR), 357 cloning vector, 417 in microarrays, 450 position-effect variegation (PEV), 95–97 post data analysis, 453 postnatal stem cells, in tissue engineering, 583–589 current approaches to, 585 delivery of stem cells, 586–588 ex vivo culture of postnatal stem cells, 585–586 local and distant endogenous stem cells, activation of, 589 reservoirs of, 583 bone marrow, 584–585 plasticity, 584 transdifferentiation, 584 potency of stem cell products, 625–626 potent costimulating cytokines stem cell factor, 152 potential stem cells, 19 preclinical regulatory considerations, 619–626 control of manufacturing process, general expectations for, 626 critical elements for developing safe stem cell-based therapy, 621–626 manufacturing and characterization issues, pertaining to stem cell products, 622–624 stem cell lines, derivation of, 624–625 stem cell products, testing of, 625–626 overview, 619–620 proof-of-concept, demonstrating, 627 resources to develop recommendations for manufacture and characterization of stem cell-based products, 620–621 code of federal regulations (CFRs), 620 guidance documents, 620 scientific interactions, 620–621 toxicological assessment, 627–628 preclinical testing, 626, 629 precursor cells, 308–309, 513–514 preimplantation development, 119–125 axis specification during preimplantation in mouse, 121–122 blastocyst formation (cavitation), 119–121 cell polarization occurs during compaction, 119 developmental potency of early mouse embryo, 122 genes important during preimplantation mouse development, 123–125 overview, 119 preimplantation embryos, 417 preimplantation genetic diagnosis (PGD), 357 primary mouse embryo fibroblast (PMEF), 367, 369 growth medium, 367 plates, mitomycin C treated, 371 preparation of, 370 preparing feeders, 369 648 primate ES cells isolation, characterization, and maintenance of, 351–362 definition, 352–353 derivation of hES cell subclones, 357–358 differentiation systems, 362 methods for hES cell culture, 358–360 overview, 351–352 primate vs mES cells, 360–362 techniques for derivation of hES cell lines, 353, 355–357 vs mES cells, 360–362 neural differentiation of, 175 primitive ectoderm, 429 primitive endoderm (PrE) lineage, 143 primitive endoderm cells, 126, 429 primordial germ cells (PGCs), 39, 65, 63, 386, 437 growth media components, 386 in mouse and human, 131–135 embryonic germ cells, 135 explanation of, 131 germ cells in genital ridge, 133–135 migration, 133 not stem cells, 131 origin of germ cell lineage, 131–133 overview, 131 procurement issues, 605–606 progenitor cells, 259, 429 in adult pancreas, 301–303 characterization, 445 and cord blood hematopoietic stem, 151–155 defining, 299, 513–514 during embryonic development of pancreas, 300–301 isolation and characterization of, 146 multipotent adult, 545–546 proneural activity, negative regulators of, 164–166 proneural cascade, 164 proneural gene cascade, 161–164 proneural gene expression, 164 proneural target genes during neuronal differentiation, divergence of, 166 proof-of-concept, demonstrating, 627 proteoglycans, 498 proximal enhancer–promoter (PEP), 50 Public Health Service Act (PHS Act), 620 purity of stem cell products, 625–626 putative stem cell markers, 194–195 PW1 Gene, 254 Q QA (quality assurance), 626 quality assurance (QA), 626 questions of justice, 610 Qur’an, 611 R radial glia, 179–180, 185 random gene disruption, 413 random insertion transgenic approach, 433 rat antibodies, unconjugated, 445 RBCs (red blood cells), 200, 217, 371 reactivation and imprinted XCI, 98 recombineering, 412 Index red blood cells (RBCs), 200, 217, 371 erythropoiesis, 217 redundant cytokine functions, 40–41 regional gene therapy, 563 religious beliefs and ethical questions, 610 religious considerations, stem cell research, 609–616 mapping terrain, 609–610 overview, 609 particular traditions, 611–614 roman catholic contributions and 14-day theory, 614–616 remyelination, 499, 505 renal cells, 148–149 renal development, 273 renal epithelial, 274 renal stem cells, 273, 281–282 reprogramming, 341 research, stem cell, 459–465 conduct of, 606 human, privately funded, 602 postponing hES cell research, 602 religious considerations, 609–616 mapping terrain, 609–610 overview, 609 particular traditions, 611–614 roman catholic contributions and 14-day theory, 614–616 therapeutic cloning research, 603–604 transplantation research, 606 reservoirs, of postnatal stem cells, 583 bone marrow, 584–585 plasticity, 584 transdifferentiation, 584 REST and miR-21, 56 REST/NRSF, 166 retinal neurons embryonic stem cells as source of, 186–187 mueller glia as source of, 185–186 retinal progenitor cells (RPCs), 185 retinoblastoma pathway, in stem cell regulation, 85 retinoic acid (RA) treatment, 187 retinopathy, 513 reverse transcriptase polymerase chain reaction (RT-PCR), 149, 213, 252, 388, 454 Reynolds, B.A., 179 rhodamine-123 (Rh-123), 446 RNA interference (RNAi), 95–96, 414 Roman Catholicism, religious considerations for stem cell research, 614–616 Rosa-26 gene trap line, 433 route, 133 RT-PCR (reverse transcriptase polymerase chain reaction), 149, 213, 252, 388, 454 RUNX1, 196 S S1P (sphingosine-1-phosphate) and PDGF, 394 safety, 625–626 assessment, preclinical evaluation supports, 626–628 assurance, control of source materials, 622–624 SAGE, 185 satellite cell microenvironment, 255, 256–257 satellite cell niche, 255 aging, 256 heterogeneity and occupancy, 255–256 satellite cells, 543, 544 extrinsic regulation, 254–257 heterogeneity, 251–252 identification, 249–251 intrinsic regulation, 253–254 self-renewal, 252–253 saxophone (sax), 63 scaffold-based tissue engineering, 573 scaffolding matrix, 561 scale-up of ESCs, in tissue engineering, 576 scarring, 555, 556 scar tissue, 561 SCF (stem cell factor), 40, 537 SCID (severe combined immunodeficiency), 351, 362, 229, 592 screening media components, 367–369 Sdf1/Cxcl12–Cxcr4, 154–155 sebaceous gland (SG), 189, 190, 191, 192, 193, 194, 196 second-degree burns, 552, 555 self-maintenance probability, 18, 19, 21 self-renewal, 189, 252, 260, 514 cord blood stem and progenitor cells, 153–154 epidermal, 551, 553, 558 implications of, 154 organ, 529–530 of satellite cells DNA segregation, 252–253 mitotic spindle orientation, 253 protein segregation, 253 reversion, 253 of stem cells, 471, 472 sensory epithelium, of eye and ear embryonic stem cells, as source of retinal neurons, 186–187 mueller glia, as source of new retinal neurons, 185–186 sequence specificity, of PEV, 95–96 serotonergic neurons, 172–173 serotonin, 181–182 severe combined immunodeficiency (SCID), 229, 351, 362, 592 sex determination, 134 SFEB (serum-free EB) protocol, 171 SG (sebaceous gland), 189, 190, 191, 192, 193, 194, 196 Shh (Sonic hedgehog), 214 SHP-2/ERK signaling, 44–45 signal transduction, 42 single-cell clones, 357–358 siRNA (small interfering RNA), 414 skeletal and cardiac muscle, regeneration of, 587 skeletal muscle stem cells, 249–257 skeletal myoblasts, 507 skeletal stem cell (SSC), 584 skeletal tissues, reconstruction of, 586–587 skeletogenesis, 223–224 skeleton, cell differentiation in, 225–226 skin grafting techniques, 525 skin stem cells, 20–22 see also hair follicle stem cells (HFSCs) skin ulcers, 523–527 SMA (smooth muscle a-actin), 230 small interfering RNA (siRNA), 414 649 Index SMCs (smooth muscle cells), 228–229, 529 SMCs (synthetic microchromosomes), 593 smooth muscle a-actin (SMA), 230 smooth muscle cells (SMCs), 228–229, 235, 529 SN–VTA (substantia nigra–ventral tegmental area), 493 solid tumor cancer stem cell, prospective isolation of, 474–476 somatic cell nuclear transfer (SCNT), 29, 341 somatic cell reprogramming, 29–31, 107–108, 604 somatic cells to pluripotent state reprogramming of, 57–58 somatic mutations, 310–312 somatic nuclear reprogramming, 441 transfer, 500 somatic stem cells, coordinate control of, 64 somatostatin, 515 Sonic hedgehog (Shh), 214 SOPs (standard operating procedures), 626 source controls, 621 Southern blotting, 431 Sox2, 29, 30, 51–53, 76–77 expression, 51–52 function in vivo, 52 and Oct4–Oct4 dimers, 52–53 and Oct4 partnership, 52 sphingosine-1-phosphate (S1P) and PDGF, 394 spinal cord embryonic, 501 injuries, 173, 177, 497–506 ES cells and neural lineage, 500 ES cell transplantation, 500–504, 505 limitations and approaches to repair and redefining goals, 498–499 novel approaches to CNS repair, 505 problem, 497 spinal cord development, 499 spinal cord organization, 497 spontaneous regeneration, 498 toward human trials, 506 spinal muscular atrophy (SMA), 173 spine, 568–569 spleen colonies, 443 marrow, 208 ontogeny of, 206 spontaneous differentiation, 229–230 spontaneous homozygotization, 413 spontaneous regeneration, spinal cord injury, 498 SSEA1 (stage-specific embryonic antigen 1), 423–425 SSEA3 (stage-specific embryonic antigen 3), 423–425 SSEA-4 surface marker, flow cytometry analysis of, 404 stage-specific embryonic antigen (SSEA1), 423–425 stage-specific embryonic antigen (SSEA3), 423–425 standard operating procedures (SOPs), 626 STAT3, 43, 76 ES cell renewal and undifferentiated state, 43–44 independent ES cell renewal, 44 and LIF, 43 STAT5, 212–214 Stat92E, 63 STATs, 42, 63 ES cell renewal, STAT3 and undifferentiated state, 43–44 FGF4 and ERK, 45 functional ablation of Grb2 in embryos and ES cells, 45 Grb2 and Gab1 adaptor proteins, 44–45 LIF and STAT3, 43 regulation, 42 SHP-2-ERK signaling, 44–45 STAT3, 43 independent ES cell renewal, 44 structure, 42 steel factor, 152 stem and progenitor cells, homing of, 154 stem cell-based products, 620–621 critical elements for developing, 621–626 stem cell-based therapies, 619–629 stem cell factor (SCF), 288, 289, 537 stem cell gene therapy, 591–596 gene addition, 592 nonviral integration strategies, 593 synthetic microchromosomes, 593 viral vectors, 592–593 genome editing, 593 overview, 591–592 requirements for successful, 593 absence of adverse effects, 596 absence of interference from endogenous defective gene product, 596 genetically corrected stem cells, 594–595 genetic modification directly in stem cells, 593–594 physiologically appropriate expression levels, 595–596 stem cell identity, chromatin status defining, 56–57 stem cell lines, derivation of, 624–625 stem cell niches, 40, 61, 299, 455–456, 530, 534 in Drosophila germline, 61 coordinate control of germline stem cell and somatic stem cell, 64 germline stem cell niche in Drosophila ovary, 62–64 overview, 61 structural components of niche, 64–65 hypothesis, 61, 311 within mammalian tissues, 65 gut epithelium, 69–70 hematopoietic system, 66–67 mammalian epidermis, 67–69 mammalian testis, 65–66 neural stem cells, 70 overview, 65 overview, 61 stem cell plasticity, 108–109 stem cell products manufacturing and characterization issues pertaining to, 622–624 testing of, 625–626 stem cell progenitors, 619 stem cell proliferation, maintenance of, 78 stem cell research, see research, stem cell stem cells, 18–19 in burns and skin ulcers, 524–526 and progenitor in retina, 185 and regenerating heart, 259–263 clinical translation of, 33 cell processing and manufacturing, 33–34 in animal models, 34 in patients, 34–35 defining, 249, 299, 513–514 differentiation, 471, 472, 628 in embryonic kidney, see cell lineages, and stem cells in embryonic kidney in extraembryonic lineages, 137–144 extraembryonic endoderm lineage, 143–144 overview, 137 trophoblast lineage, 137–141 TS cell lines, 141–143 ex vivo expansion, 82 and heart disease, 529–542 from human exfoliated deciduous teeth (SHED), 587 in vivo, cell cycle kinetics of, 81–82 microarray analysis, see microarray analysis of stem cells and differentiation migration hypothesis, 194, 205–206 primordial germ cells are not, 131 regulation, cyclin-dependent kinase inhibitors in, 83–86 self-renewal, 471, 472 sources for, 609–610 stem cell self-renewal, mechanisms of, 73–79 epigenetic regulation of, 78–79 human embryonic stem cells, self-renewal of, 79 molecular mechanism to retain ES cell selfrenewal, 74 effector molecules to retain, 78 extracellular signals for, 74–76 inner cell mass outgrowth, transcription factors involving, 77–78 transcriptional regulation of, 76–77 pluripotent stem cells, self-renewal of, 73–74 stem cell therapy, 447 embryonic vs adult stem cells, 10 potential hurdles, 9–10 therapeutic cloning, 10 stem cell zone hypothesis, 311, 317 stemness, identification of, 454–455 sterility, lab, 366 STO feeder layer, plating, 386 streaming liver model, 286 stroke, 177, 236 stromal feeder mediated neural induction, 171–172 stroma vs epithelia, 279–280 substantia nigra–ventral tegmental area (SN– VTA), 493 subventricular zone (SVZ), 489 supercoiled plasmid DNA, 410 Suppressor of Hairless (Su(H)), 165 supravital stains, 445–446 surface antigen markers, 423–428 surface antigen phenotype, 423 650 surface antigens, in situ immunofluorescence for, 427 surface markers, 404–405 susceptibility vs resistance to derivation, SVZ (subventricular zone), 489 synthetic microchromosomes (SMCs), 593 T TA (transit-amplifying) cells, 524, 538 tag and exchange methods, 414 targeted integration, 433 Tbx3, 77 T cell receptor (TCR), 207 T-cell-specific factors (Tcfs), 45 TCR (T cell receptor), 207 teeth, reconstruction of, 586–587 TEM (transmission electron microscopy), 249 tendons orthopedic applications of stem cells, 566–568 repair of, 247 teratocarcinomas, 347–348, 423, 473 teratomas, 229, 405 terminology, testing of stem cell products, 625–626 testis, mammalian, 65–66 tetraploid embryos, 433 TGFb (transforming growth factor beta), 158, 280 signaling pathway, 45–46 TGFb-1, 82, 236 thawing hES cells, 377–378, 403–404 MEFs, 399 TH EGFP knockin, 420–421 therapeutic cloning, 10, 603–604 therapies isolating desired cell types for, 575–576 multiple, and neural stem cells, 494 third-degree burns, 552, 555, 556, 557 thrombopoietin (TPO), 152, 153, 204 thymus, ontogeny of, 206–208 tissue engineering, 527, 561–562 embryonic stem cells in, 571–577 limitations and hurdles, 575–577 principles and perspectives, 571–575 postnatal stem cells in, 583 current approaches to, 585–589 reservoirs of, 583–585 uses of mesenchymal stem cells (MSCs), 246–248 tissue grafting, 433–434 tongue, stem cell organization on, 23–24 tongue proliferative unit, 23 top-down proliferation, 307, 323 topographic differentiation of fibroblasts, 456 totipotency, 429, 437, 440 toxicological assessment, 627–628 “traffic light hypothesis”, 194 transcription, 410 transcriptional regulation, 76–77, 89 transdifferentiation, 111, 441, 584 de-differentiation as prerequisite for, 114–115 model of liver cell maintenance, 297 Index of non-islet cells to islet cells, 519–520 pancreas to liver, 303–304 transfection, 409–410, 417 transforming growth factor beta (TGFb), 158, 280 transgenesis, ES cell, transgenic human embryonic stem cell clones, 410 transgenic mice, 196 transgenic mouse lines, expressor, 433 transit-amplifying (TA) cells, 524, 538 transmission electron microscopy (TEM), 249 transplantable liver repopulating cells, 293–294 transplantable matrices, 555–556 transplantations bone marrow, myogenic stem cells in, 544–547 cord blood for advantages and disadvantages of, 151 problems and possible counter measures, 152–154 of keratinocyte stem cells, 556–558 research, 606 zebrafish, 463–464 transplanted insulin-producing cells, 516 trithorax groups (trxG), 99, 100 trophectoderm, 371, 429 trophoblasts, 137–141 trophoblast stem (TS) cell, 137 tropism, in neural stem cells, 486, 487–488 trypsinization, 375–376, 383 TS cell lines, 141–143 tumorigenesis, 308, 324 type I and type II experimental design, in cDNA microarrays, 451–452 U ulcers, burns and skin, 523–528 undifferentiated human embryonic stem cells, 400, 401 Unitarian hypothesis, 309 UV irradiated sperm, 461 V Van Waardenburg disease, 357 vascular biology, ES cell differentiation culture for, 265–268 vascular endothelial growth factor (VEGF), 70, 267–268, 280, 281, 388, 527, 563, 577 vascular progenitor cells, human, 228–229, 227–231 vascular support, 247–248 vasculature, ontogeny of, 202 vasculogenesis, 199–205, 227, 526 vasculogenic embryonic cells, 227–228 vectors, viral, 592–593 VEGF (vascular endothelial growth factor), 70, 267–268, 280, 281, 388, 527, 563, 577 ventricular myocytes, 529, 535, 541 vertebrate embryo, neurogenesis in, 157–166 embryonic induction and establishment of neural tissue, 157 negative regulators of proneural activity, 164–166 neural induction, molecular bases of, 157–159 neural patterning, 160–164 neurogenesis to gliogenesis, switch from, 166 neuronal differentiation by sox proteins, regulation of, 166 overview, 157 potential links between neural patterning and neurogenesis control, 164 proneural cascade, 164 proneural gene cascade, 161–164 proneural gene expression, 164 proneural target genes during neuronal differentiation, divergence of, 166 regulation of neuronal differentiation by REST/NRSF, 166 very small embryonic-like (VSEL) stem cells, 518 viral vectors, 410, 592–593 von Willebrand (vW)1 endothelium, 202 von Willebrand (vW) factor, 231 W WB3-44 cells, 292 Weiss, S., 179 Wilms tumor suppressor gene (WTI), 278–279 Wnt/b-catenin signaling pathway, 319–320 Wnt genes, 319, 320 Wnt pathway, 196 Wnt signaling, 45, 195, 478 wound healing, gene therapy approaches in, 526–527 Wozney, John, 243 WTI (Wilms tumor suppressor gene), 278–279 X X-chromosome inactivation (XCI), 97, 287, 310, 318, 325, 353, 361, 381, 439– 441, 469 escape from, 97–98 reactivation and imprinted XCI, 98 Xist and heterochromatin assembly, 97 X-chromosome reactivation, 134 xenogeneic transplant model, 446 xenograft assay, for solid tumors, 474 Xenopus, 214, 304 Xenopus laevis, 274 xenotransplantation, 624, 625, 554, 559 Xist expression, 97, 135 XX-to-XY ratio, 361 Y yolk sac (YS), 200–201, 213 YS (yolk sac), 200–201, 213 Z zebrafish, 459–465 zinc finger transcription factor, 200 zona occludens-1 (ZO-1), 149 zona pellucida (ZP), 353, 355, 500 ZP (zona pellucida), 353, 355, 500 ... technique led to our current understanding of the bone marrow hierarchies or cell Essentials of Stem Cell Biology Copyright © 2009, Elsevier Inc All rights of reproduction in any form reserved lineages... therapeutic utility, since they rely on delivery of the reprogramming factors by retroviral transduction Viral delivery of the reprogramming factors carries the risk of tumor formation either... the nature of stem cells Stemness: Progress Toward a Molecular Definition of Stem Cells Stemness refers to the common molecular processes underlying the core stem cell properties of self-renewal