Essentials of Stem Cell Biology

PART ONE: INTRODUCTION TO STEM CELLS

1. Why Stem Cell Research? Advances in the Field

1.1 The Origins of Stem Cell Technology

1.2 Organizations that Advocate and Support the Growth of the Stem Cell Sector

1.3 Applications of Stem Cells in Medicine

1.4 Challenges to the Use of Stem Cells


2. ‘Stemness’: Definitions, Criteria, and Standards

2.1 What is a Stem Cell?

2.2 Self-Renewal

2.3 Potency

2.4 Clonality

2.5 Definition

2.6 Where do Stem Cells Come from?

2.7 Stem Cells of the Early Embryo

2.8 Ontogeny of Adult Stem Cells

2.9 How are Stem Cells Identified, Isolated, and Characterized?

2.10 Embryonic Stem Cells

2.11 Adult Stem Cells

2.12 Stemness: Progress Toward a Molecular Definition of Stem Cells


3. Pluripotent Stem Cells from Vertebrate Embryos: Present Perspective and Future Challenges

3.1 Introduction

3.2 Biology of ES and ESL Cells

3.3 Stem Cell Therapy

3.4 Summary


4. Embryonic Stem Cells in Perspective

4.1 Embryonic Stem Cells in Perspective


5. The Development of Epithelial Stem Cell Concepts

5.1 Introduction

5.2 A Definition of Stem Cells

5.3 Hierarchically Organized Stem Cell Populations

5.4 Skin Stem Cells

5.5 The Intestinal Stem Cell System

5.6 Stem Cell Organization on the Tongue

5.7 Generalized Scheme

5.8 Summary

PART TWO: BASIC BIOLOGY/MECHANISMS

6. Stem Cell Niches

6.1 Stem Cell Niche Hypothesis

6.2 Stem Cell Niches in the Drosophila Germ-Line

6.3 The Germ-Line Stem Cell Niche in the Drosophila Ovary

6.4 Germ-Line Stem Cell Niche in the Drosophila Testis

6.5 Coordinate Control of Germ-Line Stem Cell and Somatic Stem Cell Maintenance and Proliferation

6.6 Structural Components of the Niche

6.7 Stem Cell Niches Within Mammalian Tissues

6.8 Summary


7. Mechanisms of Stem Cell Self-Renewal

7.1 Self-Renewal of Pluripotent Stem Cells

7.2 Prevention of Differentiation

7.3 Maintenance of Stem Cell Proliferation

7.4 Maintenance of Telomere Length

7.5 X Chromosome Inactivation

7.6 Summary


8. Cell Cycle Regulators in Stem Cells

8.1 Introduction

8.2 Cell Cycle Kinetics of Stem Cells In Vivo

8.3 Stem Cell Expansion Ex Vivo

8.4 Mammalian Cell Cycle Regulation and Cyclin-Dependent Kinase Inhibitors

8.5 Roles of Cyclin-Dependent Kinase Inhibitors in Stem Cell Regulation

8.6 Roles of p21 in Stem Cell Regulation

8.7 Roles of p27 in Stem Cell Regulation

8.8 Other Cyclin-Dependent Kinase Inhibitors and the Retinoblastoma Pathway in Stem Cell Regulation

8.9 Relation Between Cyclin-Dependent Kinase Inhibitors and Transforming Growth Factor β-1

8.10 CKIs and Notch

8.11 Summary and Future Directions


9. How Cells Change Their Phenotype

9.1 Metaplasia and Transdifferentiation

9.2 Examples of Transdifferentiation

9.3 Barrett’s Metaplasia

9.4 Regeneration

9.5 Bone Marrow to Other Cell Types

9.6 Dedifferentiation as a Prerequisite for Transdifferentiation

9.7 How to Change a Cell’s Phenotype Experimentally

9.8 Summary

PART THREE: TISSUE AND ORGAN DEVELOPMENT

10. Differentiation in Early Development

10.1 Preimplantation Development

10.2 Cell Polarization Occurs During Compaction

10.3 Axis Specification During Preimplantation in the Mouse

10.4 Developmental Potency of the Early Mouse Embryo

10.5 Genes Important During Preimplantation Mouse Development

10.6 From Implantation to Gastrulation

10.7 The Mouse Trophectoderm and Primitive Endoderm Cells

10.8 Development of the Mouse Inner Cell Mass to the Epiblast

10.9 The Human Embryo

10.10 Implantation: Maternal Versus Embryonic Factors

10.11 The Role of Extra-Embryonic Tissues in Patterning the Mouse Embryo


11. Stem Cells Derived from Amniotic Fluid

11.1 Amniotic Fluid – Function, Origin, and Composition

11.2 Amniotic Fluid Mesenchymal Stem Cells

11.3 Amniotic Fluid Stem Cells

11.4 Conclusions


12. Stem and Progenitor Cells Isolated from Cord Blood

12.1 Addressing Delayed Time to Engraftment and Graft Failure With CB

12.2 Cryopreservation of CB Cells

12.3 Induced Pluripotent Stem Cells Generated from CB

12.4 Concluding Comments


13. The Nervous System

13.1 Introduction

13.2 Neural Development

13.3 Neural Stem Cells

13.4 Neural Differentiation of Mouse ES Cells

13.5 Neural Differentiation of Human and Nonhuman Primate ES Cells

13.6 Developmental Perspectives

13.7 Therapeutic Perspectives

13.8 Parkinson’s Disease

13.9 Huntington’s Disease

13.10 Stroke

13.11 Demyelination

13.12 Summary


14. Sensory Epithelium of the Eye and Ear

14.1 Introduction

14.2 Introduction to Progenitor and Stem Cells in the Retina

14.3 The Optic Vesicle Generates Diverse Cell Types that can Undergo Transdifferentiation

14.4 In Vivo Neurogenesis in the Posthatch Chicken

14.5 Growth of Retinal Neurospheres from the Ciliary Margin of Mammal

14.6 Prospects for Stem Cell Therapy in the Retina

14.7 Development and Regeneration of Tissues Derived from the Inner Ear

14.8 In Vivo Neurogenesis in Postembryonic Animals

14.9 In Vitro Expansion of Otic Progenitors

14.10 Prospects for Therapy


15. Epithelial Skin Stem Cells

15.1 A Brief Introduction to Mouse Skin Organization

15.2 The Bulge as a Residence of Epithelial Skin Stem Cells

15.3 Models of Epithelial Stem Cell Activation

15.4 Molecular Fingerprint of the Bulge – Putative Stem Cell Markers

15.5 Cell Signaling in Multipotent Epithelial Skin Stem Cells

15.6 Commentary and Future Directions


16. Hematopoietic Stem Cells

16.1 Embryonic Stem Cells and Embryonic Hematopoiesis

16.2 Blood Formation in Embryoid Bodies

16.3 Transformation of an EB-Derived HSC by BCR/ABL

16.4 Promoting Hematopoietic Engraftment with STAT5 and HOXB4

16.5 Promoting Blood Formation In Vitro with Embryonic Morphogens


17. Peripheral Blood Stem Cells

17.1 Introduction

17.2 Types and Source of Stem Cells in the Peripheral Blood

17.3 Endothelial Progenitor Cells

17.4 Mesenchymal Stem Cells

17.5 Therapeutic Applications of Peripheral Blood Stem Cells

17.6 Conclusions and Future Directions


18. Multipotent Adult Progenitor Cells

18.1 Pluripotent Stem Cells – Embryonic Stem Cells

18.2 Postnatal Tissue-Specific Stem Cells – Are Some More than Multipotent?

18.3 Can Pluripotency Be Acquired?

18.4 Isolation of Rodent MAPCs

18.5 Isolation of Human MAPCs

18.6 Recent Developments


19. Mesenchymal Stem Cells

19.1 The Definition of MSCs

19.2 The Stem Cell Nature of MSCs

19.3 Which Tissues Contain MSCS?

19.4 MSC Isolation Techniques

19.5 Immunomodulatory Effects of MSCS

19.6 Skeletal Tissue Regeneration by MSCS

19.7 Non-Skeletal Tissue Regeneration by MSCS

19.8 Conclusions


20. Skeletal Muscle Stem Cells

20.1 Introduction

20.2 The Original Muscle Stem Cell: The Satellite Cell

20.3 Functional and Biochemical Heterogeneity Among Muscle Stem Cells

20.4 Unorthodox Origins of Skeletal Muscle

20.5 The Muscle Stem Cell Niche

20.6 Conclusion


21. Stem Cells and the Regenerating Heart

21.1 Introduction

21.2 Recruiting Circulating Stem Cell Reserves

21.3 The Elusive Cardiac Stem Cell

21.4 Evolving Concepts of Regeneration


22. Cell Lineages and Stem Cells in the Embryonic Kidney

22.1 The Anatomy of Kidney Development

22.2 Genes that Control Early Kidney Development

22.3 The Establishment of Additional Cell Lineages

22.4 What Constitutes a Renal Stem Cell?


23. Adult Liver Stem Cells

23.1 Organization and Functions of Adult Mammalian Liver

23.2 Liver Stem Cells


24. Pancreatic Stem Cells

24.1 Introduction

24.2 Definition of Stem Cells and of Progenitor Cells

24.3 Progenitor Cells During Embryonic Development of the Pancreas

24.4 Progenitor Cells in the Adult Pancreas

24.5 Forcing Other Tissues to Adopt a Pancreatic Phenotype

24.6 In Vitro Studies

24.7 Summary


25. Stem Cells in the Gastrointestinal Tract

25.1 Introduction

25.2 Gastrointestinal Mucosa Contains Multiple Lineages

25.3 Epithelial Cell Lineages Originate from a Common Precursor Cell

25.4 Single Intestinal Stem Cells Regenerate Whole Crypts Containing all Epithelial Lineages

25.5 Mouse Aggregation Chimeras Show that Intestinal Crypts are Clonal Populations

25.6 Somatic Mutations in Stem Cells Reveal Stem Cell Hierarchy and Clonal Succession

25.7 Human Intestinal Crypts Contain Multiple Epithelial Cell Lineages Derived from a Single Stem Cell

25.8 Bone Marrow Stem Cells Contribute to Gut Repopulation After Damage

25.9 Gastrointestinal Stem Cells Occupy a Niche Maintained by ISEMFs in the Lamina Propria

25.10 Multiple Molecules Regulate Gastrointestinal Development, Proliferation, and Differentiation

25.11 Wnt/β-Catenin Signaling Pathway Controls Intestinal Stem Cell Function

25.12 Transcription Factors Define Regional Gut Specification and Intestinal Stem Cell Fate

25.13 Gastrointestinal Neoplasms Originate in Stem Cell Populations

25.14 Summary

PART FOUR: METHODS

26. Induced Pluripotent Stem Cells

26.1 Generation of iPS Cells

26.2 Molecular Mechanisms in iPS Cell Induction

26.3 Recapitulation of Disease Ontology and Drug Screening

26.4 iPS Cell Banking

26.5 Safety Concerns for Medical Application

26.6 Medical Application

26.7 Direct Fate Switch

26.8 Conclusion


27. Embryonic Stem Cells: Derivation and Properties

27.1 Derivation of Embryonic Stem Cells

27.2 Culture of Embryonic Stem Cells

27.3 Developmental Potential of Embryonic Stem Cells

27.4 Conclusion


28. Isolation and Maintenance of Murine Embryonic Stem Cells

28.1 Introduction

28.2 Maintenance of Embryonic Stem Cells

28.3 Media

28.4 Sera

28.5 Colony-Forming Assay for Testing Culture Conditions

28.6 Embryonic Stem Cell Passage Culture

28.7 Isolation of New Embryonic STEM Cell Lines

28.8 Method for Deriving Embryonic Stem Cells

28.9 Summary


29. Approaches for Derivation and Maintenance of Human Embryonic Stem Cells: Detailed Procedures and Alternatives

29.1 Introduction

29.2 Setting Up the Lab

29.3 Preparing and Screening Reagents

29.4 Mechanical Passaging of hES Cell Colonies

29.5 Derivation of hES Cells

29.6 Maintenance of Established hES Cell Cultures

29.7 Freezing hES Cells

29.8 Thawing hES Cells

29.9 hES Cell Quality Control


30. Derivation and Differentiation of Human Embryonic Germ Cells

30.1 Introduction

30.2 Human Embryonic Germ Cell Derivation

30.3 Embryoid Body-Derived Cells


31. Genomic Reprogramming

31.1 Introduction

31.2 Genomic Reprogramming in Germ Cells

31.3 Reprogramming Somatic Nuclei

31.4 Conclusions

PART FIVE: APPLICATIONS

32. Neural Stem Cells – Therapeutic Applications in Neurodegenerative Diseases

32.1 Introduction

32.2 Definition of Neural Stem Cells

32.3 Therapeutic Potential of Neural Stem Cells

32.4 Gene Therapy Using Neural Stem Cells

32.5 Cell Replacement Using Neural Stem Cells

32.6 ‘Global’ Cell Replacement Using Neural Stem Cells

32.7 Neural Stem Cells Display an Inherent Mechanism for Rescuing Dysfunctional Neurons

32.8 Neural Stem Cells as the Glue That Holds Multiple Therapies Together

32.9 Summary


33. Adult Progenitor Cells as a Potential Treatment for Diabetes

33.1 Importance of β-Cell Replacement Therapy for Diabetes and the Shortage of Insulin-Producing Cells

33.2 Potential of Adult Stem-Progenitor Cells as a Source of Insulin-Producing Cells

33.3 Defining β-Cells, Stem Cells, and Progenitor Cells

33.4 New β-Cells are Formed Throughout Adult Life

33.5 What is the Cellular Origin of Adult Islet Neogenesis?

33.6 Transdifferentiation of Nonislet Cells to Islet Cells

33.7 Pancreatic Acinar Cell Transdifferentiation

33.8 Bone Marrow Cells as a Source of Insulin-Producing Cells

33.9 Liver as a Source of Insulin-Producing Cells

33.10 Engineering Other Non-β-Cells to Produce Insulin

33.11 Attempts to Deliver Insulin Through Constitutive Rather Than Regulated Secretion

33.12 Summary


34. Burns and Skin Ulcers

34.1 Introduction

34.2 Burns and Skin Ulcers – The Problem

34.3 Epidermal Stem Cells

34.4 Stem Cells in Burns and Skin Ulcers – Current Use

34.5 Recent and Future Developments


35. Stem Cells and Heart Disease

35.1 Heart: A Self-renewing Organ

35.2 Distribution of CSCS in the Heart

35.3 Repair of Myocardial Damage by Nonresident Primitive Cells

35.4 Repair of Myocardial Damage by Resident Primitive Cells

35.5 Myocardial Regeneration in Humans


36. Stem Cells for the Treatment of Muscular Dystrophy

36.1 Introduction

36.2 Myoblast Transplantation – Past Failure and New Hope

36.3 Unconventional Myogenic Progenitors

36.4 Pluripotent Stem Cells for Future Cell-Based Therapies

36.5 Future Perspectives


37. Cell Therapy for Liver Disease: From Hepatocytes to Stem Cells

37.1 Introduction

37.2 Background Studies

37.3 Integration of Hepatocytes Following Transplantation

37.4 Clinical Hepatocyte Transplantation

37.5 Hepatocyte Bridge

37.6 Hepatocyte Transplantation in Acute Liver Failure

37.7 Hepatocyte Transplantation for Metabolic Liver Disease

37.8 Hepatocyte Transplantation – Novel Uses, Challenges, and Future Directions

37.9 Conclusion


38. Orthopedic Applications of Stem Cells

38.1 Introduction

38.2 Bone

38.3 Cartilage

38.4 Meniscus

38.5 Ligaments and Tendons

38.6 Spine

38.7 Summary


39. Embryonic Stem Cells in Tissue Engineering

39.1 Introduction

39.2 Tissue Engineering Principles and Perspectives

39.3 Limitations and Hurdles of Using ES Cells in Tissue Engineering

39.4 Summary

PART SIX: REGULATION AND ETHICS

40. Ethical Considerations

40.1 Introduction

40.2 Is it Morally Permissible to Destroy a Human Embryo?

40.3 Should we Postpone hES Cell Research?

40.4 Can We Benefit from Others’ Destruction of Embryos?

40.5 Can We Create an Embryo to Destroy it?

40.6 Should We Clone Human Embryos?

40.7 What Ethical Guidelines Should Govern hES Cell and Therapeutic Cloning Research?

40.8 Summary


41. Overview of the FDA Regulatory Process

41.1 Introduction and Chapter Overview

41.2 Brief Legislative History of FDA

41.3 Laws, Regulations, and Guidance

41.4 FDA Organization and Jurisdictional Issues

41.5 Approval Mechanisms and Clinical Studies

41.6 Meetings with Industry, Professional Groups, and Sponsors

41.7 Regulations and Guidance of Special Interest for Regenerative Medicine

41.8 FDA’s Standards Development Program

41.9 Advisory Committee Meetings

41.10 FDA Research and Critical Path Science

41.11 Other Communication Efforts

41.12 Conclusion


42. It’s Not about Curiosity, It’s about Cures: Stem Cell Research – People Help Drive Progress

42.1 Choosing Life

42.2 Size of the Promise

42.3 Personal Promises Fuel Progress

42.4 Hope Versus Hype

42.5 Giving Life

42.6 People Drive Progress

42.7 Better Health for All