Novel Concepts in iPSC Disease Modeling

The series Advances in Stem Cell Biology is a timely and expansive collection of comprehensive information and new discoveries in the field of stem cell biology.

iPSCs - Novel Concepts, Volume 15 addresses how important induced pluripotent stems cells are and how can they can help treat certain diseases.

Somatic cells can be reprogrammed into induced pluripotent stem cells by the expression of specific transcription factors. These cells have been transforming biomedical research over the last 15 years. This volume will address the advances in research of how induced pluripotent stem cells are being used for treatment of different disorders, such as liver disease, type-1 diabetes, Parkinson’s disease, macular degeneration of the retina and much more.

The volume is written for researchers and scientists in stem cell therapy, cell biology, regenerative medicine and organ transplantation; and is contributed by world-renowned authors in the field.

• Provides overview of the fast-moving field of stem cell biology and function, regenerative medicine and therapeutics
• Covers spinal cord injuries, type-1 diabetes, liver disease, Parkinson’s disease, graft vs. host disease, and much more
• Contributed by world-renown experts in the field

• Language: English
• Publisher: Academic Press
• Release date: Jan 8, 2022
• ISBN: 9780128238837

Book preview

Novel Concepts in iPSC Disease Modeling

Volume 15

Editor

Alexander Birbrair

Federal University of Minas Gerais, Department of Pathology, Belo Horizonte, Minas Gerais, Brazil

Columbia University Medical Center, Department of Radiology, New York, NY, United States

Table of Contents

Cover image

Title page

Advances in Stem Cell Biology

Copyright

Dedication

List of contributors

About the editor

Preface

Chapter 1. Induced pluripotent stem cells: novel concepts for respiratory disease modeling

List of abbreviations

Introduction

Recapitulating lung development using induced pluripotent stem cells

Modeling lung disease in the conducting airways

Modeling lung disease in the distal airspace

Modeling viral infection of the lung

Concluding remarks

Chapter 2. iPSC for modeling of metabolic and neurodegenerative disorders

Introduction

What are iPSCs?

How are iPSCs obtained?

Current iPSCs models overview

Metabolic disorders

Cardiovascular disorders

Diabetes

Neurodegenerative disorders

Future applications

Limitations

Conclusions

Chapter 3. Induced pluripotent stem cells for modeling open-angle glaucoma

Introduction

Current treatment options for POAG

Induced pluripotent stem cells as cellular models of diseases

iPSC-TM cells as a model of glaucoma

iPSC-RGCs as a model of glaucoma

Patient-derived iPSCs as a model of glaucoma

Drug discovery using iPSCs as a glaucoma model

Conclusion

Chapter 4. Patient-specific induced pluripotent stem cells for understanding and assessing novel therapeutics for multisystem transthyretin amyloid disease

Introduction

ATTR amyloidosis pathogenesis

Current standards of care for patients with ATTR amyloidosis

Limitations of current pre-clinical disease models

Developing IPSC-based models of hereditary ATTR amyloidosis

Hepatic proteostasis remodeling in IPSC-based models of ATTR amyloidosis

The clinical trial in a test tube: revolutionizing the drug discovery pathway for systemic amyloid disease

Future directions

Conclusions

Chapter 5. iPSCs for modeling choroideremia

Eye structure and function

Inherited retinal dystrophies

Choroideremia

Genetics of choroideremia

Pathophysiology of choroideremia

Animal models of choroideremia

Cellular models of choroideremia

Human induced pluripotent stem cells

Human iPSCs for choroideremia

Human iPSC-derived retinal pigment epithelium

Human iPSC-derived RPE for modeling choroideremia

Human iPSC-derived RPE for proof-of-concept studies of gene supplementation for choroideremia

Human iPSC-derived RPE for proof-of-concept studies of translational read-through for choroideremia

Future directions for modeling choroideremia

Chapter 6. Applications of human induced pluripotent stem cell and human embryonic stem cell models for substance use disorders: addiction and neurodevelopmental toxicity

Introduction

The epidemic of drug abuse and addiction

Identification of genetic targets for treatment of substance use disorders

Generation of human induced pluripotent stem cell-derived neuronal cell lines as models for drug addiction

Limitations of human induced pluripotent stem cell models of drug abuse

Use of human embryonic stem cells and human induced pluripotent stem cells as models for neurodevelopmental effects

Conclusions

Chapter 7. Induced pluripotent stem cells for modeling cardiac sodium channelopathies

Introduction

Induced pluripotent stem cell model of sodium channelopathies (Table 7.1)

Summary and future perspectives

Chapter 8. iPSCs for modeling Danon disease

Introduction

The application of iPSC-based modeling of Danon disease

Application of iPSC-cardiomyocytes to evaluate autophagic dysfunction

The application of an iPSC-based model for drug testing

Future perspectives

Chapter 9. Human-induced pluripotent stem cells for modeling of Niemann-Pick disease type C1

Introduction

Traditional models of NPC1 and rationale for human stem cell-derived models

Human-induced pluripotent stem cell-derived models of NPC1

Drug discovery applications

Conclusions and future directions

Chapter 10. iPSC-based modeling in psychiatric disorders: opportunities and challenges

Introduction

The rationale of iPSC-based disease modeling

Major results from iPSC-based modeling of psychiatric disorders

Advances in cell culture systems for iPSC-based modeling of psychiatric disorders

Uncovering causality in iPSC-based modeling of psychiatric disorders

Conclusion and outlook

Author contributions

Funding

Chapter 11. Research applications of induced pluripotent stem cells for treatment and modeling of spinal cord injury

Introduction

Application of iPSCs for SCI cell-based therapies

Application of iPSCs to generate 3D tissue for grafting into SCI

Application of iPSC-derived organoids for spinal cord modeling and research

Conclusion

Chapter 12. Functional outcomes of copy number variations of Chrna7 gene: current knowledge and new insight from induced pluripotent stem cells studies

Introduction

CHRNA7 locus and CNVs (copy number variations)

Distribution and functions of α7 nicotinic receptors in the nervous system

Clinical characteristics of CHRNA7 CNV in human patients: heterozygous deletion and duplication, homozygous deletion

Novel concepts on the functions of the α7nAChR obtained through the use of iPSC models

Conclusions

Index

Advances in Stem Cell Biology

Series Editor

Alexander Birbrair

Copyright

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Notices

Knowledge and best practice in this field are constantly changing. As new research and experience broaden our understanding, changes in research methods, professional practices, or medical treatment may become necessary.

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Dedication

This book is dedicated to my mother, Marina Sobolevsky, of blessed memory, who passed away during the creation of this volume. Professor of Mathematics at the State University of Ceará (UECE), she was loved by her colleagues and students, whom she inspired by her unique manner of teaching. All success in my career and personal life I owe to her.

My beloved mom, Marina Sobolevsky, of blessed memory (July 28, 1959–June 3, 2020)

List of contributors

C.P. Barragán-Álvarez,     Department of Medical and Pharmaceutical Biotechnology, Center for Research and Assistance in Technology and Design of the State of Jalisco, Guadalajara, Jalisco, Mexico

Laura Bernardini,     Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy

Kristen L. Boeshore,     Department of Biology, Lebanon Valley College, Annville, PA, United States

Shana N. Busch,     Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

Ben A. Calvert,     Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

Alessia Casamassa,     Cellular Reprogramming Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy

Brandon S. Cheuk,     Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, United States

A. Cota-Coronado

Department of Medical and Pharmaceutical Biotechnology, Center for Research and Assistance in Technology and Design of the State of Jalisco, Guadalajara, Jalisco, Mexico

The Florey Institute for Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia

Angela D'Anzi,     Cellular Reprogramming Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy

N.E. Díaz-Martínez,     Department of Medical and Pharmaceutical Biotechnology, Center for Research and Assistance in Technology and Design of the State of Jalisco, Guadalajara, Jalisco, Mexico

Yiqin Du

Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, United States

Department of Developmental Biology, University of Pittsburgh, Pittsburgh, PA, United States

McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States

Michael G. Fehlings

Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada

Institute of Medical Science, University of Toronto, Toronto, ON, Canada

Department of Surgery, University of Toronto, Toronto, ON, Canada

Daniela Ferrari,     Biotechnology and Bioscience Department, Bicocca University, Milan, Italy

William J. Freed,     Department of Biology, Lebanon Valley College, Annville, PA, United States

Sabrina Ghosh,     Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, United States

Richard M. Giadone,     Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, United States

Anke Hoffmann,     Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany

Che-Yu Hsu,     Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

T.S.E. Hung-Fat,     Cardiology Division, Department of Medicine, LKS Faculty of Medicine and Queen Mary Hospital, The University of Hong Kong, Hong Kong, China

Zhour Jazouli,     Institute for Neurosciences of Montpellier, University of Montpellier, Inserm, Montpellier, France

Vasiliki Kalatzis,     Institute for Neurosciences of Montpellier, University of Montpellier, Inserm, Montpellier, France

Mohamad Khazaei,     Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada

Sinem Koc-Gunel,     Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

Ajay Kumar,     Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, United States

N.G. Kwong-Man,     Cardiology Division, Department of Medicine, LKS Faculty of Medicine and Queen Mary Hospital, The University of Hong Kong, Hong Kong, China

Chun-Ting Lee,     Cellular Neurobiology Branch, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, United States

Zareeb Lorenzana,     Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

Takeru Makiyama,     Department of Cardiovascular Medicine, Kyoto University Graduate School of Medicine, Sakyo-ku, Kyoto, Japan

William Brett McIntyre

Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada

Institute of Medical Science, University of Toronto, Toronto, ON, Canada

George J. Murphy

Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, United States

Section of Hematology and Oncology, Department of Medicine, Boston University School of Medicine, Boston, MA, United States

M. Paulina Ordonez,     Department of Pediatrics, University of California, San Diego, CA, United States

E. Padilla-Camberos,     Department of Medical and Pharmaceutical Biotechnology, Center for Research and Assistance in Technology and Design of the State of Jalisco, Guadalajara, Jalisco, Mexico

Katarzyna Pieczonka

Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada

Institute of Medical Science, University of Toronto, Toronto, ON, Canada

Erik J. Quiroz

Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, United States

Edward Robinson,     Division of Genetics and Development, Krembil Research Institute, University Health Network, Toronto, ON, Canada

Jessica Rosati,     Cellular Reprogramming Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy

Amy L. Ryan

Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, United States

Christiana N. Senger,     Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States

Dietmar Spengler,     Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany

John Steele,     Department of Biological Sciences, Humboldt State University, Arcata, CA, United States

Ada Maria Tata,     Dept Biology and Biotechnologies Charles Darwin, Sapienza University of Rome, Rome, Italy

Simona Torriano,     Jules Stein Eye Institute, Department of Ophthalmology, UCLA David Geffen School of Medicine, Los Angeles, CA, United States

V. Valadez-Barba,     Department of Medical and Pharmaceutical Biotechnology, Center for Research and Assistance in Technology and Design of the State of Jalisco, Guadalajara, Jalisco, Mexico

Angelo Luigi Vescovi

Biotechnology and Bioscience Department, Bicocca University, Milan, Italy

Cellular Reprogramming Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy

R.A.N. Xinru,     Cardiology Division, Department of Medicine, LKS Faculty of Medicine and Queen Mary Hospital, The University of Hong Kong, Hong Kong, China

T.S.E. Yiu-Lam,     Cardiology Division, Department of Medicine, LKS Faculty of Medicine and Queen Mary Hospital, The University of Hong Kong, Hong Kong, China

Emma Y. Wu,     Pennsylania State University College of Medicine, Hershey, PA, United States

Michael J. Ziller,     Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany

About the editor

Alexander Birbrair

Dr. Alexander Birbrair received his bachelor's biomedical degree from Santa Cruz State University in Brazil. He completed his PhD in Neuroscience, in the field of stem cell biology, at the Wake Forest School of Medicine under the mentorship of Osvaldo Delbono. Then, he joined as a postdoc in stem cell biology at Paul Frenette's laboratory at Albert Einstein School of Medicine in New York. In 2016, he was appointed faculty at Federal University of Minas Gerais in Brazil, where he started his own lab. His laboratory is interested in understanding how the cellular components of different tissues function and control disease progression. His group explores the roles of specific cell populations in the tissue microenvironment by using state-of-the-art techniques. His research is funded by the Serrapilheira Institute, CNPq, CAPES, and FAPEMIG. In 2018, Alexander was elected affiliate member of the Brazilian Academy of Sciences, in 2019, he was elected member of the Global Young Academy (GYA), and in 2021 he was elected affiliate member of The World Academy of Sciences (TWAS). He is the Founding Editor and Editor-in-Chief of Current Tissue Microenvironment Reports, and Associate Editor of Molecular Biotechnology. Alexander also serves in the editorial board of several other international journals: Stem Cell Reviews and Reports, Stem Cell Research, Stem Cells and Development, and Histology and Histopathology.

Preface

This book's initial title was iPSCs: Recent Advances. Nevertheless, because of the ongoing strong interest in this theme, we were able to collect more chapters than would fit in one single volume, covering induced pluripotent stem cells (iPSCs) biology from different perspectives. Therefore, the book was subdivided into several volumes.

This volume Novel Concepts in iPSC Disease Modeling offers contributions by known scientists and clinicians in the multidisciplinary areas of biological and medical research. The chapters bring up-to-date comprehensive overviews of current advances in the field. This book describes the use of iPSCs to model several diseases in vitro, enabling us to study the cellular and molecular mechanisms involved in different pathologies. Further insights into these mechanisms will have important implications for our understanding of disease appearance, development, and progression. The authors focus on the modern state-of-the-art methodologies and the leading-edge concepts in the field of stem cell biology. In recent years, remarkable progress has been made in the obtention of iPSCs and their differentiation into several cell types, tissues, and organs using state-of-the-art techniques. These advantages facilitated identification of key targets and definition of the molecular basis of several disorders. Thus, this book is an attempt to describe the most recent developments in the area of iPSCs biology, which is one of the rising hot topics in the field of molecular and cellular biology today. Here, we present a selected collection of detailed chapters on what we know so far about the use of iPSCs for modeling multiple diseases. Twelve chapters written by experts in the field summarize the present knowledge about iPSC Disease Modeling.

Amy L Ryan and colleagues from University of Southern California discuss iPSCs for modeling respiratory disease. N. Emmanuel Díaz-Martínez and colleagues from Center for Research and Assistance in Technology and Design of the State of Jalisco describe iPSCs for modeling metabolic and neurodegenerative disorders. Yiqin Du and colleagues from University of Pittsburgh compile our understanding of iPSCs for modeling Open-Angle Glaucoma. George J. Murphy and colleagues from Boston University School of Medicine update us with what we know about patient-specific iPSCs for modeling amyloid disease. Vasiliki Kalatzis and colleagues from University of Montpellier summarize current knowledge on modeling choroideremia with iPSCs. Kristen L. Boeshore and colleagues from National Institute of Health talk about the modeling of substance use disorders using iPSCs. Takeru Makiyama from Kyoto University Graduate School of Medicine addresses the importance of iPSCs for modeling Cardiac Sodium Channelopathies. Hung-fat Tse and colleagues from The University of Hong Kong present the modeling of Danon Disease using iPSCs. Paulina Ordonez from University of California San Diego gives an overview of iPSCs for modeling of Niemann-Pick Disease type C1. Dietmar Spengler and colleagues from Max-Planck Institute of Psychiatry introduce what we know so far about iPSCs for modeling of psychiatric disorders. Michael G. Fehlings and colleagues from University of Toronto discuss iPSCs for Modeling of Spinal Cord Injury. Finally, Jessica Rosati and colleagues from Sapienza University of Rome focus on iPSCs for modeling functional outcomes of copy number variations in chrna7 gene.

It is hoped that the chapters published in this book will become a source of reference and inspiration for future research ideas. I would like to express my deep gratitude to my wife, Veranika Ushakova, and Ms. Billie Jean Fernandez and Ms. Elisabeth Brown from Elsevier, who helped at every step of the execution of this project.

Alexander Birbrair

Editor

Chapter 1: Induced pluripotent stem cells

novel concepts for respiratory disease modeling

Ben A. Calvert ¹ , a , Zareeb Lorenzana ¹ , Christiana N. Senger ¹ , Che-Yu Hsu ¹ , Shana N. Busch ¹ , Sinem Koc-Gunel ¹ , Erik J. Quiroz ¹ , ² , and Amy L. Ryan ¹ , ² , a       ¹ Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Southern California, Los Angeles, CA, United States      ² Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, CA, United States

Abstract

The past decade has witnessed the advent of induced pluripotency and methodology to direct these pluripotent stem cells to differentiate into many tissue-specific cell types, including those comprising the respiratory epithelium. Induced pluripotent stem cell-derived, (iPSC-derived), airway cells have expanded our capacity to replicate both respiratory development and disease. These relevant and reproducible models provide options to study disease-specific changes occurring in humans, which rodent models often do not readily recapitulate. Not only do these models use human cells, but they can also be patient-specific or engineered to reflect precise disease-causing mutations in controlled and isogenic cellular systems. Such advances represent a new era of precision medicine approaches for the evaluation and treatment of respiratory disease. This chapter presents a summary of recent advances in the generation of iPSC-derived cells, and their use in modeling human respiratory disease.

Keywords

Airways; Alveolar; Cystic fibrosis; Differentiation; Idiopathic pulmonary fibrosis; Induced pluripotent stem cells; Lung development; Organoids; Primary ciliary dyskinesia; Stem cells

List of abbreviations

Introduction

Recapitulating lung development using induced pluripotent stem cells

Early lung specification: definitive endoderm and anterior foregut endoderm

Generation of the NKX2.1 expressing primordial lung progenitor cells

Specification of proximal airway basal stem cells

Specification of distal airway alveolar type 2 stem cells

Specification of pulmonary neuroendocrine cells

Cellular plasticity in iPSC-derived airway progenitors

Modeling lung disease in the conducting airways

Cystic fibrosis

Primary ciliary dyskinesia

Inflammatory airway disease

Modeling lung disease in the distal airspace

Surfactant protein dysfunction

Alpha-1-anti-trypsin

Idiopathic pulmonary fibrosis

Lymphangioleiomyomatosis

Modeling viral infection of the lung

Concluding remarks

Acknowledgments

References

List of abbreviations

2-D    2-dimensional

3-D    3-dimensional

AAT    alpha-1-antitrypsin

AATD    alpha-1-antitrypsin deficiency

AAV6    adeno-associated virus 6

ABCA3    adenosine triphosphate binding cassette subfamily A member 3

ACE2    angiotensin-converting enzyme 2

AFE    anterior foregut endoderm

ALI    air–liquid interface

AM    alveolar macrophage

AQP5    aquaporin 5

ARDS    acute respiratory distress syndrome

AT1    alveolar type 1 cells

AT2    alveolar type 2 cells

ATP11A    ATPase phospholipid transporting 11A

BC    basal cells

BMP    bone morphogenic protein

C-KIT    tyrosine-protein kinase KIT (aka CD117, cluster of differentiation 117)

cAMP    cyclic adenosine monophosphate

Cas9    CRISPR associated protein 9

CC    club cells

CDX2    caudal type homeobox 2

CF    cystic fibrosis

CFTR    cystic fibrosis transmembrane regulator

CHIR    CHRI99021, (a GSK-3 inhibitor)

CLP    common lymphoid progenitor

CMP    common myeloid progenitor

COPD    chronic obstructive pulmonary disease

CPM    carboxypeptidase M

CRISPR    clustered regularly interspaced short palindromic repeats

CSF    colony stimulating factors

CXCR4    C-X-C motif chemokine receptor 4

DE    definitive endoderm

DMH-1    dorsomorphin homolog 1

DNAH5    dynein heavy chain 5

DPP9    dipeptidyl peptidase 9

DSP    desmoplakin

ECM    extracellular matrix

EGF    epidermal growth factor

EHT    endothelial-to-hematopoietic-transition

ERG    erythroblast transformation-specific (ETS)-related gene

ETV5    ATS variant transcription factor 5

FACS    flow activated cell sorting

FGF    fibroblast growth factor

FLT3    Fms like tyrosine kinase 3

FOXA2/M1/P2    forkhead box A2/M1/P2

GATA6    GATA binding factor 6

GFP    green fluorescent protein

GM-CSF    granulocyte-macrophage colony stimulating factor

GSK    glycogen synthase kinase

GWAS    genome-wide association studies

HAECs    human airway endothelial cells

HOPX    homeodomain-only protein homeobox

HOXA5/9/10    Homeobox A5/9/10

HPS1    Hermansky-pudlak syndrome 1 protein

HSC    hematopoietic stem cells

iAT2    induced AT2 cell

IBMX    3-isobutyl-1-methylxanthine

Id2    inhibitor of differentiation 2

IL    interleukin

ILD    interstitial lung diseases

IM    interstitial macrophage

IPF    idiopathic pulmonary fibrosis

iPSC    induced pluripotent stem cells

IRF7    interferon regulatory factor 7

JAK2    janus kinase 2

KGF    keratinocyte growth factor (or FGF7)

KLF4    krüppel like factor 4

KRT    cytokeratin

MCC    multiciliated cells

MIXL1    mix paired-like homeobox 1

MUC5B    mucin 5B

NANCI    NKX2.1 associated noncoding intergenic RNA

NDA    deoxyribonucleic acid

NGFR    nerve growth factor receptor

NKX2.1    NK2 homeobox 1

OBFC1    oligonucleotide-binding fold-containing protein 1

PAP    pulmonary alveolar proteinosis

PAX8    paired box 8

PC    phosphatidylcholine

PCD    primary ciliary dyskinesia

PDPN    podoplanin, aka T1alpha

PG    phosphatidylglycerol

PNEC    pulmonary neuroendocrine cells

POU5F1 (OCT4)    octamer-binding protein 4

PRR    pattern recognition receptor

PSC    pluripotent stem cells

RA    retinoic acid

RB    retinoblastoma protein

RNP    ribonucleoprotein

RUNX1    runt-related transcription factor 1

SARS-CoV-2    severe acute respiratory syndrome coronavirus 2

SCF    stem cell factor

SERPINA1    serpin family A member 1

SFTPC    surfactant protein C

Shh    sonic hedgehog

SMAD    similarity to drosophila gene mothers against decapentaplegic (MAD)

SOX2/17    SRY (sex determining region Y)-box 2/17

SPI1    transcription factor PU.1

STAT3    signal transducer and activator of transcription 3

TERC    telomerase RNA component

TERT    telomerase reverse transcriptase

TGFβ    transforming growth factor beta

TMPSSR2    transmembrane protease serene 2

TOLLIP    toll interacting protein

TP63    tumor protein 63

TPO    thrombopoietin

vCC    variant club cells

VEGF    vascular endothelial growth factor

Wnt    wingless/int family

WT    wild-type

Introduction

While other diseases, such as cardiovascular disease, have seen a regression in morbidity and mortality rates due to an increased number of therapeutic approaches successfully reaching the clinic, respiratory disease rates continue to increase. Despite numerous promising therapeutics emerging from preclinical trials, respiratory disease has far fewer new drugs eventually being approved for patient use. One contributing factor is the limited number of disease and patient-specific model systems available to study human respiratory disease onset and progression. Murine models have provided some of the most informative data on lung development, reviewed in Rawlins and Perl (2012). For example, lineage tracing of SRY (sex-determining region Y)-box 2 (SOX2) helped to elucidate its role in lung budding and differentiation of tracheal mesenchyme and epithelium (Que et al., 2009). Unfortunately, for many respiratory diseases, differences in human and rodent lung structure and function reflect in models that do not fully capture disease phenotypes as they occur in humans. Models of cystic fibrosis (CF) in mice, for example, complete knockouts (O'Neal et al., 1993; Snouwaert et al., 1992), ΔF508 mutants (Colledge et al., 1995; van Doorninck et al., 1995), G551D mutants (Delaney et al., 1996; Semaniakou et al., 2018), variably represent the human manifestation of the disease (reviewed extensively in McCarron et al., 2018; Wilke et al., 2011). Similarly, idiopathic pulmonary fibrosis (IPF) models, often induced by intratracheal instillation of bleomycin in rodents (Antoniu and Kolb, 2009; Carrington et al., 2018; Williamson et al., 2015), share dissimilar pathogenesis, and vary in detectable alveolar cell death and inflammation. While characterized by the development of fibrotic foci, the distribution of fibrosis differs from that in humans (reviewed in Williamson et al., 2015). Such differences in the pathophysiology of IPF in rodent models are likely one of the reasons for a complete absence of therapeutics available to increase survival in patients with IPF (Raghu et al., 2011). While some lung diseases are better recapitulated in larger animal models, such as pig and ferret models of CF (Li et al., 2006; Meyerholz et al., 2018; Pezzulo et al., 2012; Rogers et al., 2008a; Rosen et al., 2018; Sun et al., 2010; Welsh et al., 2009; Xie et al., 2018), these are costly models to develop and are therefore not suitable for high throughput studies. While these models may increase our knowledge of disease onset and pathogenesis, the value of such models in translating therapeutics successfully into the clinic is still largely unknown. Establishing a reproducible human and patient-specific model that is sustainable and scalable has the potential to accelerate therapeutic development for lung disease, particularly for rare lung diseases, is likely a valuable addition to the tool-kit for studying human lung disease pathogenesis.

Primary patient cells fulfill some of the criteria for modeling human lung disease ex vivo. Unfortunately, access to patient cells is restricted to the availability of explant lungs from patients with end-stage disease or small samples which can be obtained by bronchoscopy, limiting the number of cells that can be acquired. In vitro expansion of primary lung basal cells (BCs) while retaining their multipotent stem cell phenotype is limited, recent advances in the field are starting to elucidate methods for more robust long-term expansion of lung basal stem cells (Mou et al., 2016; Reynolds et al., 2016). Access to cells representing rare lung diseases for in vitro assays remains a significant limitation due to the low number of patients available for cell procurement. The discovery of human-induced pluripotency (induced pluripotent stem cells [iPSCs]) by the laboratories of Yamanaka and Thomson in 2007 provided a new technology that could be utilized for disease modeling in human cells, with the capacity to understand disease development and pathogenic mechanisms (Okita et al., 2007; Takahashi et al., 2007a,b; Yu et al., 2007). Directed differentiation of iPSCs can recapitulate key embryonic milestones in the development of the human lung to generate cells of the airway epithelium. Crucial studies of lung development in mice allowed us to understand some of the signaling pathways that direct lung organogenesis (Bellusci et al., 1997; Chung et al., 2018; Lu et al., 2001; Mucenski et al., 2003; Okubo and Hogan, 2004; Weaver et al., 1999, 2000; Zhang et al., 2007, 2008). Protocols involving the sequential and temporal addition of factors regulating activin/nodal, bone morphogenic protein (BMP), fibroblast growth factor (FGF), transforming growth factor bets (TGFβ), wingless (Wnt), and sonic hedgehog (Shh) signaling to pluripotent cells have evolved from early studies generating a relatively immature lung epithelium (Firth et al., 2014; Ghaedi et al., 2013; Green et al., 2011; Huang et al., 2014; Wong et al., 2012), to recent advances where functional cells can be generated and used for effective disease modeling (Ghaedi and Niklason, 2019; Happle et al., 2018; Hurley et al., 2020; Leibel et al., 2019; McCauley et al., 2017; Sahabian et al., 2019; Strikoudis et al., 2019). This chapter focuses on discussing some of the most recent advances in utilizing iPSC-derived cells to model human respiratory disease (Table 1.1).

Table 1.1

CD26, cluster of differentiation 26, also known as dipeptidyl peptidase-4 (DPP4) or adenosine deaminase complexing protein 2; CD47, cluster of differentiation 47, also known as integrin associated protein (IAP); CFTR, cystic fibrosis transmembrane regulator; iPSC, induced pluripotent stem cells; NKX2.1, NK2 homeobox 1, also known as thyroid transcription factor 1 (TTF-1); SMAD, similarity to drosophila gene Mothers Against Decapentaplegic; Wnt, wingless.

Recapitulating lung development using induced pluripotent stem cells

Among the many organs that arise from the endoderm, the lung has received considerable attention over the past few years, driven by a need to develop better disease models specific to the human respiratory system. Although in depth, lineage-tracing studies have elegantly demonstrated stages of fetal lung development in rodents, human lung development is less well-understood and rodent signaling pathways guiding lung development are not necessarily conserved humans (Bellusci et al., 1997; Hogan et al., 1997; Lu et al., 2001; Morrisey, 2018; Mucenski et al., 2003; Rawlins et al., 2008; Stabler and Morrisey, 2017; Swarr and Morrisey, 2015; Wang et al., 2013; Weaver et al., 2000; Zhang et al., 2007). Consequently, there is an incomplete understanding of the underlying mechanisms involved in early human fetal lung development. In humans, the respiratory epithelium of the lung differentiates from the anterior foregut endoderm (AFE) and the splanchnic mesoderm gives rise to the pulmonary mesenchyme. Lung development begins during weeks 4–7 of embryonic development when Wnt2/Wnt2b expressing cells in the ventral anterior mesoderm are thought to interact with the cells of the AFE (Goss et al., 2009). Additionally, BMP4 expressed in the surrounding mesenchyme, inhibits SOX2 expression in these early progenitor cells which concomitantly increases NK2 homeobox 1 (NKX2.1) expression, a key transcription factor that specifies thyroid and lung development (Domyan et al., 2011). The embryonic stage is followed by the fetal period consisting of the pseudoglandular stage (weeks 5–17), the canalicular stage (weeks 16–26), and finally the saccular stage (weeks 24 to birth). Lung alveolarization occurs during the postpartum period and continues throughout childhood (weeks 36 up to 8years Narayanan et al., 2012). The lung is partitioned into two core regions, the airways and parenchyma. The airways form the conduits between the outside world and the primary gas exchanging unit, the alveoli. The conducting airways comprise of the trachea which divides into two primary bronchi that enter the lung at each hilus. The primary bronchi then branch repeatedly into smaller bronchi and bronchioles eventually enter a terminal bronchiole. Distal airways comprise of those with a diameter of less than 2mm leading to the terminal bronchioles and the alveolar ducts (Jain and Sznajder, 2007).

In 2007, Takahashi and Yamanaka discovered that a combination of four transcriptions factors (POU5F1 (OCT4), krüppel like factor 4 (KLF4), c-Myc and SOX2) could be used to reprogram somatic, differentiated cells into pluripotent cells akin to embryonic stem cells (Takahashi et al., 2007a,b). These cells are known as iPSCs and can be generated from any accessible and proliferating cell source including fibroblasts, keratinocytes, and peripheral blood mononuclear cells (Aasen et al., 2008; Loh et al., 2009; Takahashi et al., 2007b). iPSCs have the same unique properties as embryonic stem cells including a seemingly unlimited self-renewal capacity and differentiation into all three germ layers. The differentiated progeny is attractive for the creation of disease-specific models enabling analysis of complex cellular and molecular interactions occurring during human lung development and disease manifestation and progression, in addition to being a promising source of cells for tissue regeneration. iPSCs can be patient-specific and, therefore, provide an autologous cell source that is genetically identical to the patient, allowing for the potential to engraft cells or tissue generated from these cells while avoiding the need for immune suppression. Specific differentiation of iPSCs toward cells comprising the adult lung follows a stepwise strategy striving to mimic the abovementioned stages of lung development and maturation in vitro. This results in compression of the timeline from months to days in culture. This challenge is not trivial and over the past 10 years methodology has been established and protocols refined to generate cells and structures that resemble the human adult conducting airways and more distal alveolar cells (Dye et al., 2015; Firth et al., 2014; Hawkins et al., 2017; Huang et al., 2015; Jacob et al., 2017; Konishi et al., 2016;