Professional Documents
Culture Documents
PDF Cell Biology and Translational Medicine Volume 7 Stem Cells and Therapy Emerging Approaches Kursad Turksen Ebook Full Chapter
PDF Cell Biology and Translational Medicine Volume 7 Stem Cells and Therapy Emerging Approaches Kursad Turksen Ebook Full Chapter
https://textbookfull.com/product/cell-biology-and-translational-
medicine-volume-8-stem-cells-in-regenerative-medicine-kursad-
turksen/
https://textbookfull.com/product/cell-biology-and-translational-
medicine-volume-4-stem-cells-and-cell-based-strategies-in-
regeneration-kursad-turksen/
https://textbookfull.com/product/cell-biology-and-translational-
medicine-volume-1-stem-cells-in-regenerative-medicine-advances-
and-challenges-kursad-turksen/
https://textbookfull.com/product/cell-biology-and-translational-
medicine-volume-3-stem-cells-bio-materials-and-tissue-
engineering-kursad-turksen/
Cell Biology and Translational Medicine Volume 9 Stem
Cell Based Therapeutic Approaches in Disease 1st
Edition Kursad Turksen
https://textbookfull.com/product/cell-biology-and-translational-
medicine-volume-9-stem-cell-based-therapeutic-approaches-in-
disease-1st-edition-kursad-turksen/
https://textbookfull.com/product/cell-biology-and-translational-
medicine-volume-2-approaches-for-diverse-diseases-and-conditions-
kursad-turksen/
https://textbookfull.com/product/skin-stem-cells-methods-and-
protocols-kursad-turksen/
https://textbookfull.com/product/stem-cell-renewal-and-cell-cell-
communication-methods-and-protocols-methods-in-molecular-
biology-2346-kursad-turksen-editor/
https://textbookfull.com/product/perinatal-stem-cells-biology-
manufacturing-and-translational-medicine-zhong-chao-han/
Advances in Experimental Medicine and Biology 1237
Cell Biology and Translational Medicine
Kursad Turksen
Volume 1237
Subseries Editor
Kursad Turksen
More information about this subseries at http://www.springer.com/series/15838
Kursad Turksen
Editor
This Springer imprint is published by the registered company Springer Nature Switzerland AG.
The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland
Preface
v
Contents
vii
viii Contents
Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Adv Exp Med Biol - Cell Biology and Translational Medicine (2019) 7: 1–16
https://doi.org/10.1007/5584_2019_430
# Springer Nature Switzerland AG 2019
Published online: 30 August 2019
1
2 B. A. Calvert and A. L. Ryan (Firth)
reprogram terminally differentiated cells back Yamanaka and colleagues originally generated
into a state of pluripotency, akin to that of iPSC by transducing mouse fibroblasts with Oct4,
embryonic stem cells (ESCs) found in the Sox2, Klf4 and c-Myc transcription factors via
inner cell mass of the blastocyst (Takahashi pMX based retroviral vectors. Since then, other
et al. 2007a, b; Okita et al. 2007) (Fig. 1). methods and factors have been utilized to suc-
These cells acquired an infinite capacity for cessfully induce pluripotency in a wide range of
self-replication and differentiation into cells somatic and germ line cells, these are summarized
and tissues from all germ layers, including in Table 1. Initially, lentivirus became favoured
endodermal lung progenitors. As iPSC are over retroviruses due to its capability of infecting
generated by isolating cells from somatic post-mitotic cells as well as dividing cells
tissues, they circumnavigate the ethical issues (Yamashita and Emerman 2006). Other virus
surrounding the use of ESCs (Murugan 2009). types are also used, such as adenovirus and
iPSC have revolutionized our capacity to carry Sendai virus, favoured for their non-integrating
out research in relevant human cells providing nature (Zhou and Freed 2009), helping to main-
an exceptional tool for disease modelling, as tain host genomic integrity with the original viral
well as possessing a huge potential for regener- RNA diluted with each cell division (Fusaki et al.
ative therapy. 2009). The most recent shift in technology is
Fig. 1 Pluripotent cell differentiation toward primor- SOX17 expressing definitive endoderm to anterior foregut
dial lung progenitor cells. Pluripotent stem cells are endoderm and then NKX2.1 expressing primordial lung
isolated and expanded in vitro from the inner cell mass progenitors. The pipette symbol inidcates the cytokines
of the blastocyst (Embryonic Stem Cells or ESC) or from and growth factors applied at each stage. The boxed
reprogramming of somatic cells from individuals (induced genes represent key genes expressed at each stage. The
pluripotent stem cells or iPSC). Following a stepwize red text indicates signalling that must be repressed and
differentiation protocol mimicking the key steps in green text that must be activated
embryogenesis, cells are differentiated through FOXA2,
4 B. A. Calvert and A. L. Ryan (Firth)
toward the use of non-viral methods of limitations (summarized in Table 2). While ani-
reprogramming including mRNAs (Warren et al. mal models of lung disease have substantially
2010), episomal plasmids (Okita et al. 2008), contributed to our knowledge of fundamental
recombinant proteins (Zhou et al. 2009; Kim lung biology there has been little success in the
et al. 2009) using the four original Yamanaka translation of findings into the clinic for human
factors. Other transcription factors have also use (Ma et al. 2018). Animal model studies of
found to be useful in the generation of iPSC. human diseases are often limited in the patho-
Many of these relate to the superfamilies of the genic aspects of the disease that they accurately
transcription factors identified by Yamanaka, recapitulate; for example, bleomycin instillation
such as Oct3, Sox1 and Klf2 (Yu et al. 2007). of animal models is often used to generate in vivo
models of idiopathic pulmonary fibrosis, however
does not accurately represent the onset or propa-
3 iPSC and Their Capacity gation of the disease. While informing us of some
for Disease Modelling aspects, these models do not always replicate the
complete aetiology and pathogenesis of the dis-
iPSCs have evolved rapidly as a technology, ease being studied. Primary isolated human cells
enabling the effective modelling of human dis- are difficult to expand in culture without losing
ease, complimenting the more typical approaches their phenotype with passage (Schiller and Bittner
using animal models and immortalised cell lines. 1995). Further, human tissue availability can be
Each model system has its own benefits and limited and most often acquired post-mortem.
Application of iPSC to Modelling of Respiratory Diseases 5
This leads to a finite number of cells available for chapter will focus on their application to studying
research from a limited patient population, which human lung disease.
can result in limited use in high-throughput and Genetic disorders are a prime example of
drug screening research. Also, research into pri- where iPSC benefit over conventional in vitro
mary post-mitotic cells, such as that of neurones disease modelling. Genetic diseases are often
(Frade and Ovejero-Benito 2015), are restricted to rare and have multiple subtypes, such as those
the number of cells that can be initially isolated. seen in CF (Marson et al. 2016). Whilst the spe-
This also limits the study of disease propagation cific mutations of these subtypes are documented,
and onset to what is typically an advanced disease access to patient specific material is limited,
state. severely hindering studies of disease pathology.
iPSCs provide an alternative and complimen- Instead, self-renewing iPSC can have the genetic
tary research tool that can overcome several mutation induced via state of the art gene editing
limitations of animal models, primary and technology, such as clustered regularly
immortalized human cells. Restrictions of using interspaced palindromic repeat (CRISPR)/Cas9
primary and immortalized cell lines are (Qi et al. 2013; Haurwitz et al. 2010; Wang
surmounted due to their indefinite clonal expan- et al. 2013; Cong et al. 2013). A concerted effort
sion when maintained under specific culture over the past decade has seen the evolution of
conditions with the capacity for differentiation protocols to differentiate iPSC to cells of the
into multiple cell types comprising the human respiratory epithelium (Firth et al. 2014; Wong
body (Kogut et al. 2014; Firth et al. 2015; Menon et al. 2012; Green et al. 2011; Cheng et al. 2012;
et al. 2015; Ward and Gilad 2019; Hnatiuk and Hawkins et al. 2017). This technology now
Mercola 2019; Meijer et al. 2019; Fyfe 2019; enables rare genetic disorders to be modelled in
Fiorotto et al. 2019; Hoshina et al. 2018; Mucci a relevant and human cellular system. Several
et al. 2018; Tan et al. 2018) including cells within disease states have successfully been induced in
the respiratory system. iPSC, therefore, have the iPSC including adenosine deaminase deficiency-
potential to provide a seemingly unlimited source related severe combined immunodeficiency
of patient/disease specific cells. This opens up (ADA-SCID), Shwachman-Bodian-Diamond
multiple new options for research and the prospect syndrome (SBDS), Gaucher disease (GD) type
for autologous cell therapy (Ebert et al. 2012). This III, Duchenne’s Muscular Dystrophy (DMD),
6 B. A. Calvert and A. L. Ryan (Firth)
Parkinson disease (PD), Huntington disease respiratory system also contains a natural homeo-
(HD), juvenile-onset, type 1 diabetes mellitus static microbiota, which can drastically alter dur-
(JDM) (Park et al. 2008). The concept here is to ing times of disease and stress (Dang and
develop an iPSC line and induce a disease pheno- Marsland 2019; Man et al. 2017) and is an inter-
type in the cells by knocking out/in certain genes, nal organ exposed to the exterior environment
or challenging the cells with factors that may increasing the potential for epigenetic modifica-
onset disease. The field of neuroscience has par- tion (Sakurada 2010; Hagood 2014). These
ticularly benefited from the use of iPSC (Wang features must all be considered when creating an
and Doering 2012), as obtaining primary neuro- in vitro model of respiratory disease and reflected
nal tissue is particularly challenging. Such in the advantages and limitations of any given
diseases include Alzheimer’s disease (Kondo model system. iPSC have the potential to investi-
et al. 2013), Huntington’s disease (Kaye and gate mechanisms of human lung development
Finkbeiner 2013) and schizophrenia (Brennand providing insights into the differentiation
et al. 2011). The connexion to this paradigm is pathways from stem cell to fully differentiated
that iPSC derived from patient populations with tissues. In addition, they provide an opportunity
rare genetic disorders, can be gene corrected to reverse a disease phenotype and investigate
through use of the same gene editing technology. mechanisms of disease onset.
While providing isogenic controls for in vitro The first methods describing directed differen-
evaluation this additionally opens up the potential tiation of the respiratory epithelium from iPSC
for autologous cell based therapies reducing the focused primarily on specification of the lung
need for immunosuppression and the likelihood endoderm (Cheng et al. 2012; Kadzik and
of tissue rejection. In the respiratory field, proof- Morrisey 2012; Longmire et al. 2012a). Subse-
of–principle studies have demonstrated the cor- quently, three pioneering papers were published
rection of cystic fibrosis transmembrane regulator differentiating cells to more mature cells in the
(CFTR) in CF patient derived iPSC, which were respiratory epithelium (Wong et al. 2012; Kadzik
subsequently differentiated into functional epithe- and Morrisey 2012; Firth et al. 2014). These
lial cells (Firth et al. 2015; Crane et al. 2015). studies all strived to mimic lung embryonic devel-
Providing a basis for novel iPSC based therapies opment in a dish pushing cells through
for CF patients in the future. mesendoderm, to definitive endoderm
(DE) followed by anteriorization of the ventral
foregut endoderm (AFE) to primordial NKX2.1
4 Specification of Primordial expressing lung endodermal progenitor cells
Lung Progenitors from iPSC (LP). These cells have the capacity for differenti-
ation into cells akin to that for the mature human
Directed differentiation of iPSC toward lung lung including club, goblet, multiciliated, basal,
endoderm presents its own set of challenges, alveolar and neuroendocrine cells.
which the field has made substantial progress Understanding lung development is critical to
toward elucidating over the past decade (Firth efficiently driving pluripotent cells to generate the
et al. 2014; Hannan et al. 2015; Wong and cells and structures comprising the human lung.
Rossant 2013). The lungs are a sophisticated There is still a sparsity of specific knowledge of
organ system comprising of complex structures human lung development and much of our infor-
and over 40 different cell types; they include a mation is gained from transgenic mouse models
complex vasculature, sympathetic and parasym- tracing lineage specification (Bellusci et al.
pathetic neuronal innovation, structural support 1997a, b; Weaver et al. 1999, 2003; Okubo and
and a specialized respiratory epithelium. To add Hogan 2004; Rawlins et al. 2009a, b). Lung
to this complexity, the structure of the airways organogenesis begins in the embryonic period
changes to meet its functional requirements along with independent outpouchings of the ventral
the proximal-distal axis. Similar to the gut, the wall in the primitive foregut endoderm that
Application of iPSC to Modelling of Respiratory Diseases 7
elongate and branch into the surrounding mesen- activated during gastrulation. This is mimicked in
chyme. The respiratory mesenchyme is crucial in culture using Activin A and Wnt3a or Wnt ago-
many developmental and homeostatic processes nist CHIR99021 (Kubo et al. 2004). The APS can
within the lung. It provides key signalling ligands be pushed to DE through persistent activation of
to promote the development of lung structures, nodal signalling and inhibition of bone morpho-
including alveolargenesis, airway branching and genetic protein (BMP), using DMH-1, to suppress
the vasculature. The mesenchyme is the primary mesoderm derivation (Green et al. 2011; Ogaki
source of transforming growth factor beta (TGFβ) et al. 2013). Specification of DE from the
in the developing lung (McCulley et al. 2015; mesendoderm has been optimized and results in
White et al. 2006). It is an integral component a high efficiency of DE cells from iPSC (Mfopou
for natural development and TGFβ knockout et al. 2010). In embryonic development Wnt sig-
studies demonstrate impaired lung development nalling plays an important role in many cellular
(Sanford et al. 1997). The mesenchyme also functions, including differentiation and prolifera-
provides the primary source of Wnt signalling, tion, in Vitro Wnt3A signalling is used to skew
key for branching morphogenesis of airway epi- away from SOX2 expressing ectoderm and pro-
thelium (Miller et al. 2012) (Fig. 1). mote endodermal differentiation. DE also
DE gives rise to lungs, thyroid, pancreas, liver expresses cell surfaces markers CXCR4, a che-
and intestines and is specified from the anterior mokine receptor important in cellular prolifera-
primitive streak (APS), induced from pluripotent tion and cKit that can purify the DE through
cells through strong activation of nodal and FACS sorting (Wong et al. 2010; Wang et al.
canonical wnt signaling, which are synergistically 2012) (Fig. 2).
Fig. 2 Differentiation of primordial lung progenitors above the cell types. Alveolar Type II (ATII) cells are
towards proximal and distal lung fate. iPSC derived and the progenitor cells giving rise to mature ATII and ATI
purified lung progenitor cells expressing NKx2.1 can be cells responsive for the functional alveolar unit for gas
directed toward proximal and distal fates through activa- exchange. Sox2 expressing proximal basal cells are able
tion (green) and inhibition (red) of signalling pathways to differentiate and give rise to all cells of the mature
including those driven by FGFs, BMPs and wnts. The conducting airways including secretory, basal and
markers of the specific lineages are indicated in boxes multiciliated cells responsible for mucociliary clearance
8 B. A. Calvert and A. L. Ryan (Firth)
Anterioriziation of the DE to generate the fore- tissues (Lee et al. 2001; Rossi et al. 1995;
gut, identified through SOX2 and FOXA2 Acebron et al. 1995). Although the pathways
expressing cells does not appear to critically that distinguish between these organ systems
depend on Activin A/TGF-β-signalling. Inhibi- are not well-characterised, lineages can be
tion of TGFβ is known to assist in driving AFE identified though co-expression of PAX8
(Green et al. 2011) and an inhibition of Wnt- and (thyroid, (Rossi et al. 1995) and PAX6
BMP-signalling is critical in optimizing this tran- (forebrain, (Corbin et al. 2003; Takahashi and
sition. FOXA2 is an essential transcription factor Osumi 2002).
for lung development, FOXA2 / mice do not Fibroblast Growth Factor (FGF) signalling is
develop lungs (Wan et al. 2004; Aubin et al. integral in defining lung endoderm and inducing
1997). Retinoic acid (RA), commonly used in NKX2.1 expression (Rankin and Zorn 2014;
lung differentiation protocols has dual effects Dailey et al. 2005; Xian et al. 2005). In addition,
and can either posteriorize or dorsalize the foregut sonic hedgehog (Shh) and transcriptional
creating PDX1-positive pancreatic duodenal programs of the forkhead (Fox), and GATA-
cells. Its use in in vitro differentiation protocols family members, are involved in specification of
is, therefore, not entirely clear. A number of stud- the lung from the AFE (Hogan 1999; Whitsett
ies have demonstrated the importance of RA, 1998). Differentiation towards lung progenitors
influencing micro RNAs, however, short pulses can be directed away from specification of thyroid
of RA can also maintain the stemness of iPSC progenitors through controlled FGF2 expression.
through inhibition of the canonical Wnt pathway, Studies have demonstrated that high
essential for differentiation (De Angelis et al. concentrations of FGF activate Shh expression
2018). In combination with Wnt/β-catenin, RA to generate NKX2–1 expressing lung progenitors
can act synergistically with FGF-2 and BMP-4 and thyroid (Rankin and Zorn 2014; Serra et al.
to generate CDX2-positive posterior endoderm 2017; Kurmann et al. 2015; Longmire et al.
further complicating the methods applied to 2012b). Dye et al. demonstrated that suppression
iPSC differentiation (Davenport et al. 2016). of FGF activity whilst maintaining Shh signalling
The successful generation of a primordial allowed for a more specific differentiation to lung
lung progenitor cell is accredited to the induction primed NKX2.1 expressing cells (Dye et al.
of lung transcription factor NKX2.1 (also known 2015). Sequential inhibition of TGFβ signalling,
as TTF1) (Longmire et al. 2012a; Lazzaro et al. followed by subsequent activation of FGF and
1991). The function of NKX2.1 is not entirely BMP4 signalling pathways can support further
understood. In mouse models, it is important in differentiation to lung epithelium (Longmire
the development of respiratory tissue as well as et al. 2012a).
other thoracic structures (Minoo et al. 1999;
Minoo 2000). Purification of iPSC derived
NKX2.1 primordial lung progenitor cells 5 Proximal and Distal Fate
initially proved inefficient and purification was of Lung Progenitors
limited through lack of a suitable surface anti-
gen. A recent study has shown that these Lung buds arise from the lateral part of the fore-
NKX2.1 cells can be selected using a CD47- gut prior to forming the trachea and recent data
high, CD26-low surface marker expression suggests that the progenitors at the leading tip of
profile (Hawkins et al. 2017). Alternatively, these lung buds differ in humans and mice and
Carboxypeptidase M is also expressed in these can specify both the proximal and distal regions
cells and can be used to purify a similar of the lung (Miller et al. 2018; Danopoulos et al.
population of lung progenitors (Konishi et al. 2018; Nikolic et al. 2017). To study these fate
2016; Gotoh et al. 2014). While NKX2.1 defines decisions in humans a three-dimensional
specification of lung progenitor cells, it also has organoid system has been established to culture
notable expression in the brain and thyroid fetal lung bud tips (Miller et al. 2018; Danopoulos
Application of iPSC to Modelling of Respiratory Diseases 9
et al. 2018; Nikolic et al. 2017). Cells at the the proximal airways from their distal
leading tip of these buds express NKx2.1, SOX2 counterparts that continue to selectively express
and SOX9 in humans; this contrasts with the cells SOX9 (Danopoulos et al. 2018). As discussed
in the same region of the mouse which either above, bud tip progenitors co-express both
co-express NKX2.1 and SOX2 or SOX9 (Miller SOX2 and SOX9 during psuedoglandular phase
et al. 2018). A similar population of cells has been of human embryogenetic development, however,
observed in iPSC derived lung progenitors from will become determined before development
humans (Miller et al. 2018). reaches the canalicular stages, controlled by
Detailed analysis of the regulation of proximal signals received within their proximity microen-
and distal fate decisions has been extensively vironment (Danopoulos et al. 2018).
studied in mice using lineage tracing models Currently there are no published studies spe-
(Rawlins et al. 2009b; Barkauskas et al. 2013; cifically focusing on the specification and expan-
Rock et al. 2009). In humans, we rely on the sion of an iPSC-derived basal cell. Proximal
development of robust in vitro models. Both airway basal cells are currently identified by the
fetal and iPSC derived lung bud organoids will expression of cytokeratin 5 (KRT5), TP63, nerve
differentiate when exposed to FGF7, CHIR and growth factor receptor (NGFR) and integrin alpha
Retinoic Acid, generating cells akin to those in 6 (ITGA6 or CD49f) (Daniely et al. 2004). Dur-
the human airways (Miller et al. 2018). By ing development, it appears that SMAD signaling
utilizing more sophisticated scaffold materials, plays a role in the lineage differentiation pushing
tubular airway-like structures can also be away from lung progenitor stem cells. TGFβ and
replicated in vitro, resembling that of the canalic- BMP4 mediated SMAD signaling has, however,
ular development in lung embryogenesis (Dye been demonstrated to promote the differentiation
et al. 2016). Additional factors to consider when from bud tips to a basal cell like phenotype, using
developing more complex models, is the impor- an organoid based in vitro system (Dye et al.
tance of the mesenchymal supporting cells in 2015). At this stage, SMAD inhibition promotes
controlling the fate of lung progenitors towards the maintenance of the basal cell phenotype and
a proximal or distal epithelial phenotypes. Signals further differentiation beyond a precursor cell
between the mesenchyme and epithelium are crit- (Mou et al. 2016).
ical in lung development, and supplying the exog- Another key component for differentiation to
enous growth factors to an in vitro system may be lung basal cell epithelium is NOTCH signaling
in sufficient to allow us to fully appreciate the (Rock et al. 2011). Activation of Notch signaling
signals responsible for proximal and distal human pathways is critical in embryonic development
lung fate decisions (El Agha et al. 2014). and plays various roles in a more developed sys-
tem. In the basal cell, NOTCH signaling is
involved in its further differentiation to a mature
6 Tracheo-Bronchial epithelial subtype. Maturation of airways cells is
Differentiation and Disease most commonly achieved at an “air-liquid inter-
Models face” or ALI, a platform arguably more complex
than in vitro systems for most other organ systems
Specification of distal and proximal lung cells (de Jong et al. 1994). In this system, human
requires precise spatiotemporal regulation of bronchial epithelial cells (HBEC) are seeded to
Wnt, Notch and FGF signaling pathways. The transwell inserts, allowed to grow to confluence
proximal airways, comprising of tracheal and generating an epithelial barrier with tight
bronchial cartilaginous airways, are populated junctions. Once sufficient trans-epithelial electri-
by basal cells, as the predominant progenitor cal resistance (TEER) is generated, the apical
cell, in addition to club and goblet secretory media is removed generating an apical air inter-
cells and multiciliated cells as the primary func- face. Over a 28-day period the cells undergo
tional epithelium. SOX2 expression delineates process of polarization, pseudo stratification and
10 B. A. Calvert and A. L. Ryan (Firth)
engraftment. Published data has demonstrated the providing an unprecedented access to human
successful use of iPSC-derived cells and their biology. Like any model system, they are not
regenerative therapeutic potential in a multitude without their limitations and should be used
of disorders using animal models and in vitro alongside other available systems suitable for
based techniques. These include models of liver completely addressing the specific experimental
injury (Liu et al. 2011), muscular related question at hand. For the lung, exposure of the
disorders (Kazuki et al. 2010; Tan et al. 2012), cells to the environment, a constant for the millieu
blood/immunological disorders (Suzuki et al. of cells in the airways, is not yet considered
2013), cardiovascular disease (Shiba et al. 2016) in this model system. Furthermore, epigenetic
and spinal cord injury (Nori et al. 2011), among changes causative of disease are likely wiped
others (Li et al. 2017). In the clinic, patient spe- during the reprogramming process loosing these
cific, iPSC-derived retinal epithelial cells have markers as disease phenotypes. However, by
successfully been transplanted back into patients utilising iPSC, a seemingly limitless source of
with macular degeneration, marking the first cells is available and representative of the parent
attempt of iPSC to treat a patient population genetic profile enabling both human and patient
(Mandai et al. 2017). Unfortunately, the reality specific cellular models to be developed. Further,
of this is infinitely more challenging and complex the use of iPSC allows for robust investigations
for the lung. The lung comprises of over 40 differ- into the developmental pathways involved in a
ent functional cell types forming airways, vascu- human cell-based system that would otherwise be
lature, cartilage, immune system, sympathetic and challenging. In iPSC, individual genes can be
parasympathetic neural tissues, glands and sup- manipulated and evaluated side-by-side with
portive parenchyma. In the case of lung disease, it their isogenic counterparts enabling precise
unlikely that one cell type is affected in isolation effects of specific genes to be evaluated. As
and more reasonable to think of changes more such, iPSC provide an incredibly valuable
globally with specific microenvironments model system as we progress to an era of
adapting to maximize protection and function of personalized medicine.
the lung for gas exchange. Long-term replace-
ment of cells will likely require access to the
relevant cellular niche for long-term reconstitu- 10 Concluding Remarks
tion and adaptation of the niche to reflect that of a
non-diseased lung to sustain a “healthy” Substantial progress has been made since
engrafted cell and derivatives. Progress in the Yamanaka’s discovery of induced pluripotency
field of lung regeneration has been substantial in humans in 2007. From initially identifying an
but we now need to start thinking toward more iPSC inducing minimal cocktail of transcription
complex models, which more closely recapitulate factors, to sucessful use of iPSC as a therapeutic
the in vivo cellular niche. This will require, at tool, highlights the speed at which this technlogy
minimum, collaborative efforts between has evolved. Although initial derivation of rele-
biologists, bioengineers and novel translational vant respiratory cells from iPSC lagged behing
imaging techniques. other organ systems, we still have a plethora of
methods available to study respiratory disease in a
biologically relevant cell type, overcoming the
9 The Future of iPSC shortfall of current model systems. Progress is
for Respiratory Disease currently limited by our fundamental lack of
understanding of the mechanisms controlling
iPSC present a novel, human and patient specific human lung development, the precise identity
avenue for research and therapeutic advancement. and function of human lung cell types and the
iPSC have enabled the generation of human and genetic and epigenetic control of human lung fate.
disease-related models to be created in vitro As our capacity to model human lung disease
12 B. A. Calvert and A. L. Ryan (Firth)
evolves, so will our understanding of the patho- Crane AM et al (2015) Targeted correction and restored
genesis of human lung disease. iPSC models function of the CFTR gene in cystic fibrosis induced
pluripotent stem cells. Stem Cell Rep 4(4):569–577
remain an exciting prospect. Dailey L, Ambrosetti D, Mansukhani A, Basilico C
(2005) Mechanisms underlying differential responses
Acknowledgements Thank you to Sergio Bianco in the to FGF signaling. Cytokine Growth Factor Rev 16
USC Department of Stem Cell and Regenerative Medicine (2):233–247
for production of the artwork for the schematic diagrams in Dang AT, Marsland BJ (2019) Microbes, metabolites, and
figures 1 and 2. the gut-lung axis. Mucosal Immunol 12(4):843–850
Daniely Y et al (2004) Critical role of p63 in the develop-
ment of a normal esophageal and tracheobronchial
Funding A.L.R. is funded by the Hastings Foundation, epithelium. Am J Phys Cell Physiol 287(1):C171–
Cystic Fibrosis Foundation Therapeutics (CFFT, C181
Firth15XX0, Firth17XX0) and NIH/NHLBI, R01 Danopoulos S et al (2018) Human lung branching mor-
HL139828. phogenesis is orchestrated by the spatiotemporal distri-
bution of ACTA2, SOX2, and SOX9. Am J Physiol
Lung Cell Mol Physiol 314(1):L144–L149
Davenport C, Diekmann U, Budde I, Detering N, Naujok
References O (2016) Anterior-posterior patterning of definitive
endoderm generated from human embryonic stem
Acebron A, Aza-Blanc P, Rossi DL, Lamas L, Santisteban cells depends on the differential signaling of retinoic
P (1995) Congenital human thyroglobulin defect due to acid, Wnt-, and BMP-signaling. Stem Cells 34
low expression of the thyroid-specific transcription (11):2635–2647
factor TTF-1. J Clin Invest 96(2):781–785 De Angelis MT, Parrotta EI, Santamaria G, Cuda G (2018)
Aubin J, Lemieux M, Tremblay M, Berard J, Jeannotte L Short-term retinoic acid treatment sustains
(1997) Early postnatal lethality in Hoxa-5 mutant mice pluripotency and suppresses differentiation of human
is attributable to respiratory tract defects. Dev Biol 192 induced pluripotent stem cells. Cell Death Dis 9(1):6
(2):432–445 de Jong PM et al (1994) Ciliogenesis in human bronchial
Barkauskas CE et al (2013) Type 2 alveolar cells are stem epithelial cells cultured at the air-liquid interface. Am J
cells in adult lung. J Clin Invest 123(7):3025–3036 Respir Cell Mol Biol 10(3):271–277
Barnes PJ et al (2015) Barriers to new drug development in Dowey SN, Huang X, Chou BK, Ye Z, Cheng L (2012)
respiratory disease. Eur Respir J 45(5):1197–1207 Generation of integration-free human induced pluripo-
Bellusci S et al (1997a) Involvement of Sonic hedgehog tent stem cells from postnatal blood mononuclear cells
(Shh) in mouse embryonic lung growth and morpho- by plasmid vector expression. Nat Protoc 7
genesis. Development 124(1):53–63 (11):2013–2021
Bellusci S, Grindley J, Emoto H, Itoh N, Hogan BL Dye BR et al (2015) In vitro generation of human pluripo-
(1997b) Fibroblast growth factor 10 (FGF10) and tent stem cell derived lung organoids. elife 4:e05098
branching morphogenesis in the embryonic mouse Dye BR et al (2016) A bioengineered niche promotes
lung. Development 124(23):4867–4878 in vivo engraftment and maturation of pluripotent
Brennand KJ et al (2011) Modelling schizophrenia using stem cell derived human lung organoids. elife 5:pii:
human induced pluripotent stem cells. Nature 473 e19732
(7346):221–225 Ebert AD, Liang P, Wu JC (2012) Induced pluripotent
Carey BW et al (2009) Reprogramming of murine and stem cells as a disease modeling and drug screening
human somatic cells using a single polycistronic vec- platform. J Cardiovasc Pharmacol 60(4):408–416
tor. Proc Natl Acad Sci U S A 106(1):157–162 El Agha E et al (2014) Fgf10-positive cells represent a
Chen YW et al (2017) A three-dimensional model of progenitor cell population during lung development
human lung development and disease from pluripotent and postnatally. Development 141(2):296–306
stem cells. Nat Cell Biol 19(5):542–549 Fiorotto R et al (2019) Liver diseases in the dish: iPSC and
Cheng X et al (2012) Self-renewing endodermal progeni- organoids as a new approach to modeling liver
tor lines generated from human pluripotent stem cells. diseases. Biochim Biophys Acta Mol basis Dis 1865
Cell Stem Cell 10(4):371–384 (5):920–928
Cong L et al (2013) Multiplex genome engineering using Firth AL et al (2014) Generation of multiciliated cells in
CRISPR/Cas systems. Science (New York, NY) 339 functional airway epithelia from human induced plu-
(6121):819–823 ripotent stem cells. Proc Natl Acad Sci U S A 111(17):
Corbin JG, Rutlin M, Gaiano N, Fishell G (2003) Combi- E1723–E1730
natorial function of the homeodomain proteins Nkx2.1 Firth AL et al (2015) Functional gene correction for cystic
and Gsh2 in ventral telencephalic patterning. Develop- fibrosis in lung epithelial cells generated from patient
ment 130(20):4895–4906 iPSCs. Cell Rep 12(9):1385–1390
Application of iPSC to Modelling of Respiratory Diseases 13
Frade JM, Ovejero-Benito MC (2015) Neuronal cell cycle: Jia F et al (2010) A nonviral minicircle vector for deriving
the neuron itself and its circumstances. Cell Cycle 14 human iPS cells. Nat Methods 7(3):197–199
(5):712–720 Kadzik RS, Morrisey EE (2012) Directing lung endoderm
Fujie Y et al (2014) New type of Sendai virus vector differentiation in pluripotent stem cells. Cell Stem Cell
provides transgene-free iPS cells derived from chim- 10(4):355–361
panzee blood. PLoS One 9(12):e113052 Karow M et al (2011) Site-specific recombinase strategy to
Fusaki N, Ban H, Nishiyama A, Saeki K, Hasegawa M create induced pluripotent stem cells efficiently with
(2009) Efficient induction of transgene-free human plasmid DNA. Stem Cells 29(11):1696–1704
pluripotent stem cells using a vector based on Sendai Kaye JA, Finkbeiner S (2013) Modeling Huntington’s
virus, an RNA virus that does not integrate into the host disease with induced pluripotent stem cells. Mol Cell
genome. Proc Jpn Acad Ser B Phys Biol Sci 85 Neurosci 56:50–64
(8):348–362 Kazuki Y et al (2010) Complete genetic correction of iPS
Fyfe I (2019) Mutation-specific amyloid-beta processing cells from Duchenne muscular dystrophy. Mol Ther 18
in iPSC-derived neurons. Nat Rev Neurol 15(6):310 (2):386–393
Gotoh S et al (2014) Generation of alveolar epithelial Kim D et al (2009) Generation of human induced pluripo-
spheroids via isolated progenitor cells from human tent stem cells by direct delivery of reprogramming
pluripotent stem cells. Stem Cell Rep 3(3):394–403 proteins. Cell Stem Cell 4(6):472–476
Green MD et al (2011) Generation of anterior foregut Kim JS, Choi HW, Hong YJ, Do JT (2016) Generation of
endoderm from human embryonic and induced plurip- partially reprogrammed cells and fully reprogrammed
otent stem cells. Nat Biotechnol 29(3):267–272 iPS cells by plasmid transfection. Methods Mol Biol
Hagood JS (2014) Beyond the genome: epigenetic 1357:85–95
mechanisms in lung remodeling. Physiology Kogut I, Roop DR, Bilousova G (2014) Differentiation of
(Bethesda) 29(3):177–185 human induced pluripotent stem cells into a
Hannan NR, Sampaziotis F, Segeritz CP, Hanley NA, keratinocyte lineage. Methods Mol Biol 1195:1–12
Vallier L (2015) Generation of distal airway epithelium Kondo T et al (2013) Modeling Alzheimer's disease with
from multipotent human foregut stem cells. Stem Cells iPSCs reveals stress phenotypes associated with intra-
Dev 24(14):1680–1690 cellular Abeta and differential drug responsiveness.
Haurwitz RE, Jinek M, Wiedenheft B, Zhou K, Doudna JA Cell Stem Cell 12(4):487–496
(2010) Sequence- and structure-specific RNA Konishi S et al (2016) Directed induction of functional
processing by a CRISPR endonuclease. Science multi-ciliated cells in proximal airway epithelial
(New York, NY) 329(5997):1355–1358 spheroids from human pluripotent stem cells. Stem
Hawkins F et al (2017) Prospective isolation of NKX2-1- Cell Rep 6(1):18–25
expressing human lung progenitors derived from plu- Kubo A et al (2004) Development of definitive endoderm
ripotent stem cells. J Clin Invest 127(6):2277–2294 from embryonic stem cells in culture. Development
Hnatiuk A, Mercola M (2019) Stars in the night sky: iPSC- 131(7):1651–1662
cardiomyocytes return the patient context to drug Kurmann AA et al (2015) Regeneration of thyroid func-
screening. Cell Stem Cell 24(4):506–507 tion by transplantation of differentiated pluripotent
Hogan BL (1999) Morphogenesis. Cell 96(2):225–233 stem cells. Cell Stem Cell 17(5):527–542
Hoshina A et al (2018) Development of new method to Lazzaro D, Price M, de Felice M, Di Lauro R (1991) The
enrich human iPSC-derived renal progenitors using transcription factor TTF-1 is expressed at the onset of
cell surface markers. Sci Rep 8(1):6375 thyroid and lung morphogenesis and in restricted
Hotta A et al (2009) Isolation of human iPS cells using regions of the foetal brain. Development 113
EOS lentiviral vectors to select for pluripotency. Nat (4):1093–1104
Methods 6(5):370–376 Lee BJ et al (2001) TTF-1, a homeodomain gene required
Hu K, Slukvin I (2013) Generation of transgene-free iPSC for diencephalic morphogenesis, is postnatally
lines from human normal and neoplastic blood cells expressed in the neuroendocrine brain in a develop-
using episomal vectors. Methods Mol Biol 997:163–176 mentally regulated and cell-specific fashion. Mol Cell
Huang SX et al (2015) The in vitro generation of lung and Neurosci 17(1):107–126
airway progenitor cells from human pluripotent stem Lee JH et al (2013) Surfactant protein-C chromatin-bound
cells. Nat Protoc 10(3):413–425 green fluorescence protein reporter mice reveal hetero-
Hubbard R (2006) The burden of lung disease. Thorax 61 geneity of surfactant protein C-expressing lung cells.
(7):557–558 Am J Respir Cell Mol Biol 48(3):288–298
Jacob A et al (2017) Differentiation of human pluripotent Li Y-C, Zhu K, Young T-H (2017) Induced pluripotent
stem cells into functional lung alveolar epithelial cells. stem cells, form in vitro tissue engineering to in vivo
Cell Stem Cell 21(4):472–488. e410 allogeneic transplantation. J Thorac Dis 9(3):455–459
14 B. A. Calvert and A. L. Ryan (Firth)
Liao J et al (2008) Enhanced efficiency of generating Minoo P (2000) Transcriptional regulation of lung devel-
induced pluripotent stem (iPS) cells from human opment: emergence of specificity. Respir Res 1
somatic cells by a combination of six transcription (2):109–115
factors. Cell Res 18(5):600–603 Minoo P, Su G, Drum H, Bringas P, Kimura S (1999)
Liu H, Kim Y, Sharkis S, Marchionni L, Jang Y-Y (2011) Defects in tracheoesophageal and lung morphogenesis
In vivo liver regeneration potential of human induced in Nkx2.1( / ) mouse embryos. Dev Biol 209
pluripotent stem cells from diverse origins. Sci Transl (1):60–71
Med 3(82):82ra39–82ra39 Mou H et al (2016) Dual SMAD signaling inhibition
Longmire TA et al (2012a) Efficient derivation of purified enables long-term expansion of diverse epithelial
lung and thyroid progenitors from embryonic stem basal cells. Cell Stem Cell 19(2):217–231
cells. Cell Stem Cell 10(4):398–411 Mucci A et al (2018) iPSC-derived macrophages effec-
Longmire TA, Ikonomou L, Kotton DN (2012b) Mouse tively treat pulmonary alveolar Proteinosis in Csf2rb-
ESC differentiation to Nkx2.1+ lung and thyroid deficient mice. Stem Cell Rep 11(3):696–710
progenitors. Bio Protoc 2(22):pii: e295 Murugan V (2009) Embryonic stem cell research: a decade
Lozano R et al (2012) Global and regional mortality from of debate from bush to Obama. Yale J Biol Med 82
235 causes of death for 20 age groups in 1990 and (3):101–103
2010: a systematic analysis for the global burden of Narsinh KH et al (2011) Generation of adult human
disease study 2010. Lancet (London, England) 380 induced pluripotent stem cells using nonviral
(9859):2095–2128 minicircle DNA vectors. Nat Protoc 6(1):78–88
Ma Q et al (2018) Regeneration of functional alveoli by Nemes C et al (2014) Generation of mouse induced plu-
adult human SOX9(+) airway basal cell transplanta- ripotent stem cells by protein transduction. Tissue Eng
tion. Protein Cell 9(3):267–282 Part C Methods 20(5):383–392
Man WH, de Steenhuijsen Piters WA, Bogaert D Nikolic MZ et al (2017) Human embryonic lung epithelial
(2017) The microbiota of the respiratory tract: gate- tips are multipotent progenitors that can be expanded
keeper to respiratory health. Nat Rev Microbiol 15 in vitro as long-term self-renewing organoids. elife 6:
(5):259–270 pii: e26575
Mandai M et al (2017) Autologous induced stem-cell– Nori S et al (2011) Grafted human-induced pluripotent
derived retinal cells for macular degeneration. N Engl stem-cell-derived neurospheres promote motor func-
J Med 376(11):1038–1046 tional recovery after spinal cord injury in mice. Proc
Marson FAL, Bertuzzo CS, Ribeiro JD (2016) Classifica- Natl Acad Sci U S A 108(40):16825–16830
tion of CFTR mutation classes. Lancet Respir Med 4 Ogaki S, Shiraki N, Kume K, Kume S (2013) Wnt and
(8):e37–e38 Notch signals guide embryonic stem cell differentia-
McCauley KB et al (2017) Efficient derivation of func- tion into the intestinal lineages. Stem Cells 31
tional human airway epithelium from pluripotent stem (6):1086–1096
cells via temporal regulation of Wnt signaling. Cell Ohnuki M et al (2014) Dynamic regulation of human
Stem Cell 20(6):844–857. e846 endogenous retroviruses mediates factor-induced
McCulley D, Wienhold M, Sun X (2015) The pulmonary reprogramming and differentiation potential. Proc
mesenchyme directs lung development. Curr Opin Natl Acad Sci U S A 111(34):12426–12431
Genet Dev 32:98–105 Okita K, Ichisaka T, Yamanaka S (2007) Generation of
Meijer M et al (2019) A single-cell model for synaptic germline-competent induced pluripotent stem cells.
transmission and plasticity in human iPSC-derived Nature 448(7151):313–317
neurons. Cell Rep 27(7):2199–2211. e2196 Okita K, Nakagawa M, Hyenjong H, Ichisaka T,
Menon T et al (2015) Lymphoid regeneration from gene- Yamanaka S (2008) Generation of mouse induced
corrected SCID-X1 subject-derived iPSCs. Cell Stem pluripotent stem cells without viral vectors. Science
Cell 16(4):367–372 (New York, NY) 322(5903):949–953
Mfopou JK, Chen B, Sui L, Sermon K, Bouwens L (2010) Okita K, Hong H, Takahashi K, Yamanaka S (2010)
Recent advances and prospects in the differentiation of Generation of mouse-induced pluripotent stem cells
pancreatic cells from human embryonic stem cells. with plasmid vectors. Nat Protoc 5(3):418–428
Diabetes 59(9):2094–2101 Okita K et al (2011) A more efficient method to generate
Miller MF et al (2012) Wnt ligands signal in a cooperative integration-free human iPS cells. Nat Methods 8
manner to promote foregut organogenesis. Proc Natl (5):409–412
Acad Sci U S A 109(38):15348–15353 Okubo T, Hogan BL (2004) Hyperactive Wnt signaling
Miller AJ et al (2018) In vitro induction and in vivo changes the developmental potential of embryonic
engraftment of lung bud tip progenitor cells derived lung endoderm. J Biol 3(3):11
from human pluripotent stem cells. Stem Cell Rep 10 Okuyama H et al (2019) Transplantation of multiciliated
(1):101–119 airway cells derived from human iPS cells using an
Application of iPSC to Modelling of Respiratory Diseases 15
artificial tracheal patch into rat trachea. J Tissue Eng Stadtfeld M, Hochedlinger K (2009) Without a trace?
Regen Med 13(6):1019–1030 PiggyBac-ing toward pluripotency. Nat Methods 6
Park IH et al (2008) Disease-specific induced pluripotent (5):329–330
stem cells. Cell 134(5):877–886 Strikoudis A et al (2019) Modeling of fibrotic lung disease
Qi LS et al (2013) Repurposing CRISPR as an using 3D organoids derived from human pluripotent
RNA-guided platform for sequence-specific control of stem cells. Cell Rep 27(12):3709–3723. e3705
gene expression. Cell 152(5):1173–1183 Suzuki K et al (2008) Highly efficient transient gene
Rankin SA, Zorn AM (2014) Gene regulatory networks expression and gene targeting in primate embryonic
governing lung specification. J Cell Biochem 115 stem cells with helper-dependent adenoviral vectors.
(8):1343–1350 Proc Natl Acad Sci U S A 105(37):13781–13786
Rawlins EL, Clark CP, Xue Y, Hogan BL (2009a) The Id2 Suzuki N et al (2013) Generation of engraftable
+ distal tip lung epithelium contains individual hematopoietic stem cells from induced pluripotent
multipotent embryonic progenitor cells. Development stem cells by way of teratoma formation. Mol Ther
136(22):3741–3745 21(7):1424–1431
Rawlins EL et al (2009b) The role of Scgb1a1+ Clara cells Takahashi M, Osumi N (2002) Pax6 regulates specifica-
in the long-term maintenance and repair of lung air- tion of ventral neurone subtypes in the hindbrain by
way, but not alveolar, epithelium. Cell Stem Cell 4 establishing progenitor domains. Development 129
(6):525–534 (6):1327–1338
Rock JR et al (2009) Basal cells as stem cells of the mouse Takahashi K, Yamanaka S (2006) Induction of pluripotent
trachea and human airway epithelium. Proc Natl Acad stem cells from mouse embryonic and adult fibroblast
Sci U S A 106(31):12771–12775 cultures by defined factors. Cell 126(4):663–676
Rock JR et al (2011) Notch-dependent differentiation of Takahashi K, Okita K, Nakagawa M, Yamanaka S (2007a)
adult airway basal stem cells. Cell Stem Cell 8 Induction of pluripotent stem cells from fibroblast
(6):639–648 cultures. Nat Protoc 2(12):3081–3089
Rossi DL, Acebron A, Santisteban P (1995) Function of Takahashi K et al (2007b) Induction of pluripotent stem
the homeo and paired domain proteins TTF-1 and cells from adult human fibroblasts by defined factors.
Pax-8 in thyroid cell proliferation. J Biol Chem 270 Cell 131(5):861–872
(39):23139–23142 Tammam S et al (2016) Nuclear delivery of recombinant
Sakurada K (2010) Environmental epigenetic OCT4 by chitosan nanoparticles for transgene-free
modifications and reprogramming-recalcitrant genes. generation of protein-induced pluripotent stem cells.
Stem Cell Res 4(3):157–164 Oncotarget 7(25):37728–37739
Sanford LP et al (1997) TGFbeta2 knockout mice have Tan Q, Lui PP, Rui YF, Wong YM (2012) Comparison of
multiple developmental defects that are potentials of stem cells isolated from tendon and bone
non-overlapping with other TGFbeta knockout marrow for musculoskeletal tissue engineering. Tissue
phenotypes. Development 124(13):2659–2670 Eng A 18(7–8):840–851
Schiller JH, Bittner G (1995) Loss of the tumorigenic Tan YT et al (2018) Respecifying human iPSC-derived
phenotype with in vitro, but not in vivo, passaging of blood cells into highly engraftable hematopoietic stem
a novel series of human bronchial epithelial cell lines: and progenitor cells with a single factor. Proc Natl
possible role of an alpha 5/beta 1-integrin-fibronectin Acad Sci U S A 115(9):2180–2185
interaction. Cancer Res 55(24):6215–6221 Thier M, Munst B, Edenhofer F (2010) Exploring refined
Serra M et al (2017) Pluripotent stem cell differentiation conditions for reprogramming cells by recombinant
reveals distinct developmental pathways regulating Oct4 protein. Int J Dev Biol 54(11–12):1713–1721
lung- versus thyroid-lineage specification. Develop- Thier M, Munst B, Mielke S, Edenhofer F (2012) Cellular
ment 144(21):3879–3893 reprogramming employing recombinant sox2 protein.
Shafa M et al (2018) Human induced pluripotent stem cell- Stem Cells Int 2012:549846
derived lung progenitor and alveolar epithelial cells Wan H et al (2004) Foxa2 is required for transition to air
attenuate hyperoxia-induced lung injury. Cytotherapy breathing at birth. Proc Natl Acad Sci U S A 101
20(1):108–125 (40):14449–14454
Shiba Y et al (2016) Allogeneic transplantation of iPS cell- Wang H, Doering LC (2012) Induced pluripotent stem
derived cardiomyocytes regenerates primate hearts. cells to model and treat neurogenetic disorders. Neural
Nature 538(7625):388–391 Plast 2012:346053
Si-Tayeb K et al (2010) Generation of human induced Wang P et al (2012) A molecular signature for purified
pluripotent stem cells by simple transient transfection definitive endoderm guides differentiation and isola-
of plasmid DNA encoding reprogramming factors. tion of endoderm from mouse and human embryonic
BMC Dev Biol 10:81 stem cells. Stem Cells Dev 21(12):2273–2287
Sommer CA et al (2009) Induced pluripotent stem cell Wang H et al (2013) One-step generation of mice carrying
generation using a single lentiviral stem cell cassette. mutations in multiple genes by CRISPR/Cas-mediated
Stem Cells 27(3):543–549 genome engineering. Cell 153(4):910–918
16 B. A. Calvert and A. L. Ryan (Firth)
Ward MC, Gilad Y (2019) A generally conserved response Wong JC et al (2010) Definitive endoderm derived from
to hypoxia in iPSC-derived cardiomyocytes from human embryonic stem cells highly express the
humans and chimpanzees. elife 8:pii: e42374 integrin receptors alphaV and beta5. Cell Adhes Migr
Warren L et al (2010) Highly efficient reprogramming to 4(1):39–45
pluripotency and directed differentiation of human Wong AP et al (2012) Directed differentiation of human
cells with synthetic modified mRNA. Cell Stem Cell pluripotent stem cells into mature airway epithelia
7(5):618–630 expressing functional CFTR protein. Nat Biotechnol
Weaver M, Yingling JM, Dunn NR, Bellusci S, Hogan BL 30(9):876–882
(1999) Bmp signaling regulates proximal-distal differ- Xian W, Schwertfeger KL, Vargo-Gogola T, Rosen JM
entiation of endoderm in mouse lung development. (2005) Pleiotropic effects of FGFR1 on cell prolifera-
Development 126(18):4005–4015 tion, survival, and migration in a 3D mammary epithe-
Weaver M, Batts L, Hogan BL (2003) Tissue interactions lial cell model. J Cell Biol 171(4):663–673
pattern the mesenchyme of the embryonic mouse lung. Yamashita M, Emerman M (2006) Retroviral infection of
Dev Biol 258(1):169–184 non-dividing cells: old and new perspectives. Virology
White AC et al (2006) FGF9 and SHH signaling coordi- 344(1):88–93
nate lung growth and development through regulation Yu J et al (2007) Induced pluripotent stem cell lines
of distinct mesenchymal domains. Development 133 derived from human somatic cells. Science
(8):1507–1517 (New York, NY) 318(5858):1917–1920
Whitsett J (1998) A lungful of transcription factors. Nat Yu J et al (2009) Human induced pluripotent stem cells
Genet 20(1):7–8 free of vector and transgene sequences. Science
Wilkinson DC et al (2017) Development of a three- (New York, NY) 324(5928):797–801
dimensional bioengineering technology to generate Yusa K, Rad R, Takeda J, Bradley A (2009) Generation
lung tissue for personalized disease modeling. Stem of transgene-free induced pluripotent mouse stem
Cells Transl Med 6(2):622–633 cells by the piggyBac transposon. Nat Methods 6
Wilkinson DC et al (2018) Development of a three- (5):363–369
dimensional bioengineering technology to generate Zhou W, Freed CR (2009) Adenoviral gene delivery can
lung tissue for personalized disease modeling. Curr reprogram human fibroblasts to induced pluripotent
Protoc Stem Cell Biol 46(1):e56 stem cells. Stem Cells 27(11):2667–2674
Wong AP, Rossant J (2013) Generation of lung epithelium Zhou H et al (2009) Generation of induced pluripotent
from pluripotent stem cells. Curr Pathobiol Rep 1 stem cells using recombinant proteins. Cell Stem Cell
(2):137–145 4(5):381–384
Adv Exp Med Biol - Cell Biology and Translational Medicine (2019) 7: 17–28
https://doi.org/10.1007/5584_2019_439
# Springer Nature Switzerland AG 2019
Published online: 15 November 2019
Abstract Keywords
The identification of human embryonic stem Cell therapy · Clinical trial · Gene therapy ·
cells and reprogramming technology to obtain Pluripotent stem cell · Regenerative medicine
induced pluripotent stem cells from adult
somatic cells have provided unique opportu-
nity to create human disease models, gene
Abbreviations
editing strategies and cell therapy options.
AAV Adeno-associated virus
Development of pluripotent stem cells from
AAVS1 AAV integration site 1
somatic cells and genomic manipulation tools
Cas9 CRISPR-associated system
enabled to use site specific nucleases in the cell
CCR5 CC chemokine receptor 5
therapy research. Identification of efficient
CD4 Cluster of differentiation 4
gene manipulation, safe differentiation and
CMV Cytomegalovirus
use will provide a novel strategy to treat
CRISPR Clustered regularly interspaced short
many diseases in the near future. Current avail-
palindromic repeat
able registered clinical trials clearly indicate
CRX Cone-rod homeobox
the need for pluripotent stem cell and gene
DNA Deoxyribonucleic acid
therapy treatment options. Although gene
DSB Double-strand break
editing based pluripotent stem cell research is
ESC Embryonic stem cell
a popular field for research worldwide,
FIH First-In-Human
improvement of clinical approaches for treat-
GBA Glucosylceramidase Beta
ment still remains to be investigated. In this
GCase Glucocerebrosidase
review, we summarized the current situation of
GFP Green fluorescent protein
gene editing based pluripotent cell therapy
HDR Homology-directed repair
developments and applications in clinics.
hES Human embryonic stem
hESC Human ESC
HIV Human immunodeficiency virus
H. B. Şişli, T. B. Hayal, S. Seçkin, S. Şenkal, B. K{ratl{, HPV Human papillomavirus
F. Şahin, and A. Doğan (*) HR Homologous recombination
Department of Genetics and Bioengineering, Faculty of HSC Hematopoietic stem cell
Engineering, Yeditepe University, Istanbul, Turkey
iPS Induced pluripotent stem
e-mail: aysegul.dogan@yeditepe.edu.tr
17
18 H. B. Şişli et al.
iPSC Induced pluripotent stem cell disease treatment. Owing to recent advances in
MELAS Mitochondrial myopathy, encepha- site-specific nuclease (SSN)-mediated gene
lopathy, lactic acidosis and stroke- manipulation techniques, pluripotent stem cells
like episodes might be able to use in clinical studies in the
MiPSC Mitochondrial disease patient- future. The most popular and widely used SSNs
specific induced pluripotent stem are zinc-finger nucleases (ZFNs), transcription
cell activator-like effector nucleases (TALENs), and
mtDNA Mitochondrial DNA clustered regularly interspaced short palindromic
MTS Mitochondrial targeting sequence repeat (CRISPR)/CRISPR-associated system
NHEJ Non-homologous end-joining (Cas9) (Chang et al. 2018). Site-specific double-
PITX3 Pituitary homeobox 3 strand breaks (DSBs) are introduced into the
PSC Pluripotent stem cell genomic DNA and repaired by non-homologous
RNA Ribonucleic acid end-joining (NHEJ) or homology-directed repair
RPE Retinal pigment epithelium (HDR) which results in insertion or deletion in the
sgRNA Single guide RNA targeted locus based on engineered design
SHANK3 SH3 and multiple ankyrin repeat (Hendriks et al. 2016). Combination of
domains 3 SSN-mediated gene manipulation and pluripotent
SSN Site-specific nuclease stem cell research enable modelling of develop-
TALE Tal effector protein mental pathways and diseases, modulation of cell
TALEN Transcription activator-like effector fate decision and differentiation, correction of
nuclease genetic abnormalities for certain disorders and
ZF Zinc finger avoiding immunogenicity problems. Promising
ZFN Zinc-finger nuclease trend of SSN based gene editing and pluripotent
stem cells can be adapted to clinics for cell based
therapies in the near future. Although there are
limited number of ongoing clinical research all
around the world, challenges and problems
1 Introduction
related to efficient genetic engineering of plurip-
otent stem cells still remain to be encountered for
Gene editing of pluripotent stem cells is a mile-
further human use. In this paper, recent
stone in stem cell research in terms of drug dis-
techniques especially SSNs in pluripotent stem
covery, disease modelling and regenerative
cells and current clinical trials, are reviewed.
medicine. Upon discovery of induced pluripotent
Most recent situation of the pluripotent stem cell
stem cells (IPSCs) in 2006 (Takahashi and
and gene editing in clinical trials were reviewed
Yamanaka 2006), problems associated with
and analyzed in detail.
adult and embryonic stem cells (ESCs) have
been resolved for potential future cell replace-
ment therapies. IPSCs and human ESCs
(hESCs) have similar biological properties and 2 Human Pluripotent Stem Cells
have brought an enthusiasm to basic research
and regenerative medicine. Although several Human pluripotent stem cells are divided into two
limitations exist in the therapeutic usage of plu- categories: human embryonic stem (hES) cells
ripotent stem cells, genomic technology coincides and induced pluripotent stem cells (iPSCs). hES
with stem cell technology and has brought new cells are accepted as gold standard for pluripotent
insight to pluripotent stem cell research. This is cells and the discovery of hES cells is considered
due to the need for adequate, efficient and reliable as a milestone for basic research and regenerative
cell therapy sources for tissue regeneration and medicine (Thomson et al. 1998). The story of
Gene Editing in Human Pluripotent Stem Cells: Recent Advances for Clinical Therapies 19
or Adeno-associated virus (AAV) vectors can be In the early 1980s, targeted gene studies by
used to introduce a variety of specific mutations to homologous recombination (HR) in cultured
homologous chromosomal regions (Khan et al. mammalian cells were performed (Folger et al.
2010) and can be used in research and therapy. 1982). Using the host DNA repair pathway, an
The advantage of using Toxicity and immunoge- endogenous genomic region may be replaced by
nicity are disadvantages of these type of viral the external sequence when supported by a
vectors and needs to be overcome (Wold and targeting vector via HR. A double-stranded
Toth 2013). It has led to the development of break (DSB) in genomic DNA is a form of
synthetic vectors for safety concerns as therapeu- DNA damage that requires rapid repair of cells
tic DNA. In the simplest non-viral gene delivery to preserve the integrity of the genome and the
system, “naked” DNA uses plasmid DNA (Ginn information it encodes. Repair of DSBs is
et al. 2018). achieved by non-homologous end joining
DNA vectors can be used to reprogram (NHEJ), HR, and microhomology mediated end
somatic cells to produce induced pluripotent joining (Hotta and Yamanaka 2015). The lack of
stem cells (iPSC). Jia et al. created a polycystic an ideal vector remains a major obstacle in the
minicircle connected to 2A for reprogramming treatment of human diseases. In the last few years,
factors Lin28, Oct4, Sox2 and Nanog. In this the use of non-viral vectors has increased signifi-
study, iPSC, reprogrammed with minicircle cantly (Ramamoorth and Narvekar 2015).
DNA, produced embryo bodies in culture and Induced pluripotent stem cell (iPSC) based
teratomas in immunocompromised mice. They disease modeling and cell replacement therapy
found that the yield of minicircle was higher approach has proven to be very effective in bio-
than that of plasmid DNA. Non-viral methods medical research and personalized regenerative
for generating iPS cells using excision of medicine with the resolution of new pathological
reprogramming factors using plasmids, Cre/LoxP mechanisms of a large number of monogenic
or piggyBAC transposition have been reported. diseases in recent years (Doss and Sachinidis
Efficient derivation of iPS cells without foreign or 2019) and identification of gene editing strategies
chemical elements is absolutely essential (Jia in detail.
et al. 2010). Minicircles have been used as
in vitro and in vivo targets in certain areas, includ-
ing lung epithelial cells containing enhanced GFP
3.1 Zinc Finger Nucleases (ZFNs)
(eGFP), firefly luciferase (Luc), or DNAH5,
which encode an external dynein arm protein in
Zinc fingers (ZFs) are naturally found eukaryotic
primary ciliary dyskinesia. The minicircles carry-
proteins that are dependent on zinc ion as a struc-
ing these genes exhibited higher levels of gene
tural cofactor to function (Shimberg et al. 2018).
expression compared to plasmids (Munye et al.
ZFs consist of 30 amino acid residues with
2016). Multiple recombinase systems are used to
repeats of four cysteine and/or histidine within
produce minicircles (Gaspar et al. 2015). Plasmid
their sequence (Hamed and Arya 2016). In the
contaminants in minicircle preparations may be as
field of genome engineering, Zinc Finger
high as 10% of the total yield, but this is a prob-
Nucleases (ZFNs) have been widely used as syn-
lem because it is above 1.5% allowed by health
thetic nucleases to target and edit any specific
institutions. Several methods are being developed
region found within the genome since 2003
to increase the purity of minicircle (Hou et al.
(Perez-Pinera et al. 2012). ZFNs are comprised
2015). Daneshvar et al. also created iPSCs from
of two domains including the Cys2-His2 zinc
umbilical cord mesenchymal stem cells using
finger protein domain which are series of
minicircles without the need for a feeder cell
DNA-binding motifs and a catalytic domain
layer with these four reprogramming factors (Jia
known as FokI nuclease which is a natural type
et al. 2010; Hou et al. 2015).
Gene Editing in Human Pluripotent Stem Cells: Recent Advances for Clinical Therapies 21
IIS restriction enzyme that can cleave the DNA targeted with ZFN technology in hESCs to a
within or in the proximity of its recognition locus in the human genome called AAVS1 to
sequence (Carroll 2011; Pingoud and Jeltsch allow stable gene expression. Afterwards, the
2001). Each Cys2-His2 zinc finger domain recombined hESCs have been differentiated into
recognizes 3–4 adjacent nucleotide bases, and the hematopoietic cells. Furthermore, it has been
linkage of two or three zinc finger motifs allow suggested that the introduction of CD43-GFP
binding up to 18 base pairs of DNA (Carroll 2011). reporter construct in hESCs using ZFNs is a suc-
The restriction enzyme, FokI, must form dimers in cessful gene editing tool for the expression of
order for it to apply its nuclease activity and cleave transgenes (Tiyaboonchai et al. 2014). Brigham
the DNA. Therefore, two sets of ZFNs are J. Hartley and his colleagues have established a
constructed and directed on opposite ends of the protocol to target Pituitary homeobox 3 (PITX3)
target site to allow dimerization of FokI and thus locus in hESCs by introducing ZFNs along with a
the cleavage of DNA in the specific region (Fig. 1). PITX3-EGFP-specific DNA donor vector to gen-
In many organisms including humans, ZFNs erate a PITX3 reporter cell line. This reporter cell
have been successfully utilized as a tool for line has been suggested to allow tracking and
inducing DNA double strand break and specifi- isolating the cells of interest following differenti-
cally editing targeted genes in the genome ation of hESCs for use in studies including
(Carroll 2011; Urnov et al. 2010). Manipulating in vitro Parkinson’s disease modeling or stem
the genome using ZFN technology has been cell therapy (Hartley et al. 2014). In 2015, Jia
shown to be successful with high efficiency in Liu and his colleagues have improved specific
hESCs and hiPSCs (Hockemeyer et al. 2009; protocols for implementing ZFN-based genome
Zou et al. 2009). In a study done in 2014, ZFNs editing in hESCs. Furthermore, they have shown
have been shown to be a powerful tool for that ZFNs can be efficiently expressed and
introducing and expressing transgenes in hESCs purified within 6 days and used for stimulating
at specific regions by avoiding gene silencing genomic modifications in hESCs within 2 days
during hESCs differentiation (Tiyaboonchai (Chandrasekaran et al. 2017). In 2016, Joseph
et al. 2014). CD43-GFP construct has been Collin and his colleagues have used ZFNs to
Fig. 1 The schematic representation of zinc finger nucleases. Four contiguous zinc finger proteins bind to the targeted
sequence in the human genome and the dimerized nuclease, FokI, cuts the DNA in its recognition site
Another random document with
no related content on Scribd:
nachs wist ie ’t altaid vàst, dat ie d’r was.… Moar op dag, gong ’t
weg!.. Kaik da’ ha je se weer.… Nou stonge se weer om sain.… ’n
heule bende swarte kerels!.… En nou stonge se weer an s’n strot te
trekke.… kaik!.… soo weer aldegoar sterretjes veur s’n ooge.…
huhu!.… pal d’r veur.… Enn.… nou.. kaik!.… wá’ donker ’t word.…
hoho!.… enne.… enne.. tùg dag.… was ’t strak-en-an!.. Sou die in
de hel komme?.. enne.… Spulle waa’s nooit van sain.… nooit had ie
wá’ f’rkocht.… nooit sou ie s’n spulle weer anroàke!.… Enne.… hai
sou weggaife.… teruggaife.… alles.… alles! Aa’s ie nou moar nie
dood hoefte!.… Jesis wá’ wàrm om s’n hoofd.. begon ’t weer te
gloeie, om s’n kop.—kaik!.… nog donkerder.… veur s’n ooge.…
Jesis waa’n benauwing!.…
[Inhoud]
II.
Hooge zang van werkers galmde uit, achter stekjes en rijzen, den
Juni-ochtend in. Prachtige zangklanken, die zeilden in sonore trilling
door diep luchtenblauw, uit de overal dichtgegroeide en omzonde
groente-tuinen.—In kleur-klatering goudde de aarde, en overal uit de
gaarden, van singelgroen en hagen ingesloten, dampte ochtendgoud
van jongen zomer, nevelvroege dauw, die vonkvuur schoot en
paarlen spatte tusschen grashalmen en bladeren. Achter de hagen,
als groene sierwanden tusschen elken akker òpgegroeid,
schemerden blauwkielen door, werkers die hurkten òver het
lichtverstuivend prachtgroen van aardbeibedden. [336]
MENSCHENWEE
[Inhoud]
MENSCHENWEE
DOOR
IS. QUÉRIDO
HAARLEM
DE ERVEN F. BOHN
Derde Boek
ZOMER.
[1]
[Inhoud]
EERSTE HOOFDSTUK.