Edward E. Morrisey - US grants

DESCRIPTION (provided by applicant): Early development of the lung is orchestrated by a small group of critical transcription factors including Gata6, Foxa1/2, and Nkx2.1. Genetic deletion of any of these factors significantly impairs lung endoderm differentiation and in some cases postnatal repair and regeneration. The transcriptional regulatory regions of most lung endoderm restricted genes contain functionally important Gata6, Foxa1/2, and Nkx2.1 DNA binding sites. Gata and Foxa1/2 have been shown to act as pioneer transcription factors by binding to regions of compacted chromatin and opening and priming the chromatin landscape to allow subsequent DNA binding by additional factors, resulting in the promotion of cell lineage specific gene expression. Using conditional genetic deletion in lung endoderm, we have demonstrated that Gata6 plays a central role in regulation of lung endoderm gene expression, proliferation, and branching morphogenesis. Loss of Foxa1/2 and Nkx2.1 also dramatically inhibits endoderm differentiation and branching morphogenesis. Moreover, we have demonstrated that Gata6 cooperatively regulates late lung epithelial differentiation and maturation with Nkx2.1. Gata6, Foxa1/2, and Nkx2.1 therefore form a core set of factors that we refer to as a lung restricted transcription regulatory module (TRM). However, how Gata6 cooperates with Foxa1/2 and Nkx2.1 to regulate lung endoderm specific gene expression is poorly understood, particularly in the regulation of early lung endoderm progenitor specification and differentiation. Recent unpublished data from our lab suggests that Gata6 controls lung epithelial differentiation and proliferation, in part, though regulation of the microRNA cluster miR-302/367. miR-302/367 is expressed in early embryonic development in multiple stem/progenitor cell populations and gain of function studies in vivo shows that it regulates proliferation and differentiation of early lung endoderm progenitors. Our unifying hypothesis is that Gata6 acts as an integrator of early lung endoderm progenitor development through interactions with Foxa1/2 and Nkx2.1. These interactions, in turn, regulate critical down-stream targets in lung endoderm including the microRNA cluster miR-302/367. To test this hypothesis, we propose to 1) characterize the regulation of the miR-302/367 cluster by Gata6, Foxa1/2, and Nkx2.1, 2) determine the role of miR-302/367 in lung endoderm progenitor development, and 3) determine how Gata6, Foxa1/2, and Nkx2.1 integrate regulation of early lung development and the lung endoderm transriptome. PUBLIC HEALTH RELEVANCE: A better understanding of the molecular mechanisms that regulate early lung development is directly relevant to both congenital lung disease as well as potential lung regenerative therapies. A core set of transcriptional regulators consisting of Gata6, Foxa1/2, and Nkx2.1 regulate a majority of lung specific genes and are important for adult lung homeostasis and injury repair. Thus, the studies described in our proposal will greatly enhance our knowledge of the pathways that regulate early lung progenitor development as well as airway regeneration in the adult.

DESCRIPTION (provided by applicant): The precise regulation of gene transcription in the developing airway epithelium is critical to the differentiation of epithelial cell lineages required for postnatal respiration as well as injury repair. However, little is known about the transcriptional pathways involved in regulating lung epithelial specific gene expression. The forkhead/winged-helix (also known as Fox) family of transcription factors is known to play an important role in the regulation of gene expression and cell differentiation. We have cloned a new subfamily of Fox transcription factors, Foxp1 and Foxp2, which are expressed at high levels in the embryonic and adult airway epithelium. Expression of Foxp1 is found at high levels in the distal airway epithelium and at lower levels in the proximal airway epithelium. Notably, Foxp2 is the first Fox gene described expressed exclusively in the distal airway epithelium in the lung. Preliminary analysis shows that Foxp1 and -2 repress the lung specific promoters for the SP-C and CC10 genes and that this repression activity is localized to a unique and homologous domain in the amino-terminus of both proteins that contains several putative protein-protein interaction motifs. These results lead us to hypothesize that Foxp1 and -2 regulate lung epithelial gene transcription via unique mechanisms involving transcriptional repression, possibly modulated through interaction with co-regulatory molecules. To test this hypothesis we propose to: 1) determine the precise gene and protein expression patterns of Foxp1 and -2 during development which should provide important clues as to potential down-stream transcriptional targets of these genes as well as interacting co-regulatory molecules, 2) precisely define the structural domains within Foxp1 and -2 that are important for transcriptional activity, 3) characterize the Foxp1/2-CtBP-1 interaction and its affect on the transcriptional activity of Foxp1 and -2, and 4) determine the role of Foxp1 and -2 in the development of airway epithelium through the analysis of Foxp1 and -2 deficient mice. These studies will greatly enhance our understanding of the specific transcriptional pathways that regulate lung epithelial development and differentiation as well as the mechanisms behind the pathogenesis of lung diseases, which occur due to aberrant epithelial differentiation and function.

animal colony; embryonic stem cell; tissue /cell preparation; microinjections; tissue /cell culture; genetically modified animals; laboratory mouse;

The lung arises from the foregut endoderm as an epithelial bud surrounded by mesodermal mesenchyme. Lung mesenchyme gives rise to the various lineages of pulmonary smooth muscle, including vascular smooth muscle cells (VSMCs) which are essential for blood vessel integrity. However, little is known of the molecular signaling processes that are involved in the specification and/or differentiation of VSMCs in the lung, although paracrine signaling from the endoderm has been shown to play an important rote. Proper development of the pulmonary vasculature is important in the development of the lung as a functional organ and defects in this process can lead to several human diseases including pulmonary hypertension. We have shown that inactivation of the Wnt7b gene, which is expressed in the developing airway epithelium, results in loss of vascular smooth muscle integrity in the lung, leading to perinatal hemorrhage and death. Since Wnt7b expression in the lung decreases in late gestation, we hypothesize that Wnt7b is required for proper development of VSMCs from lung mesenchyme through epithelial-mesenchymal signaling occurring early in lung development. In support of this hypothesis, we have found that the winged-helix transcription factor Foxf2, which is expressed in lung mesenchyme, is specifically down regulated in the lungs of Wnt7b/lacz-/- embryos. These results suggest that vascular smooth muscle development and integrity requires Wnt7b signaling, possibly by regulating genes such as Foxf2, which are required for proper development of VSCMs from lung mesenchyme. The goal of this proposal is to characterize the molecular mechanisms underlying Wnt7b regulation of VSMC development in the lung by addressing three questions: 1) Does Wnt7b act on definitive VSMCs or their precursors during lung vascular development?, 2) Does Wnt7b signal via canonical or non-canonical Wnt pathways in lung VMSC development and what are the global roles for these pathways in this process?, and 3) What are the down-stream effector pathways that Wnt7b influences to regulate VSMC differentiation and development? We expect that the results of these studies will lead to a better understanding of the mechanisms underlying vascular heterogeneity and, in particular, how Writ signaling regulates these developmental events.

DESCRIPTION (provided by applicant): The lung develops through a series of endoderm-mesoderm interactions that promote proper patterning of the highly complex and arborized structure required for postnatal respiration. Little is understood about how Wnt signaling promotes these early stages of lung development, whether Wnt signaling regulates specific aspects of early branching morphogenesis of the airway and vascular structures in the lung, and whether disruption of Wnt signaling can lead to human lung disease. Our preliminary data show that Wnt signaling regulates a specific type of airway branching called domain branching through the receptor Fzd2 and that disruption of domain branching leads to a phenotype resembling congenital cystic adenomatoid malformation (CCAM) in pediatric patients. Moreover, the molecular alterations that occur upon loss of Fzd2, including increased Fgf9 expression and decreased Fgf7 expression, also mimic the CCAM phenotype. Using a novel inducible cre line in the Wnt2 locus generated in our lab (Wnt2creERT2), we also show that Wnt2+ progenitors contribute to different mesenchymal lineages within the developing lung in a temporal restricted pattern and generate alveolar mesenchymal cells within the adult lung that can contribute to the generation of myofibroblasts in a model of lung fibrosis. Taken together these data suggest a critical role for Wnt signaling in two poorly understood processes in lung development and homeostasis: 1) domain branching in a temporal restricted fashion that when disrupted leads to congenital lung disease and 2) differentiation of specific mesenchymal lineages within the developing and postnatal lung through Wnt2 signaling. Using the new tools and techniques we have generated in the last round of funding we will 1) define the molecular pathways underlying the regulation of domain branching by Wnt/Fzd2 function and determine whether defects in Wnt signaling occur in CCAM lesions in humans, and 2) determine the contribution of Wnt2+ (Wnt expressing) and axin2+ (Wnt responsive) cells to lung mesenchymal development and the postnatal response to fibrotic injury models.

DESCRIPTION (provided by applicant): Lung epithelial development is transcriptionally controlled through both positive and negative regulators. Amongst these regulators, the forkhead/winged helix family or Fox family of DMA binding proteins play a central role. Our previous studies have demonstrated that Foxp1/2/4 are potent transcriptional repressors of lung gene transcription and each gene is expressed in overlapping patterns in lung epithelia. We have shown that mouse knock-out models of each of these genes demonstrate unique roles in lung, cardiac, and neural development. In the lung, Foxp2 regulates postnatal alveolarization in part through direct regulation of the alveolar epithelial type 1 cell (AEC-1) gene T1 alpha. In addition to their individual roles in development, recent evidence from our laboratory has demonstrated that Foxp1 and Foxp2 regulate lung airway morphogenesis in a compensatory manner. Foxp1/2/4 are transcriptional repressors and we have demonstrated that these factors link chromatin remodeling to target promoters through interactions with p66, a component of the NuRD (nucleosome remodeling histone deacetylase) complex. Transcriptional repression through complexes such as NuRD and their components including HDAC2 (histone deacetylase 2) are important for surfactant protein gene expression and lung epithelial maturation as our recent data on HDAC2 and the interacting homeodomain only protein (HOP) indicate. These findings demonstrate that Foxp1/2/4 play critical roles in regulation of lung epithelial specific genes, which are required for airway development and postnatal lung homeostasis. However, little is known about whether these factors act redundantly/cooperatively to regulate transcriptional targets in the lung, the mechanism of how Foxp1/2/4 repress lung gene transcription and the effect that loss of these factors has on activation and differentiation of airway progenitor cells including bronchioalveolar stem cells (BASCs) after lung injury. These questions will be addressed in the specific aims of this proposal.

DESCRIPTION (provided by applicant): This proposal seeks to utilize dramatic new advances in both epigenetic reprogramming and cardiovascular lineage/cell fate determination to inform and empower our ability to harness regenerative medicine for cardiovascular therapies. In recent years, new discoveries have significantly altered our understanding of how the heart forms. It is now clear that several cardiac progenitor populations can be identified that contribute to the adult myocardium, though the precise relationships among these populations and their distinct lineages potential remain poorly defined. The description of induced pluripotential (iPS) cells demands a rethinking of cellular plasticity and suggests the possibility of reprogramming a differentiated cell to adopt the characteristics and potential of a cardiac progenitor and subsequently a functional myocyte (16, 21, 22, 32). However, a major challenge of this research is whether reprogramming of adult cells can be directed in such a way as to dedifferentiate to a committed precardiac progenitor state without reprogramming fully to a pluripotential state. We propose to assemble a team of collaborative investigators with established expertise in cardiac development and physiology, stem cell biology and regenerative medicine to elucidate and define progressive lineage restriction during embryonic cardiac development, including the roles of Wnt and Notch signaling in cardiac progenitor biology, and to define the necessary factors for directed reprogramming of adult cells to the cardiac progenitor state. We will pursue the following aims: Compare and contrast the prospective fates of distinct cardiovascular progenitor populations in vivo to allow for an accurate spatial and temporal accounting of genetically defined populations to generate mature cardiovascular cell types during progressive lineage restriction. Characterize the ability of Wnt and Notch signaling to regulate self-renewal and differentiation in different cardiovascular progenitor subpopulations. Utilizing known information and data gathered from studies in areas 1 and 2, determine the necessary factors for producing induced cardiac progenitor (iCPC) cells and their subsequent differentiation into functional cardiac myocytes.

Recent evidence has shown that alterations in epigenetic states can alter the ability of stem cell populations to differentiate into specific cell lineages and in some circumstances lead to the de-differentiation of differentiated cell types into more pluripotent stem cells. The molecular pathways controlling such epigenetic/chromatin remodeling events are still unclear. The forkhead or Fox gene family of transcriptional regulatory factors regulate tissue specific gene transcription and are important for self-renewal and differentiation of stem/progenitor cell populations during development. We have shown that the Foxp1/2/4 subfamily of Fox factors are highly expressed in developing skin and hair follicles. Recent evidence from our lab as well as others demonstrated that Foxp1/2/4 and the related Foxp3 factor interact with chromatin remodeling complexes, including NuRD and NCoR to repress gene specific expression during cell differentiation. Evidence from our lab shows that Foxp1/2/4 interact with components of the NuRD complex, mediating transcriptional repression of important target genes in the lung and heart. Our preliminary data suggest that Foxp1/2/4-NuRD interactions have profound affects on lung development as demonstrated by defects in Foxp1-HDAC2 and Foxp2-HDAC2 compound mutant mice. These studies illustrate one of the few examples of the chromatin remodeling complex NuRD interacting with a sequence specific DNA binding transcription factor. Given these fundamental roles for Foxp1/2/4 in development of the cardiovascular and pulmonary systems, we predict that they will play a similarly critical role in regulation of hair follicle development. To explore the role of Foxp1/2/4 in skin and hair follicle development, we propose to 1) determine the roles for Foxp1/2/4 in skin and hair follicle development by deleting these genes in epidermal specific knockout mice and 2) Determine the roles for HDAC1/2 in skin and hair follicle development through in vivo loss of function analyses.

DESCRIPTION (provided by applicant): To fulfill the promise of regenerative medicine in the cardiac myogenesis field, it will be necessary to effectively manipulate expansion, differentiation, and maintenance of cardiac progenitor cells. This will be required regardless of whether translational researchers attempt to augment endogenous regenerative capacity via recruitment of progenitor cells in vivo, or whether progenitors are generated and expanded ex vivo for subsequent delivery or for the generation of tissue engineered bioprostheses. The importance of a detailed understanding of the signaling pathways important for progenitor expansion and proper differentiation is emphasized by analogous advances in the hematopoietic field, where the clinical use of GM-CSF, G-CSF and related growth factors, which regulate stem cell expansion has provided dramatic clinical impact. In the cardiovascular field, the ability to specifically regulate progenitor cell survival, expansion and differentiation is generally lacking. Moreover, a usable source of progenitors for ex vivo expansion remains elusive. To overcome this limitation, many studies have focused on the generation and characterization of cardiac progenitors from embryonic stem cells as well as induced pluripotential stem cells derived from non-cardiac fibroblasts for eventual use in tissue engineering therapies. These studies have shown that cardiac myocytes can be generated from such cell types but have also revealed that the resulting myocytes do not exhibit all of the necessary characteristics of adult cardiac myocytes. The ability to expand and controllably differentiate cardiac myocytes from ES or IPS cells is therefore limited in its uses, in part due to the lack of understanding of how cardiac progenitors expand and differentiate in vivo. The underlying thesis of the Penn/UW Consortium application is that further elucidation of the signals that mediate cardiac and hematopoietic progenitor development in the embryo provides a logical approach for the identification of factors useful for expansion and differentiation of progenitor cells ex vivo. Hence, our collaborative projects combine the analysis of two of the most vital stem cell signaling pathways, Wnt and Notch, during development and in cardiac and blood progenitors derived from pluripotential stem cells including ES and iPS cells. Nevertheless, this analysis remains undeveloped and the interactions of Wnt and Notch in the developing heart remain unexplored, although these pathways are known to interact in many other stem cell populations. These studies will interface with those described in the collaborative linked application on the role of Wnt and Notch in expansion and proper differentiation of hematopoietic stem cells (HSCs). The Aims of the UPenn cardiac portion will focus on 1) how Wnt and Notch promote cardiac progenitor expansion and differentiation in development and in ES/iPS cells and 2) defining the similarities and differences between Wnt and Notch manipulated cardiac myocytes and mature adult myocytes. Thus, the Penn/UW Progenitor Consortium proposes to characterize the ability of Wnt and Notch signaling to expand progenitors in vivo as well as ex vivo.

To fulfill the promise of regenerative medicine in the lung, it will be necessary to identify and characterize the cell lineages that affect postnatal lung epithelial repair and to effectively control their maintenance, expansion, and differentiation into mature and functional epithelial cells. Asthma and COPD are chronic lung diseases which affect the bronchiolar ainways of the lung and are leading causes of morbidity and mortality. Both diseases are thought to involve a chronic injury-repair-improper regeneration cycle that leads to the eventual breakdown of normal airway structure and function leading to loss of respiratory function. We hypothesize that epithelial progenitors within the bronchiolar airways and the pathways that regulate their expansion and differentiation are critical for proper ain/vay repair and regeneration after both chronic and acute lung injury that occurs in lung diseases such as asthma and COPD. Given the immense clinical burden imposed by asthma and COPD, we believe a focus on repair and regeneration of bronchiolar epithelium will have a significant and direct impact on human health. Moreover, a focus on pathways that can be modulated using small molecule or druggable approaches would be beneficial for directly translating basic research findings to human therapy. We propose to leverage decades of experience by leading experts in lung development, stem cell biology, and pulmonary medicine to collaboratively harness novel technologies for expansion and differentiation of endogenous lung progenitors as well as those derived from induced pluripotent stem cells (iPSCs). By focusing on new findings in the investigators laboratories involving the epigenetie regulation of bronchiolar epithelial progenitors as well as novel techniques for generation of iPSCs, the Penn component ofthe Lung Repair and Regeneration Consortium (PennLRRC) will dramatically advance the field towards the ultimate goal of generating clinically relevant therapies for promoting lung repair and regeneration. The underlying thesis of the PennLRRC Consortium is that a sophisticated understanding of basic epigenetie mechanisms involving miRNA and Hdac pathways will be critical to optimally manipulate in vivo or generate ex vivo lung progenitors and their derivatives for clinical use. RELEVANCE (See instructions): We will explore the roles for miRNA and Hdac pathways in lung regeneration and development as well as in the generation and differentitation of iPSCs for use in regenerative therapies in the lung. Since small molecule modulators of miRNA and Hdac pathways exist, we believe that investigation into how these pathways regulate lung regeneration will have an important impact on the development of new therapies for lung disease

? DESCRIPTION (provided by applicant): Pulmonary disease is the number three cause of morbidity and mortality in the Western world. Intense investigation over the last two decades has shown that many of the pathways critical for lung development are reactivated in adult disease states. Recently, non-coding RNAs have been demonstrated to play key roles in regulating lung development. Moreover, expression of many miRNAs is disregulated in adult disease states suggesting a potential role in repair/regeneration/diseases progression. This has led to the hypothesis that the non-coding RNA transcriptome may constitute a core set of regulatory factors that promote both development and proper repair/regeneration after injury and during disease remodeling in the lung. Long non-coding RNAs (lncRNAs) are thought to play key roles in regulating gene expression and, in recent studies, have been shown to regulate various developmental processes from maintaining pluripotency to regulating neural, eye, and cardiac development. LncRNAs are generally defined as RNA transcripts greater than 200 basepairs that do not encode for a polypeptide. Many lncRNAs are polyadenylated and contain multiple exon-intron structures. Some lncRNAs overlap with protein coding genes while others exists as independent transcripts between genes. The mechanism by which lncRNAs function is unclear but several studies suggest they can act either in cis or trans to either repress or enhance gene expression, possibly through interactions with chromatin remodeling complexes such as polycomb repressor complex 2 (PRC2). This suggests a role for lncRNAs in defining and modulating the epigenetic landscape to control gene expression. We have recently performed a high throughout genomic screen for lncRNAs expressed in the embryonic and adult lung using RNAseq and ChIPseq analysis. In this screen, we have chosen to focus on intergenic lncRNAs given their previously reported importance in regulating gene transcription. We have used these data to identify a lung lncRNA transcriptome containing 363 lncRNAs that likely play critical roles in lung biology. This database of lung lncRNAs provides a novel resource to identify and characterize new and important regulators of lung gene transcription and development. Our preliminary data shows that lung lncRNAs are often transcribed near transcription factors and signaling molecules critically important for lung development and homeostasis including Nkx2.1, Foxf1, and Foxa2 and are expressed in patterns similar to these genes. In particular, we show that a novel lncRNA associated with Nkx2.1 (NANCI) acts upstream of Nkx2.1 to regulate lung gene expression. These findings will have a broad impact on our understanding of the non-coding transcriptome in pulmonary development, disease and repair/regeneration.

ABSTRACT The formation of the lung alveolus is the culminative event in the development of the respiratory system. The alveoli perform the hallmark function of the respiratory system: gas exchange between the cardiovascular system and the external environment. Alveologenesis begins at approximately birth in mice, ends between 2-4 weeks of postnatal life in mice but extends several years after birth in humans. Disruptions in alveologenesis can lead to severe pediatric diseases such as bronchopulmonary dysplasia (BPD), and in the adult, defective regeneration or persistent degeneration of alveolar homeostasis can lead to chronic obstructive pulmonary disease (COPD). The mature lung alveolus contains a myriad of epithelial, endothelial, and mesenchymal cell lineages, all of which have to communicate properly to form a functional niche that efficiently exchanges gasses with the external environment. Despite the importance of the lung alveolus, we still have little information how the multifarious cell lineages within the lung alveolus communicate with each other during alveolar development or regeneration. During the previous funding period of this grant, we have identified many novel transcriptional, epigenetic, and signaling pathways that play essential roles in the development, homeostasis, and regeneration of the lung alveolus. We have also dedicated extensive effort during the first funding period in defining at a single cell level the full cellular repertoire, molecular pathways, developmental trajectories, cellular plasticity, and transient cell phenotypes that are present during alveologenesis, to derive a better understanding of this critical stage of lung development and its response to injury. These preliminary data have confirmed our previous work showing the importance of pathways such as Tgf-beta, and begun to define the molecular cues that drive development and maturation of poorly understood cell lineages including the alveolar type 1 (AT1) cell. Together, our data reveal two novel insights into AT1 cell biology: 1) AT1 cells play a central role in mediating cellular crosstalk in the developing and mature alveolus and 2) AT1 cells, but not AT2 cells, exhibit a remarkable level of lineage plasticity in response to neonatal injury and this plasticity is controlled, in part, by the Hippo pathway. Taken together, our studies highlight the central role AT1 cells play in alveolar development and homeostasis.

? DESCRIPTION (provided by applicant): Tissues respond in different ways to injury to repair and regenerate lost cells and damaged architecture. The lung responds robustly to injury through activation of spatially restricted stem/progenitor cell populations and through re-entry of differentiated cells into the cell cycle. This robust response to injury stands in contrast to the normal homeostatic state, which is remarkably quiescent. One school of thought suggests that quiescence is a default state in many tissues resulting from lack of growth stimuli as demonstrated in culture conditions. However, this does not fully explain how cells remain quiescent within a complex microenvironment in vivo during tissue homeostasis. An alternative hypothesis is that quiescence is actively maintained through as yet unknown molecular pathways. Such an active process would be important for the delicate balance between cellular quiescence required for maintaining tissue integrity during normal homeostasis and the rapid regenerative response after injury. Such information is important given that disruption in this state could lead to re-activation of cell proliferation in an uncontrolled manner and may underlie several lung diseases including pulmonary fibrosis and cancer. The Hedgehog (Hh) pathway is a hallmark signaling pathway that coordinates epithelial-mesenchymal interactions during development in multiple organs including the lung, through paracrine activation of smoothened (Smo)-mediated downstream signaling events. Of the three known Hh ligands, sonic hedgehog (Shh) is the best understood, is highly expressed during lung development, and plays an essential role in lung morphogenesis. Despite its clear role in organ development, little is known about whether or how Hh signaling coordinates epithelial-mesenchymal interactions in the adult lung to maintain tissue homeostasis or modulate injury and regeneration. Hh signaling activity has been noted in the adult lung through expression of the downstream effector Gli1, along with studies suggesting hedgehog promotes mesenchymal proliferation in vitro. However, Hh's function in normal adult tissue quiescence or its role in injury and regeneration in the lung has not been examined in in vivo models. Our preliminary data suggest that Hh signaling is active in the adult lung and is used to maintain mesenchymal quiescence during normal homeostasis as well as after injury in the proximal airways. Thus, Hh signaling plays a critical role in maintainig lung quiescence and is important in the response of the lung to injury.

Project Summary/Abstract The discovery of iPSCs provides an unprecedented opportunity for any scientist to derive an inexhaustible supply of patient-derived primary cells. These cells containing each patient's own genetic background can now be applied for in vitro human disease modeling, drug screening of personalized therapeutics, and the development of future regenerative cell-based therapies. The most valuable human clones already generated by the CTSA investigators collaborating on this proposal not only carry common disease-associated mutations and polymorphisms, but also carry knock-in fluorochrome reporters targeted to specific loci through state-of-the-art gene editing technologies. The goal of this proposal is the establishment of a CTSA network of induced pluripotent stem cell (iPSC) repositories and iPSC cores that will enable advanced disease modeling using >1000 existing normal and disease specific human cell lines and banking 6,000 additional samples procured from the 2nd and 3rd generation participants of the Framingham Study. A concerted effort for curation, sharing, and distribution of this vital resource across all CTSAs does not exist. This proposal thus creates a CTSA iPSC Network led by teams who have championed an `Open Source Biology' approach, freely sharing iPSC lines and their reprogramming reagents with more than 500 labs to date across the globe. Its goals are to make patient-derived iPSCs together with the tools and expertise for their genetic manipulation available to the greater research community on a large scale to realize their promise for extending understanding of disease and developing potential therapies. To achieve these goals, it proposes: a) national sharing of >1000 iPSC lines already derived by the CTSA teams collaborating in this proposal, representing a critical resource in high demand by both basic and clinical researchers, b) development and support of formalized education and training programs able to nationally disseminate the expertise required to fully harness these new tools and differentiate them into the wide diversity of human cell lineages, c) maintenance and sharing of open source gene-editing tools and gene edited iPSC lines that will enable CTSA investigators to manipulate the human genome at will, and d) derivation for national sharing of additional iPSC lines generated from the most densely clinically and genetically phenotyped cohort of individuals currently followed in the USA today: the ~6,000 participants of the second and third generations of the Framingham Study.

PROJECT SUMMARY (CELL CULTURE AND iPS CORE) The Cell Culture and iPS Core (CCiC) facility is unique on the University of Pennsylvania campus and in the region. It serves a tremendous need by Center of Molecular Studies in Digestive and Liver Diseases (abbreviated as CMSDLD, which is the NIDDK P30 Digestive Diseases Research Core Center) members for services and technologies underlying Specific Aims related to primary cells and established cell lines, 3D culture systems (organotypic culture and organoids), manipulating gene expression in cell lines through RNA interference and CRISPR/Cas9, and the application of induced pluripotent stem cells (iPS) that have been genetically reprogrammed to an embryonic stem cell-like condition and differentiating such cells to discrete lineages (GI, pancreas, liver). Furthermore, the CCiC provides a rich repository of c cell lines (2D and 3D) that are well annotated for identity, passage and free of Mycoplasma infection thereby providing quality control, rigor and reproducibility. The CCiC provides standardized protocols and regular orientation and instruction, which prove to be cost-effective measures. There are emerging projects related to the use of iPS technology to correct disease states in enteroids and hepatocytes, remarkable illustrations of translational medicine fueled by the CCiC. Through its services, technologies, quality control and time/cost-effectiveness, the CCiC advances the CMSDLD's vision and missions on behalf of members/associate members/personnel.

PROJECT SUMMARY The lung develops through a series of mesoderm-endoderm interactions that promote proper patterning of the highly complex and arborized structure required for postnatal respiration. We have previously demonstrated the necessity of Wnt signaling in specification of respiratory endoderm through the actions of multiple components of the Wnt pathway including Wnt2/2b and ?-catenin. Later in development, our lab has demonstrated that Wnt signaling is essential for branching point formation in the developing airways, proximal- distal patterning of the developing lung epithelium, and regulating development of smooth muscle lineages within the lung. Thus, Wnt signaling plays multifarious roles in lung development, both in epithelial and mesenchymal lineages. Despite what we have learned about Wnt signaling in lung development, little is known about its role in the adult lung and in particular what role this pathway plays in lung homeostasis or after acute injury. In the mammalian lung, the alveolus is the primary site of gas exchange. Lineage tracing studies have shown that the two primary epithelial lineages of the lung alveolus, alveolar type 1 (AT1) and type 2 (AT2) cells, derive from a common progenitor early in lung endoderm development. Previous studies have also demonstrated that AT2 cells, or a subpopulation within this lineage, can act as a resident progenitor for the adult alveolus through its facultative ability to self-renew and differentiate into AT1 cells after injury. The alveolus also contains a heterogeneous mixture of mesenchymal cells of which little is known. The lack of comparative analysis of the various lung mesenchymal lineages has limited our understanding of the functional cellular heterogeneity of the alveolar niche. Our preliminary studies have defined a progenitor lineage within the overall Sftpc+ cell population, which we have named the alveolar epithelial progenitor (AEP) cell. AEPs express most of the markers of AT2 cells including Sftpc, but unlike the majority of AT2 cells, they also express Axin2, a Wnt signaling target gene and one of the most accurate readouts of Wnt signaling activity. In the adult lung, AEPs comprise approximately 20% of the total AT2 population and using both RNA-seq and ATAC-seq, our unpublished data shows that they have a strikingly distinct transcriptome and epigenome from non-AEP AT2s. In parallel, we have begun to define mesenchymal lineage heterogeneity in the lung using multiple paracrine signaling cell lineage reporters. Using these methods, we have identified a mesenchymal alveolar niche cell (MANC) that are spatially and functionally positioned to promote AT2 self-renewal and differentiation. Together with the characterization of the AEP lineage, we have begun to unravel the cellular and molecular heterogeneity in the lung alveolus. The data from our studies has raised the hypothesis that signaling between distinct mesenchymal (MANCs) and epithelial (AEPs) cells in the alveolus is critical for adult lung homeostasis and regeneration after injury.

ABSTRACT The respiratory system is architecturally complex and comprised of many compartments or niches responsible for unique functions during respiration. While the human respiratory system exhibits a significant level of similarity with rodents such as mice, it contains unique compartments and structures that are poorly understood but likely to be important in understanding disease etiology and progression. As an example, the heterogeneity along the proximal-distal axis of the human airway is significantly different than in the mouse, which may underlie the lack of appropriate rodent models for many human lung diseases. This lack of understanding is similar for the human pulmonary vasculature, where few animal models of diseases such as pulmonary hypertension exist. A detailed analysis of these compartments and others in the developing human lung will result in the identification of new cell lineages and molecular signatures of individual cells across the proximal-distal axis of the airways and along the pulmonary vasculature. These data will need to be coupled with high resolution imaging techniques to build a cellular atlas of the developing human lung. One of the major goals of Phase 2 of the LungMAP Consortium, which was originally initiated in 2014, is to define the unique architectural, cell, and gene expression complexities of the developing human lung using sophisticated and emerging technologies including single cell analytics. Given the spatially specific architectural complexities of the human lung, we propose to focus on three important compartments or niches: 1) the proximal airways, 2) the distal airways and alveolus including the terminal and respiratory bronchioles (TBs and RBs), and 3) the pulmonary vasculature. We will utilize multi-modal genomic, epigenomic, and proteomic techniques to define the cellular and molecular heterogeneity in these three niches at the single cell level, and disseminate this information to allow investigators to extract cell-cell crosstalk that defines and maintains these three niches in the developing human lung. Our group has developed and applied novel genomic and imaging tools and designed interactive web applications to display and interrogate multi- dimensional data that allows for specific, interactive, and continuous ongoing analysis of the data generated in the LungMAP Consortium. Importantly, our group has demonstrated the ability to define cell-cell interactions within specific lung niches by integrating genomic data with high resolution imaging. The ultimate goals of our proposal are to 1) identify and map the cell lineages within three critical niches of the developing human respiratory system, 2) define their spatial organization in relation to each other, 3) provide novel datasets to allow researchers to identify the cell-cell interactions that are critical for their postnatal development, and 4) organize and display the data for broad access throughout the scientific community using multi-dimensional genomic and proteomic analysis tools.

PROJECT SUMMARY ? CORE C The Cell Culture and iPS Core (CCiC) of this program (P01) project is unique at the University of Pennsylvania and amongst other institutions that are part of the P01. The CCiC will serve the P01 investigators and their laboratory personnel through interrelated Specific Aims to meet their strong and compelling needs related to murine and human esophageal primary cell cultures, establishing esophageal cell lines (normal, premalignant and cancer cells, normal fibroblasts and cancer-associated fibroblasts), esophageal 3D culture systems (organotypic 3D culture and 3D organoids), manipulating gene expression in cell lines (inducible retroviral/lentiviral vectors, the PiggyBac transposon system, RNA interference, and the CRISPR/Cas9 system), and preclinical drug testing for translation to personalized medicine. The CCiC provides a rich repository of esophageal and non-esophageal cell lines (2D and 3D) that are well annotated for identity, passage and free of Mycoplasma infection thereby providing quality control, rigor and reproducibility. Additionally, the CCiC generates standardized protocols and regular orientation and instruction (for all Projects), which prove to be cost-effective measures. Furthermore, the CCiC will instruct and conduct services related to induced pluripotent stem (IPS) cells that have been genetically reprogrammed to an embryonic stem cell-like condition and differentiating such cells to discrete gastrointestinal cell lineages. Through its services, technologies, quality control and time/cost-effectiveness, the CCiC advances the vision and missions of this P01 project.

ABSTRACT The respiratory system is comprised of multiple unique and spatially distinct compartments that respond to injury and diseases states differently based on their cellular and extracellular composition. The alveolar compartment or niche is responsible for the majority of gas exchange with the external environment in the lungs and is an area that is dramatically altered during lung diseases such as chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Within the alveolus, there are at least two major mature epithelial cell types, alveolar type 1 (AT1) and alveolar type 2 cells (AT2), as well as various mesenchymal cells including Pdgfra+/Axin2+ mesenchymal alveolar niche cells (MANCs), Axin2+ myofibroblast precursor cells (AMPs), and poorly defined vascular endothelial cell populations. Despite our increasing knowledge of the cell types that comprise the lung alveolus, we have little information on how they communicate with each other or how their progenitor-differentiated progeny relationships are ultimately regulated. To address these questions, we propose to characterize the genetic pathways of the mature adult lung to better understand the transcriptional and epigenetic mechanisms underlying lung homeostasis and regeneration. Our preliminary data has identified two new and important transcriptional regulators of alveolar epithelial homeostasis and regeneration: Tfcp2l1 and Klf5. Our preliminary data suggest that Tfcp2l1 and Klf5 regulate the self-renewal of AEP and AT2 cells and their differentiation into AT1 cells, in opposing manners. Tfcp2l1 is essential in restricting AT2 differentiation into the AT1 lineage whereas Klf5 is essential for licensing the ability of AT2 cells to differentiate into AT1 cells after acute injury. Moreover, our preliminary data suggests that Tfcp2l1 marks the AEP sublineage in a manner similar to how Lgr5 marks the intestinal stem cell. Together, these data provide critical insight into the molecular and cellular orchestration of alveolar homeostasis and regeneration through the engagement of cell type specific transcriptional pathways that regulate self-renewal and differentiation of epithelial cell lineages.

PROJECT SUMMARY (CELL CULTURE AND iPS CORE) The Cell Culture and iPS Core (CCiC) facility is unique on the University of Pennsylvania campus and in the region. It serves a tremendous need by Center of Molecular Studies in Digestive and Liver Diseases (abbreviated as CMSDLD, which is the NIDDK P30 Digestive Diseases Research Core Center) members for services and technologies underlying Specific Aims related to primary cells and established cell lines, 3D culture systems (organotypic culture and organoids), manipulating gene expression in cell lines through RNA interference and CRISPR/Cas9, and the application of induced pluripotent stem cells (iPS) that have been genetically reprogrammed to an embryonic stem cell-like condition and differentiating such cells to discrete lineages (GI, pancreas, liver). Furthermore, the CCiC provides a rich repository of c cell lines (2D and 3D) that are well annotated for identity, passage and free of Mycoplasma infection thereby providing quality control, rigor and reproducibility. The CCiC provides standardized protocols and regular orientation and instruction, which prove to be cost-effective measures. There are emerging projects related to the use of iPS technology to correct disease states in enteroids and hepatocytes, remarkable illustrations of translational medicine fueled by the CCiC. Through its services, technologies, quality control and time/cost-effectiveness, the CCiC advances the CMSDLD's vision and missions on behalf of members/associate members/personnel.