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Young Wook Chun, PhD
Training focus:Micro-environmental regulation of EMT for heart valve tissue engineering
Training start day:09/01/2010 Co-mentors:W. David Merryman, PhD Joey V. Barnett, PhD
Heart valve tissue engineering is complicated as it requires the marrying of biomaterials with well-defined biomechanical properties to valve interstitial cells (VICs), which are the most prevalent cells in the heart valve leaflet tissue. The VICs exhibit a dynamic phenotype ranging from quiescent fibroblast-like cells to activated VICs, or myofibroblasts. Thus, controlling their phenotype within an engineered environment is challenging. Further, the current understanding of VIC pathobiology and mechanobiology is limited. My work initially focuses on elucidating the gene regulatory network of the VIC population in both chick and mouse embryo models in order to parse the essential genes that give rise to this unique phenotype. After the in vivo studies, I plan on developing in vitro engineered biomaterial environments that can be used to assess the mechanical input (ECM compliance and roughness, shear stress, planar strain) into these gene networks, both in regards to epithelial-mesenchymal transformation (EMT) of the endocardial cell population that ultimately forms the cushion and the VIC population. A key component of the in vitro portion of this work is the nanomodification of biomaterial surfaces to control VIC function. |
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Behzad Gerami-Naini, PhD
Training focus:Tooth formation from human embryonic stem cells in a three-dimensional (3D) in vitro model
Training start day:03/01/2009Co-mentors:Richard Maas, MD, PhD David Mooney, PhD
The mammalian dentition, like many organs, develops through a series of sequential and reciprocal interactions between epithelial and mesenchymal tissues. The ability of human embryonic stem cells (hESCs), mouse embryonic stem cells (mESCs) and induced pluripotent stem cells (iPS cells) to differentiate into various cell types in vitro, such as neural progenitors, pancreatic progenitors, and trophoblast cells provides a powerful platform to study mechanisms of organogenesis such as those mediating odontogenesis, in vitro. In my project, I will test the hypothesis that under correct spatial and temporal programming of the cellular microenvironment, hESCs can be directed along the odontogenic pathway to form tooth germs in vitro. This hypothesis will be tested using the following two specific aims. Specific Aims: a) To investigate whether three-dimensional (3D) epithelial-mesenchymal interactions can augment the odontogenic differentiation of hESCs, mESCs and iPS cells. b) To evaluate the role of specific signaling molecules on the directed differentiation of stem cells within these 3D extracellular matrix (ECM) arrays. |
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Joshua Ho, PhD
Training focus:Integrative ChIP-seq analysis for developmental biologyTraining start day:06/01/2010Co-mentors:Peter Park, PhD Richard Maas, MD, PhD
Stem cell differentiation is regulated by a set of highly coordinated regulatory pathways mediated by various protein-DNA events at the genomic and epigenomic levels. Recently, large-scale genome-wide mapping of various in vivo protein-DNA interactions has been made possible by advances in chromatin immunoprecipitation (ChIP) followed by massively parallel sequencing (ChIP-seq). However, we currently do not have a systematic analysis framework for comparing and integrating multiple ChIP-seq profiles in the context of two-group, multi-group, factorial, and time-series experimental designs that are pertinent to many developmental biology studies. In this project, I aim to develop practical bioinformatics methods for analysis of ChIP-seq profiles, and systematically apply them to understand the gene regulatory dynamics underlying organ development. In particular, I will leverage the data being generated from various participating and collaborating laboratories of SysCODE to build an integrative view of the molecular mechanisms leading to the development of heart valve, tooth germs, and pancreatic islets. |
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Charles W. O'Donnell, PhD
Training focus:Computational Discovery of Pancreatic Islet Reprogramming Factors
Training start day:06/15/2011Co-mentors:Douglas Melton, PhD David Gifford, PhD
The ability to reprogram diverse cell types into therapeutically useful states remains an unrealized promise of regenerative medicine. This is due partly to our incomplete understanding of the signaling and transcriptional networks that control cellular competence, determination, and differentiation. However, recent efforts have demonstrated the efficient production of pancreatic progenitor cells from embryonic stem cells using morphogen-guided in vitro differentiation. Building on this, we will model how morphogen and exogenous factors can be used to directly drive the mature pancreatic beta cell fate. With our collaborators, gene expression, chromatin structure, and key regulator binding will be characterized for developmental and factor-induced states using high-throughput sequencing methods such as RNA-seq, DNase-seq, and ChIP-seq. Further proteomic interaction information will be incorporated into the model based on existing databases, physics models, and novel experimental enhancer discovery techniques. The integration of such diverse data sources will require new algorithmic prediction techniques, and will offer a more complete view of the mechanisms for cell type specification. |
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Ivan Rebustini, PhD
Training focus:Regulation of progenitor/stem cells during tooth morphogenesis by micro-RNAs
Training start day:06/13/2011Co-mentors:Richard Maas, MD, PhD Peter Park, PhD
Non-coding elements of the genome such as micro-RNAs (miRNAs) have emerged as important regulators of progenitor/stem cell maintenance during organ morphogenesis; however, it is currently unknown how miRNAs regulate dental progenitor/stem cells. Early tooth morphogenesis requires epithelium and mesenchyme interactions via a well-established Gene Regulatory Network (GRN) involving Wnt and BMP signaling, however it is undefined how miRNAs regulate this GRN during tooth development. Therefore, the focus of my project is to define the role of miRNAs in progenitor/stem cells maintenance, and establishing an integrative study encompassing miRNA regulation of GRN involved in early tooth morphogenesis. Addressing the roles of miRNAs during dental progenitor/stem cells maintenance is necessary, in order to develop strategies to repair damaged dentition by restoring an early miRNA-regulated GRN in situ. The experimental approaches involved in this research include: 1. Screen for miRNA expression during embryonic mouse tooth morphogenesis using high throughput deep sequencing RNA-Seq technique, and identifying known and discovering novel miRNAs expressed during specific stages of tooth morphogenesis; 2. Perform target prediction, and search for the corresponding targets of selected miRNAs using the microarray-based ToothCODE database; 3. Confirm the miRNA targets, using gain- and loss-of-function approaches in ex vivo early tooth organ cultures; 4. Search for a miRNA expression signature for the early tooth germ, when compared to other embryonic organs of SysCODE interest such as pancreatic islet and heart valve; 5. Use progenitor/stem cell markers to isolate progenitor stem cell populations and to define the identity and function of miRNAs in maintaining the stem cell population niche. |
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Shilpa Sant, PhD
Training focus:Biomaterials engineering to study epithelial mesenchymal interaction during tooth development
Training start day:02/01/2011Co-mentors:Ali Khademhosseini, PhD Richard Maas, MD, PhD
Epithelial mesenchymal interactions play a key role in the development of various tissues such as tooth, lungs, and kidneys. For instance, various stages in tooth development namely, thickening of oral ectoderm followed by the bud, cap, bell stages and finally the calcification stage, are all a result of the inductive signaling interactions between the epithelium and the underlying mesenchyme. Dental epithelium interacts with the dental mesenchyme through various biochemical signalling to start the budding process. Such an orchestration continues throughout tooth morphogenesis till the formation of the root, enamel and dentin. Thus, to mimic an in vivo microenvironment, it is necessary to engineer a three-dimensional (3D) scaffold with controlled spatial and temporal biochemical signals. The goal of my work is to engineer biomaterials with spatially controlled biochemical signals, specifically FGF8/Wnt and BMP4 to mimic the instructive role of epithelial cells in odontogenesis. In this work, I plan to use various synthetic/natural hydrogels that can support mesenchymal cell viability and proliferation. Further, I plan to generate gradients of various morphogens either alone or in combinations to mimic the role of epithelium in tooth morphogenesis. |
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Kerstin Seidel, PhD
Training focus:Identification of new markers for the incisor stem cell niche
Training start day:06/25/2011Co-mentors:Richard Maas, MD, PhD Ophir Klein, MD, PhD
The mouse incisor provides an excellent model system to study the biology of adult stem cells. However, markers that allow a clear discrimination between different cell types in the incisor stem cell niche have not yet been identified. This lack of markers hampers analyses of stem cell behavior, and therefore our goal is to identify novel, cell type specific markers by analyzing the gene co-expression network organization in the proximal incisor. Our approach involves generating a large number of expression profiles of individual micro-dissected tissue samples and subjecting them to a weighted gene co-expression network analysis. Gene co-expression modules identified in heterogeneous tissues are often related to distinct biological processes and can be driven by discrete cell types; therefore we will investigate whether the identified modules are enriched for the few known markers of specific cell types in the tooth by cross referencing published gene expression data. Starting with the highest ranked factors of each of the presumed cell-type specific modules, the cell type specificity will be validated by visualizing gene expression patterns in the incisor. The results of this study will provide a wealth of new biomarker information and enhance our understanding of the cellular diversity that is present in the incisor stem cell system. |
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Richard Sherwood, PhD
Training focus:Building a Transcriptional and Signaling Network of Pancreatic Specification
Training start day:12/01/2009Co-mentors:Richard Maas, MD, PhD David Gifford, PhD
While embryonic stem (ES) cells have been touted as a promising therapeutic tool, their efficient differentiation into therapeutically relevant cell types has yet to be achieved. The root cause behind this failure is the lack of understanding of how cells are progressively specified during normal embryonic development. The goals of my project are twofold: to advance ES cell differentiation toward therapeutically relevant pancreatic cell types and to understand basic developmental processes such as cell fate specification and determination at a molecular level. In order to achieve these goals, I have broken down development along the pancreatic lineage into discrete steps based on a detailed understanding of embryonic pancreatic development, and I am focusing on obtaining a mechanistic understanding of how intercellular signaling pathways and transcription factors, the master regulator genes of development, coordinate each progressive step both in embryos and in ES cells. I use techniques such as chromatin immunoprecipitation followed by high- throughput sequencing (ChIPseq), co-immunoprecipitation followed by mass spectrometry (IP-MS), and genome-wide transcriptional profiling to understand where relevant developmental transcription factors bind in the genome, what their transcriptional partners are, and how they affect expression of all other genes. I am collaborating with computational biologists to build a predictive model of development that combines cell signaling inputs and transcriptional interactions discovered in our system. |
