Pluripotent stem cells hold enormous promise for biomedicine. Indeed the recent development of induced pluripotent stem cell (iPSC) procedures allows the generation of patient-specific pluripotent cells from any individual. Induced pluripoten stem cells closely resemble their embryo-derived counterparts, embryonic stem cells (ESC). Currently, however, the exact degree of identity between ESC and iPSC is unclear. Human (h) iPSC are genetically identical to the person of origin and thus, carry the exact complement of genetic variables that cause or predispose the patient to disease. This enables the development of exciting and unprecedented avenues to model disease etiology, better diagnostic and pharmaceutical reagents and in time, defined mature cell populations suitable for transplantation-based therapies. In order to realize the potential of pluripotent cells a detailed, quantitative understanding of their regulatory mechanisms is critical. By their nature, complex biological systems cannot be understood using reductionist approaches. Rather, systems biology paradigms that merge global experimental technologies with computational approaches are required to reveal how a cell processes biological information to affect a change in fate. Together with our computational colleagues we have developed such a systems approach and applied it to study the regulation of mouse (m) ESC, the founding and best-characterized member of the pluripotency pantheon. In the current proposal we will extend our studies to define how biological information is processed by mESC over time after a defined perturbation. We will focus on transcriptional regulators such as Nanog, Esrrb and Tbx3, and others that are necessary for pluripotency and measure their functions at the epigenetic, transcriptional, mRNA, microRNA and proteomic levels. The interactions among these factors in regulatory modules will also be explored. These studies will provide an unprecedented dynamic view of ESC regulation. In a sense, how individual pluripotent cells traverse the """"""""Waddington Landscape"""""""" will be measured and visualized. Other genetic loss-of-function studies will be pursued to identify the complete panel of protein-coding gene-products that together function to maintain the pluripotent """"""""state"""""""" and its transitions. We will also apply novel analytical tools to identify molecules that alter ESC properties in subtle and previously undefinable ways. Selected candidate molecules have already emerged and will be studies in detail. Finally, the existence of multiple alternative pluripotency regulatory network configuration will be explored and the roles of biological """"""""noise"""""""" as well as stochasticity in ESC regulation will be addressed.
This project will provide a quantitative and comprehensive view of how pluripotent stem cells process molecular information during fate decisions. Such a view is necessary for the realization of the enormous medical promises of pluripotent stem cells, and will serve as a firm foundation for the development of disease models, novel diagnostic tool as well as pharmaceutical compounds. Ultimately, these studies will also impact on the derivation of defined cell populations for regenerative medicine applications.
|Freire, Ana G; Waghray, Avinash; Soares-da-Silva, Francisca et al. (2017) Transient HES5 Activity Instructs Mesodermal Cells toward a Cardiac Fate. Stem Cell Reports 9:136-148|
|Brosh, Ran; Hrynyk, Iryna; Shen, Jessalyn et al. (2016) A dual molecular analogue tuner for dissecting protein function in mammalian cells. Nat Commun 7:11742|
|Waghray, Avinash; Saiz, Néstor; Jayaprakash, Anitha D et al. (2015) Tbx3 Controls Dppa3 Levels and Exit from Pluripotency toward Mesoderm. Stem Cell Reports 5:97-110|
|Gingold, Julian A; Coakley, Ed S; Su, Jie et al. (2015) Distribution Analyzer, a methodology for identifying and clustering outlier conditions from single-cell distributions, and its application to a Nanog reporter RNAi screen. BMC Bioinformatics 16:225|
|Papatsenko, Dmitri; Lemischka, Ihor R (2015) NetExplore: a web server for modeling small network motifs. Bioinformatics 31:1860-2|
|Lee, Dung-Fang; Su, Jie; Kim, Huen Suk et al. (2015) Modeling familial cancer with induced pluripotent stem cells. Cell 161:240-54|
|Papatsenko, Dmitri; Darr, Henia; Kulakovskiy, Ivan V et al. (2015) Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal. Stem Cell Reports 5:207-20|
|Kim, Huen Suk; Bernitz, Jeffrey M; Lee, Dung-Fang et al. (2014) Genomic editing tools to model human diseases with isogenic pluripotent stem cells. Stem Cells Dev 23:2673-86|
|Gingold, Julian A; Fidalgo, Miguel; Guallar, Diana et al. (2014) A genome-wide RNAi screen identifies opposing functions of Snai1 and Snai2 on the Nanog dependency in reprogramming. Mol Cell 56:140-52|
|Xu, Huilei; Ang, Yen-Sin; Sevilla, Ana et al. (2014) Construction and validation of a regulatory network for pluripotency and self-renewal of mouse embryonic stem cells. PLoS Comput Biol 10:e1003777|
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