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.

Public Health Relevance

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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM078465-07
Application #
8642649
Study Section
Development - 2 Study Section (DEV2)
Program Officer
Haynes, Susan R
Project Start
2007-09-01
Project End
2016-03-31
Budget Start
2014-04-01
Budget End
2015-03-31
Support Year
7
Fiscal Year
2014
Total Cost
$447,312
Indirect Cost
$183,411
Name
Icahn School of Medicine at Mount Sinai
Department
Biology
Type
Schools of Medicine
DUNS #
078861598
City
New York
State
NY
Country
United States
Zip Code
10029
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
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
Zhang, Yue Shelby; Sevilla, Ana; Wan, Leo Q et al. (2013) Patterning pluripotency in embryonic stem cells. Stem Cells 31:1806-15
Xu, Huilei; Baroukh, Caroline; Dannenfelser, Ruth et al. (2013) ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. Database (Oxford) 2013:bat045
Binda, Olivier; Sevilla, Ana; LeRoy, Gary et al. (2013) SETD6 monomethylates H2AZ on lysine 7 and is required for the maintenance of embryonic stem cell self-renewal. Epigenetics 8:177-83
Gaspar-Maia, Alexandre; Qadeer, Zulekha A; Hasson, Dan et al. (2013) MacroH2A histone variants act as a barrier upon reprogramming towards pluripotency. Nat Commun 4:1565
Lee, Dung-Fang; Su, Jie; Sevilla, Ana et al. (2012) Combining competition assays with genetic complementation strategies to dissect mouse embryonic stem cell self-renewal and pluripotency. Nat Protoc 7:729-48
Ang, Yen-Sin; Tsai, Su-Yi; Lee, Dung-Fang et al. (2011) Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell 145:183-97
Ang, Yen-Sin; Gaspar-Maia, Alexandre; Lemischka, Ihor R et al. (2011) Stem cells and reprogramming: breaking the epigenetic barrier? Trends Pharmacol Sci 32:394-401

Showing the most recent 10 out of 15 publications