The long-term goal of this grant is to reveal molecular mechanisms by which particular cell type choices are made in multipotent progenitor cells in the mammalian embryo. The research seeks to understand how extracellular signals converge on progenitor cells to induce a cell fate choice and how multipotent progenitors gain the competence to choose certain fates and be excluded from others. Since the vast majority of embryonic progenitors, adult stem cells, and perhaps cancer progenitors in the body are multipotent, not pluripotent, understanding the principles by which multipotent progenitors gain their special competencies and limitations is of fundamental biomedical importance. As a model system, we investigate the specification of liver progenitors from multipotent foregut endoderm cells in the early mouse embryo. These studies identified the concept that pioneer transcription factors help establish cell type competency by opening up local domains of chromatin at silent liver target genes in the endoderm. We hypothesize that transcription factors that convert differentiated cells to pluripotency can function as pioneer factors. Recently, we discovered co-regulators that modify chromatin architecture with FoxA pioneer factors and revealed the basis by which Fox proteins, compared to other factors, scan the genome in the living cell nucleus. In addition, we discovered a dynamic signaling network that induces the hepatic fate In multipotent endoderm, and more recently have traced the inducing signals down to the chromatin of recipient target genes. Our integrative view is enabled by our development of new cell sorting capacities from early embryos and scaled-down molecular biology and chromatin immunoprecipitation technology. Finally, we can now trace the fate and function of different types of progenitor cells in the mammalian foregut. We performed genomic expression analysis of different patches of endoderm cells and then made cre-ER transgenes driven by the differentially expressed genes. Our basic findings have been translated by many other laboratories to explain how pioneer factors enable cancer cells to be hormone responsive and to differentiate embryonic stem cells into endoderm cells and liver cells. Further work from this grant is anticipated to provide insights into the mechanisms of cell programming and the means by which different progenitor types can be programmed to particular cell fates.
improvements in the ability to program progenitor cells and stem cells, and to reprogram differentiated cells, will provide therapies for human diseases, allow researchers to investigate early manifestations of disease genomes. and to screen for drugs that ameliorate cellular dysfunction. To enable such possibilities, my grant investigates the normal genetic regulatory mechanisms by which mammalian cell type specification occurs, so that the efficiency of therapeutic and diagnostic cell programming can be enhanced.
|Iwafuchi-Doi, Makiko; Donahue, Greg; Kakumanu, Akshay et al. (2016) The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation. Mol Cell 62:79-91|
|Hsu, H-T; Chen, H-M; Yang, Z et al. (2015) TRANSCRIPTION. Recruitment of RNA polymerase II by the pioneer transcription factor PHA-4. Science 348:1372-6|
|Kim, Jungsun; Zaret, Kenneth S (2015) Reprogramming of human cancer cells to pluripotency for models of cancer progression. EMBO J 34:739-47|
|Xu, Cheng-Ran; Li, Lin-Chen; Donahue, Greg et al. (2014) Dynamics of genomic H3K27me3 domains and role of EZH2 during pancreatic endocrine specification. EMBO J 33:2157-70|
|Iwafuchi-Doi, Makiko; Zaret, Kenneth S (2014) Pioneer transcription factors in cell reprogramming. Genes Dev 28:2679-92|
|Zaret, Kenneth S (2014) Genome reactivation after the silence in mitosis: recapitulating mechanisms of development? Dev Cell 29:132-4|
|Bhatia, Sangeeta N; Underhill, Gregory H; Zaret, Kenneth S et al. (2014) Cell and tissue engineering for liver disease. Sci Transl Med 6:245sr2|
|Zaret, Kenneth S (2014) At the revolution with Fred Sherman. Mol Cell Biol 34:922-5|
|Lagha, Mounia; Mayeuf-Louchart, Alicia; Chang, Ted et al. (2013) Itm2a is a Pax3 target gene, expressed at sites of skeletal muscle formation in vivo. PLoS One 8:e63143|
|Kim, Jungsun; Hoffman, John P; Alpaugh, R Katherine et al. (2013) An iPSC line from human pancreatic ductal adenocarcinoma undergoes early to invasive stages of pancreatic cancer progression. Cell Rep 3:2088-99|
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