I am interested in understanding the relationship between normal development and mechanisms of disease. I therefore built a strong foundation in molecular biology, biochemistry and developmental genetics as a graduate student. As a postdoctoral fellow, I have used the digestive tract as a model system to study fundamental developmental questions of stem cell renewal and differentiation in fetal and adult mice. Notch signaling plays critical roles in these processes. Using powerful mouse genetic tools, I have demonstrated roles for Notch signaling and its key downstream intestine-restricted transcription factor Atoh1 in gut stem and progenitor cell proliferation, dedifferentiation and cancer, leading t 4 first-author publications. To further understand mechanisms of gastrointestinal cell response to Notch signaling in epithelial cells, I now aim to investigate transcription factors that act downstream of Notch signaling. To systemically identify novel transcription factors that play important roles in intestinal cell differentiation and study the underlying transcriptional mechanisms, I will learn and apply the new genome-wide approach of chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-Seq). I will analyze genome-wide binding of the secretory transcription factors Atoh1 and Tcf4, and test specific mechanistic hypotheses regarding their interactions in cell replication and in differentiation of te intestinal secretory cell lineage. In the stomach, which does not express the crucial downstream factor Atoh1, I will test the novel hypothesis that a stomach-restricted homologue, Ascl1, acts downstream of Notch signaling to regulate epithelial cell proliferation and enteroendocrine differentiation. The studies I propose will hence provide novel and significant insights into central mechanisms of gastrointestinal epithelial differentiation and help illuminate the molecular basis of diseases ranging from congenital disorders and inflammation to cancer.
I aim to become an independent principal investigator in the area of gastrointestinal biology, with expertise in lineage differentiation. A K99/R00 award will facilitate my transition to full independence through sequential mentored and independent phases. In the short-term, this award will allow me to learn new technologies including ChIP-Seq and bioinformatics analysis, hence broadening my expertise to include knowledge of systems biology and genomics, under the mentorship of Ramesh Shivdasani. His lab has successfully completed projects and published important papers that apply such approaches, providing a perfect training environment. Furthermore, the exceptional institutional environment at the Dana-Farber Cancer Institute and Harvard Medical School will further enable my transition to independence by providing institutional programs, facilities, opportunities for collaboration, and broad mentorship My mentorship committee includes world-leading Harvard faculty in the fields of gastrointestinal biology, transcription and genomics to provide guidance and support towards developing my own research program. Furthermore, the Harvard Stem Cell Institute and the Center for Functional Cancer Epigenetics (CFCE) at Dana-Farber Cancer institute will not only give me outstanding opportunities to refine my methods but will also allow me to interact and collaborate with eminent scientists in stem cell biology and epigenomics. Thus, a K99/R00 award will provide critical support at a crucial stage in my career and permit me to make a long-term commitment toward studying the unique biology that underlies gastrointestinal diseases. In the long-term future as a successful independent investigator, I will devote myself to understanding basic mechanisms of gastrointestinal diseases, leading collaborative efforts with clinical and computational biologists, and educating the next generation of basic and clinical scientists.

Public Health Relevance

The gastrointestinal surface is continually replenished through the activity of stomach and intestinal stem cells that differentiate into specialized cell types. Although these cells harbor the risk of developing diseases such as cancer and inflammation, understanding of their molecular regulation is incomplete. This proposal for a K99/R00 award focuses on important organ-specific transcription factors, i.e., proteins that control hundreds of other genes, and I propose to study how these proteins function within a prominent developmental signaling pathway known as Notch. These studies will help define molecular mechanisms of gastrointestinal cell differentiation and identify new targets for therapy of digestive tract diseases.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
Career Transition Award (K99)
Project #
Application #
Study Section
Diabetes, Endocrinology and Metabolic Diseases B Subcommittee (DDK)
Program Officer
Carrington, Jill L
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Dana-Farber Cancer Institute
United States
Zip Code
Kim, Tae-Hee; Saadatpour, Assieh; Guo, Guoji et al. (2016) Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5(+) Intestinal Stem Cells. Cell Rep 16:2053-60
Kim, Tae-Hee; Li, Fugen; Ferreiro-Neira, Isabel et al. (2014) Broadly permissive intestinal chromatin underlies lateral inhibition and cell plasticity. Nature 506:511-5
Kim, Tae-Hee; Shivdasani, Ramesh A (2012) Stem cell niches: famished Paneth cells, gluttonous stem cells. Curr Biol 22:R579-80
Kim, Tae-Hee; Escudero, Silvia; Shivdasani, Ramesh A (2012) Intact function of Lgr5 receptor-expressing intestinal stem cells in the absence of Paneth cells. Proc Natl Acad Sci U S A 109:3932-7