The epithelia of the intestine and colon provide a barrier against gut microbiota, which can modify the growth, metabolism, and cell fate decisions of epithelial cells in profound ways. Emerging evidence suggests that, to meet this unique challenge, the epithelial cells are quite plastic, capable of dedifferentiating into stem cells in order to maintain the tissue?s regenerative capacities and proper homeostasis. However, the mechanisms by which (1) epithelial cells respond to different microbes and their derived metabolites and (2) the epigenetic regulatory elements that drive this plasticity are largely unknown. Addressing these two fundamental questions will enable us to understand the robustness of epithelial stem cell regulation. Within the scope of the R35, we are developing platform technologies to address these two fundamental questions. First, we have been developing a 2D organoid based screening assay to investigate host- microbial interactions in a high-throughput fashion. The 2D fluorescent organoid assay allows us to plate different gut bacterial strains on the apical (luminal) side of monolayer organoid cells, while fluorescent probes enable readout of bacterial and host cell states during their interactions. Second, we have been developing an epigenetic CRISPR-dCAS9 organoid screening platform. Guided by epigenetic profiling including ATAC-seq and Mint-ChIP, high-throughput guide RNA (gRNA) libraries are designed to target lineage-specific chromatin regions. By measuring enriched gRNAs from regenerated stem cells isolated based on fluorescent markers, we will systematically identify regulatory elements that drive de-differentiation and plasticity. To accomplish these two tasks, we are requesting two essential pieces of equipment. First, we need a fluorescent plate reader, which will allow us to measure the fluorescent signals from reporters in bacteria, organoid cells, and the CRISPR/dCAS9 constructs. We were using the plate reader in the departmental teaching lab previously, which has recently moved and is now unavailable. Second, we hope to purchase an IncuCyte imaging system, which provides automated capabilities for time-series quantification of bacterial/organoid growth and lineage commitment dynamics. The equipment will enable us to develop the two organoid-based screening platforms and to identify novel mechanisms that regulate host-microbial interactions and cell fate plasticity.

Public Health Relevance

A fluorescent plate reader and an IncuCyte live imaging system are requested to develop two organoid screening technology platforms within the scope of the R35 project. The first project will develop 2-D intestinal and colonic organoid assays to screen host-microbial interactions. The second project will develop an epigenetic CRISPR-dCAS9 screening platform to identify regulatory elements that drive call fate plasticity and de-differentiation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Unknown (R35)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1)
Program Officer
Gibbs, Kenneth D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Duke University
Biomedical Engineering
Biomed Engr/Col Engr/Engr Sta
United States
Zip Code
Bu, Pengcheng; Chen, Kai-Yuan; Xiang, Kun et al. (2018) Aldolase B-Mediated Fructose Metabolism Drives Metabolic Reprogramming of Colon Cancer Liver Metastasis. Cell Metab 27:1249-1262.e4
Chen, Kai-Yuan; Srinivasan, Tara; Lin, Christopher et al. (2018) Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids. Conf Proc IEEE Eng Med Biol Soc 2018:2378-2381
Kadur Lakshminarasimha Murthy, Preetish; Srinivasan, Tara; Bochter, Matthew S et al. (2018) Radical and lunatic fringes modulate notch ligands to support mammalian intestinal homeostasis. Elife 7:
Chen, Kai-Yuan; Shen, Xiling; Diehl, Anna Mae (2018) Prometheus revisited. J Clin Invest 128:2192-2193
Chen, Kai-Yuan; Srinivasan, Tara; Tung, Kuei-Ling et al. (2017) A Notch positive feedback in the intestinal stem cell niche is essential for stem cell self-renewal. Mol Syst Biol 13:927
Klose, Christoph S N; Mahlak├Áiv, Tanel; Moeller, Jesper B et al. (2017) The neuropeptide neuromedin U stimulates innate lymphoid cells and type 2 inflammation. Nature 549:282-286
Barth, Bradley B; Henriquez, Craig S; Grill, Warren M et al. (2017) Electrical stimulation of gut motility guided by an in silico model. J Neural Eng 14:066010