Current Research and Scholarly Interests
Cancer biology and oncogene discovery in organoid cultures.
We have successfully established primary 3D organoid cultures of diverse tissues and used them to achieve the first in vitro conversion of primary intestine, stomach and pancreas tissue to adenocarcinoma (Ootani et al, Nat Med 2009; Li et al, Nat Med 2014) amongst others. These organoid systems comprise an robust in vitro system which we are exploiting for the functional validation of putative oncogenic loci which are identified in whole-genome cancer surveys such as TCGA. We collaborate extensively with systems biologists to interrogate large-scale cancer genomics datasets in organoids using barcoded screening methods, which are identifying new oncogenes against which we then attempt to develop new therapies. Further, we have established large biobanks of organoids from clinical cancer biopsies with relevance to tumor modeling and predication of patient responses to therapeutics. We also apply organoid models to cancer drug discovery and drug resistance.
Organoids for regenerative medicine.
We are also interested in using organoids as a method to grow mini-organs that can be transplanted into recipients for regenerative medicine purposes. We are establishing proof-of-principle for human or mouse organoid transplantation, ultimately to effect phenotypic correction of diseases.
Intestinal stem/progenitor biology.
The complete regeneration of the epithelial lining of the intestine every 5-7 days renders the intestine a model system for studying stem cell behaviors. We are investigating the regulation of the intestinal stem cell (ISC) compartment by extracellular signals such as Wnts, using adenoviral and conditional knockout approaches. We have defined R-spondins as dominant regulators of the ISC niche with Wnts playing a more permissive role using lineage tracing, bioengineered Wnts and single cell RNA-seq approaches (Yan et al., Nature, 2017a; Janda et al, Nature 2017b). We have found that Bmi1+ ISC are strongly injury-inducible versusthe homeostatic function of Lgr5+ ISC (c.f. Yan et al, PNAS 2012, Barry et al, Nature 2013) and have enteroendocrine characteristics (Yan et al., Stem Cell, 2017). Further, we have derived robust organoid methods for prolonged culture of and ex vivo expansion of primary intestine and other GI organs, with preservation of ISCs and recapitulation of the Wnt- and Notch-dependent ISC niche, even allowing peristalsis (Ootani et al, Nat Med 2009; Li et al Nat Med 2014).
Angiogenesis and the blood-brain barrier
We are interested in determining functions of novel molecules regulating angiogenesis including receptors such as GPCRs, microRNAs and secreted molecules. We found that GPR124 is essential for developmental brain angiogenesis (Kuhnert et al, Science 2010) and that GPR124 is critical for maintaining blood-brain barrier integrity during stroke and brain tumor growth (Chang et al, Nat Med 2017). We have several active projects in stroke and blood-brain barrier (BBB) basic biology and therapeutic development. We have previously exploring the functions of the endothelial miRNA miR-126 in adults using conditional ko mice (Kuhnert et al, Development 2008) and have extensive interests in pharmacologic inhibition of novel targets for anti-angiogenic therapy of cancer and ocular disorders.
Endothelial cell regulation of physiology,
How do endothelial cells regulate physiology of their host organs? The liver hepatocyte appears particularly responsive to its host endothelial cells per VEGF regulation of hepatocyte Epo synthesis, erythropoiesis (Tam et al, Nat Med 2006) and metabolic pathways. We have found that FDA-approved VEGF inhibitors such as aflibercept improve glucose tolerance and can treat animal models of diabetes, by stimulating cross-talk between the hypoxia and insulin signaling pathways, with sensitization of hepatic insulin signaling (Wei et al., Nature Med 2013a; Taniguchi et al., Nat. Med., 2013b).