Chemical and Functional Genomic Approaches to Stem Cell Biology and Regenerative Medicine
Recent advances in stem cell biology may make possible new approaches for the treatment of a number of diseases including cardiovascular disease, neurodegenerative disease, musculoskeletal disease, diabetes and cancer. These approaches could involve cell replacement therapy and/or drug treatment to stimulate body’s own regenerative capabilities by promoting survival, migration, proliferation, differentiation and reprogramming of endogenous stem/progenitor cells. However, such approaches will require identification of renewable cell sources of engraftable functional cells, an improved ability to manipulate their fate in vitro and in vivo, as well as a better understanding of the signaling pathways that control their fate.
Equipped with high throughput screening platform and large arrayed molecular libraries—combinatorial chemical libraries, genome-scale cDNA (for gain-of-function) and siRNA (for loss-of-function) libraries, we have been developing and integrating chemical and functional genomic tools to study stem cell biology and regeneration. Our current works have focused on screening these libraries to identify and further characterize small molecules and genes that can control stem cell fate in various systems, including (i). Self-renewal regulation of embryonic and adult stem cells; (ii). Directed and step-wised differentiation of ESC toward neuronal, cardiac and pancreatic lineages; (iii). Directed neuronal differentiation and subtype neuronal specification of human and rodent neural stem cells; (iv). Cellular plasticity and reprogramming of lineage-restricted somatic cells to multipotent and pluripotent states; (v). Functional proliferation of adult cardiomyocytes and pancreatic beta cells; (vi). Developmental signaling pathways (i.e. Wnt, Hh, BMP and FGF) and epigenetic mechanisms (histone and DNA de/methylation). (vii). Development of new technologies for stem cell derivation and gene targeting. Moreover, major efforts are devoted to characterize the molecular mechanism of these identified small molecules and genes using various approaches, including detailed structure-activity-relationship (SAR) studies, affinity chromatography for target identification, transcriptome profiling, proteomics analysis, chemical/genetic epistasis, and biochemical and functional assays in vitro and in vivo. So far, functional small molecules and/or genes have been identified and are being characterized in each of the above twenty plus distinct biological processes involving regulation of stem/progenitor cells. More recent examples include identification and characterization of distinct small molecules for hESC self-renewal and clonal expansion/survival; dopaminergic neuron specification from mESCs; derivation of rat ESCs; reprogramming of somatic cells to pluripotent state (iPS cells); definitive endoderm and pancreatic induction; chemically defined monolayer conditions for self-renewal of ESCs and their directed differentiation to cardiac lineages; proliferation of human beta cells; and regulating Wnt signaling. Those studies may ultimately facilitate the therapeutic application of stem cells and the development of small molecule drugs to stimulate tissue and organ regeneration in vivo.
Shown are synthetic small molecules and natural products that bind to nuclear receptors (all-trans retinoic acid and dexamethasone), histone-modifying enzymes and DNA-modifying enzymes (trichostatin A, BIX 01294 and 5-azacytidine), and protein kinases and signalling molecules (reversine, purmorphamine, 16,16-dimethyl prostaglandin E2, forskolin, QS11, BIO, cyclopamine, neuropathiazol, pluripotin and Y-27632). Reproduced with permission from Macmillan Publishers, Ltd: Nature, Xu et al., 453, 338-344, copyright 2008.