Research in my lab focuses on two major themes: gene regulation during brain development and the genetic basis of inner ear morphogenesis. Both areas of investigation use mouse models to study mechanisms of human congenital disorders including brain malformations and hearing loss.
gene regulation, enhancers, Shh, brain development, hearing loss, cochlea, genetics, genomics, gene therapy
Description of Research
Enhancers regulating Sonic hedgehog (Shh) brain expression
Cis-acting regulatory sequences are required for proper temporal and spatial control of gene expression. Variation in gene expression is highly heritable and a significant determinant of human disease susceptibility. The diversity of human genetic diseases attributed, in whole or in part, to mutations in non-coding regulatory sequences is on the rise. Improvements in genome wide methods of associating genetic variation with human disease and predicting DNA with cis-regulatory potential are two of the major reasons for these recent advances. Research in my laboratory employs genetic, genomic and biochemical approaches to uncover the cis and trans acting determinants of Shh expression in the mouse and human CNS. The temporal and spatial control of Shh expression from defined signaling centers is critical for establishing the identity of neurons in discrete positions along the dorsoventral axis of the neural tube. In the absence of Shh function, ventral midline development is perturbed resulting in holoprosencephaly (HPE), a structural brain malformation, as well as neuronal patterning and path finding defects. Central to the understanding of ventral neural tube development is how Shh transcription is regulated in the CNS. Previous work in my lab employed an enhancer trap assay to uncover six CNS specific enhancers distributed over 500kb whose combined activity covered most sites of Shh transcription in the mouse neural tube including the ventral forebrain (Jeong et al., 2006). These Shh regulatory elements were subsequently used as tools to further dissect Shh brain function (Jeong et al., 2008; Geng et al., 2008; Jeong et al., 2011; Trowe et al., 2013) and determine the evolutionary origin of Shh regulatory sequences, which in some cases predate the chordate phylum (Yao et al., 2016). A particular highlight of these studies was our demonstration that mouse embryos lacking Shh in the prospective hypothalamus exhibit key features of septo-optic dysplasia (SOD), a congenital disorder characterized by pituitary, optic nerve, and midline brain malformations (Zhao et al., 2012). We further revealed that prenatal ethanol exposure increases SOD risk through spatiotemporal perturbations in Shh signaling activity (Kahn et al., 2017). These finding suggest that reduced Shh signaling underlies the pathogenesis of SOD and represents a later manifestation of a Shh dependent phenotype compared to HPE. Whole exome sequencing studies are currently underway to identify novel pathogenic mutations associated with human cases of SOD. These brief examples of my lab’s work are meant to emphasize our expertise in deciphering complex regulatory circuits controlling brain specific gene expression in normal and disease states.
Genomic architecture of Shh dependent cochlear morphogenesis
A second focus of research in my laboratory addresses the genetic programs underlying inner ear morphogenesis. Congenital malformations of the inner ear are a significant cause of hearing loss and vestibular dysfunction in humans. My research program is strongly motivated by the premise that a detailed understanding of the cellular and molecular mechanisms underlying inner ear development should not only improve our fundamental knowledge of how this complex structure is assembled, but may also profoundly improve the way inner ear disorders are treated in the future. The principal components for hearing (cochlea) and balance (vestibulum) are formed from ventral and dorsal outgrowths, respectively, of a common bilateral structure, the otocyst. Organization of the inner ear into auditory and vestibular components is established early in development and is heavily influenced by surrounding tissues. The proximity of the otocyst to the hindbrain suggested that extracellular signals that pattern the CNS might also polarize the otic epithelium along its dorsoventral axis. Previous work in my laboratory determined the specific contributions of Shh and Wnt signaling pathways in promoting cochlear and vestibular development, respectively. We demonstrated that Shh acts directly on the otic epithelium to regulate the outgrowth of the cochlear duct (Riccomagno et al., 2002; Bok et al., 2007; Brown et al., 2011), whereas Wnt signaling is essential for vestibular morphogenesis and sensory hair cell specification (Riccomagno et al., 2005; Rakowiecki and Epstein 2013; Brown et al., 2015). More recent studies identified novel downstream effectors of Shh signaling that are active during cochlear duct outgrowth. In comparing the mRNA expression profile between control and Shh signaling mutants, we identified an intriguing set of genes with highly enriched functions in cochlear morphogenesis and sensory development. The gene regulatory networks acting downstream of Shh in the inner ear are currently being elucidated using a variety of genome wide approaches, including ChIP-seq, RNA-seq and ATAC-seq. In addition, targeted mutations have been engineered in mice for a select number of Shh dependent genes, some of which result in hearing loss. Gene therapy protocols are also being developed to treat hearing loss in these mice.
Several rotation projects related to the stated goals of the lab are currently available. Contact Dr. Epstein for more information.
Alex Rohacek (Graduate Student)
Tanya Corman (Graduate Student)
Staci Rakowiecki (Research Specialist)
Victor Muthu, Ph.D. (Postdoctoral Fellow)
Tingfang Chen, Ph.D. (Postdoctoral Fellow)
Sixing Chen, M.Sc. (visiting scholar)
Rohacek AM, Bebee TW, Tilton RK, Radens CM, McDermott-Roe C, Peart N, Kaur M, Zaykaner M, Cieply B, Musunuru K, Barash Y, Germiller JA, Krantz ID, Carstens RP, Epstein DJ.: ESRP1 Mutations Cause Hearing Loss due to Defects
in Alternative Splicing that Disrupt Cochlear
Development. Developmental Cell 43: 318-331, 2017.
Kahn, B.M., Corman, T.S., Lovelace, K., Hong, M., Krauss, R.S. and Epstein, D.J. : Prenatal ethanol exposure in mice phenocopies Cdon mutation by impeding Shh function in the etiology of optic nerve hypoplasia. Disease Models and Mechanisms 10: 29-37, 2017.
Yao, Y., Minor, P.J., Zhao, Y-T., Jeong, Y., Pani, A.M. King, A.N., Symmons, O., Gan, L., Cardoso, W.V., Spitz, F., Lowe, C.J. and Epstein, D.J.: Cis-regulatory architecture of a brain-signaling center predates the origin of chordates. Nature Genetics 48: 575-580, 2016.
Brown, A.S., Rakowiecki, S.M., Li, J.Y. and Epstein, D.J. : The cochlear sensory epithelium derives from Wnt responsive cells in the dorsomedial otic cup. Developmental Biology 399: 177-187, 2015.
Trowe, M-O., Zhao, L., Weiss, A-C., Christoffels, V., Epstein, D.J.* and Kispert, A.* : Inhibition of Sox2-dependent activation of Shh in the ventral diencephalon by Tbx3 is required for the formation of the neurohypophysis
Development 140: 2299-2309, 2013 Notes: *corresponding authors.
Rakowiecki, S. and Epstein, D.J. : Divergent roles for Wnt/β-catenin signaling in epithelial maintenance and
breakdown during semicircular canal formation.
Development 140: 1730-9, 2013.
Zhao, L., Zevallos, S., Rizzoti, K., Jeong, Y., Lovell-Badge, R. and Epstein, D.J.: Disruption of SoxB1 dependent Sonic hedgehog expression in the hypothalamus causes Septo-Optic Dysplasia.
Developmental Cell 22: 585-596, 2012.
Jeong, Y., Dolson, D. K., Waclaw, R. R., Matise, M. P., Sussel, L., Campbell, K., Kaestner, K. H., Epstein, D. J.: Spatial and temporal requirements for sonic hedgehog in the regulation of thalamic interneuron identity. Development 138(3): 531-41, 2011.
Brown, A. S., Epstein, D. J.: Otic ablation of smoothened reveals direct and indirect requirements for Hedgehog signaling in inner ear development. Development 138(18): 3967-76, 2011.
Bok, J., Dolson, D. K., Hill, P., Ruther, U., Epstein, D. J., Wu, D. K.: Opposing gradients of Gli repressor and activators mediate Shh signaling along the dorsoventral axis of the inner ear. Development 134(9): 1713-22, 2007.
Jeong, Y., El-Jaick, K., Roessler, E., Muenke, M., Epstein, D. J.: A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers. Development 133(4): 761-72, 2006.
Jeong, Y., Leskow, F. C., El-Jaick, K., Roessler, E., Muenke, M., Yocum, A., Dubourg, C., Li, X., Geng, X., Oliver, G., Epstein, D. J.: Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nature Genetics 40(11): 1348-53, 2008.
Riccomagno, M. M., Takada, S., Epstein, D. J.: Wnt-dependent regulation of inner ear morphogenesis is balanced by the opposing and supporting roles of Shh. Genes & Development 19(13): 1612-23, 2005.
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Last updated: 11/07/2017
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