David R. Hyde Professor; Kenna Director of the Zebrafish Research Center

Mechanisms underlying Retinal Development and Regeneration
David R. Hyde

Research Interests:

My lab studies retinal development and regeneration of retinal neurons from resident adult stem cells in zebrafish. The retina is an excellent model because it is an easily accessible portion of the central nervous system and may have implications in the development and regeneration of other regions of the CNS, such as the brain. Furthermore, the resident adult stem cells in the zebrafish retina are also present in the retina and brain of all vertebrates, including humans. Thus, understanding how the zebrafish regenerates lost neurons may lead to therapies to treat several human neurological diseases, such as macular degeneration and retinitis pigmentosa in the retina or Alzheimer’s and Parkinson’s disease.

Various treatments can be used to damage the adult zebrafish retina, resulting in the loss of different types of retinal neurons. Retinal damage induces the resident Müller glia to dedifferentiate/reprogram and proliferate to produce neuronal progenitor cells (NPCs), which continue to proliferate and migrate to the damaged retinal layer and specifically differentiate into the neuronal class that was lost. Because these Müller glia-derived NPCs can differentiate into any type of retinal neuron, they must be pluripotent and represent adult stem cells. The regeneration is highly specific, with the number of proliferating Müller glia and NPCs proportional to the number of dying neurons and the NPCs differentiating into primarily only the neuronal cell types that were lost. This suggests that signals must stimulate the initiation of the regeneration response, regulate the extent of Müller glia and NPC proliferation, and communicate the type and number of retinal neurons that were lost.

Using a combination of microarray, RNA-seq, and proteomic experiments, we identified a number of proteins/genes that are required for various aspects of regeneration, including Müller glia reprogramming and proliferation, NPC proliferation, and migration. We determined that tumor necrosis factor-alpha (TNFα ), produced in dying retinal neurons, stimulates Müller glia proliferation, while Notch signaling represses Müller glia proliferation. When TNFα is injected into an undamaged eye and Notch signaling is blocked, Müller glia reenter the cell cycle to produce NPCs that commit to neuronal lineages, even without retinal damage. Thus, expression of TNFα and repression of Notch signaling are necessary and sufficient to stimulate a regeneration response. We also determined that Sox2 is required and sufficient for Müller glia reprogramming. These three proteins regulate the expression and activation of two transcription factors that are both necessary for Müller glia proliferation, Ascl1a (Achete scute-like 1a) and Stat3. While Stat3 is expressed in all Müller glia in the light-damaged retina, Ascl1a is only expressed in proliferating Müller glia. It is unclear what regulates the differential expression patterns of Stat3 and Ascl1a during retinal regeneration.

While several proteins required for regeneration are also necessary for retinal development, other regeneration proteins either have different or no function in development. This demonstrates that regeneration is not simply a recapitulation of the normal developmental process. However, we do study the functions of our regenerative candidate proteins in development because it can inform us of their potential roles and reveal what are the similarities and differences between development and regeneration.

In addition to using transcriptomic and proteomic approaches to study regeneration, we are developing novel genetic approaches to identify genes required for regeneration and study their function. We also create transgenic lines to study the expression patterns of candidate genes and their proteins. We are starting to use genome editing to generate conditional knockout and overexpression mutant lines to control the loss and expression of specific candidate genes at different points prior to and during retinal regeneration. This will allow us to distinguish between the function of specific proteins early (Müller glia reprogramming and proliferation) and late (NPC proliferation and neuronal commitment) during regeneration. We are also using a variety of genetic and molecular approaches to study the epigenetic changes during Müller glia reprogramming, as well as live cell imaging of cultured retinas to follow the dynamic nuclear and cellular movements during regeneration. Through these state-of-the-art approaches, we are elucidating the molecular and cellular processes that regulate neuronal regeneration in zebrafish retina and throughout the CNS.



  • Director of the Center for Stem Cells and Regenerative Medicine 2014-Present
  • Rev. Howard J. Kenna, C.S.C. Memorial Director of the Center for Zebrafish Research 2001-Present
  • Professor, Department of Biological Sciences, University of Notre Dame, IN 2000-Present
  • Director,  University of Notre Dame Zebrafish Research Facility, IN 1995-2001
  • Associate Professor, Department of Biological Sciences, University of Notre Dame, IN 1995-2000
  • Assistant Professor, Department of Biological Sciences, University of Notre Dame, IN 1988-1995
  • Senior Research Fellow, Division of Biology, California Institute of Technology, CA 1988
  • Postdoctoral Research Fellow, Division of Biology, California Institute of Technology, CA 1985-1988
  • Ph. D. Biochemistry, Pennsylvania State University, PA 1985
  • B.S. Biochemistry, Michigan State University, MI 1980


Recent Papers:

  • Conner, C., Ackerman, K.M., Lahne, M., Hobgood, J.S., and Hyde, D.R. (2014). TNFα expression and repressing Notch signaling are sufficient to mimic retinal regeneration by inducing Müller glial proliferation to generate committed progenitor cells. J. Neurosci. 34: 14403-14419.
  • Rajaram, K., Harding, R., Hyde, D.R., and Patton, J.G. (2014). miR-203 regulates progenitor cell proliferation during adult zebrafish retina regeneration. Dev. Biol. 392:393-403.
  • Rajaram, K., Harding, R.L., Bailey, T., Patton, J.G., and Hyde, D.R.(2014). Dynamic miRNA expression patterns during retina regeneration in zebrafish: reduced dicer or miRNA expression suppresses proliferation of Müller glial-derived neuronal progenitor cells. Dev. Dyn. 243: 1591-1605.
  • Gorsuch, R.A. and Hyde, D.R. (2014). Regulation of Müller glial dependent neuronal regeneration in the damaged adult zebrafish retina. Exp. Eye Res. 123:131-140.
  • Nelson, C.M., Ackerman, K.M., O’Hayer, P., Bailey, T.J., Gorsuch, R.A. and Hyde, D.R. (2013). Tumor necrosis factor-alpha is produced by dying retinal neurons and is required for Müller glia proliferation during zebrafish retinal regeneration. J. Neurosci. 33:6524-6539.
  • Gemberling, M., Bailey, T.J., Hyde, D.R., and Poss, K.D. (2013). The zebrafish as a model for complex tissue regeneration. Trends in Genetics. 29: 611-620.
  • Nelson, C.M., Gorsuch, R.A., Bailey, T.J., Ackerman, K.M., Kassen, S.C., and Hyde, D.R. (2012). Stat3 Defines Three Populations of Müller Glia and Is Required for Initiating Maximal Müller Glia Proliferation in the Regenerating Zebrafish Retina. J. Comp. Neurol. 520: 4294-4311. .