Dynamic Bayesian Network Analysis Reveals Unique and Conserved Elements of Genetic Circuitry Governing Two Different Cell-Specific Regenerative Paradigms in the Retina

Abstract

Regeneration—the capacity to replace lost body parts—has fascinated scientists since the time of Aristotle. Regenerative phenomena became popular with observationalists during the 18th and 19th centuries and a fertile ground for experimentation. In fact, early regenerative biology practitioners such as Abraham Trembley (1710-1784) and his colleagues have been credited with establishing the foundations of modem experimental biology. However, interest faded during the 20th century in part due to the rise of Genetics and later reinforced by the dominance of mammalian model species which have a limited capacity for tissue replacement. At the start of the 21st century, a confluence of “stem cell promise” and new genetic manipulation techniques applicable to a broad range of species has rekindled the field. (Rosenthal, 2003) One aspect, however, remains a consistent and somewhat limiting theme: the emphasis on large-scale injury paradigms (e.g., limb loss). Conversely, the diseases most often cited as potential therapeutic beneficiaries of stem cell/regenerative research advances are typically linked to the loss of specific cell types (e.g., Parkinson’s disease, Type 1 diabetes). We and others have begun to explore cell-specific regenerative paradigms in order to increase understanding of how the loss of individual cell types is detected, how the response to cell loss is regulated, and ultimately how cell-type specific regeneration can be promoted. The goal of this project is to identify genetic networks that regulate the 12 regeneration of individual retinal neuron subtypes. Visual impairment is cited as the second most feared disease following cancer (Office, 2004). While currently considered ‘irreversible’ in mammals, including humans, we posit that retinal cell loss can be ‘cured’ by stimulating dormant regenerative capacities of adult neural stem cells located in the eye (Das et al., 2006); i.e., that reparative therapeutic strategies can be developed that restore visual function to patients by replacing cells lost to degenerative disease or ocular trauma. We developed a system for studying cell-specific loss and replacement in the zebrafish retina, a highly regenerative species (Poss, Wilson, & Keating, 2002), as a means of understanding how the regenerative potential retinal stem cells is regulated. Mammals, including humans, have a limited innate capacity for retinal regeneration (Das et al., 2006). However, recent data suggests that the potential for regeneration is retained in mammals; treatments with discrete molecular factors can enhance retinal cell replacement in mammalian disease models and human retinal stem cells can give rise to new neurons in cell culture. In addition, key cellular and molecular mechanisms governing retinal regeneration appear to be conserved between fish and mammals (e.g., Muller glia acting as injury-induced retinal stem cells) (Reh & Fischer, 2006). Accordingly, we sought to identify genes and genetic networks which regulate the regeneration of individual retinal cell subtypes using temporally resolved differential expression assays combined with cutting-edge statistical methods for establishing connectivity patterns in genetic circuits. By defining pathways which stimulate retinal stem cells to respond to cell losses in a regenerative manner, we aspire to further the development of novel therapies aimed at reversing vision loss in humans.