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R.H. Farkas, J. Qian, J.L. Goldberg, H.A. Quigley, D.J. Zack; Profiles of Gene Expression in Highly Purified Retinal Ganglion Cells in the Rat . Invest. Ophthalmol. Vis. Sci. 2004;45(13):668.
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© ARVO (1962-2015); The Authors (2016-present)
Purpose:The phenotypes of specialized cells arise, in part, from the unique gene expression patterns the cells exhibit. A partial profile of genes expressed by retinal ganglion cells (RGCs) was obtained through EST sequencing. To better understand the functions of these RGC genes, both in terms of ganglion cell physiology and the functions of the genes themselves, we examined where else in the nervous system, and at what levels, these genes where expressed. Methods: EST sequencing was performed on a cDNA library constructed from RGCs isolated by immunopanning. Comparative gene expression clustering between RGCs and 13 different neural regions (Su et al., 2002; http://expression.gnf.org/cgi–bin/index.cgi) was carried out using ‘Cluster’ and ‘TreeView’ (M. Eisen). RESP18 and DDAH1 antibodies were gifts of Drs B.A. Eipper and M. Vasak, respectively. For candidate gene genomic mapping the mRNA alignment program, SPIDEY, was used. Results: Clustering of 4,791 RGC ESTs identified 2,360 unique gene clusters. Of these, 60% represented known genes, while 27% were either uncharacterized genes or ESTs. The remaining 13% were previously undiscovered sequences that might contain novel genes of particularly importance to RGCs. Unexpectedly, one of the largest clusters, ‘regulated endocrine–specific protein 18’ (RESP18), was a neuroendocrine–specific gene highly over–expressed in hypothalamus. RESP18 immunoreactivity was found mainly in the RGC layer. DDAH1, a gene involved in nitric oxide metabolism, was localized to RGC and amacrine layers. Hierarchical clustering was used to visualize overall RGC gene expression patterns compared to expression profiles generated by Su et al. from affymetrix microarrays from 13 separate neuronal regions. A prominent subset of RGC genes was specifically over–expressed in both dorsal root and trigeminal ganglia, regions known to share similar genetic regulatory hierarchies with RGCs. To narrow the search for candidate disease related genes, RGC genes were mapped to known disease loci for optic neuropathies. Conclusions: This work represents a first step in developing a gene expression profile of retinal ganglion cells, and more generally, is one of the first efforts to profile gene expression in a purified neuronal population. Hierarchical clustering revealed a striking pattern of RGC genes that were preferentially expressed in dorsal root and trigeminal ganglia. Sensory ganglia share transcription factors such as the Brn–3 family, and we speculate that the clustered genes might be regulated by such shared factors.
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