PURPOSE: To obtain and analyze the gene expression profiles of the retina following optic nerve transection (ONT). METHODS: An axotomy animal model was generated by taking a cross section of the optic nerve with care not to damage the adjacent blood supply. The extent of cell loss was evaluated by counting cells in the ganglion cell layer (GCL) of flat-mounted retinas stained with cresyl violet. Gene expression profiles of control and ONT retinas were analyzed with Agilent's rat oligo microarray slides. Differentially expressed genes were identified from three independent experiments and clustered based on their functions with expression analysis systematic explorer software. Real-time quantitative and semiquantitative RT-PCR were used to validate changes in gene expression levels. RESULTS: Gene expression changes in axotomized retinas were analyzed with rat oligo microarray slides containing 22,575 oligonucleotide probes that represent over 20,000 genes and expressed sequence tags (ESTs). The expression of 493 genes was increased more than 1.5 fold, including 85 that were upregulated more than 2 fold, and the expression of 113 genes was decreased 1.5 fold or more, including 21 that were downregulated more than 2 fold. Differentially expressed genes were clustered based on their functions. Several novel genes expressed in the GCL have been identified and their expression patterns in different tissues were analyzed. Among the genes differentially regulated in retinas with induced retinal ganglion cell (RGC) death, we have identified 13 genes that are mapped to known glaucoma loci and can be considered for mutation screening in patients with inherited forms of glaucoma. CONCLUSIONS: The gene expression profiles of the ONT retinas can be used to identify RGC-expressed genes, which may be essential for the morphological and physiological characteristics of RGCs. The results of this study can also be used to evaluate the molecular changes taking place in the retina in response to RGC loss.
PURPOSE: To obtain and analyze the gene expression profiles of the retina following optic nerve transection (ONT). METHODS: An axotomy animal model was generated by taking a cross section of the optic nerve with care not to damage the adjacent blood supply. The extent of cell loss was evaluated by counting cells in the ganglion cell layer (GCL) of flat-mounted retinas stained with cresyl violet. Gene expression profiles of control and ONT retinas were analyzed with Agilent's rat oligo microarray slides. Differentially expressed genes were identified from three independent experiments and clustered based on their functions with expression analysis systematic explorer software. Real-time quantitative and semiquantitative RT-PCR were used to validate changes in gene expression levels. RESULTS: Gene expression changes in axotomized retinas were analyzed with rat oligo microarray slides containing 22,575 oligonucleotide probes that represent over 20,000 genes and expressed sequence tags (ESTs). The expression of 493 genes was increased more than 1.5 fold, including 85 that were upregulated more than 2 fold, and the expression of 113 genes was decreased 1.5 fold or more, including 21 that were downregulated more than 2 fold. Differentially expressed genes were clustered based on their functions. Several novel genes expressed in the GCL have been identified and their expression patterns in different tissues were analyzed. Among the genes differentially regulated in retinas with induced retinal ganglion cell (RGC) death, we have identified 13 genes that are mapped to known glaucoma loci and can be considered for mutation screening in patients with inherited forms of glaucoma. CONCLUSIONS: The gene expression profiles of the ONT retinas can be used to identify RGC-expressed genes, which may be essential for the morphological and physiological characteristics of RGCs. The results of this study can also be used to evaluate the molecular changes taking place in the retina in response to RGC loss.
Authors: Justin P Templeton; Mohamed Nassr; Felix Vazquez-Chona; Natalie E Freeman-Anderson; William E Orr; Robert W Williams; Eldon E Geisert Journal: BMC Neurosci Date: 2009-07-30 Impact factor: 3.288