Eyes without ON transection underwent TES for 1 hour, and were removed at different selected time points from 1 hour to 10 days. The retinas were dissected from the eyes in a shallow bath of cold phosphate buffered saline (PBS) and were stored at −80°C until use. Total RNA was then extracted (RNeasy Mini Kit; Qiagen, Hilden, Germany) from pooled retinas and quantified (Gene Quant II; Amersham Pharmacia Biotech, Piscataway, NJ), as previously described.
20
RT-PCR and Northern blot analysis were performed as previously described.
21 For RT-PCR, 5 μg of total RNA was reverse transcribed using oligo (dT) reverse transcriptase (Ready-To-Go You-Prime First-Strand Beads; Amersham Biosciences). The cDNAs were amplified for 25 to 30 cycles of 30 seconds at 95°C, 30 seconds at 55°C, and 60 seconds at 72°C. The sequences of the primers used were: IGF-1 forward, 5′-TGGACGCTCTTCAGTTCGTG-3′, reverse, 5′-GTTTCCTGCACTTCCTCTAC-3′; IGF-1R forward, 5′-CAGCTGCAACCACGAGGCTG-3′, reverse, 5′-GGTTCACAGAGGCGTACAGC-3′; BDNF forward, 5′-AGAGCTGCTGGATGAGGACC-3′, reverse, 5′-CCAGTGCCTTTTGTCTATCG-3′; TrkB forward, 5′-CTTGGAGAAGGAGCCTTTGG-3′, reverse, 5′-CAACCCGGTAGTAGTCGGTG-3′; bFGF forward, 5′-CGGCAGCATCACTTCGCTTC-3′, reverse, 5′-CAGTATGGCCTTCTGTCCAG-3′; FGFR-1 forward, 5′-ACCTGATCTCGGAGATGGAG-3′, reverse, 5′-TGGTGGGTGTAGATCCGGTC-3′; CNTF forward, 5′-TGAGGCAGAGCGACTCCAAG-3′, reverse, 5′-GCTCTCAAGTGCTGAGATTC-3′; CNTFR forward, 5′-TTGGGTCACAACACCACGGC-3′, reverse, 5′-CCAAGGAGCTGGTGGTGCTG-3′; and β-actin forward, 5′-TGCCCATCTATGAGGGTTACG-3′, reverse, 5′-TAGAAGCATTTGCGGTGCGGTGCACG-3′.
For Northern blot analysis, total RNA (10 μg) was isolated from the retina at each time point by electrophoresis on 1.0% agarose-formaldehyde gels and transferred overnight onto polyvinylidene difluoride (PVDF) membranes (Millipore Corp., Bedford, MA). The membrane was prehybridized for 1 hour at 65°C in hybridization buffer (0.9 M NaCl, 90 mM sodium citrate [pH 7.0]) containing 5× Denhardt’s solution, SDS (0.5%), and heat-denatured salmon sperm DNA (100 ng/mL). The cDNA probe was radiolabeled with [32P]dCTP (NZ522; PerkinElmer Life and Analytical Sciences, Boston, MA, with the Random Primer DNA Labeling Kit, ver. 2; Takara Bio, Shiga, Japan). After hybridization overnight at 65°C in hybridization buffer containing radiolabeled cDNA probe (5 ng/mL), filters were washed twice with 2× SSC, 0.5% SDS and 0.2× SSC, 0.5% SDS for 60 minutes at 65°C, exposed to x-ray film (Fuji Film, Kanagawa, Japan), and subjected to autoradiography. Autoradiograms were quantified by image analysis (Scion Image; Scion Corp., Frederick, MD). The relative expression levels of IGF-1 mRNA in the retinas after TES were compared with the expression in the control retina, which was normalized to 1.0. Data from three independent experiments are given as the mean ± SD.