Tissue processing of corneas and TG, total RNA extraction, and RNA yield were performed as we have described elsewhere.
26 31 Briefly, 1000 ng of total RNA was reverse-transcribed with random hexamer primers and murine leukemia virus (MuLV) reverse transcriptase (High Capacity cDNA Reverse Transcription Kit; Applied Biosystems [ABI], Foster City, CA), in accordance with the manufacturer’s recommendations.
The differences in expression levels of gK, gB, LAT (stable 2kb LAT intron), CD4, CD8, IFN-γ, granzyme A (GzmA), and granzyme B (GzmB) were evaluated using custom-made gene-expression primers (TaqMan; ABI), described later. Relative copy numbers for the gK, gB, and LAT transcripts were calculated by using standard curves generated from the plasmids pGEM-gK1040, pAc-gB1, and pGEM5317, respectively. In all experiments, GAPDH was used for normalization of transcripts.
Expression levels of the various transcripts were evaluated with commercial gene-expression assays (TaqMan; ABI) with optimized primer and probe concentrations. Primer probe sets consisted of two unlabeled PCR primers and the FAM dye–labeled probe (TaqMan MGB; ABI) formulated into a single mixture. In addition, all cellular amplicons included an intron–exon junction to eliminate signal from genomic DNA contamination. The assays for cellular transcripts were (1) CD4 (assay IMm00442754_m1), amplicon length, 72 bp; (2) CD8 (α chain; assay Mm01182108_m1), amplicon length, 67 bp; (3) GAPDH (assay Mm999999.15_G1), amplicon length, 107 bp; (4) GzmA (assay Mm00439190_m1), amplicon length, 77 bp; (5) GzmB (assay Mm00442834_m1) amplicon length, 95 bp; and (6) IFN-γ (assay Mm00801778_m1; all from ABI) amplicon length, 101 bp.
Expression levels of HSV-1 gK, gB, and LAT were similarly evaluated by using custom-made gene-expression assays (TaqMan; ABI). The gB primers and probe were forward primer, 5′-AACGCGACGCACATCAAG-3′; reverse primer, 5′-CTGGTACGCGATCAGAAAGC-3′; and probe, 5′-FAM-CAGCCGCAGTACTACC-3′. The gK primers and probe were forward primer, 5′-GGCCACCTACCTCTTGAACTAC-3′; reverse primer, 5′-CAGGCGGGTAATTTTCGTGTAG-3′; and probe, 5′-FAM-CAGGCCGCATCGTATC-3′. The LAT primers and probe were forward primer, 5′-GGGTGGGCTCGTGTTACAG-3′; reverse primer, 5′-GGACGGGTAAGTAACAGAAGTCTCTA-3′; and probe, 5′-FAM-ACACCAGCCCGTTCTT-3′. The amplicon lengths for gB, gK, and LAT were 72, 82, and 81 bp, respectively.
Quantitative real-time PCR was performed with a sequence-detection system (Prism 7900HT; ABI) in 384-well plates, as we described previously.
26 31 Real-time PCR was performed in triplicate for each tissue sample. The threshold cycle (C
t) values, which represents the PCR cycle at which there is a noticeable increase in the reporter fluorescence above baseline, were determined with sequence-detection system software (SDS 2.2 Software; ABI). In each experiment, an estimated relative copy number of each target gene was calculated with standard curves generated from plasmids containing the gene of interest: pGem-gK,
11 pAc-gB1,
32 and pGem-5317. Briefly, each plasmid DNA template was serially diluted 10-fold, such that 5 μL contained from 10
3 to 10
11 copies of the desired gene, then subjected to PCR (TaqMan; BD Biosciences) with the same set of primers as the test samples. By comparing the normalized threshold cycle of each sample with the threshold cycle of the standards, we determined the copy number for each reaction.