Total RNA isolated from conjunctival tissues and from fibroblasts of control and OCP conjunctiva was used to detect the relative expression of m-CSF mRNA. The principle of real-time quantitative PCR has been described elsewhere.
24 25 The quantification of transcription of real-time PCR takes advantage of the 5′ nuclease activity of DNA polymerase (Ampli
Taq Gold; PE-Applied Biosystems, Foster City, CA). Total RNA was extracted from conjunctival tissues and conjunctival fibroblasts with an RNA isolation kit (Qiagen, Valencia, CA). The primers and probe used for detecting m-RNA for m-CSF are as follows: forward, TGC AGC GGC TGA TTG ACA; reverse, TTC AAC TGT TCC TGG TCT ACA AAC TC, probe (
TaqMan; PE-Applied Biosystems); FAM (reporter dye)-TCA GAT GGA GAC CTC GTG CCA AAT TAC ATT-TAMRA (quencher dye). Each PCR reaction contained equivalent amounts of total RNA. Real-time PCR was performed in duplicate with a kit used according to the manufacturer’s recommendation (
TaqMan One-Step RT-PCR Master Mix Reagents; PE-Applied Biosystems). All the reactions were controlled by standards (nontemplate control and standard positive control). While extracting the total RNA from conjunctival fibroblasts, we routinely used DNase to prevent DNA contamination. When real-time PCR was performed without addition of reverse transcriptase, no PCR product was detected, either for m-CSF or the housekeeping gene. Amplified PCR products were sequenced (at the core facility of Harvard Institute of Medicine, Boston, MA), and showed a complete homology with the corresponding sequence of the human m-CSF gene. The quantity of mRNA was calculated by normalizing the threshold cycle level (
C T) of m-CSF to the
C T of the housekeeping genes 18S ribosomal RNA or glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of the same RNA probe, according to the following formula: the mean 18S or GAPDH
C T (each multiplex PCR was performed in duplicate) was subtracted from the mean m-CSF
C T level. This result represents the change in
C T (Δ
C T). This Δ
C T is specific and can be compared with the Δ
C T of a calibration sample (for example, control conjunctiva or control conjunctival fibroblasts). The subtraction of control Δ
C T from the Δ
C T of OCP samples or fibroblasts is referred to as ΔΔ
C T. The relative quantification of expression of m-CSF in conjunctival tissues and fibroblasts isolated from the conjunctiva of patients with OCP (in comparison with that in the control) was determined by 2
−ΔΔC T . For all the probes, the quencher dye was 6-carboxy-tetramethylrhodamine (TAMRA), and the reporter dye was 6-carboxy fluorescein (FAM) for m-CSF and VIC for 18S and GAPDH.