Quantitative analysis of mucin transcripts was carried out by
MIMIC competitive PCR (Clontech). The method is a co-PCR reaction with
target cDNA and a competing exogenous template serving as an internal
standard.
19 20 21 The competitive MIMIC template is a dsDNA
construct with ends engineered to be complimentary to the mucin
primers, but containing a nonhomologous central sequence
(v-
erbB). Coamplification of a constant amount of
conjunctival cDNA in the presence of serial dilutions of this internal
standard allows for quantification of mucin mRNA.β
2-Microglobulin (β
2M),
a ubiquitously expressed protein, was used as a “housekeeping gene”
for comparative purposes. After reverse transcription, 1 μl (∼1 ng)
of conjunctival cDNA was amplified and analyzed. Primers for both MUC2
and MUC5AC were as previously published.
21 Primers forβ
2M were purchased from Clontech. PCR
parameters consisted of an initial denaturation at 94°C for 10
minutes to heat activate the DNA polymerase (Amplitaq Gold; Perkin
Elmer, Foster City, CA). This was followed by 30 cycles of denaturation
at 94°C for 1 minute (40 cycles for MUC2), annealing at 59°C for 1
minute for MUC2 (60°C for MUC5AC, 54°C forβ
2M), and extension at 72°C for 1 minute with
a final extension at 72°C for 7 minutes. MgCl
2 was included at 2.5 mM for β
2M and MUC5AC (1.5
mM for MUC2). Identities of PCR products were confirmed by sequencing.
After electrophoresis in 1% agarose, bands corresponding to target
cDNAs and MIMIC competitors were stained with ethidium bromide and
photographed with Polaroid Type 667 film. The photographs were
digitized with an Epson Action Scanner II digital image processor
and analyzed using SigmaGel (Jandel, San Rafael, CA) software. Levels
of mucin and β
2M PCR products were determined by
densitometric analysis and normalized to corresponding MIMIC standards.
Results of MUC2 and MUC5AC amplification were compared to those
obtained from β
2M amplification to determine the relative
abundance of mucin transcripts. Reported numbers of transcripts are
based on the assumption of 100% efficiency of cDNA synthesis although
actual efficiency is lower. Therefore, the estimated transcript numbers
represent the minimum number of mucin-specific mRNAs in the tissue
samples.