Total cellular RNA was prepared using ISOGEN (NIPPON GENE, Toyama,
Japan) according to the manufacturer’s protocol. In brief, surgical
materials were homogenized in 1 ml of ISOGEN, and 200 μl of
chloroform was added. After centrifugation at 4°C, the aqueous phase
was collected, and total RNA was precipitated with an equal volume of
isopropanol. RNA was then dissolved in 10 μl of water treated with
diethyl pyrocarbonate.
We calculated the relative amount of RNA in each case by quantifying
the amplified β-actin cDNA fragment because total amount of RNA
extracted in each case was below the limit of the ordinary measurement
with a UV photometer due to the minute size of the tissue. Two μl of
the solution containing total RNA was reverse-transcribed with a
First-Strand cDNA Synthesis Kit (Pharmacia Biotech, Uppsala, Sweden) at
37°C for 1 hour in a 15-μl reaction volume containing random
hexadeoxynucleotide primer and Moloney Murine Leukemia Virus reverse
transcriptase. A 2-μl aliquot of the reaction product was subjected
to 30 cycles of PCR for amplification of β-actin cDNA. Density of the
band of amplified β-actin cDNA was measured in each case, and the
relative amount of total RNA extracted from each tissue was calculated.
Based on the above results, we adjusted the starting amount of RNA for
further RT–PCR analysis on the expression of VEGF, VEGF-R1, VEGF-R2,
neuropilin-1, and β-actin. RNA was reverse-transcribed as described
above, and PCR was performed at 30 cycles in a 50-μl reaction volume
containing 800 nM of each primer, 100 μM of dNTP, and 5 U Taq DNA polymerase (TOYOBO, Tokyo, Japan) in a thermal
controller (Mini Cycler; MJ Research, Watertown, MA). The thermal cycle
was 1 minute at 94°C; 2 minutes at either 64°C (VEGF), 64°C
(VEGF-R1), 63°C (VEGF-R2), 63°C (neuropilin-1), or 67°C
(β-actin); and 3 minutes at 72°C, followed by 3 minutes at 72°C.
The nucleotide sequences of the PCR primers were 5′-TGC CTT GCT GCT CTA
CCT CC-3′ (forward, on exon 1) and 5′-TCA CCG CCT CGG CTT GTC AC-3′
(reverse, on exon 8) for VEGF; 5′-GAT GTT GAG GAA GAG GAG GAT T-3′
(forward) and 5′-AAG CTA GTT TCC TGG GGG TAT A-3′ (reverse) for
VEGF-R1; 5′-GAT GTG GTT CTG AGT CCG TCT-3′ (forward) and 5′-CAT GGC TCT
GCT TCT CCT TTG-3′ (reverse) for VEGF-R2; 5′-CAA CGA TAA ATG TGG CGA
TAC T-3′ (forward) and 5′-TAT ACT GGG AAG AAG CTG TGA T-3′ (reverse)
for neuropilin-1; 5′-TGA CGG GGT CAC CCA CAC TGT GCC CAT CTA-3′
(forward) and 5′-CTA GAA GCA TTT GCG GTG GAC GAT GGA GGG-3′ (reverse)
for β-actin. The above RT–PCR analysis enabled us to discriminate
each isoform of VEGF by the difference in size of each amplified DNA
fragment. The expected sizes of the amplified cDNA fragments of
VEGF121, VEGF145,
VEGF165, VEGF189,
VEGF206, VEGF-R1, VEGF-R2, neuropilin-1, andβ
-actin were 0.41, 0.48, 0.54, 0.61, 0.66, 1.1, 0.56, 0.82, and 0.66
kb, respectively. An aliquot of the PCR product was electrophoresed in
a 1.5% agarose gel and stained with ethidium bromide.
To confirm the specific amplification from the target mRNAs, the
RT–PCR products were subcloned into the pBluescript KS vector
(Stratagene, La Jolla, CA) and were analyzed by sequencing with
fluorescent T7 primer (Amersham Pharmacia Biotech, Buckinghamshire, UK)
using a Thermo Sequenase fluorescence-labeled primer cycle sequencing
kit (Amersham Pharmacia Biotech) and ALF DNA sequencer II (Amersham
Pharmacia Biotech).