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(Received for publication, January 12, 1996, and in revised form, March 8, 1996)
From the Division of Human Immunology, Hanson Centre for Cancer
Research, Institute of Medical and Veterinary Science, Frome Road,
Adelaide 5000, South Australia, Australia
Granulocyte-macrophage colony-stimulating factor
(GM-CSF) is a hemopoietic growth factor that is expressed in activated
T cells, fibroblasts, macrophages, and endothelial cells. Although
GM-CSF does not appear to be essential for normal hemopoiesis,
overexpression of GM-CSF has been implicated in the pathogenesis of
some diseases such as myeloid leukemia and chronic inflammation. An
NF- Cytokines are a rapidly growing family of proteins that act as
local or systemic intercellular regulatory factors. They are involved
in various developmental and differential processes and are important
in the immune response to infection and injury. However, cytokines are
also implicated in the pathology of many clinical conditions including
septic shock, parasitic infections, chronic inflammation,
atherosclerosis, and cancer (1). Granulocyte-macrophage
colony-stimulating factor is a cytokine involved in the control of
survival, proliferation, and differentiation of hemopoietic progenitor
cells as well as in the functional activation of mature myeloid cells
(reviewed in Ref. 2). GM-CSF1 expression
occurs in different cell types, including fibroblasts and endothelial
cells in response to proinflammatory agents such as tumor necrosis
factor and interleukin-1 (IL-1), monocytes in response to endotoxin,
and activated T cells (reviewed in Ref. 3).
Despite the clinical application of GM-CSF as an activator of
hemopoietic cell production after bone marrow transplantation, evidence
has accumulated to suggest that GM-CSF may play a role in the
pathogenesis of several disease conditions, in particular myeloid
leukemia and chronic inflammation (4, 5, 6, 7). GM-CSF was found to be
abnormally expressed in atopic patients and in patients with rheumatoid
arthritis (4, 5). In terms of leukemia, GM-CSF has been shown to be
produced by some leukemic clones in an autocrine fashion in
vitro, and the growth of the cells in vitro depends on
the presence of GM-CSF (8). Recent in vivo experiments have
also shown that GM-CSF increased the blast cell counts in 9 of 12 acute
myeloid leukemia patients (9). Taken together these data suggest that
it would be of significant therapeutic importance to be able to
modulate GM-CSF gene expression.
Synthetic oligonucleotides are attracting increasing interest as tools
for specific manipulation of gene expression and have potential
therapeutic application. Several strategies that employ short nucleic
acid fragments targeted to different intracellular components are
currently under investigation with variable success (reviewed in Ref.
10). The ``antigene'' (11) strategy is based on inhibition of
transcription of the selected gene by oligonucleotide-directed
intermolecular DNA triple helix formation either through prevention of
regulatory proteins binding to the control regions (12) or by acting as
transcriptional repressors (13). Triplex formation may have certain
advantages over the other oligonucleotide-mediated strategies, as there
are fewer target molecules per cell and it is expected to be more
selective. In vitro experiments demonstrated that the
formation of such sequence-specific structures can inhibit DNA
replication (14) or block transcription factors binding to the gene of
interest and thereby directly affect transcription initiation (15).
Triplex-forming oligonucleotides (TFOs) were also found to repress
transcription in intact cells, resulting in highly specific inhibition
of the synthesis of promoter reporter gene targets (16, 17, 18).
Predominantly polypurine:polypyrimidine (Pur:Pyr) sequences have been
shown to be suitable targets for intermolecular triple helices.
Different structures of base triplets have been described, forming two
groups of DNA triple helices. Both have the third strand binding in the
major groove of the duplex DNA through Hoogsteen (Y*RY motif) or
reverse Hoogsteen (R*RY motif) base pairing. The best studied Y*RY
type, formed by the addition of a polypyrimidine third strand, consists
of C+*G:C and T*A:T base triads with the third strand
parallel to the purine-rich strand of the underlying duplex (19, 20).
These triplexes are stable only under acidic pH, but that condition can
be partly overcome by methylation of the third strand cytosines (22).
Stable R*RY type triplexes have been shown to form at physiological pH
in the presence of divalent cations, where oligonucleotide interaction
with double-stranded DNA involves G*G:C, A*A:T, or T*A:T triads with an
antiparallel orientation of the third strand (21). TFO binding to the
DNA duplex target appears to be highly sequence-specific, as
triplex-forming oligos have been shown to recognize unique sites in the
yeast chromosome (23).
The human GM-CSF gene contains an enhancer located approximately 3 kilobases from the transcription start site (24) and a proximal
promoter spanning at least the first 120 bp from the transcription
initiation site (3, 25). Activation of the human GM-CSF promoter in T
cells appears to be tightly regulated by induction and binding of
multiple transcription factors including NF- Here we attempted to modulate transcription from the GM-CSF gene by DNA
triple helix formation within the promoter region. A triplex-forming
oligodeoxynucleotide was targeted to a 15-bp purine-rich sequence that
overlaps the Oligodeoxyribonucleotides
were synthesized by the
The HTLV-1 tax expression plasmid (pcTax) used was a gift
from Dr. Warner Greene (Gladstone Institute, San Francisco, CA) and has
been previously described (28). The reporter construct pGMluc contains
620 bp of the GM-CSF promoter (27). The reporter plasmid pIL3luc,
containing a 670-bp ( Double-stranded
oligodeoxyribonucleotides were end-labeled with
[
The probe for DNase I
footprinting was prepared by digesting the pGMluc plasmid with
SalI, dephosphorylated with alkaline phosphatase, and
radiolabeling with [ Triplex formation was performed as
described above using 33P-end-labeled double-stranded
fragments of the GM-CSF gene promoter and immunoglobulin The Jurkat T cell
line was cultured in RPMI medium containing 10% fetal calf serum and
supplemented with L-glutamine and penicillin/gentamycin
antibiotics. Cells were transfected by electroporation at 270 V and a
capacitance of 960 microfarads using a Bio-Rad gene pulser. 5 × 106 cells in 350 µl of RPMI containing 20% fetal calf
serum were used per transfection. Ten µg of HTLV-1 tax
expression vector and 5 µg of pGMluc or pIL3luc reporter plasmid was
used per transfection. Twenty-four hours posttransfection, TFO GM3 or
control oligonucleotide GMc was added (where indicated in the figure
legends) to the culture medium. Cells were cultured for an additional 2 h, stimulated at a final concentration of 20 ng/ml PMA and 2 µM calcium ionophore, and harvested 8 h later.
Cells used for
the luciferase reporter assay were activated and exposed to
oligonucleotides as described above and lysed by three freeze/thaw
rounds 8 h after stimulation with PMA/Ca2+ ionophore. Three
µg of total protein from the cell lysates was used per luciferase
assay according to a procedure previously described (31). Light
emission was measured using a scintillation counter with the
coincidence circuit switched off.
Jurkat T cells were transfected, treated with oligonucleotides (where
indicated), and activated with PMA/Ca2+ ionophore, as
described above. Total RNA was purified using guanidine isothiocyanate
8 h after cell stimulation. The method for quantitating specific
mRNA by RNase protection and the vectors for antisense RNA
synthesis have been previously described (32). Ten µg of total RNA
was used for each assay with 33P-labeled antisense probe.
Specific bands were quantified using a Molecular Dynamics
PhosphorImager and normalized against glyceraldehyde-3-phosphate
dehydrogenase as internal control.
The concentration of GM-CSF protein in the supernatants of
the cell samples, used for RNase protection assay was quantified by
enzyme-linked immunosorbent assay (Quantikine R & O Systems Inc.,
Minneapolis, MN) according to the manufacturer's instructions. The
detection limit for this assay was 1.5 pg/ml.
It was previously shown that triple helix formation by
oligonucleotides can inhibit DNA-protein interaction at specific
regions by only overlapping and not spanning the entire protein binding
site (16). The 15-bp sequence from The ability of these oligonucleotides to form triplexes was analyzed by
gel mobility shift assay and DNase I footprinting. A radiolabeled 30-bp
fragment of the GM-CSF promoter from To further confirm the selectivity and specificity of the GM3 TFO, a
DNase I footprinting assay was performed. Fig. 3 shows
that triplex formation by GM3 protected from DNase I digestion, in a
concentration-dependent manner, only the targeted sequence
of 15 bp within a 489-bp SalI/MscI fragment of
the GM-CSF gene promoter. The DNase I footprint occurred at 4 µM concentration of the specific TFO, and full protection
was obtained at 16 µM (Fig. 3, lanes 3 and
4), which is consistent with the affinity of GM3 for its
target duplex observed in the gel shift assay. The nonspecific oligomer
GMc did not allow any protection of the target from DNase I-mediated
degradation even at a concentration of 20 µM. These data
suggest that oligonucleotide GM3 forms a stable and sequence-selective
triple helix with its double-stranded target from the GM-CSF gene
proximal promoter.
The effect of triplex formation by GM3 on the
ability of NF-
Jurkat T cells transfected with the HTLV-1 tax expression
plasmid contain NF- These results indicate that triplex formation specifically prevents
binding of NF- It was shown previously (17, 36) that short
single-stranded oligonucleotides, when applied to the culture medium,
can internalize into cells and equilibrate the concentration inside and
outside the cell membrane within a few hours. This phenomenon is not
universal and varies depending on the cell type used in the experiment
possibly as a consequence of different mechanisms of oligonucleotide
uptake (reviewed in Ref. 37). When Jurkat T cells were incubated with
an intrinsically 32P-labeled oligonucleotide we also found
that the intracellular concentration of the oligomer reached
approximately 50% of that in the culture medium after 2 h and
approximately 80% after 5 h of incubation (data not shown).
To investigate the effect of triplex formation on GM-CSF gene
transcription in cell culture, 3
The specific triplex-forming oligonucleotide GM3 demonstrated a 65%
inhibition of the reporter gene activity from pGMluc at a concentration
of 1 µM, whereas no effect was detected when cells
transfected with pGMluc were treated with GMc at the same concentration
of 1 µM (Fig. 5). Also no significant differences in
luciferase activity induced by the IL-3 promoter were detected when
cells transfected with pIL3luc were exposed to medium alone, GM3, or
GMc at the highest concentrations (Fig. 5)
We used RNase protection assays to determine whether the GM3
oligonucleotide, targeted to form a triple helix within the GM-CSF
promoter, would selectively suppress the induction of mRNA from the
endogenous GM-CSF gene. The effect on the response of the GM-CSF gene
to PMA/Ca2+ ionophore treatment and HTLV-1 Tax
expression in combination with PMA/Ca2+ ionophore was
measured. Jurkat T cells transiently transfected with HTLV-1
tax or untransfected were preincubated for 2 h with
triplex-forming oligonucleotide GM3 or control oligomer GMc at the
indicated concentrations (Fig. 6). After stimulation for
a further 7 h with PMA/Ca2+ ionophore, total RNA was
extracted and assayed. GM-CSF mRNA levels in PMA/Ca2+
ionophore-stimulated cells were significantly reduced when cells were
treated with GM3 at 2.4 µM concentration compared with
samples exposed to the culture medium only or to the control GMc
oligomer at the highest concentration. (Fig. 6). GM3 was also effective
when the expression of GM-CSF mRNA was synergistically activated by
HTLV-1 Tax and PMA/Ca2+
ionophore2 (Fig. 6). GM3 caused up to 70%
reduction of the GM-CSF mRNA level induced by PMA/Ca2+
ionophore and up to 50% decrease after activation with HTLV-1
Tax and PMA/Ca2+ ionophore together (Fig. 6).
Concentrations of immunoreactive GM-CSF in the supernatants of cells
stimulated with both stimuli and treated with GM3, but not GMc, were
also decreased by an average 45% with the highest concentration of GM3
(from an average 560 ± 13 pg/ml (mean ± S.D.) to an average 320 ± 16 pg/ml in two experiments) in accordance with mRNA levels in the
cells. In the same cell samples, concentrations of IL-3 mRNA were
not affected either by TFO GM3 or by control GMc oligonucleotides
regardless of the type of activation used (Fig. 6).
These results lead to the conclusion that a 3 We show here that a triplex-forming oligonucleotide can repress
transcription from a reporter construct containing the human GM-CSF
gene promoter and more importantly can reduce expression from the
endogenous GM-CSF gene in Jurkat T cells. Moreover, we show that GM-CSF
protein concentrations in cell supernatants were reduced in parallel
with the GM-CSF mRNA levels. Although there are many reports of
triplex formation inhibiting transcription from reporter gene
constructs, only a few reports describe the inhibition of human
endogenous gene expression in cell culture (17, 40, 41, 42).
The TFO binds to a sequence overlapping a The effect of the TFO GM3 appears to be specific for the GM-CSF gene
and has no effect on a reporter construct containing the IL-3 promoter
or on mRNA levels from the endogenous IL-3 gene. The gene for IL-3
responds to the same stimuli as GM-CSF in T cells (38, 44). This
implies that the TFO is not blocking NF- It is also worth noting that the GM3-targeted DNA sequence covers a G/C
element (see Fig. 1) that represents a putative Sp1 binding site. The
Sp1 protein has been implicated in the transcriptional activation of
numerous genes, and the Sp1 site was found to be important in the
expression of murine GM-CSF (45). The G/C region of the human gene has
a 2-bp difference with the functional site in mouse and appears to be a
weak Sp1 binding site.3 However, blocking
of Sp1 binding to the GM-CSF promoter by the TFO may also contribute to
the observed inhibitory effect of GM3 on the expression of the
gene.
We have also shown that the GM3 oligonucleotide caused a slightly
greater decrease in the GM-CSF mRNA levels in Jurkat T cells
induced by PMA/Ca2+ ionophore than in cells activated by
both PMA/Ca2+ ionophore and the HTLV-1 transactivator Tax.
Costimulation of GM-CSF expression by these two stimuli has been shown
to have a strong synergistic effect leading to high levels of gene
transcription.2 The overexpression of Tax significantly
increases binding of NF- The observed relatively high KD (>10
µM) of the GM3 oligonucleotide binding to its duplex
target could be due to the one mismatch in the otherwise
homopurine-homopyrimidine sequence of the double-stranded DNA.
Pyrimidine interruptions in the purine tract of the targeted DNA
sequence have been shown to be significantly unfavorable for triplex
formation because of loss of Hoogsteen hydrogen bonding (21) and can
increase the value of the relative binding affinity of the third strand
by approximately 1 order of magnitude (49). The central location of the
interruption in the purine sequence of the duplex, as seen in the
target on the GM-CSF promoter, has been also found to cause greater
distortion in the stability of the DNA triplex than the same mismatch
situated at the end of the targeted site (49, 50). Another factor that
may contribute to the relatively low affinity of GM3 for its target DNA
is the stretch of eight consecutive guanines in the TFO, which makes
this oligonucleotide highly susceptible to self-aggregation through the
formation of G-tetrades (51, 52). It also should be noted that some
degradation of the triplex may occur during the course of
electrophoresis, thus increasing the value of the KD
observed.
In a number of previous studies it has been noted that the
extracellular concentration of the TFO required for inhibition of
target gene transcription in intact cells was in the range of 10-25
µM (17, 18, 40), which was 10-50 times the dissociation
constant for triplex formation in vitro. The data presented
in this study are not consistent with these observations. A significant
decrease of GM-CSF mRNA levels by GM3 was achieved at a
concentration of 2.4 µM of the TFO in the culture medium,
which was below the KD value observed in the binding
gel shift assays. This may be attributed to the intrinsic properties of
the GM3 oligonucleotide sequence. But this finding may also be
explained by the possible changes in the chromatin structure upon
activation of the inducible GM-CSF gene that could make the target
duplex in the gene promoter more easily accessible for the exogenous
oligonucleotide and thus promote more efficient triplex formation by
GM3.
50-70% of cases of acute myeloid leukemia have been shown to depend
on GM-CSF for proliferation both in vitro (8) and in
vivo (9) and also for engraftment into SCID mice (53). A specific
antagonist of GM-CSF/receptor interactions can block the growth of
acute myeloid leukemia cells in vitro (54), as can
antibodies against GM-CSF (55) and its receptor (56). It has been
suggested, in fact, that paracrine production of GM-CSF is responsible
for progression of the disease (57). Furthermore, 20-30% of acute
myeloid leukemia cases constitutively produce and respond to GM-CSF
(39, 58, 59), suggesting that it can also act in an autocrine manner.
The GM3 TFO may, therefore, have a potential therapeutic role in
blocking either the paracrine or autocrine production of GM-CSF in
cases of acute myeloid leukemia. The detection of GM-CSF mRNA in
the bronchoalveolar lavage of atopic patients and GM-CSF protein in the
synovial fluid of rheumatoid arthritis patients (4, 5) suggests another
role for the therapeutic use of TFOs that block GM-CSF
transcription.
We gratefully acknowledge Dr. Roy Himes for
the pGMluc plasmid, Dr. Peter Cockerill for the pIL3luc plasmid, Dr.
Steve Gerondakis for the recombinant p65 protein, and Dr. Tim Hercus
for performing the enzyme-linked immunosorbent assay. We also thank
Professors Angel Lopez and Mathew Vadas for critical review of the
manuscript and helpful comments.
Volume 271, Number 24,
Issue of June 14, 1996
pp. 14438-14444
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.

B/Rel binding site within the GM-CSF promoter, termed the
B
element appears to be important for controlling expression in reporter
gene assays in response to a number of stimuli in T cells. We
investigated oligonucleotide-directed triple helix formation across
this regulatory sequence as a potential tool to inhibit GM-CSF gene
transcription. A 15-base oligonucleotide, GM3, was targeted to a
purine-rich region in the GM-CSF proximal promoter, which overlaps the
B element. Gel mobility shift assays and DNase I footprinting
demonstrated that GM3 formed a sequence-specific collinear triplex with
its double-stranded DNA target. Triplex formation by GM3 blocked
recombinant and nuclear NF-
B proteins binding to the GM-CSF element.
GM3 also caused selective inhibition of the human T-cell lymphotrophic
virus-1 Tax transactivator-induced luciferase activity from a reporter
construct driven by the GM-CSF promoter in Jurkat T cells. Finally, GM3
greatly reduced the concentration of endogenous GM-CSF mRNA induced
by different stimuli in Jurkat T cells but did not affect interleukin 3 mRNA levels in the same cells. We conclude that the
B element in
the GM-CSF promoter plays a central role in the transcriptional
activation of the endogenous GM-CSF gene. Colinear triplex formation
acts as a selective transcriptional repressor of the GM-CSF gene and
may have potential therapeutic application in cases of undesirable
overexpression of this protein.
B/Rel, AP-1, and NFAT
proteins (25, 26, 27). The GM-CSF promoter contains two binding sites for
the NF-
B/Rel family of transcription factors, the CK-1 element,
which binds only specific members of the family such as p65 (Rel-A) and
c-Rel (Rel), and the
B element that binds mainly classical NF-
B
p65/p50 (NF-
B1) complexes (26, 27). The
B element appears to play
a central role in the response of the GM-CSF promoter to T cell
receptor type signals as well as HTLV-1 Tax activation in T-cells (25,
27)
B-element. Sequence specificity of the third strand
coupling to its duplex target was investigated, as well as the ability
of triplex formation to inhibit recombinant and nuclear NF-
B
proteins binding to the GM-CSF promoter. We also evaluated the effect
of the triplex-forming oligomer on luciferase activity from GM-CSF
promoter-driven reporter constructs and on endogenous GM-CSF mRNA
and immunoreactive protein levels in activated Jukart T-cells and show
that triplex formation can selectively suppress human GM-CSF gene
expression.
Oligonucleotides and Plasmids
-cyanoethylphosphoramidite method on an
Applied Biosystems synthesizer (Applied Biosystems, Foster City, CA)
using solid support for nonmodified oligomers or solid support coupled
with 3
-amino-modifier (Glen Research, Sterling, VA) for oligomers with
a propanolamine group at the 3
terminus. Deprotected oligonucleotides
were purified by preparative 12-20% gel electrophoresis.
Concentrations were determined by absorption measurements at 260 nm
using molar extinction coefficients. Oligonucleotide sequences are
presented in Fig. 1b.
Fig. 1.
The GM-CSF proximal promoter (A)
and oligodeoxynucleotides used in this study (B). Map
of the GM-CSF gene proximal promoter with previously identified
functionally important elements or conserved elements shown by
shaded boxes. The 15-bp target site (
80 to
65) for
triplex formation is indicated. An arrow indicates the
transcription initiation point. B, GM is a 30-mer from
90
to
60 in the GM-CSF gene promoter used as a duplex target in gel
shift assays. The underlined sequence indicates the region
targeted for triplex formation with a point of ``mismatch'' shown in
small capitals. Ig
is a 27-mer (3931-3957) containing
the NF-
B consensus site from the immunoglobulin
gene enhancer
used as a control duplex. Shaded in both double-stranded
oligomers are the NF-
B protein binding sites. The GM3
oligonucleotide was designed to bind to the target site as a third
strand, and GMc was used as a control oligonucleotide.
550 to +120) polymerase chain reaction fragment
of human IL-3 gene promoter made using
J1-16 genomic clone (24) was
provided by Dr. Peter Cockerill (IMVS, Adelaide, S.A., Australia).
-32P]ATP and T4 polynucleotide kinase. TFOs (specific
and control) were heated at 65 °C for 5 min to prevent
self-association and placed on ice. Triplex formation was assessed by
incubating for 2 h at 20 °C 0.2 ng of double-stranded probe with the
indicated concentrations of TFOs (see legend for Fig. 2) in 89 mM Tris borate (pH 8.0), 20 mM
MgCl2, and 10% sucrose followed by electrophoresis through
a 12% native acrylamide gel for 16 h at 4 °C. Both gel and running
buffer contained 89 mM Tris borate (pH 8.0) and 20 mM MgCl2.
Fig. 2.
Gel mobility shift assay of triplex
formation. End-labeled duplexes (~0.2 ng), GM, and Ig
were
preincubated alone (lanes 5 and 7) or with GM3 at
10 µM (lanes 1 and 6), 3 and 1 µM (lanes 2 and 3, respectively),
or GMc at 10 µM (lane 4) and assayed by
electrophoresis through a native 12% polyacrylamide gel for 18 h at
4 °C. Arrows show the mobility of double-stranded
(D) and triple-stranded (T) DNA.
-33P]ATP using T4 polynucleotide
kinase. After a second digest with MscI the 489-bp probe was
purified on a 2% agarose gel. Triplex formation reactions were
performed under the same conditions as described for the triplex band
shift assays and were then digested with DNase I at a concentration of
1 unit/µl for 30 s. Digestion was stopped by adding 20 mM
EDTA and 0.2% SDS. A + G chemical sequencing of the probe was carried
out according to the Maxam-Gilbert method (29). Samples were then
electrophoresed through 6% denaturing gels, dried, and visualized
using a Molecular Dynamics PhosphorImager.
gene
enhancer (see Fig. 1). After initial incubation for triplex formation
of approximately 0.2 ng of the probe with specific or control
single-stranded oligonucleotides as described above recombinant p65
(27) or nuclear extracts from transfected and stimulated Jurkat T cells
(prepared according to Ref. 30) were added, and samples were incubated
for a further 30 min at 20 °C. The composition of the protein
binding buffer was 25 mM Tris (pH 7.6), 0.5 mM
dithiothreitol, 0.5 mM EDTA, 60 mM NaCl, and 1 µg of poly(dI-dC) for the recombinant p65. Ten mM
MgCl2 was also present in the binding reaction for the
nuclear proteins. Electrophoresis was carried out on 5% native
polyacrylamide gels containing 0.25 × TBE buffer at 190 V for 90 min
for samples with the recombinant p65 and 0.5 × TGE buffer at 150 V for
3 h using nuclear extracts.
Oligonucleotide Design and Triplex Formation on the GM-CSF
Promoter
80 to
65, which overlaps the
B element in the GM-CSF gene proximal promoter (Fig.
1a) was targeted to form an intermolecular
triple helix. This sequence contains only one ``mismatch'' in an
otherwise Pur:Pyr tract and is 72% G-rich, properties that have been
demonstrated to be essential for stable triplex formation. A
triplex-forming oligonucleotide GM3 (Fig. 1b) was designed
according to the rules previously described in numerous studies (17,
33, 34, 35), i.e. T opposite A:T pairs and G opposite G:C pairs
with its orientation antiparallel to the purine strand of the
underlying duplex target. G was also put opposite the interrupting C:G
pair, as it has been shown to be tolerated in this triplex motif (17,
33). As a control, an oligomer GMc of random sequence of G and T
residues with the same length as GM3 was used (Fig. 1b).
90 to
60 (GM, Fig.
1b), which encompassed the TFO target and overlapping
B
element, was incubated with increasing concentrations of the GM3
oligonucleotide in the presence of Mg2+ and subjected to
electrophoresis on native polyacrylamide gels also containing
Mg2+ followed by autoradiography. Triplex formation was
concentration-dependent (Fig. 2) but
occurred only at the higher concentrations of specific TFO and with
apparent KD >10 µM. However no
triplex formation was observed when control GMc oligonucleotide was
incubated with GM even at the highest concentration (Fig. 2). GM3 was
also incubated with a control double-stranded oligonucleotide
containing the
B element from the immunoglobulin
gene (Ig
),
and no triplex formation was detected (Fig. 2).
Fig. 3.
DNase I footprint analysis of the specificity
of triplex formation on the GM-CSF promoter. A 489-bp fragment of
GM-CSF gene promoter, 33P-labeled at one end, was incubated
with TFO GM3 or control oligonucleotide GMc at the concentrations
indicated above each lane followed by DNase I
digestion. For the control DNase I digest, the promoter fragment was
incubated in the absence of oligonucleotides under the same conditions
(lane 2). A G + A Maxam-Gilbert sequencing reaction
(lane 1) was run beside DNase I digests to precisely map the
DNase I footprint. The target sequence for triplex formation by GM3 is
indicated in brackets.
B/Rel proteins to bind to the
B element within the
30-bp fragment of the GM-CSF promoter was examined by gel mobility
shift assay. The radiolabeled double-stranded oligonucleotide was
incubated in the absence or presence of increasing concentration of GM3
followed by incubation with recombinant p65 protein or nuclear extracts
from HTLV-1 Tax-expressing Jurkat T cells. The formation of the
recombinant p65-DNA complex was inhibited by TFO GM3 in a
concentration-dependent manner (Fig.
4a). The GMc unrelated oligomer that could
not form a triplex did not have any significant effect on p65
interaction with the GM-CSF promoter fragment (Fig. 4a,
lane 9). p65 protein binding to the Ig
control probe was
not significantly affected by the GM3-specific oligonucleotide,
used at the highest concentration (Fig. 4a, lane
10)
Fig. 4.
Effect of the triplex formation on
recombinant (A) and nuclear (B) NF-
B protein
binding to the GM-CSF gene promoter fragment containing the
B-element. A, effect of the TFO GM3 on the binding to DNA
of purified recombinant truncated p65. Arrows indicate the
p65-DNA complex and unbound free probes. Mobility shift assays were
carried out on native polyacrylamide gels using 33P-labeled
double-stranded DNA fragments from GM-CSF promoter (GM) and
immunoglobulin
gene enhancer (Ig
) containing the
B consensus
sequence. Double-stranded probes (~0.2 ng) were preincubated alone or
with oligonucleotides at the following concentrations: GM3 at 10 µM (lanes 4 and 10), 3, 1, 0.3, and
0.1 µM (lanes 5-8, respectively), and GMc at
10 µM (lane 9) followed by further incubation
with recombinant p65. B, triplex formation by GM3 inhibits
nuclear NF-
B protein binding to the DNA. Nuclear extracts were
isolated from nonstimulated (N/S) or HTLV-1 Tax expressing
Jurkat T cells (tax). An arrow indicates the
B-like DNA-protein complex. Mobility shift assays were performed as
described above for the recombinant p65, except that nuclear NF-
B
proteins were used. TFO and control oligomer were added to the
double-stranded probes at the following concentrations: GM3 at 10 µM (lane 5), 3, 1, and 0.3 µM
(lanes 6-8, respectively), and GMc at 10 µM
(lane 9) The figure shows only the region of the
gel containing inducible
B-like DNA-protein complex and some
constitutive DNA-protein complexes with similar electrophoretic
mobility. Identification of specific DNA-NF-
B complexes was
performed by competition with 20 ng of unlabeled Ig
in both assays
(panel A, lane 2, and panel B,
lane 3).
B/Rel complexes that can bind to the GM-CSF
B
element (Fig. 4b) (27). The specific NF-
B complex was
determined by competition with an excess of cold Ig
oligomer
containing the
B consensus sequence (Fig. 4b, lane
3). Several constitutive DNA-protein complexes were also detected
under the conditions used (Fig. 4b). Preincubation of the
probe with increasing concentrations of GM3 inhibited the appearance of
the
B-DNA specific complex in a concentration-dependent
manner (Fig. 4b, lanes 5-8), whereas no effect
was detected with control GMc oligomer at the highest concentration
(Fig. 4b, lane 9).
B/Rel transcription factors (either recombinant or
nuclear proteins) to the
B element of the GM-CSF gene promoter. It
is interesting to note that constitutive proteins binding to the GM
fragment used as a probe in the gel retardation assay were also blocked
by the related TFO but not by the control oligonucleotide (Fig.
4b). This fact could be viewed as additional evidence that
the observed inhibition of NF-
B protein binding to the DNA probe was
due to triplex formation at the targeted site and not TFO-NF-
B
protein interactions.
-amino-derivatized (specific and
control) oligomers were directly added to the culture medium at the
indicated concentrations (Fig. 5). 3
-modification with
a primary amino group has been shown to significantly increase the
resistance of natural phosphodiester oligodeoxynucleotides to nuclease
degradation (17). Two luciferase reporter constructs were used to
analyze the ability of the TFO to inhibit inducible transcriptional
activity in Jurkat T cells. A 620-bp GM-CSF promoter reporter vector
(pGMluc) containing the triplex target site and a plasmid with 670 bp
of the IL-3 gene promoter (pIL3luc), which does not have a sequence
capable of forming a DNA triplex with GM3, were transfected into Jurkat
T cells together with an HTLV-1 tax expression vector. Both
IL-3 and GM-CSF promoter activities are induced by HTLV-1 Tax (38).
After 24 h, TFO GM3 and control oligomer GMc were added to the culture
medium at the concentrations shown in Fig. 5, and cells were cultured
for an additional 8 h and then harvested.
Fig. 5.
Effect of TFOs on the transcriptional
activation from luciferase reporter constructs containing GM-CSF and
IL-3 genes promoters. pGMluc, pIL3luc, and expression plasmid
pcTax have been described previously. Five µg of reporter plasmid was
cotransfected by electroporation into Jurkat T cells together with 10 µg of pcTax. Twenty-four hours after transfection, cells were treated
with medium alone, GM3, or GMc at the indicated concentrations.
Columns show relative levels of transcriptional induction
upon stimulation from the luciferase reporter gene. The reporter gene
activities in transfected cells stimulated by overexpression of Tax and
treated with only medium were assigned a value of 100%. Tax expression
lead to an average of 250-fold induction for pGMluc and 223-fold
induction for pIL3luc over the level in unstimulated cells.
Columns and error bars on the graph (mean ± S.E.) represent combined data from seven measurements in three
independent experiments for pGMluc and five measurements in two
independent experiments for pIL3luc.
Fig. 6.
Triplex formation by GM3 affects expression
from the endogenous GM-CSF gene in Jurkat T cells activated by
different stimuli. Untransfected Jurkat T cells or Jurkat T cells
transfected with 10 µg of pcTax were treated with specific TFO GM3 or
control GMc at the indicated concentrations and stimulated with
PMA/Ca2+ ionophore. Total cellular RNA was purified, and
the levels of the mRNAs of interest were assessed by PhosphorImager
quantitation of bands, obtained from mRNA protection by
33P-labeled antisense probes. Glyceraldehyde-3-phosphate
dehydrogenase mRNA levels in each sample were used as an internal
reference for normalizing GM-CSF and IL-3 mRNA concentrations. The
columns on the graph represent relative levels of GM-CSF and
IL-3 mRNA in cells stimulated with PMA/Ca2+ ionophore
or HTLV-1 Tax together with PMA/Ca2+ ionophore. GM-CSF and
IL-3 mRNA levels in cells stimulated and not treated with
oligonucleotides were assigned a value of 100%. The error
bars show standard deviations of the results obtained in two
independent experiments.
-amino derivatized
oligodeoxyribonucleotide, directed to form a triple helix with a 15-bp
target sequence overlapping the NF-
B binding site in the GM-CSF
promoter, significantly inhibits transcription from the endogenous gene
in human T cells, and this inhibition appears to be oligomer- and
gene-specific.
B element and blocks
in vitro protein binding to this site. This is consistent
with the previous mutation analysis of the GM-CSF promoter in our
laboratory showing that this
B element is required for the response
of the promoter to PMA/Ca2+ ionophore activation (25) and
to transactivation by the HTLV-1 Tax protein (27) in reporter gene
assays. The data presented here confirm these results for the
endogenous gene. Activation of the GM-CSF gene by PMA/Ca2+
ionophore is also mediated via NFAT/AP-1 binding sites in both the
promoter and enhancer (25, 43). HTLV-1 Tax, on the other hand, requires
the
B element as well as the adjacent CK-1 element for promoter
induction but does not activate NFAT/AP-1 sites (27).2 The
fact that the GM3 TFO inhibits the response of the endogenous gene to
both PMA/Ca2+ ionophore and Tax/PMA/Ca2+
ionophore costimulation suggests a central role for this
B element
in GM-CSF gene transcriptional activation.
B or other transcription
factor function in general but is acting selectively through triplex
formation on the GM-CSF promoter.
B/Rel transcription factors to the
B
element in the GM-CSF promoter compared with that seen with
PMA/Ca2+ ionophore,2 which may make it more
difficult for the TFO to compete with proteins for binding to the
target site. In addition, NFAT/AP-1 sites and the CK-1 element all
contribute to this high level of synergism, and it may by more
difficult to block gene activation via a single site. In order to
achieve complete inhibition of GM-CSF transcription it may be necessary
to use TFOs that block not only the
B element but also NFAT/AP-1
sites in the gene enhancer or promoter since we have shown that all of
these elements are required for full activation of the gene (25, 27,
43).2 It may be also possible to increase the affinity of
TFO binding to the target site on the GM-CSF promoter. This may be
achieved by using, for instance, oligonucleotides coupled to an
intercalating agent (46, 47) or an oligomer that is linker-substituted
at the position of the ``mismatch'' in the duplex target (48).
*
This work was supported by a grant from the National Health
and Medical Research Council of Australia. The costs of publication of this
article were defrayed in part by the
payment of page charges. The article
must therefore be hereby marked
``advertisement'' in
accordance with 18 U.S.C. Section
1734 solely to indicate this fact.
To whom correspondence should be addressed: Div. of Human
Immunology, Institute of Medical and Veterinary Science, Box 14, Rundle
Mall, P.O., Adelaide, 5000 South Australia, Australia. Tel.: 61 8 222 3475; Fax: 61 8 232 4092; E-mail:
fshannon{at}immuno.imvs.sa.gov.au.
1
The abbreviations used are: GM-CSF,
granulocyte-macrophage colony-stimulating factor; IL, interleukin; TFO,
triplex-forming oligonucleotides; bp, base pair(s); PMA, phorbol
12-myristate 13-acetate; HTLV, human T-cell lymphotrophic virus.
2
Himes, S. R., Katsikeros, R., and Shannon, M. F. (1996) J. Virol., in press.
3
P. Cockerill, personal communication.
©1996 by The American Society for Biochemistry and Molecular Biology, Inc.
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