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*
Department of Experimental Pathology, and
Graduate Program in Immunology and Molecular Pathogenesis and Genetics and Molecular Biology, Emory University School of Medicine, Atlanta, GA 30322; and
Department of Chemistry, Williams College, Williamstown, MA 02167
| Abstract |
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mRNA is strictly dependent on cell activation signals in both T and
mast cell lines. In contrast, the ß isoform is expressed at very low
constitutive levels in both cell types but is only up-regulated in
response to mast cell activation signals delivered through the Fc
RI
or via calcium ionophores. These results demonstrate another level of
regulation within the NF-AT family that can contribute to cell
type-specific gene expression. | Introduction |
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The existence of multiple NF-AT proteins that can recognize the same DNA element raises questions regarding their in vivo function. The overlapping expression patterns of some of these proteins and their similar in vitro binding and trans-activation activities on promoter elements of NF-AT-regulated genes argue that these factors are largely redundant. However, several lines of evidence support the idea that family members may also have cell-specific and/or gene-specific activities. 1) Outside the regions of high homology, the NF-AT family members have quite diverse sequences, providing the opportunity for interaction with unique cofactors required for the transcription of a subset of NF-AT-regulated genes. 2) Tissue-restricted expression of some individual family members and their isoforms has also been observed. For example, NF-AT3 is expressed at very low levels in the thymus, whereas NF-AT4 is strongly expressed at this site 14, 15, 16 . Likewise, isoforms of NF-AT3 show distinct expression patterns: the 3-kb form is expressed predominantly in the placenta, lung, kidney, testis, and ovary, and the 4.5-kb form is expressed in the heart and colon 14 . 3) Recent studies using antisera that can distinguish family members reveal the existence of NF-AT binding specificity. Timmerman et al. showed that while NF-AT1 and NF-AT2 can bind equally well to either the IL-2 or IL-4 promoter in in vitro DNA binding assays, NF-AT3 and NF-AT4 exhibit at least a 10-fold lower affinity 20 . Similarly, NF-ATx was shown to be the major component of IL-2 promoter DNA-protein complexes in double-positive thymocytes 21 .
The most compelling argument for gene-specific activities of NF-AT comes from the phenotypic analysis of NF-ATp- and NF-ATc-deficient mice. Stimulated T lymphocytes from NF-ATc-/- mice have an impaired ability to produce IL-4 22, 23 . The production of Ig isotypes associated with Th2 responses is also diminished 22 . Expression of other NF-AT-regulated genes in T cells, such as IL-2, was only slightly affected. These data demonstrate that IL-4 gene expression is a specific target of regulation by NF-ATc 22, 23 . In contrast, although the kinetics of IL-4 expression by activated T cells are delayed in NF-ATp-deficient mice, IL-4 production is significantly enhanced overall compared with that observed in wild-type animals. NF-AT4-/- animals produce relatively normal amounts of Th1 and Th2 cytokines such as IL-4, but positive selection of T cells is defective 22 . These results suggest the possibility that IL-4 transcription is positively regulated by NF-ATc and is repressed by NF-ATp 24, 25 .
In this study we provide evidence for cell-type specific expression of
NF-ATc isoforms. These studies were prompted by our earlier observation
that the NF-AT-mediated regulation of IL-4 gene transcription in mast
cells exhibits striking differences compared with that of T cell IL-4
transcription 2 . Although the transcription of IL-4 in both cell
types is dependent on an NF-AT site between -88 and -60 in the murine
IL-4 gene, the protein-DNA complexes that form at this site are
distinct. Unlike the T cell IL-4 complex that also contains activating
protein-1 (AP-1), these Jun/Fos family members are not present
in the mast cell NF-AT complex. DNA affinity purification and Western
blot experiments also revealed differences in the size and regulation
of the mast cell NF-AT protein associated with this site. These data
suggested the possibility that this NF-AT was either a unique isoform
or the product of a previously undescribed gene. Our efforts to address
this issue led to the isolation of several NF-AT cDNA clones from a
murine mast cell library. Here we report the full sequence of two
murine NF-ATc isoforms, designated NF-ATc.
and -ß. Each form shows
unique features in sequence and expression pattern compared with the
previously described human NF-ATc genes 26 . In addition, murine T and
mast cells exhibit striking differences in the relative expression of
NF-ATc.
and NF-ATc.ß. This is due in part to the different
inducibilities of these isoforms in response to TCR- and
Fc
RI-mediated signaling. The selective expression of NF-ATc isoforms
may contribute to cell- and/or gene-specific transcription of molecules
that function in inflammation and that have not been previously
appreciated in knockout experiments.
| Materials and Methods |
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The sequences of the murine NF-ATc.
(accession no. AF087434)
and NF-ATc.ß (accession no. AF049606) were deposited in the
GenBank database.
cDNA cloning
A murine mast cell cDNA library was constructed in the
gt11
(Clontech, Palo Alto, CA.) vector. Poly(A)+ mRNA from
stimulated (ionomycin for 90 min) CFTL15 mast cells 27 was used as
the template for first-strand cDNA synthesis using both oligo(dT) and
random hexamer primers. The library was screened at low stringency (2x
SSC/0.5% SDS at 55°C) with a murine NF-ATp probe obtained by RT-PCR
amplification of murine EL-4 T cell RNA. The probe contained sequences
corresponding to nucleotides 10381517 within the rel
similarity domain (RSD) of NF-ATp 28 . Positive clones were purified,
and inserts were subcloned into pBluescript plasmids for further
analysis. Sequencing of both strands of the cDNA inserts was performed
using the dideoxynucleotide chain termination method with reagents from
U.S. Biochemical Corp. (Cleveland, OH).
RNase protection analysis
Total RNA samples from cell lines and murine tissues (from
unimmunized C3H/HeNCr mammary tumor virus (MTV)-
mice) were isolated using the RNA-STAT reagent according to the
manufacturers instructions (Tel-Test, Friendswood, TX). RNase
protection assays were performed using NF-ATc.
(nucleotides 10196
in the
sequence) and NF-ATc.ß (nucleotides 15161 in ß
sequence) cDNA fragments as templates for the synthesis of antisense
RNA labeled to high sp. act. with [32P]UTP (Riboprobe
kit, Promega, Madison, WI). Full-length RNA probes were gel-purified
and hybridized (5 x 105 cpm) to 10 µg of total RNA
overnight at 45°C in 40 mM PIPES (pH 6.4), 400 mM NaCl, 1 mM EDTA,
and 80% formamide in a total volume of 30 µl. Samples were incubated
for 1 h at 30°C after addition of 350 µl of digestion buffer
(10 mM Tris (pH 7.5), 5 mM EDTA, 300 mM NaCl, 0.14 µg of RNase T1,
and 1 µg of RNase A). Proteinase K (5 µl of 10 mg/ml stock) and SDS
(10 µl of 20% solution) were added and incubated for an additional
30 min at 37°C. Samples were extracted with phenol/chloroform,
precipitated, resuspended in gel loading buffer, and analyzed by 6%
denaturing PAGE. Densitometric quantitation of relative mRNA expression
levels was performed using the National Institutes of Health Image
program.
Northern blot analysis
The murine tissue Northern blots were purchased from Clontech.
For analysis of expression in cell lines, 10 µg of total RNA or 2
µg of poly(A)+ RNA was electrophoresed on a 1%
formaldehyde gel and transferred to nitrocellulose. DNA probes were
labeled by random hexamer priming and hybridized as described
previously 29 . The NF-ATc-specific probe corresponds to nucleotides
11621727 based on the NF-ATc.ß sequence shown in Fig. 1
and contains a significant portion of the
RSD. The murine ß-actin probe includes nucleotides 147332 of the
published sequence 30 . The IL-4 cDNA probe corresponds to nucleotides
40412 31 .
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CFTL15 is an IL-3-dependent murine mast cell line derived from
fetal liver cells and was previously described 27 . Bone
marrow-derived mast cells (BMMC) were isolated from BALB/c bone marrow
cultured in IL-3 and stem cell factor. After 4 wk the cells were
analyzed by flow cytometry for the surface expression of c-Kit and
Fc
RI. The c-Kit levels were determined using directly conjugated
anti-CD117-phycoerythrin (PharMingen, San Diego, CA). Expression of
the high affinity Fc
was assessed using a two-step staining
procedure. Cells were first incubated with purified mouse IgE (Sigma).
After three washes, a second IgE bound to Fc
R was detected using a
rat anti-mouse IgE-FITC Ab (PharMingen). Data were acquired on a
FACS caliber flow cytometer (Becton Dickinson, San Jose, CA) gating on
propidium iodide-negative cells. Data were analyzed using
CellQuest software (BDIS; Becton Dickinson). P815 and ABFTL3 are
transformed mast cells that express IL-4 mRNA constitutively 29 . EL-4
is a murine thymoma line 32 that was obtained from American Type
Culture Collection (Manassas, VA). D011.10 Th1 and Th2 cell lines were
derived from the OVA-specific TCR transgenic mouse 33 . M12.4.1 B
cells were a gift from Dr. Paul Rothman 34 ; L929 fibroblast cells
were obtained from American Type Culture Collection and have been
previously described 35 . Mast cells were activated by culturing with
the calcium ionophore, ionomycin (1 µg/ml; Calbiochem, La Jolla, CA)
or by cross-linking the high affinity Fc
R by priming the cells with
1 µg/ml purified anti-DNP IgE (Sigma) for 2 h followed by
activation with 5 µg/ml DNP-keyhole limpet hemocyanin (Calbiochem).
In some experiments mast cells were cultured for 2 days with IgE before
stimulation. T cells were stimulated with 1 µg/ml ionomycin and 20
ng/ml PMA (Sigma) or with Ag (2.5 x 105/ml BALB/c
spleen cells, 104 U/ml IL-2, and 0.5 µM
OVA323339 peptide) for the indicated periods of time.
| Results |
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and ß isoforms that differ only at
their N-termini
To identify NF-AT genes expressed in mast cells, a cDNA probe
derived from the murine NF-ATp RSD was used to screen both oligo(dT)-
and random hexamer-primed CFTL15 murine mast cell libraries at low
stringency. Approximately 1.6 x 105 plaques were
screened. Several clones were characterized, including one that
corresponded to NF-ATp. The majority of the cDNAs analyzed were
homologous to human NF-ATc.ß, an isoform identified in Raji B cells
26 . The longest clone is comprised of 3435 nucleotides, which
includes an approximately 1.3-kb 3' untranslated region (3'UTR) that is
unrelated to the 3'UTR of human NF-ATc (Fig. 1
). Within the coding
region, this cDNA exhibits >83% identity overall at the DNA level
with the human gene (Fig. 2
A). The
cDNA encodes a protein of 704 amino acids (aa) with a predicted
molecular mass of 70 kDa. A comparison of amino acid sequences reveals
that NF-ATc is highly conserved in human and mouse. There is 96.7%
identity and 98% similarity within the RSD (encoded by aa 408684),
which contains the DNA binding domain. The amino-terminal region (aa
1407) contains three serine/proline (SP) motifs and is 83%
identical and 91% similar to its human NF-ATc.ß homologue. A short
C-terminal region (aa 685704) does not show similarity to the
reported sequence of human NF-ATc.
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homologue 13 were also isolated. It is notable that unlike
the human cDNAs that encode isoform-specific amino acids at both the N-
and C-terminal portions of the proteins 26 , the differences between
murine NF-ATc.
and -ß were limited to the 5' end. In NF-ATc.
cDNAs, sequences specifying the first 27 aa of NF-ATc.ß are replaced
by nucleotides that can potentially encode 39
isoform-specific
amino acids (Fig. 2
probe, and RT-PCR using
murine T and mast cell cDNA and primers derived from the murine NF-ATc
common region and the human NF-ATc.
5'UTR. However, it is likely
that these sequences exist. A recent report indicates that, like the
human
isoform, a murine homologue isolated from T cells contains
nucleotides that specify an additional 3 aa 36 . These sequences
include an in-frame AUG codon in a context that is suboptimal for
protein translation initiation (cggAUGc) 37 . This upstream AUG is
used for the translation initiation of a minor NF-ATc protein species
in human T cells. Our clones contain the downstream AUG, which lies in
an optimal context (accAUGa) and initiates the major form of human
NF-ATc.
translation 37, 38 . A comparison of the murine and human
-specific sequences shows that they share 80% identity and 80%
similarity (Fig. 2NF-ATc expression differs in human and murine tissues
Previous Northern blot analysis with human tissues, using probes
that distinguish the
and ß isoforms, reveal that NF-ATc.ß mRNA
is approximately 4.5 kb in size and is preferentially expressed in
spleen, testis, and ovary; the
isoform is encoded by a 2.7-kb mRNA
and is detected predominantly in the thymus and peripheral blood
leukocytes 26 . In murine tissues, probes derived from both the 5'
region (not shown) and the RSD (Fig. 3
A) hybridize with two closely
migrating mRNA species of about 4.5 kb, suggesting that both the
and ß isoforms mRNAs are of similar size. Levels of murine NF-ATc RNA
are highest in spleen, lung, and skeletal muscle. Detectable, but much
lower, expression was observed in heart, brain, liver, and kidney.
There was no detectable expression in mouse testis, unlike results
reported for human NF-ATc.
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NF-ATc.
and -ß mRNA are differentially expressed
Results from Northern analyses are consistent with the idea that
there is cell- and tissue-specific expression of NF-ATc isoforms. RNase
protection assays were performed using probes that can distinguish
between the
and ß isoforms of NF-ATc to explore this possibility.
The integrity of the RNA in the samples was verified in parallel
reactions using a ß-actin probe (data not shown). As shown in Fig. 4
, the ß isoform is strongly expressed in
heart, spleen, and kidney, whereas
-specific mRNA is present only in
spleen. Neither isoform is present at detectable levels in liver or
brain. However, RNA samples from these tissues did protect a band of 70
bp corresponding to the region of the ß probe that is shared with
, indicating the presence of an additional isoform(s) of NF-ATc in
the sample.
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isoform is strictly
dependent on cell activation in a variety of both T and mast cell lines
(Fig. 5
receptor or activation with calcium ionophore induces NF-ATc.
mRNA
in BMMC and CFTL15 mast cells (Fig. 5
mRNA is only weakly expressed in P815 and ABFTL3 transformed
mast cell lines.
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Steady state levels of NF-ATc isoforms are differentially regulated in activated T and mast cells
The apparent differences in NF-ATc inducibility between these
distinct cell types could be explained simply by cell-specific
differences in the kinetics of activation. To assess this possibility,
T and mast cell lines were stimulated for various times, and total RNA
was isolated for use in RNase protection assays. As shown in Fig. 6
, maximal expression of NF-ATc.
was
observed between 1 and 2.5 h, and then rapidly fell to
undetectable levels in CFTL15 mast cells. In the T cell lines tested,
the maximal expression of the
isoform message was observed between
2 and 3 h. There were also notable time-dependent differences in
the expression of NF-ATc.
in the T cell lines; by 6 h
poststimulation, little
-specific RNA was detected in Th1 cells,
whereas detectable amounts persisted for at least 24 h after
stimulation in Th2 cells and for 48 h in EL-4 cells.
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Cell type-specific differences in mRNA stability exist
To investigate the contribution of differences in mRNA
stability to the cell-specific expression patterns we observed, CFTL15
mast cells and EL-4 T cells were stimulated for 2 h before
treatment with actinomycin D to block ongoing transcription. Total mRNA
was then isolated at 0.5-h intervals, and steady state levels were
assessed by RNase protection. As shown in Fig. 7
A, both NF-ATc.
and -ß mRNA
persisted in CFTL15 mast cells at peak levels for at least 2 h
after actinomycin D treatment. In fact, NF-ATc.
mRNA persisted much
longer in actinomycin D-treated cells (Fig. 7
B), suggesting
that an mRNA-destabilizing product is transcribed concomitantly with
NF-ATc in mast cells. NF-ATc.
mRNA expression in EL-4 cells is much
more labile. Within 30 min of blocking transcription, levels of steady
state mRNA are reduced by more than half. These data indicate that the
persistence of NF-ATc.
expression in T cells is dependent in part on
ongoing transcription.
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| Discussion |
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and NF-ATc.ß isoforms were
isolated from a murine mast cell library 13, 26 . Like the human
isoforms, the murine cDNAs are distinguished by isoform-specific
sequences at the 5' end of the coding region. These sequences are
highly related to the human sequences. Murine NF-ATc.
and NF-ATc.ß
cDNAs are otherwise identical and do not contain the isoform-specific
differences in sequences 3' of the RSD that characterize the human
sequences. In fact, the murine sequences located 3' of the RSD are
unique and share no homology at the DNA or protein level with human
NF-ATc.
and -ß. The murine NF-ATc.
DNA sequence reported here
is similar, but not identical, with cDNAs derived from activated T
cells reported by Pan et al. 36 .
In addition to the variants described in this report, it is likely that
other NF-ATc isoforms exist. Although RNase protection assays
demonstrate that brain and liver do not express appreciable amounts of
either form, a protected band corresponding to the sequences encoding
the common region was observed (Fig. 4
). Similarly, several smaller
mRNAs ranging in size from about 4.0 to <2.0 kb were easily detected
in P815 cells by Northern blot analysis (Fig. 3
B) despite
the lack of an
- or ß-specific signal in these cells (Fig. 5
, A and B). A subset of these small mRNA species
was also observed in normal mast cells, suggesting that they are not
unique to transformed mast cells. Western blot data likewise provide
evidence for the existence of multiple protein isoforms of NF-ATc. We
previously described a single anti-NF-ATc-reactive species of
approximately 56 kDa in unstimulated mast cells and two additional
proteins between 120 and 160 kDa whose expression is activation
dependent 2 . In studies by Lyach et al., at least three proteins of
distinct m.w. were observed in activated T cells using NF-ATc-specific
antisera 38 . Whether these are generated by alternative splicing, the
use of alternative promoters, or the selective utilization of
translation start sites remains to be determined.
Why do multiple NF-ATc isoforms exist? We speculate that the unique
regions of the NF-ATc isoforms confer distinct functions to these
proteins. Structure-function studies have demonstrated that the
N-terminal domain of NF-ATp (aa 1415), human NF-ATc.
(aa 1418),
and the N- and C-terminal domains of NF-ATx function as
trans-activation domains 39, 40, 41 . It is possible that
unique domains act to attract unique coactivators. In support of this
theory is the finding that p300/CREB binding protein can be recruited
by NF-ATp 39 . In addition, we showed that AP-1 associates exclusively
with the IL-4 promoter NF-AT complex in T cells but not in mast cells
despite equivalent expression of these proteins in both cell types 2 .
Proteins such as c-Maf, NF-AT-interacting protein-45, and GATA-3, which
have been described as essential cofactors for IL-4 gene expression in
T cells, are also candidates for a role in cell type-specific
coactivation 42, 43, 44 . The existence of multiple isoforms that contain
unique functional domains expands the potential repertoire of
coactivators that can cooperate with NF-ATc to achieve selective gene
expression in a given cell type.
Previous studies demonstrate that the regulation of NF-AT activity occurs at several levels (for a review, see 9 . All family members appear to undergo activation-dependent trans-location from the cytoplasm to the nucleus. These events require the calcium-dependent phosphatase, calcineurin, which acts on cytoplasmic NF-AT through direct protein-protein interactions and allows the shuttling of NF-AT to the nucleus. A nuclear kinase, glycogen synthase kinase-3, regulates the export of NF-AT back to the cytoplasm 19 . Tissue-specific expression patterns of NF-AT family members and their isoforms also regulate the range of NF-AT-responsive genes that can be influenced in any given cell type 9 . NF-ATp, NF-AT3, and NF-AT4/x are constitutively expressed in target tissues and are not subject to control by cell activation signals. In contrast, NF-ATc mRNA and protein expression are dependent on stimulation in human T cells 12, 13, 15, 16, 38 .
The results presented here demonstrate that additional levels of NF-AT
regulation exist. In murine T cells and mast cells, activation through
the TCR or high affinity Fc
R is absolutely required for the
expression of NF-ATc.
. In contrast, although the ß isoform is
expressed at low constitutive levels in most of the cell lines we
analyzed, only the mast cells demonstrate a significant increase in
steady state mRNA levels upon stimulation. The clear-cut differences in
expressions of the
and ß isoform mRNAs in response to activation
signals support the hypothesis that distinct promoters responsive to T
cell and/or mast cell activation signals contribute to the selective
expression of these factors. We also provide evidence that mechanisms
exist to differentially regulate mRNA half-life. Blocking transcription
with actinomycin D prolongs the expression of NF-ATc.
, but not -ß,
in mast cells, indicating that an active destabilizing agent functions
to down-regulate steady state mRNA levels.
The analysis of cytokine responses in NF-ATc-deficient mice
demonstrates that this factor is responsible for IL-4 production in
activated T cells 10, 11 . Our data support the idea that NF-ATc.
,
but not -ß, is involved in IL-4 transcription in Th2 cells. This
conclusion is based on the observation that NF-ATc.ß is only
minimally expressed in T cells and that the kinetics of NF-ATc.
closely parallel the expression of IL-4 in these cells (data not
shown). Furthermore, cloning of NF-ATc from both human and murine T
cells resulted in the isolation of cDNAs corresponding only to
NF-ATc.
, indicating that this is the predominant NF-AT isoform
expressed in this cell lineage 13, 36 .
Because the mast cell population was not affected by NF-ATc gene targeting in NF-ATc-/- mice, its in vivo role in mast cell IL-4 gene transcription has not been addressed. The current studies were initiated to identify the NF-AT factor(s) associated with the IL-4 promoter in mast cells. However, the identity of this factor is still elusive. DNA affinity purification experiments demonstrate that the major protein associated with the IL-4 NF-AT site between -88 and -60 is 41 kDa, a size not observed in analysis of anti-NF-ATc-reactive proteins by Western blot. Furthermore, this protein was reactive with NF-ATp antisera, although the specificity/cross-reactivity of both NF-ATp and NF-ATc antisera have not been rigorously tested. Given the prevalence of both isoforms in mast cells as well as activation kinetics that correlate with IL-4 expression, it is likely that NF-ATc plays a role. We are currently exploring the possibility that the shorter NF-ATc mRNAs encode this smaller protein associated with the IL-4 promoter in mast cells. A better understanding of the NF-ATc chromosomal gene will allow the targeting of isoform-specific sequences to assess their roles in vivo.
| Acknowledgments |
|---|
| Footnotes |
|---|
2 The sequences of the murine NF-ATc.
(accession no. AF087434) and NF-ATc.ß (accession no. AF049606) were deposited in the GenBank database. ![]()
3 Address correspondence and reprint requests to Dr. Melissa A. Brown, Department of Experimental Pathology, Emory University, 1639 Pierce Dr., Atlanta, GA 30322. E-mail address: ![]()
4 Abbreviations used in this paper: NF-AT, NF of activated T cells; Fc
R1, high affinity Ig E receptor; RSD, rel similarity domain; BMMC, bone marrow-derived mast cells; UTR, untranslated region. ![]()
Received for publication September 1, 1998. Accepted for publication December 3, 1998.
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transcripts. Mol. Cell. Biol. 11:5551.This article has been cited by other articles:
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C.-W. Chow, C. Dong, R. A. Flavell, and R. J. Davis c-Jun NH2-Terminal Kinase Inhibits Targeting of the Protein Phosphatase Calcineurin to NFATc1 Mol. Cell. Biol., July 15, 2000; 20(14): 5227 - 5234. [Abstract] [Full Text] |
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R. Chen, T. F. Burke, J. E. Cumberland, M. Brummet, L. A. Beck, V. Casolaro, and S. N. Georas Glucocorticoids Inhibit Calcium- and Calcineurin-Dependent Activation of the Human IL-4 Promoter J. Immunol., January 15, 2000; 164(2): 825 - 832. [Abstract] [Full Text] [PDF] |
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M. A. Sherman, T. Y. Nachman, and M. A. Brown Cutting Edge: IL-4 Production by Mast Cells Does Not Require c-maf J. Immunol., August 15, 1999; 163(4): 1733 - 1736. [Abstract] [Full Text] [PDF] |
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