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* Ethel Percy Andrus Gerontology Center, and Division of Molecular & Computational Biology, The University of Southern California, Los Angeles, CA 90089-0191, USA; and
DNA Array Unit, Research Resources Branch, National Institute on Aging, NIH, 5600 Nathan Shock Drive, Baltimore MD 21224-6825, USA
1Correspondence: Ethel Percy Andrus Gerontology Center, University of Southern California, 3715 McClintock Avenue, Los Angeles, CA 90089-0191, USA. E-mail: kelvin{at}usc.edu
| ABSTRACT |
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Key Words: calcipressin 1 sod 1 oxidative stress Downs syndrome
| INTRODUCTION |
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Calcineurin is a calcium/calmodulin activated serine/threonine phosphatase (PP2B) that is an important enzyme in Ca2+-dependent eukaryotic signal transduction pathways (5)
. It plays important roles in immune stimulation, and calcineurin-dependent signal transduction pathways have been extensively characterized during T cell activation (6)
. Calcineurin transduction pathways are also well characterized in yeast, where the protein promotes growth in high calcium environments by dephosphorylation of the Tcn1p transcription factor (7
8
9)
. Calcineurin plays a critical role in cellular responses to various extracellular signals and environmental stresses, and it is important in the regulation of apoptosis (9
10
11
12
13)
, memory processes (14
15
16)
, and skeletal and cardiac muscle growth and differentiation (17
, 18)
. In plants calcineurin mediates salt adaptation (19)
. Since the DSCR1(Adapt78) protein, "Calcipressin 1" can regulate calcineurin activity, it is likely to be involved as an antagonist in many of the above processes.
The DSCR1(Adapt78) gene consists of 7 exons, four of which (exons 14) can be alternatively spliced to produce a number of different mRNA isoforms (20)
. These isoforms may have different expression patterns, functions, and different regulation mechanisms. For example, expression of exon 2 has been detected in fetal, but not adult human brain (2)
, and calcineurin can induce expression of DSCR1(Adapt78) isoform 4 mRNA but does not appear to induce the other isoforms (21)
.
DSCR1(Adapt78) was discovered as a gene associated with transient adaptation to oxidative stress and calcium stress (1)
, and we have recently demonstrated that it can actually provide stress protection. However, we also observed that this gene is overexpressed in Alzheimers disease and Downs syndrome, indicating that its expression can also be harmful. Therefore, we hypothesized that although acute and transient DSCR1(Adapt78) overexpression may protect against calcium-mediated stresses, its chronic overexpression can cause cell damage (22
23
24)
. The mechanisms by which DSCR1(Adapt78) can protect or harm cells are still unclear. Here, using regulated expression of a DSCR1(Adapt78) transgene, followed by microarray analysis, we have tried to identify pathways and targets affected by its expression.
| METHODS |
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Doxycycline regulated DSCR1(Adapt78) expression system
DSCR1(Adapt78) isoform 1 fragment, produced by LA RT-PCR as we described previously (23)
, was inserted into a pTRE vector from Clontech Laboratories, Inc. (Palo Alto, CA). PC-12 tet-off cells from Clontech Laboratories, Inc., stably transfected with "regulator plasmid," were next transfected with the pTRE carrying DSCR1(Adapt78) fragment to finally produce a double-stable cell line in which the DSCR1(Adapt78) transgene could be turned off by doxycycline. All procedures were performed as described in the tet-off gene expression user manual from Clontech Laboratories, Inc.
PC-12 cell culture
PC-12 cells were cultivated in media containing 85% DMEM, 10% horse serum, 5% antibiotic free fetal bovine serum (Clontech Laboratories, Inc.), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin sulfate. PC-12 tet-off cells, stably transfected with "regulator plasmid," were maintained in media additionally containing 50 µg/ml G418. The double-stable cell line carrying both the "regulator plasmid" and the DSCR1(Adapt78) transgene was maintained in media additionally containing 50 µg/ml G418 and 50 µg/ml hygromycin. Cells were cultivated in a humidified 10% CO2 atmosphere at 37°C. The DSCR1(Adapt78) transgene was turned off by application of 0.02 µg/ml doxycycline to the media.
RNA isolation
Total RNA was extracted using the TRIzol reagent (Life Technologies, Inc., Rockville, MD). RNA concentration was quantified spectrophotometrically, and relative content was further confirmed on ethidium bromide-stained gels. Integrity of the RNA was estimated by agarose gel electrophoresis; only RNA samples displaying discrete 28S and 18S RNA bands were used in our experiments.
Northern hybridization
Samples containing 10 µg of total RNA were subjected to electrophoresis through 1% agarose formaldehyde gels, blotted to nylon membranes (Oncor) with HETS (CINNA/BIOTECX), and cross-linked by ultraviolet radiation. The membranes were prehybridized for 4 h and then hybridized for 15 h in Hybrizol I (Oncor) at 42°C. After hybridization, they were washed with 2xSSC plus 0.1% SDS at room temperature for 1 and 10 min, then with 0.1xSSC plus 0.1% SDS at 60°C for 10 and 30 min. The membranes were exposed, developed, and scanned using the PhosphorImager system (Molecular Dynamics, Sunnyvale, CA). To rehybridize RNA gel blots, probes were removed by washing the membranes in a solution of 0.1xSSC, 0.1% SDS, and 10 mM Tris-HCl (pH 7.0) at 90°C for 10 min. To quantify the levels of DSCR1(Adapt78) mRNA, the membranes were scanned and the hybridization signal measured using ImageQuant software (Molecular Dynamics). Each signal was recalculated according to the amount of RNA actually loaded on the gels. The amount of RNA loaded was controlled in two ways. First, the gels were stained with ethidium bromide, photographed under UV light, and the amount of 28S and 18S was evaluated. Second, membranes were hybridized with a GAPDH probe. Probes containing [
-32P]dCTP-labeled DNA were prepared using the High Prime system (Boeringer Mannheim, Germany). A PCR fragment corresponding to DSCR1(Adapt78) isoform 1 was used to prepare the DSCR1(Adapt78) probe and a PCR-fragment consisting of GAPDH exons 7 and 8 was used to prepare GAPDH probes. PCR fragments were prepared as we described previously (23)
.
Microarray construction and use
A 15,000 human cDNA clone set of IMAGE Consortium clones (http://image.llnl.gov) available from Research Genetics (Huntsville, AL, USA) was sorted for genes relevant to signal transduction, immune function, and neurological importance. A focused set of 1152 genes for each array type was PCR amplified and printed in duplicate at high density onto nylon membranes. The NIA immunoarray (25)
and the NIA Neuroarray (26)
have been described previously. cDNAs arrayed for the Signal Transduction array include receptor genes of the tyrosine kinase, tyrosine phosphate, and G-protein-coupled classes; intracellular signaling molecules, including MAP kinases, serine-threonine kinases, GTPase-activating proteins, and SH3/SH2 docking proteins. Marker genes from the cell cycle, Jak-Stat, NF
B, and P13/AKT pathways are included as well. Total RNA from experimental samples was used to synthesize 33P-labeled cDNAs by reverse transcription, according to protocols described in http://www.grc.nia.nih.gov/branches/rrb/dna.htm. All three array types were simultaneously hybridized with
-33P-dCTP-labeled cDNA probes overnight at 55°C in 4 ml of hybridization solution. Hybridized arrays were rinsed in 50 ml of 2xSSC and 1% SDS twice at 55° for 15 min each. The microarrays were exposed to phosphorimager screens for 13 days. The screens were then scanned in a Molecular Dynamics STORM PhosphorImager (Sunnyvale, CA) at 50 µm resolution. ImageQuant software (Molecular Dynamics, Sunnyvale, CA) was used to convert the hybridization signals on the image into raw intensity values, and the data thus generated were transferred into Microsoft Excel spreadsheets predesigned to associate the ImageQuant data format to the correct gene identities.
Data processing
Raw intensity data for each experiment was normalized independently for each array type by Z score transformation as described previously (27)
. Briefly, intensity data are first, log10 transformed and then used for the calculation of Z scores. Z scores are calculated by subtracting the average gene intensity (within a single experiment) from the raw intensity data for each gene, and dividing that result by the standard deviation of all the measured intensities. Significant changes in gene expression were calculated by the Z ratio method (28)
. In brief, gene expression differences between any two experiments are calculated by taking the difference between the observed gene Z scores. Z ratios then express these differences in terms of their relationship to the standard deviation of the distribution of all of the observed gene changes. The calculated Z ratios for a given comparison are rank ordered on this basis and a Z ratio of ±1.96 is inferred as significant (p<0.05).
DSCR1(Adapt78) antibody and Western blot analysis
Using the predicted open reading frame sequence of DSCR1(Adapt78), we designed a C-terminal 16-amino-acid peptide that was used as an antigen to immunize rabbits. We added a cysteine to the N terminus of this peptide (KIIQTRRPEYTPIHLS) and then conjugated the peptide to keyhole limpet hemocyanin. Polyclonal antibodies were raised commercially (ProSci, Inc., Poway, CA) by injection of this complex into rabbits. Serum from one of the immunized rabbits was affinity purified on a column with the covalently attached DSCR1(Adapt78) peptide that was used for immunization. Western blot analysis was performed, following the protocol from ProSci, Inc., using an ECL-detection system from Amersham. Final dilution of the purified antibody for Western blot analysis was 1:500. Our antibody specifically recognized calcipressin1 (the dscr1/adapt78 protein) as a single band.
Sod 1 assay
Activity of the sod 1 enzyme (intracellular Cu,Zn SOD) was measured by the cytochrome c reduction assay as described in (29)
. Cells were disrupted in water and whole homogenates were used for assays. Total concentration of protein in homogenates was measured using the protein reagent from Bio-Rad Laboratories (Hercules, CA). The sod 2 enzyme was inactivated using dodecyl sulfate, which does not affect sod 1.
| RESULTS |
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5 h after stress is initiated and then gradually down-regulated to basal levels. Here, we also time-regulated DSCR1(Adapt78) expression to mimic its expression during stress conditions. The tet-off gene expression system (Clontech Laboratories, Inc.), which employed doxycycline regulated transgene expression, was used in these experiments (Fig. 1
1 week in media without doxycycline, and then doxycycline was added (to inhibit the transgene) for 0, 1, 3, 6, 9, 24, or 48 h. Expression of the DSCR1(Adapt78) transgene was significantly down-regulated in 3 h and almost completely inhibited as early as
6 h (Fig. 1B
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Genes affected by DSCR1(Adapt78) down-regulation
Following the shutdown of DSCR1(Adapt78) transgene overexpression, we analyzed the time course of expression of other genes, using cDNA microarrays. Total RNA samples, isolated at different time points of DSCR1(Adapt78) transgene shutdown (Fig. 1
), were used as microarray probes for Fig. 2
. Three different microarray types were used in this study: immunoarray, neuroarray, and signal transduction array (see Experimental Procedures). Each array was run in triplicate, and all experiments were repeated twice. Data were processed, normalized, and Z scores were calculated to evaluate expression of each gene as described in Experimental Procedures. Please, see SOD1 gene expression Z scores for example (Fig. 3
A).
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Although expression of most genes was unaffected, DSCR1(Adapt78) down-regulation caused up-regulated expression of some genes, down-regulation of others, as well as transient gene regulation (Fig. 2
). It is interesting that among those transiently regulated was the gene encoding for DNA cytosine-5 methyltransferase. It was up-regulated at 1 and 3 h of DSCR1(Adapt78) down-regulation, its high levels of expression remained unchanged at 3, 6, and 9 h, and then it was decreased again at 24 h, and diminished to basal levels at 48 h. DNA cytosine-5 methyltransferase can methylate DNA and thus can down-regulate transcriptional activity of other genes. It is possible that regulation of DNA cytosine-5 methyltransferase is an early event through which DSCR1(Adapt78) may execute various transient responses to oxidative stress.
Somatostatin I precursor and several other mRNAs in PC-12 cells were gradually up-regulated from 0 to 48 h following DSCR1(Adapt78) down-regulation. In contrast, genes encoding superoxide dismutase 1 (SOD1), NF
B inducing kinase (NIK), and others, were gradually down-regulated. Note that the DSCR1(Adapt78) signal was also gradually decreased (Fig. 2
), proving the reliability of our techniques. Remarkably, DSCR1(Adapt78) down-regulation caused down-regulated expression of several protein kinase-encoding genes. The DSCR1(Adapt78) product, calcipressin 1, was previously demonstrated to antagonize the action of the serine/threonine phosphatase, calcineurin (3
, 4)
, and here, we see that it can additionally regulate the expression of other protein kinases. In the present study, we have focused on the SOD1 gene; however, regulation of protein kinases and other genes by DSCR1(Adapt78) will be the subject of future studies.
DSCR1(Adapt78) regulates SOD1
SOD1 mRNA levels were gradually down-regulated following shutdown of DSCR1(Adapt78) transgene overexpression (Fig. 3A
). This also caused lowered production of sod 1 protein (Fig. 3B
). On the basis of this observation, we hypothesized that DSCR1(Adapt78) might also induce SOD1 expression. We next overexpressed the DSCR1(Adapt78) transgene and found that production of sod 1 protein was indeed up-regulated when DSCR1(Adapt78) was overexpressed (Fig. 4
). Using Western blot analysis, we estimate that, following 24 h of DSCR1(Adapt78) overexpression, sod 1 protein levels were
78% higher than they were before DSCR1(Adapt78) overexpression (Fig. 4
). These results were further confirmed by comparison of sod 1 enzyme activity in cells overexpressing calcipressin 1 with control cells (Fig. 4D
). Sod 1 activity was up-regulated
70% following 24 h of DSCR1(Adapt78) overexpression. Considering that sod 1 levels in the brains of Downs syndrome patients are elevated by
50%, compared with controls (32)
, this is very significant increase.
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To demonstrate that induction/down-regulation of SOD1 is not due to the doxycycline withdrawal from/addition into the cell culture medium, we ran similar experiments using the parent PC-12 cell line, in which the plasmid carrying our DSCR1(Adapt78) transgene was missing. The same doxycycline concentration in the medium was used (0.02 µg/ml). Doxycycline did not affect either calcipressin 1 or sod 1 protein levels in these cells (Fig. 3C
), confirming that SOD1 was regulated by DSCR1(Adapt78), and not by doxycycline.
It seems that DSCR1(Adapt78) expression in cells is tightly regulated. This gene is normally expressed at a low level, and it is induced by stress. Its expression is rapidly turned off when stress is withdrawn. Similarly, DSCR1(Adapt78) is feedback-regulated in our expression system. In the PC-12 cells used in our study, its level rose after withdrawal of doxycycline from the cell growth medium, then it reached maximal levels in
6 h, and later was slightly decreased but remained above the endogeneous level (Fig. 4
). It is likely that cells recognize and down-regulate high levels of DSCR1(Adapt78) expression, which may be harmful for them. Sod 1 protein levels (Fig. 4
), however, continued to gradually rise, even when calcipressin 1 levels were down-regulated. Rapid regulation of DSCR1(Adapt78) expression is probably facilitated by both DSCR1(Adapt78) mRNA and protein (calcipressin 1) rapid degradation in cells. We estimate that DSCR1(Adapt78) mRNA half-life is not longer than 2 h (Fig. 1
) and calcipressin 1 half-life is not longer than 6 h (Fig. 3B
). The half-life of the sod 1 protein, in contrast, is much longer, around 24 h (33)
depending on cell type. This might explain why sod 1 protein levels continued to rise at the 24 h time point, even when calcipressin 1 levels no longer increased.
| DISCUSSION |
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50% compared with controls (32)
Earlier, we (24)
and others (3)
observed that the DSCR1(Adapt78) gene, which is localized in the Downs syndrome candidate region, is overexpressed in brains from Downs syndrome patients. Because DSCR1(Adapt78) causes overexpression of SOD1, it is likely that an elevated level of sod 1 in Downs syndrome brains might be due, at least in part, to DSCR1(Adapt78) overexpression. This hypothesis is also in agreement with the observation that both SOD1 (41)
and DSCR1(Adapt78) (23
, 24)
are highly expressed in the same type of brain cellsneurons. This fact also suggests that neurons might be the most vulnerable cells in Downs syndrome, in which elevated levels of sod 1, due to the gene triplication, might be additionally magnified due to elevated levels of calcipressin 1. In fact, neurological pathologies are the most common manifestations in Downs syndrome, and it seems that oxidative stress and neuronal damage occur already in utero (39)
.
We have recently demonstrated that DSCR1(Adapt78) is also overexpressed in Alzheimers disease (24)
. Downs syndrome subjects commonly develop Alzheimers disease in their later years of life (42)
and these two diseases might have common pathways. It is possible that DSCR1(Adapt78) overexpression also causes elevated levels of sod 1 and consequently damage in Alzheimers disease. This hypothesis, however, remains to be tested.
The mechanism by which DSCR1(Adapt78) may regulate SOD1 expression is unknown; however, there are indications that the DSCR1(Adapt78) protein, calcipressin 1, may also be a transcriptional factor. So far, calcipressin 1 has been demonstrated to bind to, and down-regulate the activity of calcineurin (3
, 4)
. However, binding and regulation of calcineurin might be not the only function or even the major function of the DSCR1(Adapt78) gene product. A stretch of
80 amino acids near the N terminus of DSCR1(Adapt78) protein family members shows similarity with an RNA recognition motif, which is found in many RNA binding proteins and in a few single-stranded DNA binding proteins, (43)
suggesting that DSCR1(Adapt78) might be a transcriptional factor. Additionally, the dynamic of calcipressin 1 localization within the cells also indicates that it might be a transcriptional factor: When produced, it is transported from the cytoplasm, and it accumulates in the nuclear compartment (4)
.
In conclusion, we have demonstrated a new pathway for the regulation of SOD1 expression via DSCR1(Adapt78). DSCR1(Adapt78) is known to be up-regulated during oxidative stress, and in disease states involving chronic inflammation. Our data may help to better understand mechanisms of sod 1 expression and its relationship to human diseases such as Downs syndrome and Alzheimer disease.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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Received for publication June 24, 2003. Accepted for publication September 9, 2003.
| REFERENCES |
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