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Virology |
Basic Research Laboratory, Virus Tumor Biology Section, National Cancer Institute, Bethesda, Maryland 20892 [C. A. P-M., M. R., P. C., J. D., C. G., J. N. B.]; Unite dEpidemiologie et Physiopathologie des Virus Oncogenes, Batiment SIDA-Retrovirus, Institut Pasteur, 75724, Cedex 15, Paris, France [R. M., A. G.]; and Advanced Technology Center, National Institutes of Health, Gaithersburg, Maryland [C. W.]
| ABSTRACT |
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763 genes that had differentially regulated expression in at least three of five HTLV-I cell lines. Classification of these genes into functional groups including cellular receptors, kinases, phosphatases, cytokines, signal proteins, and transcription factors provides insight into genes and pathways that are differentially regulated during HTLV-I transformation. | INTRODUCTION |
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The mechanism of oncogenic transformation of host T lymphocytes in ATL remains unclear, and to date there is no effective treatment for this disease. However, as with other cancers, altered gene expression of networks of genes are linked to ATL initiation and progression. Several studies (8, 9, 10, 11) have established that the viral transcriptional activator protein Tax plays a critical role in cellular transformation. Tax not only activates expression of viral genes via the viral LTR, but has also been reported to affect the expression or activity of several cellular genes. Several of these genes encode proteins involved in cell growth and cell death including proto-oncogenes, growth factors and their receptors, CDKs, and CDK inhibitors (8, 9, 10, 11) .
In more recent studies, a role for the HTLV-I accessory proteins, p12, p30, and p13 in gene activation and cell signaling have been demonstrated. All three proteins have been shown to play a role in vivo for viral infectivity and replication (12, 13, 14, 15, 16) . In addition, the p12 protein has been implicated in the MHC class I-mediated immune response and T-cell signaling (16, 17, 18) . The viral protein p13 has also recently been reported to regulate cellular signaling pathways (19) . Finally, the p30 protein is reported to play a role in transcriptional regulation with the use of Gal4-p30 fusion constructs (20) .
DNA microarray technology has facilitated the development of a more complete and inclusive analysis of gene expression profiles in response to many stimuli for a variety of biological systems. Harhaj et al. (21)
and de La Fuente et al. (22)
used Atlas human cDNA arrays to analyze gene expression patterns in HTLV-I-infected PBMCs compared with uninfected PBMCs or HTLV-I-transformed C8166 cells compared with nonvirally transformed CEM cells, respectively. Ng et al. (23)
have used NIH OncoChip cDNA arrays to analyze gene expression patterns of
2000 human genes in Tax-expressing Jurkat T lymphocytes. These studies have looked at small numbers of samples and identified a few candidate genes important for HTLV-I-induced pathogenesis. We have chosen GeneChip microarrays (Affymetrix, Inc.), containing oligonucleotide hybridization probes representative of >7000 genes, to perform a more comprehensive examination of the expression profiles for HTLV-I-immortalized and -transformed cell lines and compared these with the expression profile of normal activated PBLs. The results presented here extend earlier studies by identifying a significant number of new genes that have altered expression in HTLV-I-transformed cells compared with activated PBLs. We have identified several new response pathways involving G2/M checkpoint control factors, DNA replication and licensing factors, transcriptional regulators, and kinase/phosphatase signaling molecules that are deregulated in HTLV-I-infected cells. Moreover, we found that by analyzing several HTLV-I cell lines, gene expression changes attributable to individual cell types were decreased.
| MATERIALS AND METHODS |
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RNA Isolation and Probe Preparation.
mRNA was isolated from total RNA by the RNeasy and Oligotex mRNA isolation procedures as outlined by the manufacturer (Qiagen). Experimental procedures for GeneChip were performed according to the Affymetrix GeneChip Expression Analysis Technical Manual (Affymetrix). Briefly, double-stranded cDNA was synthesized from mRNA with the SuperScript Choice system (Life Technologies, Inc.) and a T7-(dT) 24 (GENSET) primer. In vitro transcription was performed on the cDNA to produce biotin-labeled cRNA with an Enzo Transcription Kit (Enzo) as described by the manufacturer. The cRNA was linearly amplified with T7 polymerase, the biotinylated cRNA was cleaned with an RNeasy Mini Kit (Qiagen), fragmented to 50200 nucleotides, and then hybridized to Affymetrix Hu6800 arrays. The arrays were then processed on the Affymetrix fluidics station and scanned on an HP GeneArray scanner. The intensity for each probe set of the array was captured with Affymetrix GeneChip Software, according to standard Affymetrix procedures. To determine the quantitative RNA level, the average differences representing the perfectly matched minus the mismatched for each gene-specific probe set was calculated. The GeneSpring Software (SiliconGenetics) was also used to examine the differential gene expression.
RT-PCR.
Total cellular RNA was isolated with Rnazol B (Tel-Test) as described by the manufacturer. RNA (5 µg) was converted to cDNA with RETROscript (Ambion) as described by the manufacturer. Samples were then PCR amplified with SuperTaq Plus polymerase (Ambion) to quantitate individual genes. The PCR primers for Tax were as follows: 5'-TGTTTGGAGACTGTGTACAAGGCG-3' and 5'-CAGGCTGTCAGCGTGACGG-3'. The primers for IL-2R
were as follows: 5'-GGTCCCAGGCAGAGAATCATA-3' and 5'-AGAGGGAGAAGGGATGGAGGT-3'. PCR products were separated by agarose gel electrophoresis and quantitated with Fluorchem (Imgen Technologies).
Transfections.
Jurkat T cells were transiently transfected by electroporation with 4 µg of the Cdc25C promoter construct (C290-, C75-, CC51-, and C75M1-Luc) in the absence or presence of Tax (8 µg) as described previously (24)
. Luciferase activity was measured on a Berthold Luminometer and normalized to protein concentration.
| RESULTS |
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Expression Profiling of Normal and HTLV-I mRNA.
Using GeneSpring Software, we performed a "cluster" or "tree" analysis of the cell gene-expression profiles. A hierarchical clustering (Fig. 1)
, which allowed visualization of a set of samples or genes by organizing them into a mock-phylogenetic tree, was performed for individual genes (across the top) and for each sample (down the side). In this tree, genes (or samples) having similar gene-expression patterns are clustered together. How far across the tree one goes until a subtree is found containing both genes (samples) is a measure of how closely correlated those genes (samples) are to each other. As expected, the gene-expression profile of the activated PBLs was most closely related to their unactivated counterparts (Fig. 1
, lines A and B) and was distinct from the HTLV-I-infected cells (Fig. 1
, lines CG). It is interesting to note that the overall gene-expression profile of two HTLV-I-transformed cells lines, HUT102 and C81, fell into a closely related gene-expression cluster. This suggests that they are more closely related to each other than they are to the HTLV-I-immortalized cells. The HTLV-I-immortalized cell lines, Bes, obtained from the PBL culture of this ATL patient, and ACH.WT, lymphocytes immortalized with an infectious clone of HTLV-I, fell into a similar cluster. Interestingly, the HTLV-I-immortalized cell line Champ, also obtained through PBL culture of an ATL patient, fell into a separate cluster distinct from the HTLV-I-transformed cells (C81 and Hut102) and the HTLV-I-immortalized cells (Bes and ACH.WT). The shading across each sample/bar is an indication of the gene-expression levels for each of the 7300 genes. For each cell sample, a unique expression pattern emerges (Fig. 1)
. A section of the tree has been expanded to show an example of how individual genes performed. As shown, the genes GATA-2, PON2, and PLAGL2 are all overexpressed in the HTLV-I-infected cells as compared with the PBL samples. This form of clustering allows one to identify groups of genes that are expressed either similarly or opposite to the control sample.
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. IL-2R
plays a pivotal role in the ability of HTLV-I-transformed cells to proliferate (26, 27, 28, 29)
. Tax has been demonstrated to activate expression of IL-2R
through activation of the nuclear factor
B pathway (29)
. Not unexpectedly therefore, we found that IL-2R
expression was elevated in each of the HTLV-I-infected cells (Table 1)
expression was increased 738-fold in the HTLV-I samples as compared with the activated PBLs (Table 1)
mRNA in the HTLV-I-transformed cells was confirmed by quantitative PCR (Fig. 2, B and C)
mRNA expression.
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was elevated 510-fold in the HTLV-I-infected cell samples. The level of IL-15R
expression was elevated in four of the various HTLV-I-infected cell samples (Table 1)
expression in the C81 HTLV-I-transformed T-cell line was as low as was seen in the activated lymphocyte cells. Thus, the level of IL-15R
expression in different HTLV-I-infected cells may vary significantly. These results are consistent with RNA and protein levels reported previously (30)
. Of the microarray reports, ours is the first to demonstrate differential IL-15R
expression. To note, the IL-2Rß chain common to both IL-15R
and IL-2R
signaling is also increased in the HTLV-I-infected cells except in the C81 sample (Table 1)
Overexpression of Cellular Cytokines or Signal Molecules.
In agreement with the proposed IL-15 paracrine/autocrine loop (30
, 31)
, we observed an increase in the level of IL-15 mRNA in four of five HTLV-I-transformed cells. These results are consistent with the work of Azimi et al. (31
, 32)
who demonstrated that the IL-15 promoter is transactivated by Tax and the level of IL-15 mRNA is increased 34-fold in HTLV-I-transformed cells lines. C81 cells appear to be an exception because the level of IL-15 mRNA expression is very low in this cell line.
In addition to the overexpression of cytokines including SCYA1, SCYA17, SCYA22, and P40 T-cell growth factor, there were also several signal pathway gene products that had increased expression (Table 1)
. We have previously shown that Tax activates expression of parathyroid hormone-releasing protein (PTHrP; see Ref. 33
). In our current analysis, we see a 25-fold increase in PTHrP gene expression (Table 1)
. Our microarray analysis shows that TNF
(GenBank accession no. M16441) expression is elevated in C81, HUT102, and ACH-WT lymphocytes, which are immortalized with an infectious clone of HTLV-I. In contrast, very low levels of TNF
expression were observed in the Bes and Champ RNA samples.
We also observed that the expression level of gp34 was elevated in the HTLV-I-infected cells. This type II membrane protein belongs to the TNF superfamily (TNFSF4) and has been shown to stimulate T-cell proliferation and cytokine production. At slightly lower levels, we observed the elevated expression of TNFSF7 (CD27L), which also plays a role in T-cell activation. We saw an increase in the cell surface molecules CD58 and CD59 (Table 1)
. Many cell-surface signaling molecules were also decreased in expression in the HTLV-I-infected cells as compared with activated PBLs. These include integrin molecules (ITGAM, ITGAE, and CD11A), the adhesion molecule PECAM1, CD47, CDW52, CD37, CD27, CD7, CD20, CD16, and CD72 (Table 1)
; all of which play a role in lymphocyte signaling.
Overexpression of Kinases/Phosphatases in HTLV-I-infected Cells.
Phosphorylation has been shown to play a key role in regulating protein activity and cellular responses. Several kinases were overexpressed in the HTLV-I-transformed cells including mitogen-activated protein kinase family members PRKM7 and mitogen-activated protein kinase 3 (MARK3); tyrosine kinase Lyn; cell cycle regulatory kinases CDK4, CDK7, and CDK2; and CK1
. The overexpression of CK1
is of interest because we have recently demonstrated that the amino terminus of p53 is hyperphosphorylated at serine 15 and one other amino acid within amino acids 119 (34
, 35) . Sakaguchi et al. (36)
and Dumaz et al. (37)
have shown that threonine 18 can be phosphorylated by CK1
. Interestingly, phosphorylation of threonine 18 is dependent on prior phosphorylation of serine 15 (37)
. The overexpression of Lyn is consistent with previous reports that Tax transactivates the promoter of this src family gene (38)
.
Recently, Ng et al. (23)
reported increased levels of the MLK3 using cDNA arrays to study Tax-regulated genes in transformed Jurkat T lymphocytes. The studies by de La Fuente et al. (22)
comparing a Tax/HTLV-I-expressing cell line (C81) with a transformed T-cell line (CEM), also noted an increase in MLK3. In contrast, our results, like those of Harhaj et al. (21)
using Atlas (Clontech) filter arrays and Ruckes et al. (25)
using subtractive hybridization, do not show differential expression of MLK3 in HTLV-I-infected cells compared with activated donor PBLs. The levels of MLK3 expression we observed are highlighted in Table 1
. One explanation for the difference is the choice of control cells. The first studies use transformed cells, whereas our studies and those of Harhaj et al. (21)
and Ruckes et al. (25)
compared the HTLV-I-infected cells with activated PBLs. Perhaps nonviral transformed T-cells have a down-regulation of MLK3 and thus the Tax-expressing cells artificially appear to have an increase in MLK3.
Our studies are the first to show that the dual specific phosphatases DUSP2, DUSP4, and DUSP5 are increased
10-fold in the HTLV-I-infected cells as compared with the activated PBLs. These phosphatases have been implicated in the mitogenic signaling pathways involving erk1 and erk2 (39, 40, 41)
and may play an important role in regulating signaling in the HTLV-I-infected cells.
Likewise, INPP1 is increased
10-fold in the HTLV-I-infected cells over activated PBLs. Inositol signaling is an important component of cellular processes including proliferation, differentiation, and apoptosis (42, 43, 44)
. INPP1 acts on both Ins(1
,4)
P2 and Ins(1
,3
,4)
P4, which are key intermediary metabolites in several pathways such as DNA replication and cell cycle progression (42, 43, 44)
. INPP1 overexpression has recently been correlated with human colorectal cancer (45)
.
Overexpression of Transcription Factors.
The HTLV-I Tax protein functions as a transcriptional transactivator of the viral LTR and several cellular promoters. Transcriptional activation by Tax is attributable, in part, to protein-to-protein interactions leading to enhanced DNA binding or transcriptional activity or increased nuclear accumulation of active transcription factors, causing activation of CREB, nuclear factor
B, and SRF. Tax has also been shown to stabilize the indirect binding of coactivator proteins such as CBP to the DNA, leading to an increase in transcription initiation and reinitiation. Our microarray data revealed the increased expression of
32 transcription regulators in the HTLV-I cells. Not all of these genes are likely to be directly activated by Tax, but may represent "secondary" effects of HTLV-I infection because of changes in cell metabolism and cell proliferation.
In recent reports, Harhaj et al. (21)
and Ruckes et al. (25)
analyzed the regulation of transcription factors in HTLV-I positive cells. Transcription factors of the Jun family including junB, Jun, and JUND, B94, Ets2, CDK7 (TFIIH), GTF2A1, Rel, and GATA-2 were overexpressed in the range of 314-fold. The results of our study are consistent with these reports. All of these transcription factors, with the exception of TAFII31 and YB-1, were found to be up-regulated in the HTLV-I cells (Table 1)
. Also included in our transcription factor group were several members of the CREB transcription factor group including ATF3, ATF6, and cAMP-responsive element modulator (CREM). As stated above, CREB/ATF plays an important role in HTLV-I-LTR transcription and thus viral expression and replication.
Consistent with the work of Sharma et al. (46)
, the transcriptional activator IRF4 which binds to the IFN-stimulated response element in the immunoglobulin
light chain enhancer and plays a role in ISRE-targeted signal transduction mechanisms specific to lymphoid cells, is up-regulated up to 17-fold. Interestingly, IRF5 is also increased 3-fold in HTLV-I-transformed cells, whereas the family members IRF1 and IRF3 are decreased compared with PBLs (Table 1)
. This suggests that HTLV-I-infection may impact only a subset of IRF-regulated genes.
Altered Expression of Members of the Cell Cycle Machinery.
Several members of the cell cycle machinery have altered expression in HTLV-I-infected cells compared with control PBLs. The expression of the Cdc25C tyrosine phosphatase was increased 36-fold (Table 1)
in HTLV-I-transformed cells. This protein functions as a dose-dependent inducer of mitotic control. It is required for progression of the cell cycle, through dephosphorylating Cdc2, activating kinase activity (Fig. 3A)
. The fact that cyclin B and Cdc2 (CDK1) expression are also increased may further indicate a deregulation of G2/M cell cycle control.
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13-fold. Deletion of the upstream promoter region to -75 reduced promoter activity, but did not diminish Tax transactivation (Fig. 3C)
As with many oncogenic factors, deregulated checkpoint control occurs at several stages within the cell cycle. In addition to the increase in G2/M phase regulatory factors, we see an increase in DNA replication licensing and elongation factors including MCM2, HsMCM6, MCM7, Cdc28 kinase 1 and 2, Cdc18L, RFC3, and RFC4 (Table 1)
. As described previously (49, 50, 51, 52)
, we see increased expression of the cell cycle regulators PCNA (27-fold), p21 (25-fold), CDK2 (26-fold), CDK4 (17-fold), and thioredoxin (27-fold). Concomitant with an increase in cdk levels, there is a decrease in the cdk inhibitor p19 (Table 1)
. Together these results suggest that HTLV-I infection impacts several steps in cell cycle regulation.
Expression of Genes That Regulate Apoptosis.
Experiments from numerous laboratories have defined apoptotic pathways and gene products that function to inhibit or accelerate cellular apoptosis. For example, HIAP-1 acts to repress apoptosis in mammalian cells, presumably by inhibiting the activity of caspases involved in cell death (53
, 54)
. Interestingly, HIAP-1 and API1 (55
, 56)
are overexpressed 58-fold in HTLV-I cells. API1 functions in the cell to inhibit the action of specific caspases in the induction of cell death (55
, 56)
. We also found that the apoptosis inhibitor BCL2L1 (Bcl-xL) was overexpressed in HTLV-I cells 47-fold. Similar to the findings of Ruckes et al. (25)
, we also find increased expression of the anti-apoptotic factor I-309. In contrast to the results of Harhaj et al. (21)
, we did not detect the overexpression of other apoptosis inhibitors such as dad1, ddlc1, HSP27, or NKEF in HTLV-I cells compared with activated T-cells.
In addition to the overexpression of genes that inhibit apoptosis, we also found genes that induce apoptosis were down-regulated. For example, the expression of caspase-8, a cysteine protease that functions in the initiation of the apoptotic proteolytic pathway (57 , 58) is repressed in the HTLV-I cells. Depletion or inactivation of caspase-8 in cells is reported to prevent p53 transcription-independent apoptosis and significantly attenuate overall cell death induced by wild-type p53 (59) . Similarly, caspase-4 and -6 expression was down-regulated in the HTLV-I cells.
Repressed Genes.
It has been shown that decreases, as well as increases, in cellular gene expression are important regulatory events. Previous studies (21, 22, 23)
have identified a limited number of repressed genes. In our study, we have identified 420 genes which are decreased 2-fold or greater in the HTLV-I cells are compared with control PBLs (on-line data supplement). Interestingly, several protein kinases were down-regulated in expression as compared with activated PBLs (Table 1)
. Very striking was the down-regulation of several protein kinase C isoforms including, ß1, ß2,
, eta,
, and protein kinase C-like 2 kinase. Protein kinase C is a family of at least 10 structurally related enzymes that have been implicated in a variety of cellular responses. The protein kinase C (PKC) substrate inositol 1,4,5-triphosphate 3-kinase was also down-regulated, further suggesting that control of the pathway used in normal T-cell activation has been repressed in HTLV-I-infected cells.
| DISCUSSION |
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7300 genes in activated and HTLV-I-infected lymphocytes. Several new genes that have deregulated expression in HTLV-I-transformed cells have been identified including cellular receptors, cytokines, apoptosis inhibitors, kinases, checkpoint regulators, and transcription factors. Because all of the HTLV-I cells used in these studies are stably infected, it is not possible at this time to distinguish which genes are deregulated during the initial immortalization/transformation events and which genes are induced as the result of secondary effects of HTLV-I infection. In addition, a clear distinction between HTLV-I-immortalized versus -transformed cells cannot be made at this point and requires analysis of more HTLV-I-infected samples.
In examining the expression profiles, however, we noted several compelling changes. In particular, several alterations have occurred in the cell cycle/DNA repair pathways. We noted changes in the factors controlling G2/M progression. Specifically, we have identified for the first time that mRNA expression of the Cdc25C tyrosine phosphatase was increased in HTLV-I-transformed cells. This protein phosphatase functions as a dose-dependent inducer of mitotic control (Fig. 3)
. Cdc25C is activated by hyperphosphorylation of the N-terminal domain. Several kinases, including Chk1, phosphorylate Cdc25C at Ser216 (60)
. Ser216 is phosphorylated throughout interphase, but not in mitosis. Ser216-phosphorylated Cdc25C is recognized and bound by 14-3-3, which may sequester Cdc25C in the cytoplasm, preventing it from interacting with Cdc2. At the appropriate time in the cell cycle, hypo- or unphosphorylated Cdc25C dephosphorylates Cdc2, activating kinase activity. The fact that cyclin B and Cdc2 (CDK1) expression are also increased may further indicate a deregulation of G2/M cell cycle control. It will be of interest to examine the phosphorylation state of Cdc25C and Cdc2 in the HTLV-I-transformed cells.
As noted previously, several changes in the cytokine/cytokine receptor signal cascades are altered in HTLV-I-infected cells (for reviews see Refs. 9, 10, 11
). We have extended these studies and have shown the expression profiles of several cytokines and their receptors including IL-15, IL-15R
, IL-6, IL-6R, IL-7, and IL-7R, as well as T-cell signaling molecules. Importantly, kinases and phosphatases, known to play a role in signaling cascades, are also altered in HTLV-I-infected cells. Further investigation is needed to determine which pathways result in cellular immortalization/transformation and which are a result of immortalization/transformation.
The data presented in this study represents the most comprehensive analysis of gene expression patterns in HTLV-I-transformed cells to date. Of the 7300 genes analyzed in this study, the expression of
763 genes was deregulated >2-fold in the HTLV-I-transformed cells. Analysis of the deregulated genes, in terms of known function, allows several important conclusions. First, there is no single regulatory pathway that is solely targeted for activation/inactivation in the stably transformed cell. Rather, a network of interrelated pathways including cell proliferation, T-cell signaling, and immune regulation are deregulated. Second, there appear to be multiple alterations in the cell death/survival pathway that have occurred. Several proteins that increase the rate of apoptosis are down-regulated in the HTLV-I-transformed cell. Moreover, several proteins that inhibit apoptosis were up-regulated. Clearly, the overall pattern is to disrupt the cell cycle regulatory points and favor survival of the cell. Whether the pattern of gene expression is the same in all cells within the transformed cell population or whether what we are seeing is a global pattern of individual gene expression changes within the population await further analysis. It is also clear that the analysis of gene expression in the initial stages of infection and transformation would be of tremendous value in defining key transformation pathways.
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| FOOTNOTES |
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1 Supplementary data for this article is available at Cancer Research Online(http://cancerres.aacrjournals.org). ![]()
2 To whom requests for reprints should be addressed, at Basic Research Laboratory, Virus Tumor Biology Section, National Cancer Institute, 9000 Rockville Pike, Bethesda, MD 20892. Phone: (301) 496-0986; Fax: (301) 496-4951; E-mail: bradyj{at}mail.nih.gov ![]()
3 The abbreviations used are: HTLV-I, human T-cell lymphotropic virus type-I; ATL, adult T-cell leukemia; LTR, long terminal repeat; CDK, cyclin-dependent kinase; PBMC, peripheral blood mononuclear cell; PBL, peripheral blood lymphocyte; PHA, phytohemagglutinin; IL, interleukin; RT-PCR, reverse transcription-PCR; IL-2R
, IL-2 receptor
; TNF, tumor necrosis factor; CK1
, casein kinase 1
; MLK, mixed-lineage kinase; DUS, dual-specificity phosphatase; INPP1, inositol phosphate-1-phosphatase; CREB, cAMP-responsive element binding protein; ATF, activating transcription factor. ![]()
Received 11/15/01. Accepted 4/15/02.
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