Transcription Profile of Cells Infected with Human T-Cell Leukemia Virus Type I Compared with Activated Lymphocytes1
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[CANCER RESEARCH 62, 3562–3571, June 15, 2002] Transcription Profile of Cells Infected with Human T-cell Leukemia Virus Type I Compared with Activated Lymphocytes1 Cynthia A. Pise-Masison, Michael Radonovich, Renaud Mahieux, Pramita Chatterjee, Craig Whiteford, Janet Duvall, Claire Guillerm, Antoine Gessain, and John N. Brady2 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 d’Epidemiologie 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 vivo for viral infectivity and replication (12–16). In addition, the p12 protein has been implicated in the MHC class I-mediated immune Human T-cell leukemia virus type I (HTLV-I) is the etiologic agent for response and T-cell signaling (16–18). The viral protein p13 has also adult T-cell leukemia and the neurological disorder tropical spastic para- recently been reported to regulate cellular signaling pathways (19). -paresis/HTLV-I-associated myelopathy. CD4؉ T lymphocytes, the pri mary hosts for HTLV-I, undergo a series of changes that lead to T-cell Finally, the p30 protein is reported to play a role in transcriptional activation, immortalization, and transformation. To gain insight into the regulation with the use of Gal4-p30 fusion constructs (20). genetic differences between activated and HTLV-I-infected lymphocytes, DNA microarray technology has facilitated the development of a we performed Affymetrix GeneChip analysis of activated and HTLV-I- more complete and inclusive analysis of gene expression profiles in infected cells. Using the Hu6800 GeneChip, we identified ϳ763 genes that response to many stimuli for a variety of biological systems. Harhaj et had differentially regulated expression in at least three of five HTLV-I cell al. (21) and de La Fuente et al. (22) used Atlas human cDNA arrays lines. Classification of these genes into functional groups including cellular to analyze gene expression patterns in HTLV-I-infected PBMCs com- receptors, kinases, phosphatases, cytokines, signal proteins, and transcrip- pared with uninfected PBMCs or HTLV-I-transformed C8166 cells tion factors provides insight into genes and pathways that are differen- compared with nonvirally transformed CEM cells, respectively. Ng et tially regulated during HTLV-I transformation. al. (23) have used NIH OncoChip cDNA arrays to analyze gene expression patterns of ϳ2000 human genes in Tax-expressing Jurkat INTRODUCTION T lymphocytes. These studies have looked at small numbers of sam- ples and identified a few candidate genes important for HTLV-I- HTLV-I3 is the etiologic agent of an aggressive and fatal disease induced pathogenesis. We have chosen GeneChip microarrays (Af- termed ATL and of the neurodegenerative disease tropical spastic fymetrix, Inc.), containing oligonucleotide hybridization probes paraparesis/HTLV-I-associated myelopathy (1–4). HTLV-I has also representative of Ͼ7000 genes, to perform a more comprehensive been less closely associated with uveitis, arthritis, infectious derma- examination of the expression profiles for HTLV-I-immortalized and titis, and immunosuppression (5–7). The principle target for HTLV-I -transformed cell lines and compared these with the expression profile infection in the lymphoid system are mature CD4ϩ CD45ROϩ T of normal activated PBLs. The results presented here extend earlier lymphocytes, although other cell types of lymphoid origin have been studies by identifying a significant number of new genes that have infected by HTLV-I in vitro, including CD8ϩ T cells, B cells, and altered expression in HTLV-I-transformed cells compared with acti- macrophages (8–11). vated PBLs. We have identified several new response pathways The mechanism of oncogenic transformation of host T lymphocytes involving G2/M checkpoint control factors, DNA replication and in ATL remains unclear, and to date there is no effective treatment for licensing factors, transcriptional regulators, and kinase/phosphatase this disease. However, as with other cancers, altered gene expression signaling molecules that are deregulated in HTLV-I-infected cells. of networks of genes are linked to ATL initiation and progression. Moreover, we found that by analyzing several HTLV-I cell lines, gene Several studies (8–11) have established that the viral transcriptional expression changes attributable to individual cell types were de- activator protein Tax plays a critical role in cellular transformation. creased. 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 MATERIALS AND METHODS growth and cell death including proto-oncogenes, growth factors and their receptors, CDKs, and CDK inhibitors (8–11). Cell Cultures. We isolated PBMCs from healthy, HTLV-I-negative donors using Ficoll density gradient centrifugation. After removal of macrophages, In more recent studies, a role for the HTLV-I accessory proteins, cells were stimulated for 18 h with PHA (2 g/ml) and then grown in RPMI p12, p30, and p13 in gene activation and cell signaling have been 1640 medium supplemented with 10% fetal bovine serum, 100 units/ml demonstrated. All three proteins have been shown to play a role in penicillin-streptomycin, 2 mM glutamine, and 50 units/ml IL-2. Activated cells were expanded for 2 weeks and then total RNA was isolated. Resting cells Received 11/15/01; accepted 4/15/02. were expanded for 2 weeks, washed twice in culture medium not containing The costs of publication of this article were defrayed in part by the payment of page PHA and IL-2, and total RNA was isolated 3 days later. HTLV-I-immortalized charges. This article must therefore be hereby marked advertisement in accordance with cells, Champ (ATL), Bes (ATL), and ACH.WT, were grown in complete 18 U.S.C. Section 1734 solely to indicate this fact. 1 Supplementary data for this article is available at Cancer Research Online (http:// medium supplemented with 50 units/ml IL-2. HTLV-I-transformed cells, C81 cancerres.aacrjournals.org). and Hut102, were grown in complete medium. 2 To whom requests for reprints should be addressed, at Basic Research Laboratory, RNA Isolation and Probe Preparation. mRNA was isolated from total Virus Tumor Biology Section, National Cancer Institute, 9000 Rockville Pike, Bethesda, RNA by the RNeasy and Oligotex mRNA isolation procedures as outlined by MD 20892. Phone: (301) 496-0986; Fax: (301) 496-4951; E-mail: [email protected]. 3 The abbreviations used are: HTLV-I, human T-cell lymphotropic virus type-I; ATL, the manufacturer (Qiagen). Experimental procedures for GeneChip were per- adult T-cell leukemia; LTR, long terminal repeat; CDK, cyclin-dependent kinase; PBMC, formed according to the Affymetrix GeneChip Expression Analysis Technical peripheral blood mononuclear cell; PBL, peripheral blood lymphocyte; PHA, phytohem- Manual (Affymetrix). Briefly, double-stranded cDNA was synthesized from ␣ ␣ agglutinin; IL, interleukin; RT-PCR, reverse transcription-PCR; IL-2R , IL-2 receptor ; mRNA with the SuperScript Choice system (Life Technologies, Inc.) and a TNF, tumor necrosis factor; CK1⑀, casein kinase 1 ⑀; MLK, mixed-lineage kinase; DUS, dual-specificity phosphatase; INPP1, inositol phosphate-1-phosphatase; CREB, cAMP- T7-(dT) 24 (GENSET) primer. In vitro transcription was performed on the cDNA responsive element binding protein; ATF, activating transcription factor. to produce biotin-labeled cRNA with an Enzo Transcription Kit (Enzo) as de- 3562 Downloaded from cancerres.aacrjournals.org on September 24, 2021. © 2002 American Association for Cancer Research. GENE EXPRESSION PROFILES OF HTLV-I-INFECTED CELLS scribed by the manufacturer. The cRNA was linearly amplified with T7 polym- obtained through PBL culture of an ATL patient, fell into a separate erase, the biotinylated cRNA was cleaned with an RNeasy Mini Kit (Qiagen), cluster distinct from the HTLV-I-transformed cells (C81 and Hut102) fragmented to 50–200 nucleotides, and then hybridized to Affymetrix Hu6800 and the HTLV-I-immortalized cells (Bes and ACH.WT). The shading arrays. The arrays were then processed on the Affymetrix fluidics station and across each sample/bar is an indication of the gene-expression levels scanned on an HP GeneArray scanner. The intensity for each probe set of the array for each of the 7300 genes. For each cell sample, a unique expression was captured with Affymetrix GeneChip Software, according to standard Af- pattern emerges (Fig. 1). A section of the tree has been expanded to fymetrix procedures. To determine the quantitative RNA level, the average dif- ferences representing the perfectly matched minus the mismatched for each gene- show an example of how individual genes performed. As shown, the specific probe set was calculated. The GeneSpring Software (SiliconGenetics) was genes GATA-2, PON2, and PLAGL2 are all overexpressed in the also used to examine the differential gene expression. HTLV-I-infected cells as compared with the PBL samples. This form RT-PCR. Total cellular RNA was isolated with Rnazol B (Tel-Test) as of clustering allows one to identify groups of genes that are expressed described by the manufacturer. RNA (5 g) was converted to cDNA with either similarly or opposite to the control sample. RETROscript (Ambion) as described by the manufacturer. Samples were then From the expression data, we compiled a list of genes deregulated PCR amplified with SuperTaq Plus polymerase (Ambion) to quantitate indi- an average of 2-fold or greater in at least three of five HTLV-I- vidual genes. The PCR primers for Tax were as follows: 5Ј-TGTTTG- infected cell lines, as compared with activated PBLs (Table 1 and Ј Ј Ј GAGACTGTGTACAAGGCG-3 and 5 -CAGGCTGTCAGCGTGACGG-3 . on-line data supplement1). A 2-fold cutoff was chosen based on The primers for IL-2R␣ were as follows: 5Ј-GGTCCCAGGCAGAGAAT- statistical information provided by Affymetrix.