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Department of Cancer Biology, Lerner Research Institute [Y. X., Z. W., J. M., S. P., G. C., R. H. S.], and Urological Institute [E. A. K.], Cleveland Clinic Foundation, Cleveland, Ohio 44195; Translational Genomics Research Institute, Phoenix, Arizona 85004 [J. D. C., J. M. T.]; and Brady Urological Institute, Johns Hopkins Medical Institutions, Baltimore, Maryland 21287 [W. B. I.]
| ABSTRACT |
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| INTRODUCTION |
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2; Ref. 3
]. The only well-established function of 25A is the activation of RNase L. Although 25A compounds generally vary in length from two to five or more adenylyl residues, the principal products observed in IFN-treated and virus-infected cells are the inactive diadenylate, ppp5'A2'p5'A, and the active tri- and tetra-adenylate species [ppp5'A(2'p5'A)2 and ppp5'A(2'p5'A)3; Ref. 4
]. These oligonucleotides are unusual in nature because even though nonenzymatic synthesis of nucleic acids favors 2',5' linkages, the vast majority of internucleotide linkages formed enzymatically are 3',5', including mature species of RNA and DNA (5)
. Exceptions are 2' to 5' junctions in lariat RNA splicing intermediates, a 2',5'-phosphodiester linkage in DNA-RNA complexes known as multicopy single-stranded DNAs, and 25A (3
, 6 , 7)
. Because 25A is the only known nucleic acid with two or more consecutive 2',5' linkages it occupies a unique place in nucleic acid biology by providing an unambiguous signal to RNase L, resulting in cleavage of single-stranded RNA. A large number of 25A analogues has been described previously with modifications of the bases, riboses, internucleotide linkages, 5'-phosphoryl groups, and 2',3' termini (reviewed in Ref. 5
). Nevertheless, development of biostable and potent small molecule activators of RNase L that are convenient to synthesize and purify have remained elusive. Natural 25A molecules are very efficiently degraded by a combination of 5'-phosphatase and 2',5'-phosphodiesterase activities present in cells and in serum. Therefore, stabilization of the 25A molecule to catabolic enzymes while retaining RNase L activation ability was an important goal in the present study.
RNase L, the target of 25A, is a 741-amino acid protein (human form) with a bipartite domain structure in which the N-terminal half represses the RNase domain in the COOH-terminal region (Fig. 1
; Ref. 8
). The repressor half consists of nine ankyrin repeats. 25A binding to the repressor region of RNase L relieves the inhibition caused by the ankyrin repeats, presumably as a result of inducing a conformational change in the enzyme that unmasks the dimerization and RNase domains (9)
. The seventh and eighth ankyrin repeat contain a duplicated P-loop-like motif (GKT) implicated in mediating binding to 25A (10)
. RNase L also contains several protein kinase-like domains in its COOH-terminal half. The kinase-like and RNase domains of RNase L are homologous to the Ire1 proteins, with both kinase and endoribonuclease activities, that function in the unfolded protein response (9)
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A, resulting in a methionine to isoleucine missense mutation in the translational start codon, thus preventing translation (1)
; 795G
T, converting a glutamic acid within the 25A binding domain of RNase L to a stop codon (E265X; Refs. 1
and 11
); and 471
AAAG, causing a frameshift at codon 157 and a translation stop after seven additional codons (Refs. 12
and 13
; Fig. 1
T (E265X) or 471
AAAG mutation (1
, 12)
. In addition, there exists among prostate cancer cases and controls several missense variants in RNase L (Fig. 1
A) in unselected (including both familial and nonfamilial) prostate cancer cases (15)
. An expanded study was performed on DNA isolated from 423 unselected prostate cancer cases and 454 unaffected sibling controls. A significant association of the R462Q variant with cases was observed (P = 0.011). The odds ratios indicated that carrying one copy of the R462Q variant gene increased the risk of prostate cancer by
1.5-fold, whereas having two variant alleles doubled the risk. Results implicated R462Q in up to 13% of cases, which if confirmed would make it the most prevalent genetic marker for prostate cancer. Therefore, R462Q could be an important risk marker for prostate cancer in the general male population. Here, we have investigated the impact of RNase L activated by novel 25A analogues on apoptosis of the human prostate cancer cell lines PC3, DU145, and LNCaP, derived from metastases of brain, bone, and lymph node, respectively. Results show that 25A analogues have the ability to induce apoptosis of such late-stage prostate cancer cells. In addition, among eight naturally occurring missense variants evaluated, only R462Q significantly decreased RNase L activity. The deficiency in the R462Q variant was correlated to a decrease in enzyme dimerization to the active form and a reduction in the ability to cause apoptosis. Our findings support the association of RNase LR462Q with prostate cancer risk while also highlighting the ability of RNase L activators to induce death of prostate cancer cells derived from late-stage tumors.
| MATERIALS AND METHODS |
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Oligonucleotide Synthesis.
Chemical syntheses of the oligonucleotides were performed on 1-µmol columns (Glen Research) using an ABI model 380B automated DNA synthesizer (Applied Biosystems). After syntheses, the columns were removed from the instrument and the supports were transferred to screw-capped vials (4 ml; Wheaton, Millville, NJ). The supports were treated with 3 ml of ammonium hydroxide/ethanol solution (3:1, v/v) for 2 h at room temperature and then at 55°C for 8 h. The solutions were dried in vacuo on a Savant Speed-Vac. The residues were treated with 1 M tetrabutylammonium fluoride in tetrahydrofuran solution (Aldrich, St. Louis, MO) overnight. Tetrahydrofuran was removed using Speed-Vac. Compounds were dissolved in 1 ml of water and vortex mixed. The crude products were purified by HPLC3
on a polystyrene reverse phase column (PRP-100; Hamiliton Co., Reno, NV). Solvent A was 10 mM tetrabutylammonium dihydrogenphosphate (pH 7.5) in water, and solvent B was 10 mM tetrabutylammonium dihydrogenphosphate (pH 7.5) in acetonitrile:water (8:2, v/v). Elution was with a convex gradient of 580% solvent B in solvent A in 60 min at a flow rate of 1.5 ml/min. Fractions containing the compounds were pooled, dried, and then desalted on Sep-Pak columns (Waters Corp., Milford, MA), using 80% methanol as eluent. The tetrabutylammonium salt was transformed into the sodium salt by ion-exchange using Dowex 50W (sodium form; Bio-Rad, Hercules, CA).
Natural 25A [p3(A2'p)nA, where n = 1 to
3] was prepared enzymatically from ATP using hexahistidine-tagged and -purified recombinant porcine Mr 42,000 25A synthetase (a gift from R. Hartmann, Cleveland Clinic, Cleveland, OH; Ref. 17
). Individual 25A oligomers were purified using reverse-phase HPLC.
Determining the Stability of the 25A Analogues in Human Serum.
The stability of 25A compounds (each at 47.8 µM) was determined by incubation in 700 µl of human serum (Sigma-Aldrich, St. Louis, MO), diluted to 800 µl with water at 37°C. Aliquots (100 µl) were removed at 0, 1, 2, 4, 7, and 24 h, heated to 100°C for 5 min, centrifuged 10 min at 10,000 x g at 24°C, and the supernatant removed for HPLC analysis. 25A compounds and their degradation products were analyzed by HPLC on an Ultrasphere ODS column (4.6 x 250 mm) (Beckman).
Cell Culture and Transfections.
Hey1B (human ovarian carcinoma), DU145, PC3, and LNCaP cells were grown in RPMI 1640 supplemented with streptomycin-penicillin and 10% heat-inactivated fetal bovine serum. L929 (mouse fibroblast) and HeLa M cells (human cervical epithelial cells) were grown in DMEM supplemented with streptomycin-penicillin and 10% heat-inactivated fetal bovine serum. Mouse JM03 cells were isolated from a spontaneous rhabdomyosarcoma from RNase L-/- p53-/- mice.4
Transfection of 25A compounds was performed using Lipofectamine 2000 (Invitrogen) according to the manufacturers protocol. Briefly, cells were plated 1 day before transfection, so that the cells are
7080% confluent at the time of transfection. 25A was diluted into Optima media (Invitrogen) and then mixed with Lipofectamine 2000 for
20 min. The mixture was added to the cells, incubated at 37°C for 35h, then the media was replaced with complete media plus serum.
Site-directed Mutagenesis of RNase L.
The RNase L point mutants were constructed using the QuikChange XL Site-Directed Mutagenesis Kit from Stratagene. Briefly, a full-length coding sequence DNA for human RNase L in pGEX-4T-3 vector (8)
was used as template for mutagenesis. The template plasmid was denatured and annealed with the two synthetic oligonucleotide primers containing the desired mutations. Using the nonstrand-displacing action of Pfu-Turbo DNA polymerase, we extended and incorporated the mutagenic primers, resulting in nicked circular strands. The methylated, nonmutated parental DNA template was digested with DpnI. The circular, nicked double-stranded DNA was transformed into XL10-Gold ultracompetent cells (Statagene). After transformation, the XL10-Gold ultracompetent cells repair the nicks in the mutated plasmid. All mutants were confirmed by DNA sequencing analysis.
Expression and Purification of GST-RNase L Fusion Proteins.
Briefly, the cDNAs for wild-type or mutant forms of RNase L in plasmid pGEX4-T-3 were transformed into Escherichia coli DH5
(8)
. The transformed bacteria were grown at 37°C to A595 = 0.5 before being induced with 0.1 mM isopropyl-1-thio-ß-D-galactpyranoside for 3 h. Harvested cell pellets were washed with PBS and resuspended in PBS-C (8)
. The suspended cells were sonicated on ice, and Triton X-100 was added to a final concentration of 1% (v/v). The supernatants were collected after centrifugation at 16,700 x g for 20 min at 4°C. Purification of fusion proteins were performed as described by the manufacturer of glutathione-Sepharose 4B (Pharmacia).
Activation of Purified Recombinant RNase L.
Substrate for in vitro RNase L assays was C7UUC12 (prepared on an ABI DNA synthesizer and purified as described above), labeled at its 3' terminus with [5'-32P]-pCp (3000 Ci/mmole; DuPont/New England Nuclear) with T4 RNA ligase (Life Technologies, Inc.; Ref. 18
). Briefly, 0.1 µg of purified GST-RNase L (wild type or R462Q) was incubated in the presence or absence of 0.1, 1, 10, and 100 nM 25A analogue on ice for 30 min. Reaction mixtures were incubated further with 80 nM C7UUC12-[32P]pCp for 30 min at 30°C. RNA was analyzed in sequencing gels to measure the extent of RNA degradation. The ratios of degraded RNA substrate to the intact RNA was quantitated in a phosphorimager.
Monitoring RNase L-mediated rRNA Cleavages in Intact Cells.
The cell-based RNase L assay was performed as described previously (1)
. Briefly, cells were transfected with 25A using Lipofectamine 2000 (Invitrogen) at the concentrations indicated in the figure legends. After a 3- to 5-h incubation, media were removed and cells were washed twice in 5 ml of PBS. Total RNA was isolated from transfected cells using the Trizol reagent according to manufacturers protocol and was quantitated by measuring absorbance at 260 nm. RNA (1 µg) was separated on RNA chips and analyzed with an Agilent Bioanalyzer 2100 (Agilent Technologies). The peak areas of 28S and 18S rRNA and their main cleavage products were measured using the Bio Sizing program (version A.02.01 S1232).
Cell Viability Assays.
The viability of cells was determined using the colorimetric CellTiter 96 Aqueous Cell Proliferation Assay, as described (19)
. Briefly, cells were seeded in 96-well culture plate (5 x 103 cells per well) and transfected with various forms of 25A at different concentrations. At 18 h after transfection, 50 µl of CellTiter 96 Aqueous reagent (40% v/v dilution in PBS) were added to each well. Plates were incubated at 37°C for 3 h, and absorbance was measured at 490 nm with a 96-well plate reader (model Spectra Max 340; Molecular Devices, Menlo Park, CA).
Western Blots.
Protein (100 µg) in cell extracts were separated in 10% polyacrylamide/SDS gels for detection of RNase L, PARP, or ß-actin or 12% polyacrylamide/SDS gels for caspase 3. The proteins were transferred to Immobilon-P membrane (Millipore), incubated with monoclonal antibody to human RNase L (20)
, or polyclonal antibody to human cleaved caspase 3 (Chemicon) or polyclonal antibody to PARP (Cell Signaling), or monoclonal antibody to ß-actin (Sigma) for 1 h. Membranes were washed with PBS with 1% Tween 20 and incubated with goat antimouse antibody or goat antirabbit antibody tagged with horseradish peroxidase (Life Technologies, Inc.) for 1 h. Proteins in the blots were detected by enhanced chemiluminesence (Amersham).
Binding of 2',5'-Oligoadenylates to RNase L.
A 32P-labeled and bromine-substituted 25A analogue, p(A2'p)2(br8A2'p)2A3'[32P]pCp (probe), was cross-linked to GST-RNase L (human; 0.4 µg) or to RNase L in crude cell extracts (200 µg) under UV light, as described (21)
. The RNase L fusion proteins or cell extracts were incubated with the probe, 105 cpm (specificity, 3000 Ci/mmol), in 50 µl of buffer on ice for 60 min. Samples were exposed to 308-nm light to induce covalent cross-linking to RNase L on ice for an additional 60 min. Protein separation was by electrophoresis in SDS/10% polyacrylamide gels, followed by autoradiography of the dried gels.
RNase L/RNase L Interaction Assays.
The RNase L dimerization assay was performed as described previously (8)
. Briefly, E. coli cell extracts (100 µg of protein) containing GST-RNase L or GST-RNase LR462Q were incubated with 60 µg of extract containing human recombinant (untagged) RNase L produced in insect cells (22)
in the presence or absence of different concentrations of 25A on ice for 1 h. BSA (250 µg) and 5 µl of 20% (v/v) glutathione sepharose 4B was added, and the mixtures were incubated with shaking at room temperature for 20 min, with gentle vortexing every 5 min, followed by washing three times with PBS-C (8)
. The immobilized proteins were eluted with SDS/gel sample buffer with boiling for 5 min, separated by electrophoresis in SDS/8% polyacrylamide gels, transferred to nitrocellulose membrane, and probed with monoclonal antibody to human RNase L (20)
.
| RESULTS |
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AAAG), causing a frameshift and stop codon (12)
. In addition, the LNCaP cells are heterozygous for R462Q and D541E missense variants. RNase L in PC3 cells is homozygous for the wild-type accession sequence (NM021133), whereas in DU145 cells are heterozygous for a G296V missense variant of RNase L. Effects on cell viability of transfecting 25A compounds were determined by tetrazolium conversion (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxy-phenyl)-2-(4-sulfonyl)-2H-tetrazolium) assays. A PS 25A (compound 4) had a 10-fold enhanced anticellular effect on the DU145 cells compared with a natural phosphodiester (compound 1) (Fig. 2)
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35%, whereas the other variants had slightly less activity (
20%) than the wild-type enzyme. In contrast, the RNase LR462Q variant was reduced in activity by
3-fold compared with wild-type RNase L (Fig. 6B)
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3-fold reduced rate of RNA cleavage compared with wild-type RNase L, consistent with our previous findings (15)
. To investigate the cause of the deficiency, 25A-binding activity was measured by covalent cross-linking of a radioactively labeled, bromine-substituted 25A analogue under UV light (21)
. However, the R462Q and wild-type enzymes had equivalent levels of 25A binding activity (Fig. 8)
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and actinomycin D (Fig. 10
2-fold in cells expressing RNase LR462Q, whereas caspase 3 cleavage was undetectable, despite expression of similar levels of RNase L and RNase LR462Q. These findings suggest that the association of RNase LR462Qwith prostate cancer risk (11
, 15) correlates with deficient enzymatic activity and consequently in a decreased ability to induce apoptosis.
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| DISCUSSION |
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Apoptosis of Prostate Cancer Cell Lines by 25A Activation of RNase L.
Results show that 25A activation of RNase L leads to RNA damage-mediated apoptosis in the metastatic prostate tumor cell lines DU145, PC3, and, to a lesser extent, LNCaP. Whereas PC3 and DU145 cells are homozygous for fully active forms of RNase L, the LNCaP cells have a deletion/frameshift mutation in one RNASEL allele. LNCaP cells express normal levels of RNase L as the result of allelic compensation. Nevertheless, LNCaP cells were less sensitive to 25A treatments than the other two cell lines. For instance, 25A produced 39, 27, and 19% rRNA breakdown in the DU145, PC3, and LNCaP cells, respectively (Fig. 3)
. Three days of 25A treatment reduced cell viability by 98% and 95% in the DU145 and PC3 cells, respectively, whereas about half of the LNCaP cells survived under identical treatments (Fig. 5)
. PARP cleavage in response to 25A was also greater in the DU145 and PC3 cells than in the LNCaP cells (Fig. 4A)
. 25A activation of RNase L has been shown to lead to release of cytochrome c from mitochondria and to caspase 3-dependent apoptosis (19)
. In these studies, caspase 3 cleavage in response to 25A treatment occurred to a greater extent in DU145 cells than in the PC3 and LNCaP cells (Fig. 4B)
. Therefore, PARP cleavage was a better indicator of cell death than caspase 3 cleavage. These results suggest that in the LNCaP cells a truncated RNase L produced from the mutant allele may act as an inhibitor of RNase L or that the LNCaP are less efficient in 25A uptake than the DU145 and PC3 cells. However, transfection of a fluorescein-tagged 25A into the three cell lines did not show a large difference in transfection efficiencies as measured by cytofluorimetry (data not shown). Therefore, it remains possible that the LNCaP cells produce a RNase L-truncated polypeptide that acts as dominant negative.
The R462Q Variant of RNase L Has a Reduced Capacity to Induce Apoptosis in Response to 25A.
Three inactivating mutations and an additional nine missense variants in RNASEL have been observed collectively in prostate cancer cases and/or in controls (Fig. 1)
(1
, 11
, 13, 14, 15, 16)
. All three inactivating mutations (M1I, E265X, and
157) and six missense variants (G59S, I97L, I220V, V247M, G296V, and S322F) map to the N-terminal half of RNase L that binds 25A, whereas the remaining three missense variants (R462Q, Y529C, and D541E) are in the protein kinase-like region. No mutations or variants have been observed in the RNase domain (Fig. 1)
. Among the missense mutants that have been examined in prostate cancer cases (S406F, D541E, I97L, and R462Q), only the R462Q variant has been shown to be associated with prostate cancer risk or aggressiveness (11
, 14
, 15)
. To determine the effect of the various missense mutations on enzyme activity, the wild-type and mutant forms of RNase L were compared after expression in mouse JM03 cells, isolated from a spontaneous rhabdomyosarcoma from RNase L-/- p53-/- double gene knockout mice. The R462Q variant showed the lowest levels of enzyme activity, approximately one-third of wild-type RNase L. The Y529C variant was reduced by
35%, whereas the other variants showed similar activity to the wild-type enzyme. These findings are consistent with genetic evidence implicating, thus far, only R462Q in prostate cancer risk.
A deficiency in RNase LR462Q was investigated further in this study using recombinant purified protein. Enzyme kinetics indicated a 3-fold reduction in catalytic rate compared with wild-type enzyme, consistent with our previous results (15)
. Whereas 25A binding activity was unaffected, the defect was related to a decreased capacity of the enzyme to dimerization into its active form. Previously, we found that another amino acid residue in the protein kinase-like domain of RNase L, K392, was required for dimerization (27)
. Our current results support a role for the protein kinase homology region in enzyme dimerization. The R462Q mutation reduced the ability of RNase L to cause apoptosis in response to activation by 25A as measured by cleavage of PARP and caspase 3 (Fig. 10)
. Therefore, the association of the R462Q mutant with prostate cancer risk correlates with a deficiency in apoptosis. These findings lend additional support to the notion that the tumor suppressor function of RNase L is related to its apoptotic activity.
| ACKNOWLEDGMENTS |
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| FOOTNOTES |
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1 Supported by USPHS Grants CA44059 and CA62220 from the Department of Health and Human Services. ![]()
2 To whom requests for reprints should be addressed, at Department of Cancer Biology, NB40, The Lerner Research Institute, The Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH 44195. Phone: (216) 445-9650; Fax: (216) 445-6269; E-mail: silverr{at}ccf.org ![]()
3 The abbreviations used are: HPLC, high-performance liquid chromatography; PARP, poly(ADP-ribose) polymerase; GST, glutathione S-transferase; PS, phosphorothioate. ![]()
4 J. Murakami and R. H. Silverman, unpublished observations. ![]()
Received 7/15/03. Accepted 9/ 2/03.
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