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Molecular Oncology Program, Spanish National Cancer Center (CNIO), Madrid, Spain
| ABSTRACT |
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50% reduction in the amount of Ku86 protein was achieved 72 hours after transfection with Ku86-specific small interference RNAs. This decrease in Ku86 levels resulted in a rapid loss of cell viability characterized by increased apoptosis and decreased mitotic index in the cell population. Importantly, Ku86 knockdown was concomitant with a significant loss of telomeric sequences and with increased chromosomal aberrations, including chromatid-type fusions involving telomeric sequences. These findings demonstrate a role for Ku86 in regulating telomere length and telomere capping in human cells, which, in turn, could impact on cancer and aging. | INTRODUCTION |
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A role for Ku proteins in telomere protection and telomere length regulation has been demonstrated in various eukaryotic systems, including yeast, plants, and mice. However, the outcomes of Ku86 deletion seem to greatly vary in these different organisms, suggesting significant differences in telomere biology. In particular, yeast defective for Ku proteins shows loss of telomeric repeats and deregulation of the G-strand overhang (16) , whereas plants deficient for Ku proteins show massive telomere elongation, as well as elongation of the G-strand overhang (17 , 18) . Mice defective in Ku86 are viable but show premature aging (19, 20, 21) . Mouse embryonic fibroblasts derived from Ku86-deficient mice show increased frequencies of telomere fusions (5 , 7, 8, 9 , 14) and a premature senescence-like arrest in culture (22) , suggesting a role for Ku86 in telomere capping. Interestingly, mice and plants share the outcome that Ku abrogation results in telomerase-mediated telomere elongation, indicating that Ku acts as a negative regulator of telomerase in these organisms (9 , 17 , 18 , 23) . An independent study, however, suggested that abrogation of mouse Ku86 leads to telomere shortening (5) .
In marked contrast to mice, Ku86 deletion in human somatic cells is lethal (24) , suggesting that Ku86 may have differential roles in human and mouse cells, as is also indicated by the fact that human cells have 50-fold more DNA-PKcs activity than mouse cells (25) . To study the role of Ku86 at human telomeres, we have used small interference RNA technology to knock down Ku86 levels in HeLa cells. A 50% reduction in Ku86 protein was achieved 72 hours after transfection with Ku86-specific small interference RNAs. This decrease in Ku86 levels resulted in a rapid loss of cell viability characterized by an increased apoptosis and a decreased proliferation index. Similar results were obtained when using the same small interference RNA duplexes on SAOS and U2OS cells or when targeting additional Ku86 sequences using short hairpin RNA vectors. Importantly, Ku86 knocked-down cells showed a marked loss of telomeric sequences and increased chromatid-type fusions involving telomeres produced by leading-strand synthesis. These findings demonstrate an important role for Ku86 at human telomeres and reveal differences in telomere biology between mouse and human cells.
| MATERIALS AND METHODS |
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Transient Transfection of Small Interference RNAs
The small interfering RNA sequences used for targeted silencing of human Ku86 were selected as described (26)
and supplied by Dharmacon (Dallas, TX) as double-stranded small interference RNA. Two different small interference RNAs were selected against Ku86 sequences: siKu861 targeted 195 bases downstream the start codon (AAT CCC CTT TCT GGT GGG GAT) and siKu862 targeted 465 bases downstream the start codon (AAA TGT GAC ATC TCC CTG CAA). As a control duplex, we used the Scramble Sequence small interference RNA duplex II (siScramble-2), which was designed and provided by Dharmacon. BLAST-search1
and search at the ensembl-database2
ruled out homology of the selected Ku86-specific small interference RNA sequences with other gene sequences.
HeLa, SAOS, and U2OS transfections were performed as described previously (ref. 27 ; and Dharmacon technical bulletin). Briefly, cells at a confluency of 30% to 50% were transfected with the selected small interference RNAs using Oligofectamine reagent (Invitrogen, Carlsbad, CA) following the manufacturers instructions.
Ku86 Knock Down Using Short Hairpin RNA Vectors
The short hairpin RNA constructs used for targeted silencing of human Ku86 were selected following the recommendations of OligoEngine (Seattle, WA) and cloned into a pSUPER-retro vector (pRS; kind donation from Dr. Rene Bernards, NKI, Amsterdam; ref. 28
). Four different short hairpin RNAs were designed from the Ku86 sequence: shKu86 2.7, shKu86 3.4, shKu86 4.2, and shKu86 5.4. The sequences for short hairpin RNAs are: ATG TGA CAT CTC CCT GCA A for shKu86 2.7, GGT GAT AAC CAT GTT TGT A for shKu86 3.4, CCA GGT TCT CAA CAG GCT G for shKu86 4.2, and GAG CAT AGA CTG CAT CCG A for shKu86 5.4.
As controls, cells were transfected with empty pSUPER-retro and pSUPER-retro expressing a short hairpin RNA specific for green fluorescent protein (pRSGFP). Transfections were performed with the FuGENE (Roche, Basel, Switzerland) transfection reagent following the manufacturers instructions. After 48 hours, transfected cells were selected using 2 µg/mL puromycin. Seventy-two hours after transfection cells were recovered for the different experiments.
Western Blot Assays
Whole-cell extracts and nuclear extracts were obtained at the indicated times after transfection as described (29)
. Protein concentration was determined by Bio-Rad DC Protein Assay (Bio-Rad, Munich, Germany). Two to 20 µg of protein extracts were separated on SDS-8% polyacrylamide electrophoresis gel and transferred to nitrocellulose membranes (Bio-Rad). The antibodies used were an anti-Ku86 monoclonal antibody (Kamiya biomedical company, Seattle, WA), an anti-Ku70 monoclonal antibody (Kamiya biomedical company), an anti-TRF2 polyclonal antibody (SF08, kindly provided by Eric Gilson, Lyon, France), an anti-ß-actin monoclonal antibody (Sigma, St. Louis, MO), and an anti- poly(ADP-ribose) polymerase monoclonal antibody (Serotec, France). Antibody binding was detected after incubation with goat antirabbit or antimouse horseradish peroxidase-coupled antibody by using enhanced chemiluminescence. The results were scanned and intensity bands were quantified using NIH image 1.62 software.
Scoring of Chromosomal Abnormalities
Quantitative Fluorescence In situ Hybridization.
The indicated numbers of metaphases from each cell culture (
200) were scored for chromosomal aberrations by superimposing the telomere image on the 4', 6-diamidino-2-phenylindole chromosome image in the TFL-telo software (gift from Dr. Peter Lansdorp, The Terry Fox Laboratory, Vancouver, British Columbia, Canada).
Chromosome Orientation-Fluorescence In situ Hybridization.
Chromosome orientation-fluorescence in situ hybridization (CO-FISH) was performed as described previously (15)
. Metaphase spreads were photographed on a Leitz Leica DMRB fluorescence microscope.
Telomere Length Analysis
Quantitative Fluorescence In situ Hybridization.
Metaphase and interphase nuclei were prepared for quantitative FISH and hybridized as described (9)
. To correct for lamp intensity and alignment, images from fluorospheres (fluorescent beads; Molecular Probes) were analyzed using the TFL-Telo software (gift from Dr. Peter Lansdorp). Images were captured using Leica quantitative FISH software at 1,500 millisecond integration time in a linear acquisition mode to prevent oversaturation of fluorescence intensity and recorded using a COHU CCD camera on a Leica Leitz DMRB fluorescence microscope. Under this capturing conditions, the fluorescence of individual telomeres as short as 500 bp can be detected and quantified. The TFL-Telo software was used to quantify the fluorescence intensity of telomeres from at least 10 metaphases of each data point. The images of metaphases were captured on the same day, in parallel, and scored blindly.
To convert arbitrary units of fluorescence into kilobases, telomere fluorescence values were extrapolated from the telomere fluorescence of LY-R (R cells) and LY-S (S cells) lymphoma cell lines of known lengths of 80 and 10 kb, respectively (30) . We established a linear correlation (r2 = 0.999) between the fluorescence intensity of the R and S telomeres with a slope of 38.6. The calibration-corrected telomere fluorescence intensity was calculated as described (9) .
G-Strand Overhang Assay.
Cells were included in agarose plugs following instructions provided by the manufacturer (Bio-Rad). After overnight digestion in LDS buffer [1% LDS, 100 mmol/L EDTA (pH 8.0), and 10 mmol/L Tris (pH 8.0)], the plugs were digested with 0 or 100 units of mung bean nuclease for 15 minutes. Then the plugs were digested with MboI overnight and run on pulse field electrophoresis gels as described (31)
. The sequential in-gel hybridizations in native and denaturing conditions were carried out as described before (9)
. Quantification of the G-strand overhang radioactive signals was carried out using a STORM 860 Phosphoimager (Molecular Dynamics, Amersham Biosciences, United Kingdom) using the software provided by the manufacturer. These values were corrected by the telomere signal in denaturing gel conditions.
Telomerase Assay.
S-100 extracts were prepared from mock and siKu862 transfected cells, and a modified version of the telomeric repeat amplification protocol assay was used to measure telomerase activity (31)
. An internal control for PCR efficiency was included (TRAPeze kit Oncor).
Determination of In vivo Apoptosis by Annexin V Labeling.
At the selected time points after transfection with mock, siScramble-2, or siKu862, cells were harvested by trypsinization, and 100,000 cells were used for labeling. Cells were washed with PBS and resuspended in 100 µL of binding buffer (AnnexinV-FITC kit, Immunotech, Marseille, France). After addition of 5 µL of FITC-conjugated Annexin V and 10 µL of propidium iodine, cells were incubated on ice for 10 minutes in the dark. After the addition of 400 µL of binding buffer, samples were analyzed by flow-cytometry (BD FACSCalibur, BD Biosciences, San Jose, CA).
Statistical Analysis
Students t Test.
A Student t test with "two-tails," "two-samples of unequal variance" (or Welchs correction), was used to calculate the statistical significance of the observed differences. GraphPad Prism v.3.0a and Microsoft Excel v.2001 were used for the calculations.
For Students t test the differences are considered significant for P < 0.05, very significant for P < 0.01, highly significant for P < 0.001, and extremely significant for P < 0.0001.
| RESULTS AND DISCUSSION |
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80% of Ku86 protein levels in siScramble-2 transfected cells (Fig. 1A)
53.2 ± 2.1% and 46.1 ± 2.9% of those present in mock-transfected cells and siScramble-2-transfected cells, respectively (Figs. 1, AC)
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SiKu862 duplexes were also used to knock down Ku86 protein levels in two additional human tumor cell lines, SAOS and U2OS (Materials and Methods). Ku86 and Ku70 protein levels were significantly decreased in SAOS and U2OS cell lines transfected with the siKu862 duplexes compared with the corresponding controls transfected with the siScramble-2 duplex (Fig. 1D)
.
To confirm the results obtained with small interference RNA duplexes, additional Ku86 sequences were targeted using four independent short hairpin RNA vectors: shKu86 2.7, shKu86 3.4, shKu86 4.2, and shKu86 5.4 (Materials and Methods; Fig. 2
). All of the shKu86 vectors were able to reduce Ku86 protein levels in HeLa cells 72 hours after transfection (Fig. 2A)
. The shKu86 5.4 construct was selected for additional analysis, because it showed the highest decrease of Ku86 protein levels. In particular, 72 hours after transfection with shKu86 5.4, Ku86 and Ku70 protein levels were 59.0 ± 7.3% and 65.0 ± 7.4%, respectively, of those present in cells transfected with a control short hairpin RNA vector with sequences against green fluorescent protein (pRSGFP, Fig. 2B
).
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A similar loss of viability, as determined by a decreased mitotic index, was observed when additional Ku86 sequences were targeted in HeLa cells using four independent short hairpin RNA vectors: shKu86 2.7, shKu86 3.4, shKu86 4.2, and shKu86 5.4 (Fig. 3E)
.
In summary, knocking down Ku86 protein levels to
50% of the normal levels with the siKu862 duplex leads to a decrease in cell viability, which is concomitant with increased cell death and decreased cell proliferation. This loss of cell viability is not apparent when Ku86 levels are
80% (siKu861 duplex in Fig. 1A
) suggesting the existence of a threshold value for Ku86 protein levels beyond which cells start losing their viability. Altogether, these results indicate that Ku86 is required for the viability of human cells, in agreement with previous reports using a human Ku86 knockout cell line (24)
. The important role of Ku86 in human cells is in contrast with the fact that Ku86-deficient mice are viable (20)
, thus suggesting differences in the role of Ku86 in humans and mice (see below).
Knocking Down Ku86 Protein Levels in Human Cells Results in Telomere Shortening.
To study the impact of knocking down human Ku86 protein levels on telomere length, we performed quantitative FISH with a PNA-telomere probe on metaphases prepared from cells transfected with either siScramble-2 or siKu862 duplexes at 72 hours after transfection (Fig. 4A
; Materials and Methods). A clear decrease in telomere length was observed in metaphases prepared from siKu862transfected cells compared with cells transfected with the siScramble-2 duplex at 72 hours after transfection (Fig. 4A)
. The decrease in telomere length was highly significant (Students t test P < 0.0001) after comparing >2,240 telomere values for each condition. The telomere shortening observed in siKu862 transfected cells was concomitant with an increase in signal-free ends (chromosome ends with no detectable TTAGGG signal as indicated by quantitative FISH). In particular, siKu862transfected cells showed a total of 10.7% of signal-free ends compared with 4.3% in the case of siScramble-2transfected cells (Fig. 4A)
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These results were confirmed when additional Ku86 sequences were targeted using short hairpin RNA vectors. In particular, HeLa cells transfected with shKu86 5.4, which we have shown previously to have 59 ± 7.3% and 65 ± 7.5% of Ku86 and Ku70 protein levels, respectively, compared with pRSGFP-transfected cells at 72 hours after transfection, also showed a highly significant shortening of telomeres as shown in Fig. 4C
(Students t test P < 0.0001).
In summary, these results show that a decrease in the Ku86 protein levels leads to a significant and rapid telomere shortening in human cells, thus suggesting that Ku86 is very important for telomere length maintenance in human cells. This finding is in contrast with Ku86 deletion in mice or plants, which leads to telomerase-mediated telomere elongation (17 , 23) . These differential effects of Ku86 abrogation on telomere length in human and mouse cells suggest important differences in telomere biology between these two species and, in particular, on the roles of Ku86 at the telomere.
Next, we used in-gel hybridization in native conditions to examine the integrity of the telomeric G-strand overhang in Ku86 knocked-down cells (Materials and Methods). However, no significant difference in the intensity of the G-strandspecific signals was detected between siKu862transfected cells and cells transfected with the siScramble-2 duplex (data not shown). Interestingly, the G-strand overhang has been shown to be elongated in Ku-deficient Saccharomyces cerevisiae mutants, as well as in Ku86-deficient plants (18 , 34) , but to retain its normal length in Ku86-deficient mice (5 , 9 , 23) . The differential impact of Ku86 deletion on the G-strand overhang integrity, again suggests differences in telomere biology among these various organismal systems, and, in particular, on the role of Ku86 at telomeres.
Normal Levels of In vitro Telomeric Repeat Amplification Protocol Telomerase Activity in Human Cells with Knocked Down Ku86 Protein Levels.
It has been shown recently that human Ku70/Ku86 complex interacts with the catalytic component of telomerase, hTert, thus suggesting that Ku proteins may also regulate telomerase activity in human cells (35)
. To investigate whether the telomere shortening shown by human cells knocked down for Ku86 was the result of down-regulation of telomerase activity, we measured telomerase activity levels using the telomeric repeat amplification protocol assay in mock-transfected and in siKu862transfected cells (Materials and Methods). However, telomerase activity was similar in mock-transfected cells and in cells transfected with the siKu862 duplex (data not shown), indicating that knockdown of Ku86 protein in human cells does not alter the in vitro activity of the telomerase complex. This does not exclude, however, that human Ku86 could regulate the action of telomerase at telomeres, as it has been shown before for mouse and plant Ku86 proteins (17
, 23)
. In this regard, the fact that cells knocked down for Ku86 have shorter telomeres than the noninterfered controls may suggest that Ku86 has a role in the recruitment of telomerase to human telomeres or in the protection of telomeres from exonuclease activities.
Cells Knocked Down for Ku86 Show Increased Chromatid-type Fusions With Telomere Signals at the Fusion Point and Preferentially Involving Telomeres Produced by Leading-strand Synthesis.
To investigate the putative role of human Ku86 in telomere capping, we studied chromosomal aberrations spontaneously arising in siKu862transfected cells, as well as in mock-transfected cells and cells transfected with the control siScramble-2 duplex. For quantification of chromosomal aberrations we used two independent techniques, telomere quantitative FISH and chromosome orientation FISH (Materials and Methods). First, we performed telomere quantitative FISH on >200 metaphases from each siKu862 and siScramble-2transfected cell, as well as from the corresponding mock-transfected cells, at 72 hours after transfection (Materials and Methods; Table 1
). siKu862transfected cells showed a 2-fold increase in interchromosomic chromatid-type fusions compared with the mock-transfected cells and the cells transfected with the siScramble-2 duplex, 0.02 and 0.01 fusions per metaphase, respectively (Table 1
; Fig. 5
, for example). Of notice, these chromatid-type fusions always showed telomere signals at the fusion point as determined by quantitative FISH (indicated with an arrow in Fig. 5
). It is unlikely that these fusions resulted from an intact chromatid fused to one with critically short telomeres, because properly capped/normal-length telomeres are protected from DNA repair events. Therefore, the existence of end-to-end chromatid fusions with telomeres at the fusion point suggests that they were produced by telomere uncapping rather than by critical telomere shortening. These results are in agreement with the fact that Ku86-interfered cells show normal levels of telomerase activity (see above), as well as with previous findings showing that Ku86-deficient mice show increased end-to-end fusions with long telomeres at the fusion point (9
, 22
, 23)
. Also in agreement with this notion, siKu862transfected cells did not show significantly increased frequencies of dicentric chromosomes lacking telomere signals at the fusion point compared with the mock-transfected cells (Table 1
; Fig. 5
, for example).
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In summary, these results show an
2-fold increase in chromatid-type fusions in the Ku86 knocked-down cells compared with the controls, thus indicating a role for human Ku86 in telomere capping and, in particular, in the capping of telomeres produced by leading-strand synthesis.
Concluding Remarks and Significance.
The results presented here suggest a role for Ku86 in telomere length maintenance and telomere capping in human somatic cells. In particular, Ku86 knockdown by using siKu86 duplexes results in significant telomere shortening and increased chromatid-type fusions involving telomeres with detectable TTAGGG signals. It is possible that part of these effects could be also mediated by the expected down-regulation of the Karp1 transcript, which encodes for a longer isoform of Ku86 in human cells (37)
. The fact that most of the chromatid-type fusions present in human cells knocked-down for Ku86 involve telomeres produced by leading-strand synthesis suggests a role for human Ku86 in the processing of telomeres produced by leading-strand synthesis, similar to that proposed before for DNA-PKcs and TRF2 (15)
. In addition, Ku86 knockdown results in a fast loss of telomeric sequences. This is in marked contrast to Ku86 deletion in mice or plants, which resulted in telomerase-dependent telomere elongation, pointing to significant differences in telomere biology between different organisms.
The roles of human Ku86 in telomere length maintenance and telomere capping, predict that hypomorphic mutations of Ku86 could dramatically impact on aging and cancer in humans. Finally, through its simultaneous roles on telomere biology and double-strand break repair, Ku86 depletion may increase the sensitivity to DNA damaging agents in a synergistic manner, because short telomeres have been shown to result in increased sensitivity to ionizing radiations (29) .
Of note, importantly, the results presented here agree with findings reported recently by Myung et al. (38) , using a different experimental approach.
| FOOTNOTES |
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The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
Requests for reprints: Maria Blasco, Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre (CNIO), Madrid 28029, Spain. E-mail: mblasco{at}cnio.es
1 Internet address: http://www.ncbi.nlm.nih.gov/BLAST/. ![]()
2 Internet address: http://www.ensembl.org/Homo_sapiens/blastview. ![]()
Received 4/19/04. Revised 8/ 2/04. Accepted 8/ 4/04.
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