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EMBRYONIC STEM CELLS: CHARACTERIZATION SERIES |
aLaboratory for Genomic Programming, RIKEN Center for Developmental Biology, Kobe, Japan;
bDepartment of Life Science, Graduate School of Science and Technology, Kobe University, Kobe, Japan;
cLaboratory for Stem Cell Biology, Center for Developmental Biology, Kobe, Japan;
dCellular Biochemistry, Animal Resource Sciences/Veterinary Medical Sciences, The University of Tokyo, Tokyo, Japan;
eTranscriptome Research Center, National Institute of Radiological Sciences, Chiba-shi, Japan;
fGraduate School of Agricultural Science, Tohoku University, Sendai, Japan
Key Words. Nuclear transfer • Cloning • Embryonic stem • Reprogramming
Correspondence: Teruhiko Wakayama, Ph.D., 2-2-3 Minatojima-minamimachi Chuo-ku, Kobe 650-0047, Japan. Telephone: 81-78-306-3049; Fax: 81-78-306-0101; e-mail: teru{at}cdb.riken.jp
Received on October 31, 2005;
accepted for publication on May 3, 2006.
First published online in STEM CELLS EXPRESS May 11, 2006.
| ABSTRACT |
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| INTRODUCTION |
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However, it remains unclear whether these somatically derived NT-ESCs are identical to the ESCs derived from early, normally fertilized embryos. Many NT-ESC lines differentiate into germ cells in chimeric mice [6, 7, 11], the strongest evidence to date that these cells have the same potential as ESCs. By contrast, most, if not all, cloned animals show serious fetal and postnatal abnormalities, perhaps resulting from defects in early genome activation [12], and many exhibit placentomegaly [13, 14]. Although imprinted gene expression patterns appeared normal in apparently "normal" cloned mice [15], they still exhibited epigenetic defects [1618], often including obesity [19] and premature death [20]. DNA microarray analysis revealed that 4%12% of expressed genes in the cloned placentas differed in expression levels from controls [21, 22]. However, those abnormalities seem to indicate epigenetic reprogramming errors, not DNA damage, because they were not transmitted to the next generation [19, 23]. Because NT-ESC lines are established using the same procedures, it is possible that they will also exhibit epigenetic defects.
Interestingly, NT-ESC lines can be established with success rates 10 times higher than reproductive cloning [68, 11, 13, 24]. We have previously reported that the success rate of the procedure depends on the mouse strain: hybrid strains are more tolerant of cloning than inbred strains, such as C57BL/6 and C3H/He, which are in common use in mouse genetic studies but which have never been cloned successfully [25]. However, NT-ESC lines can be established with high rates irrespective of donor mouse strain, tissue type, or sex [11]. Therapeutic cloning is thus at least an order of magnitude more successful than reproductive cloning [8, 26]. Thus, either most NT-ESC lines have been established from NT-embryos with negligible reproductive potential (Fig. 1A) or most NT-embryos die during or after implantation because of abnormal placental development, which does not involve ESCs. If these somatic NT-ESC lines have inherent abnormalities, such as epigenetic defects, there may be potential risks in their clinical use, and the scientific discoveries based on these NT-ESCs might be of limited utility.
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| MATERIALS AND METHODS |
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All animals (obtained from Japan SLC Inc., Shizuoka, Japan, http://www.jslc.co.jp) were maintained in accordance with the animal experiment handbook at the RIKEN Center for Developmental Biology, Kobe, Japan.
NT and Establishment of NT-ESC Lines
Oocytes were collected from 8- to 10-week-old female BDF1 mice. Cultured tail-tip fibroblasts [13], fresh isolated cumulus cells [24], or testicular Sertoli cells [28] were used as nuclear donors [10, 2023]. NT was performed as described [24]. Briefly, a group of oocytes (usually 30) was transferred to a droplet (approximately 10 µl) of HEPES-CZB containing 5 µg/ml cytochalasin B, which had been previously placed under mineral oil in the operation chamber on the microscope stage. After an oocyte was held by an oocyte-holding pipette, its zona pellucida was "drilled" by applying several piezo pulses to the tip of an enucleation pipette [24, 29]. The metaphase II chromosome-spindle complex, distinguished as a translucent spot in the ooplasm, was drawn into the pipette with a small amount of accompanying ooplasm and gently pulled away from the oocyte until a stretched cytoplasmic bridge was pinched off. After the spindles of oocytes in one group were removed (which took approximately 10 minutes), they were transferred into cytochalasin B-free CZB and kept there for up to 2 hours at 37.5°C [24]. The donor cell was drawn in and out of the injection pipette until the cell membrane was broken. In some cases, a few piezo pulses were applied to break the plasma membrane. After a cumulus cell nucleus was drawn deep into the pipette, another cell nucleus was drawn into the same pipette. Within a few minutes, several nuclei were lined up within a single pipette and were injected one by one into an "empty" oocyte at room temperature. After NT, the reconstructed oocytes were activated by 10 mM SrCl2 in Ca2+-free CZB medium in the presence of 5 g/ml cytochalasin B and 1% dimethyl sulfoxide and cultured for 4 days in potassium simplex optimized medium (Specialty Media, Lavallette, NJ, http://www.specialtymedia.com).
When they had developed to the morula or blastocyst stages, embryos were used to establish NT-ESC lines as described [6, 11] with a slight modification: 20% knockout serum replacement and 0.1 mg/ml adrenocorticotropic hormone (American Peptide Company, Sunnyvale, CA, http://www.americanpeptide.com) were added to the ESC medium instead of fetal calf serum [30]. Briefly, morulae/blastocysts were treated with acid Tyrodes solution to remove the zona pellucida and placed in 96 multiwell dishes with mouse embryonic fibroblasts (ICR origin) for more than 10 days. Proliferating outgrowths were dissociated using trypsin digestion and replated on fibroblasts until stable cell lines grew out. We used these NT-ESCs within eight passages for all subsequent experiments and did not perform any clonal selection. The effects of sex or organ of the donor cells on the establishment rate of NT-ES lines has been reported previously [7, 8, 11]. More detailed protocols of mouse NT and NT-ESC establishment were published elsewhere [31, 32].
Sequential Establishment of NT-ESCs
For the sequential establishment of NT-ESCs, the original somatic cell nuclei were collected from 10-week-old BCF1 female cumulus cells. When an NT-ESC line was established from those cloned embryos, it was used as a donor for the NT procedure [6, 33] to establish the next series of NT-ESC lines; this was repeated up to eight times. In all experiments, the original donors were used within five to eight passages. We designated the original NT-ESC lines as S1, the second-series NT-ESC lines as S2, and so on until S9.
Production of Cloned Offspring and Tetraploid Complementation Chimeric Offspring
We used four NT-ESC lines (designated BDmt-2, BDmt-4, B6fc-1, and B6fc-2), which were derived from the nuclei of BDF1 male tail-tip fibroblasts and C57BL/6 cumulus cells, and two male ESC lines derived from BDF1 embryos. They were selected according to the percentage of normal karyotypes, or to coincide with other experiments, and used at between four and eight passages. For cloning, NT from NT-ESCs was as described above. For the production of chimeric offspring, NT-ESCs were introduced into the blastocoels of normal (3.5 days post copulation [dpc]) or tetraploid blastocysts from BALB/c or ICR strain mice using a piezo-actuated microinjection pipette [6]. Tetraploid embryos were produced by the electrofusion of two-cell embryos [34]. Cloned and chimeric embryos were transferred into the uteri of day-2.5 pseudopregnant ICR strain females and examined at 19.5 dpc by Caesarian section.
Immunohistochemistry
We used the appropriate manufacturers staining procedures throughout. Alkaline phosphatase staining was according to the manufacturers protocol (Sigma-Aldrich, St. Louis, http://www.sigmaaldrich.com). Immunohistochemistry was performed using the following antibodies: anti-Oct3/4 (monoclonal 1:100; Santa Cruz Biotechnology, Inc., Santa Cruz, CA, http://www.scbt.com); anti-Nanog (monoclonal 1:200; ReproCELL Inc., Tokyo, http://reprocell.com/en); anti-SSEA-1 and -3, (monoclonal 1:100; Chemicon, Temecula, CA, http://www.chemicon.com); anti-SSEA-4 (monoclonal 1:100; Santa Cruz Biotechnology, Inc.), and anti-platelet-derived growth factor-receptor-
(PDGFR-
) (S1) (both 1:100; provided by S. I. Nishikawa). Alexa Fluor 488-, 350-, or 568-labeled secondary antibodies (Molecular Probes, Eugene, OR, http://probes.invitrogen.com) were used for detection as appropriate.
Flow Cytometric Analysis
NT-ESCs and fertilized ESCs were dispersed in 10 µl of goat serum (Sigma-Aldrich). After a 20-minute incubation on ice, the cells were mixed with staining buffer (phosphate-buffered saline containing 0.2% bovine serum albumin) containing anti-SSEA-1 antibody (0.1 µg/106 cells), anti-SSEA-4 (0.1 µg/106 cells), and PDGFR-
(0.2 µg/106 cells). Subsequently, the cells were washed and resuspended in staining buffer containing Alexa Fluor 488-conjugated anti-mouse IgM (BD Biosciences, Franklin Lakes, NJ, http://www.bdbiosciences.com) or anti-allophycocyanin-conjugated anti-mouse IgG (BD Biosciences). After a 30-minute incubation on ice, the cells were analyzed using a FACSaria Cell Sorter (BD Biosciences).
Karyotype Analysis by Giemsa and Spectral Karyotyping with Fluorescent In Situ Hybridization Painting
Chromosomes from NT-ESCs were stained using Giemsa and spectral karyotyping with fluorescent in situ hybridization (SKY-FISH) chromosome painting techniques (Applied Spectral Imaging Inc., Vista, CA, http://www.spectral-imaging.com) according to the manufacturers protocols. All NT-ESC and ESC lines were used within eight passages. More than 50 metaphase nuclei (for Giemsa staining) or 1520 metaphase nuclei (for SKY-FISH staining) were examined for each cell line.
DNA Methylation Analysis
Methylation status at specific loci, detected by restriction landmark genomic scanning, was evaluated using a combination of methylation-sensitive restriction enzyme digestion and quantitative real-time polymerase chain reaction (PCR) [3538]. We used 10 NT-ESC lines: BDfc-1, -3, -4, -5, and -11 derived from cumulus cells of BDF1 mice, and B6fc-1 to -5 derived from cumulus cells of C57BL/6 mice. These were the lines first established in our laboratory and used for all subsequent gene expression experiments (DNA arrays and high-coverage gene expression profiling [HiCEP]). For controls, five lines of the same genetic background fertilized ESCs (BDES-1, -2, and -5 cells from BDF1 mice and lines B6ES-1 and B6ES-2 from C57BL/6 mice) were used. Genomic DNA of NT-ESCs and ESCs was digested using PstI and then treated with NotI. Each primer set for PCR was designed to amplify regions that included NotI sites. Ten nanograms of genomic DNA, treated with or without NotI, was analyzed by real-time PCR using the appropriate primers. The amount of undigested DNA both in NotI-treated and untreated genomic DNA was estimated by real-time PCR with SYBR green PCR Master Mix using ABI Prism 7,000 and 7,500 Sequence Detection Systems (Applied Biosystems, Foster City, CA, http://www.appliedbiosystems.com) according to the manufacturers protocols. The methylation ratio at each RLGS (Restriction Landmark Genomic Scanning) locus was defined as the proportion of the amount of undigested DNA in the NotI-treated genome to that in the untreated one. The initial amount of DNA in the reaction mix was normalized using control primer sets, which amplify sequences without NotI sites. For all samples, we performed at least three independent PCR amplifications in duplicate. Table 1 is annotated with NotI restriction sites obtained using the UCSC (University of California, Santa Cruz) genome browser (accessed March 2005).
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Significance analysis of microarray (SAM) data [41] was performed using the affy and siggenes modules of the Bioconductor suite. The specific commands and outputs of the analysis are available on request as a command and a log file. Relationships between the individual ESC samples were calculated as modified all-against-all Euclidean distances, based on the expression of different sets of probe sets selected for their variability in expression across the ESC lines, using functions of the eXintegrator analysis system. Probe sets with high covariations of individual probe pair profiles (calculated as the analysis of variance score), and with high coefficients of variance across the set of ESC samples used in this study, were selected and used to calculate all-against-all distances for the individual samples. Distances were calculated as Euclidean distances of the mean of individually normalized probe pair profiles (with a variance of 1 and a mean of 0 across the samples) mapped to a sigmoid curve. Representations of the individual samples were then mapped to positions in a two-dimensional (2D) field based on the set of distances using an error minimization algorithm [27].
Gene Expression Analyzed by HiCEP
Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany, http://www1.qiagen.com) from NT-ESCs derived from C57BL/6 female cumulus cell nuclei or from DBA/2 male tail cell nuclei (B6fc-1, B6fc-2, DBAmt-1, and DBAmt-2) and ESCs derived from C57BL/6 female embryos or DBA/2 male embryos (B6ES-1, B6ES-2, DBAES-1, and DBAES-5). The HiCEP procedure was performed as described [42]. Briefly, 1 µg of total RNA treated with DNase I was converted to cDNA using the SuperScriptIII First Strand Synthesis system (Invitrogen) with 5'-biotinylated oligo(dT) primers. Double-strand cDNA was prepared, digested with MspI, and trapped by avidin bound to magnetic beads. After the fragments digested by MspI (except for most of the 3'-region bearing oligo(dT)-biotin) were washed off, a synthetic adaptor was ligated, and the trapped templates were digested by MseI. The resulting solution was used as a template for 256 runs of selective PCR. The products were denatured and loaded on an ABI PRISM 3100 electrophoresis system (Applied Biosystems).
| RESULTS |
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. All NT-ESC lines were positive for ESC-specific markers, and negative for differentiation markers, in a pattern similar to fertilized ESCs (Table 1). We also examined the levels of SSEA-1, SSEA-4, and PDGFR-
by cell sorting, but only SSEA-1 was produced by all NT-ESC lines (Fig. 1C). Thus, once established, all these NT-ESC lines showed phenotypes that were almost identical to fertilized embryo-derived ESCs. The karyotypes of NT-ESC lines were normal when examined using Giemsa and SKY-FISH (i.e. 42 of 50 NT-ESC lines [87%] had normal karyotypes in 44%100% of the cells) (means were 64.6% by Giemsa staining and 61.4% by SKY-FISH; Table 1). These data are within the normal range for ESC lines (58%70% and 40%60%, respectively; Table 1, control ESCs) [43]. Four of the NT-ESC lines had only 10%20% normal karyotypes. Another four NT-ESC lines had no normal karyotypes, one line showed trisomy in chromosome 1, two lines showed trisomy in chromosome 11, and one line showed Y-chromosome deletions in all examined cells (Fig. 1D). These aneuploid NT-ESC lines could not be distinguished by morphology or by immunostaining for the ESC markers.
Physical Damage to Nuclei of NT-ESC Lines
We next examined whether donor somatic cell nuclei were damaged by the NT procedure. To do this, we performed sequential NT using nuclei from NT-ESCs and repeated this several times to amplify any possible damage from the procedures. However, the success rates of NT and cell line establishment did not decrease by the ninth series (Fig. 1B and supplemental online Table S2) and no karyotype abnormalities were observed by SKY-FISH staining (supplemental online Table S3). On the other hand, we could not generate cloned mice from somatic cell nuclei beyond six generations [44]. Thus, the process of NT in itself at least did not cause the karyotype abnormalities in the NT-ESC lines, but there may have been damage that can be revealed only by full-term development.
Similarity of NT-ESC Lines by Tissue-Dependent and Differentially Methylated Region Assay
Next, we used DNA methylation assays to examine the epigenetic status of NT-ESCs. We previously reported that, even when newborn cloned mice appear normal, a few tissue-dependent and differentially methylated regions (T-DMRs) are aberrantly methylated [16]. There are many T-DMRs dispersed throughout the genome [45], and DNA methylation patterns are specific for different cell types [35]. We selected 26 loci (Table 1) belonging to five subgroups (D, M, UM, TM, and TUM) for DNA methylation analysis. These include the target loci of DNA methyltransferases 3a and 3b in ESCs (D in Fig. 2A), loci that are hypermethylated (M in Fig. 2B) or hypomethylated (UM in Fig. 2B) in most cell types, and loci that are hypermethylated (TM in Fig. 2C) or hypomethylated (TUM in Fig. 2C) in ESCs [36]. We examined 10 NT-ESC lines derived from BDF1 or C57BL/6 female mice (supplemental online Fig. 1) and compared them with five female ESC lines from the same genetic background. As shown in Figure 2, all 26 loci showed very similar methylation patterns in all NT-ESC and ESC lines examined. Although we did not examine the loci of imprinted genes, each T-DMR pattern is known to be cell type-specific [35]. This suggests that there were few or no differences between NT-ESCs and fertilized ESCs in terms of DNA methylation status.
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The two NT-ESC lines we established were compared against two control ESC lines (NT-ESC vs. contESC) also established in this laboratory as well as against a range of ESCs (NT-ESC vs. total ESC). To determine the number of genes that are expected to be differentially expressed between different ESC lines, we also grouped all ESC lines established by us and compared these with the E14 ESC line (NT-ESC + contESC vs. E14) and the E14 and ESVJ lines considered as a group (NT-ESC + contESC vs. E14 + ESVJ). We also compared the E14 line against the ESVJ line to give an indication of the numbers of genes that were differentially expressed between two established and well-characterized ESC lines.
These comparisons are shown in Figure 3A, where we have plotted the number of probe sets classified as differentially expressed (minus the estimated number of false calls) between the indicated groups of ESCs for delta values between 0.2 and 2. Far more differences were found between different established ESC lines (i.e., between E14 and ESVJ) at all delta values than between NT-ESC and contESC lines, indicating that the NT-ES lines do not differ to a greater degree either from each other or from ES lines, as compared with the differences between ES lines.
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We also used the Affymetrix, Inc., array data to determine the relationships between different samples obtained. A set of probes that were variably expressed across the ESC lines was used to calculate distance measurements between the individual samples. These distances were then used to map the individual samples to positions in 2D space in a manner that conserved the intersample distances (Fig. 3B). This analysis is analogous to a classical cluster analysis but is able to better indicate the complete set of relationships between individual samples. The results of this analysis agree with those of the SAM analysis. All ESCs (NT-ESC or contESC) derived in this laboratory are similar to each other but are different to the E14 and ESVJ established lines. The largest difference indicated by the SAM analysis is observed between the E14 and ESVJ lines. We also performed this analysis using different sets of probes, but the results did not differ markedly (data not shown).
We next used HiCEP to examine gene expression patterns (Fig. 4A, 4B). This technique can distinguish less than 20% (1.2-fold) differences in gene expression, with very few false-positive peaks and high coverage. It can detect more than 70% of all transcripts, including noncoding transcripts [42]. We identified approximately 18,000 peaks in these cell lines and following scatter-plot analysis revealed a close similarity in gene expression between ESCs and NT-ESCs. The Pearson coefficients of correlation (r values) were .8501 (B6ES-1 vs. B6ES-2), .9213 (B6fc-1 vs. B6fc-2), .8720 (B6fc-1 vs. B6 ES-1), and .9471 (B6fc-1 vs. B6ES-2) (Fig. 4C). Although genome-wide observation detected some variation in gene expression between ESCs and NT-ESCs, a similar level of variation was also observed between different ESC lines, suggesting that the observed differences are not due to the cloning procedure per se. However, this does not necessarily mean that there are no differences in gene expression between ESCs and NT-ESCs. Subsequently we performed a precise analysis of individual peaks and found six for which the expression levels in both fertilized ESC lines were three times as great as the C57BL/6-derived NT-ESC lines and three peaks in which expression level in the NT-ESCs was three times as great as in the ESC lines (Fig. 4A). We subsequently repeated this experiment, using ESC and NT-ESC lines established from DBA2 strain mice, but could not confirm this difference between the ESCs and NT-ESCs (Fig. 4B). Although one might expect to find variation between cells derived from different strains, given that all fertilized ESC lines are considered as functionally equivalent, those differences should not be functionally relevant. Furthermore, if differences in expression found between NT-ESCs and ESCs are to be considered to have some functional significance, the genes responsible should not be variably expressed across several different ESC lines. This evidence gives credence to the notion that these NT-ESCs are similar to fertilized ESCs.
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| DISCUSSION |
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The DNA microarray profiles and HiCEP experiments demonstrate that all ESCs (NT-ESC or contESC) derived in this laboratory are similar to each other but are different to the E14 and ESVJ established lines. Only insignificant differences in gene expression between the NT-ESC and other ESC lines were found here, with the minor differences probably resulting from subtle variations in sample-to-sample preparations. Smith et al. [49] and Brambrink et al. [50] also demonstrated that bovine and mouse cloned embryonic cells closely resemble naturally fertilized embryos, respectively, using global gene expression profiles. Even if NT-ESCs may inherit some undetectable epigenetic abnormalities, the similarities of NT-ESCs and ESCs in terms of molecular and other characteristics indicate that murine therapeutic cloning can provide a reliable model for preclinical stem cell research.
Finally, we examined the differentiation potential of NT-ESCs by tetraploid complementation. If NT-ESCs are able to differentiate normally to all embryonic cell types, the resulting 4n chimeric mice should have healthy phenotypes; the strongest evidence for normality of NT-ESCs. We found the rates of generating healthy offspring derived from NT-ESC or ESC lines to be similar (Table 2) [7, 51], and all those mice show germline transmission at adulthood. Thus, our experiment clearly demonstrates that, like fertilized ESCs, NT-ESCs can differentiate into all normal embryonic tissues in vivo. To establish an NT-ESC line, a cloned blastocyst must be cultured for more than 1 month in vitro. During this period, survival of the cloned embryo is independent of most developmentally related gene expression and of placental development; it might be able to proceed gradually to obtain the normal pattern of gene expression [12, 15]. Another possibility is that some of the cloned embryos possess only a few normally reprogrammed cells [12], and these few cells are insufficient to sustain a viable term fetus to term. However, viable NT-ESCs can be established even from those few normal cells during 1 month of culture. Alternatively, in reproductive cloning, the cloned embryos must express all the appropriate genes and exhibit relatively normal placental development immediately after implantation. This more stringent set of criteria may account for the higher developmental failure rates of presumably incompletely reprogrammed cloned embryos after implantation. However, recently, we have found that the success rate of cloned mice from several NT-ESC nuclei were different, even those established from the same donor at the same time [8]. This suggests that NT-ESC lines have similar in vitro differentiation potential to ESCs but that the extent of reprogramming differs between cell lines.
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| ACKNOWLEDGMENTS |
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| REFERENCES |
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