Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

Induced pluripotent stem cells (iPSCs) offer immense potential for regenerative medicine and studies of disease and development. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. However, it remains unknown how complete the reestablishment of ES-cell-like DNA methylation patterns is throughout the genome. Here we report the first whole-genome profiles of DNA methylation at single-base resolution in five human iPSC lines, along with methylomes of ES cells, somatic cells, and differentiated iPSCs and ES cells. iPSCs show significant reprogramming variability, including somatic memory and aberrant reprogramming of DNA methylation. iPSCs share megabase-scale differentially methylated regions proximal to centromeres and telomeres that display incomplete reprogramming of non-CG methylation, and differences in CG methylation and histone modifications. Lastly, differentiation of iPSCs into trophoblast cells revealed that errors in reprogramming CG methylation are transmitted at a high frequency, providing an iPSC reprogramming signature that is maintained after differentiation.     

Genotyping of Rhesus SCNT pluripotent stem cell lines

Somatic cell nuclear transfer (SCNT) into enucleated oocytes has emerged as a technique that can be used to derive mouse embryonic stem cell lines with defined genotypes. In this issue Byrne et al. report the derivation of two SCNT Rhesus macaca male stem cell lines designated CRES-1 and CRES-2. Molecular studies detailed in their paper provides supporting evidence that the chromosome complement of CRES-1 and CRES-2 was genetically identical to the male cell donor nucleus and that the mitochondrial DNA originated from different recipient oocytes. In this validation paper, we independently confirm that both stem cell lines were indeed derived by SCNT.     

Developmental reprogramming after chromosome transfer into mitotic mouse zygotes

Until now, animal cloning and the production of embryonic stem cell lines by somatic cell nuclear transfer have relied on introducing nuclei into meiotic oocytes. In contrast, attempts at somatic cell nuclear transfer into fertilized interphase zygotes have failed. As a result, it has generally been assumed that unfertilized human oocytes will be required for the generation of tailored human embryonic stem cell lines from patients by somatic cell nuclear transfer. Here we report, however, that, unlike interphase zygotes, mouse zygotes temporarily arrested in mitosis can support somatic cell reprogramming, the production of embryonic stem cell lines and the full-term development of cloned animals. Thus, human zygotes and perhaps human embryonic blastomeres may be useful supplements to human oocytes for the creation of patient-derived human embryonic stem cells.     

Nanog promotes transfer of pluripotency after cell fusion

Through cell fusion, embryonic stem (ES) cells can erase the developmental programming of differentiated cell nuclei and impose pluripotency. Molecules that mediate this conversion should be identifiable in ES cells. One candidate is the variant homeodomain protein Nanog, which has the capacity to entrain undifferentiated ES cell propagation. Here we report that in fusions between ES cells and neural stem (NS) cells, increased levels of Nanog stimulate pluripotent gene activation from the somatic cell genome and enable an up to 200-fold increase in the recovery of hybrid colonies, all of which show ES cell characteristics. Nanog also improves hybrid yield when thymocytes or fibroblasts are fused to ES cells; however, fewer colonies are obtained than from ES x NS cell fusions, consistent with a hierarchical susceptibility to reprogramming among somatic cell types. Notably, for NS x ES cell fusions elevated Nanog enables primary hybrids to develop into ES cell colonies with identical frequency to homotypic ES x ES fusion products. This means that in hybrids, increased Nanog is sufficient for the NS cell epigenome to be reset completely to a state of pluripotency. We conclude that Nanog can orchestrate ES cell machinery to instate pluripotency with an efficiency of up to 100% depending on the differentiation status of the somatic cell.     

Embryonic stem cell as nuclear donor could promote in vitro development of the heterogeneous reconstructed embryo

The nucleus of a somatic cell could be dedifferentiated and reprogrammed in an enucleated heterogeneous oocyte. Some reconstructed oocytes could develop into blastocysts in vitro, and a few could develop into term normally after transferred into foster mothers, but most of cloning embryos fail to develop to term. In order to evaluate the efficacy of embryonic stem cell as nucleus donor in interspecific animal cloning, we reconstructed enucleated rabbit oocytes with nuclei from mouse ES cells, and analyzed the developmental ability of reconstructed embryos in vitro. Two kinds of fibroblast cells were used as donor control, one derived from ear skin of an adult Kunming albino mouse, and the other derived from a mouse fetus. Three types of cells were transferred into perivitelline space under zona pellucida of rabbit oocytes respectively. The reconstructed oocytes were fused and activated by electric pulses, and cultured in vitro. The developmental rate of reconstructed oocytes derived from embryonic stem cells was 16.1%, which was significantly higher than that of both the adult mouse fibroblast cells (0%-3.1%, P < 0.05) and fetus mouse fibroblast cells (2.1%-3.7%, P < 0.05). Chromosome analysis confirmed that blastocyst cells were derived from ES donor cell. These observations show that reprogramming is easier in interspecific embryos reconstructed with ES cells than that reconstructed with somatic cells, and that ES cells have the higher ability to direct the reconstructed embryos development normally than fibroblast cells.     

Comparative pluripotency analysis of mouse embryonic stem cells derived from wild-type and infertile hermaphrodite somatic cell nuclear transfer blastocysts

Therapeutic cloning, whereby embryonic stem cells （ESCs） are derived from patient-specific cloned blastocysts via somatic cell nuclear transfer （SCNT）, holds great promise for treating many human diseases using regenerative medicine. Teratoma formation and germline transmission have been used to confirm the pluripotency of mouse stem cells, but human embryonic stem cells （hESCs） have not been proven to be fully pluripotent owing to the ethical impossibility of testing for germ line transmis- sion, which would be the strongest evidence for full pluripotency. Therefore, formation of differentiated cells from the three somatic germ layers within a teratoma is taken as the best indicator of pluripotency in hESC lines. The possibility that these lines lack full multi- or pluripotency has not yet been evaluated. In this study, we established 16 mouse ESC lines, including 3 genetically defective nuclear transfer- ESC （ntESC） lines derived from SCNT blastocysts of infertile hermaphrodite F1 mice and 13 ntESC lines derived from SCNT blastocysts of normal F1 mice. We found that the defective ntESCs expressed all in vitro markers of pluripotency and could form teratomas that included derivatives from all three germ layers, but could not be transmitted via the germ line, in contrast with normal ntESCs. Our results in- dicate that teratoma formation assays with hESCs might be an insufficient standard to assess full pluripotency, although they do define multipotency to some degree. More rigorous standards are required to assess the safety of hESCs for therapeutic cloning.     

Copy number variation and selection during reprogramming to pluripotency

The mechanisms underlying the low efficiency of reprogramming somatic cells into induced pluripotent stem (iPS) cells are poorly understood. There is a clear need to study whether the reprogramming process itself compromises genomic integrity and, through this, the efficiency of iPS cell establishment. Using a high-resolution single nucleotide polymorphism array, we compared copy number variations (CNVs) of different passages of human iPS cells with their fibroblast cell origins and with human embryonic stem (ES) cells. Here we show that significantly more CNVs are present in early-passage human iPS cells than intermediate passage human iPS cells, fibroblasts or human ES cells. Most CNVs are formed de novo and generate genetic mosaicism in early-passage human iPS cells. Most of these novel CNVs rendered the affected cells at a selective disadvantage. Remarkably, expansion of human iPS cells in culture selects rapidly against mutated cells, driving the lines towards a genetic state resembling human ES cells.     

DNA methylation status of H19 and Xist genes in lungs of somatic cell nuclear transfer bovines

In somatic cell nuclear transfer （SCNT） technologies, the donor cell＇s nuclei need to be epigenetically reprogrsmmed for embryonic development. The incomplete reprogramming of donor cell nuclei has been Implicated as s primary reason for the low efficiency of SCNT. DNA methylstion is s major epigenetic modification of the genome that regulates crucial aspects of genome function, including establishment of genomic imprinting. In order to make sure whether the DNA methylstion reprogramming is efficient in SCNT animals, we analyzed the DNA methylstion status of two imprinting genes, H19 and Xist, in lungs of deceased SCNT bovines that died within 48 h of birth using bisulfite sequencing analysis. Our findings demonstrated that cloned bovines showed significantly lower DNA methylstion of H19 than controls （P〈0.05）, and three tested CpGs sites （1, 2, 3） exhibited unmethylstion in one cloned bovine （9C3）; however, Xist showed similar DNA methylation levels between clones and controis, and both showed hypermethylstion （96.11% and 86.67%）.     

Monoclonal mice generated by nuclear transfer from mature B and T donor cells

Cloning from somatic cells is inefficient, with most clones dying during gestation. Cloning from embryonic stem (ES) cells is much more effective, suggesting that the nucleus of an embryonic cell is easier to reprogram. It is thus possible that most surviving clones are, in fact, derived from the nuclei of rare somatic stem cells present in adult tissues, rather than from the nuclei of differentiated cells, as has been assumed. Here we report the generation of monoclonal mice by nuclear transfer from mature lymphocytes. In a modified two-step cloning procedure, we established ES cells from cloned blastocysts and injected them into tetraploid blastocysts to generate mice. In this approach, the embryo is derived from the ES cells and the extra-embryonic tissues from the tetraploid host. Animals cloned from a B-cell nucleus were viable and carried fully rearranged immunoglobulin alleles in all tissues. Similarly, a mouse cloned from a T-cell nucleus carried rearranged T-cell-receptor genes in all tissues. This is an unequivocal demonstration that a terminally differentiated cell can be reprogrammed to produce an adult cloned animal.     

Scriptaid affects histone acetylation and the expression of development-related genes at different stages of porcine somatic cell nuclear transfer embryo during early development

Although the somatic cell nuclear transfer(SCNT) technique has been used extensively for cloning and generating transgenic pigs,the cloning efficiency is still very low.It has been proposed that the low efficiency of this technique is the result of incomplete epigenetic reprogramming and abnormal gene expression during early embryonic development.In this study,we investigate the effect of Scriptaid,a low-toxicity histone deacetylase inhibitor,on the developmental competence of porcine SCNT embryos.We found that treating SCNT embryos with 500 nmol/L Scriptaid for 15 h after activation significantly enhanced the blastocyst formation rate(27.7%) compared with the untreated group(control)(12.2%,P<0.05).Using an immunofluorescence technique to measure the average fluorescence intensity,we also found that treating SCNT embryos with Scriptaid increased the level of histone acetylation on histone H3 at lysine 14(acH3K14).Furthermore,treating embryos with Scriptaid increased the expression level of three genes that play important roles during embryonic development(Oct4,Klf4 at the blastocyst stage and Nanog at the 4-cell stage).Moreover,the expression level of the apoptosis-related gene Caspase-3 was significantly lower in the Scriptaid-treated SCNT embryos compared with the control SCNT embryos at the 4-cell and blastocyst stages.In conclusion,these results indicate that Scriptaid treatment improves the development and nuclear reprogramming of porcine SCNT embryos.     

Apoptosis of transgenic cloned and recloned bovine blastocysts

Apoptosis plays an important role in preimplantation embryonic development. Investigating mechanisms of apoptosis can provide useful information for obtaining high-quality embryos and help to improve cloning efficiency. Here, we investigated the incidence of blastomere apoptosis in transgenic blastocysts generated by somatic cell nuclear transfer (SCNT) and recloning using a terminal deoxynucleotidyl transferase-mediated d-UTP nick end-labeling (TUNEL) assay. Transgenic recloned embryos were the second generation SCNT embryos derived from the somatic cells of a transgenic SCNT calf. The blastocyst rate of transgenic SCNT embryos was lower than that of nontransgenic SCNT embryos. The incidence of apoptosis in transgenic SCNT embryos was higher than that of nontransgenic SCNT embryos. The blastocyst rate and the incidence of apoptosis in transgenic recloned embryos were similar to nontransgenic SCNT embryos. The process of donor cell transfection and drug selection may decrease the developmental capacity of transgenic SCNT embryos. Serial cloning did not influence the developmental capacity of transgenic recloned embryos.     

实验用小型猪胎儿成纤维细胞和骨髓间充质细胞为核供体生产转基因克隆胚胎

目的比较不同类型体细胞对生产转基因克隆胚胎效率的影响。方法利用脂质体介导的方法将质粒pEGFP-N1转染到五指山小型猪胎儿成纤维细胞和骨髓间充质细胞,经过G418筛选后均获得了阳性细胞株。然后分别以两种类型转基因细胞以及未转基因细胞为核供体进行体细胞核移植,比较不同类型供体细胞克隆胚胎的囊胚发育率。结果胎儿成纤维细胞和骨髓间充质细胞克隆胚的囊胚发育率差异不显著(P>0.05,8.3%vs.7.1%);转基因胎儿成纤维细胞(9.6%)和转基因骨髓间充质细胞(9.9%)克隆胚胎的囊胚发育率差异不显著(P>0.05,9.6%vs.9.9%);每一种类型供体细胞转基因与否对克隆胚的囊胚发育率无影响(P>0.05)。结论通过体细胞核移植技术,小型猪骨髓间充质细胞与胎儿成纤维细胞均可有效地生产转基因囊胚。     

Nuclear transfer using nonquiescent adult fibroblasts from a bovine ear

The natural reproduction of mammal is sexual reproduction, which needs fertilization involving sperm and oocyte. Nuclear transfer provided an asexual reproduction method for mammal. Donor cells used in previous experiments of nuclear transfer were mostly from undifferentiated or non-terminally differentiated cells, such as embryonic or fetal cells. However, since Wilmutet al. obtained a viable lamb by transfer of an adult sheep somatic cell into an enucleated oocyte, nuclear transfer using adult somatic cell has been successful in several species. Wilmutet al. suggested that it was a key factor for the success of somatic nuclear transfer to induce the donor cells into GO phase (“GO-phase hypothesis”). In order to verify the Gophase hypothesis, nonquiescent adult fibroblasts from a bovine ear were transferred into enucleated bovine oocytes. The experiments showed that the rate of electrofusion after micromanipulation was above 50%, the cleaving rate was 54.5% and 9.1% of those reconstructed embryos developed to 32-cell stage. These results indicate that for cattle, nuclei from nonquiescent adult somatic cells introduced into enucleated oocytes are at least capable of supporting early development.     

Nuclear reprogramming by nuclear transplantation and defined transcription factors

In the past ten years, great breakthroughs have been achieved in the nuclear reprogramming area. It has been demonstrated that highly differentiated somatic cell genome could be reprogrammed to a pluripotent state, which indicates that differentiated cell fate is not irreversible. Nuclear transplantation and induced pluripotent stem (iPS) cell generation are the two major approaches to inducing reprogramming of differentiated somatic cell genome. In the present review, we will summarize the recent progress of nuclear reprogramming and further discuss the potential to generate patient specific pluripotent stem cells from differentiated somatic cells for therapeutic purpose. Supported by the National High Technology Research and Development Program of China (Grant No. 2005AA210930)     

兔ES样细胞系的建立及其特性分析

报道从２３７枚家兔胚胎中建成７个可连续传代的ＥＳ样细胞系。建系条件为，使用小鼠原始胚胎成纤维细胞（ＭＥ）作饲养层，以含１０％胎年血清和１０％兔血清的ＤＭＥＭ／Ｆ１２为培养基，添加白血病抑制因子（ＬＩＦ）或上皮生长因子（ＥＧＦ），胚龄为９０，９６ｈ。该细胞系的细胞。在许多方面类似于小鼠ＥＳ细胞，具干细胞的形态特征，呈集落型生长，可连续传代并保持其形态特征，具有一定的自发分化和诱导分化的能力，悬浮培养