Mayumi Oda

Generation of induced pluripotent stem cells from human terminally differentiated circulating T cells.

A manuscript has appeared online demonstrating isolation of iPSCs from peripheral blood, including a single line that showed evidence for both TCR-β and TCR-γ rearrangement by PCR (Kunisato, A., Wakatsuki, M., Shinba, H., Ota, T., Ishida, I., and Nagao, K. [2010]. Direct generation of induced pluripotent stem cells from human non-mobilized blood. Stem Cells Dev., in press. Published online May 24, 2010. 10.1089/scd.2010.0063).

Placentomegaly in cloned mouse concepti caused by expansion of the spongiotrophoblast layer

Abstract Hypertrophic placenta, or placentomegaly, has been reported in cloned cattle and mouse concepti, although their placentation processes are quite different from each other. It is therefore tempting to assume that common mechanisms underlie the impact of somatic cell cloning on development of the trophoblast cell lineage that gives rise to the greater part of fetal placenta. To characterize the nature of placentomegaly in cloned mouse concepti, we histologically examined term cloned mouse placentas and assessed expression of a number of genes. A prominent morphological abnormality commonly found among all cloned mouse placentas examined was expansion of the spongiotrophoblast layer, with an increased number of glycogen cells and enlarged spongiotrophoblast cells. Enlargement of trophoblast giant cells and disorganization of the labyrinth layer were also seen. Despite the morphological abnormalities, in situ hybridization analysis of spatiotemporally regulated placenta-specific genes did not reveal any drastic disturbances. Although repression of some imprinted genes was found in Northern hybridization analysis, it was concluded that this was mostly due to the reduced proportion of the labyrinth layer in the entire placenta, not to impaired transcriptional activity. Interestingly, however, cloned mouse fetuses appeared to be smaller than those of litter size-matched controls, suggesting that cloned mouse fetuses were under a latent negative effect on their growth, probably because the placentas are not fully functional. Thus, a major cause of placentomegaly is expansion of the spongiotrophoblast layer, which consequently disturbs the architecture of the layers in the placenta and partially damages its function.

High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers

Many genome-wide assays involve the generation of a subset (or representation) of the genome following restriction enzyme digestion. The use of enzymes sensitive to cytosine methylation allows high-throughput analysis of this epigenetic regulatory process. We show that the use of a dual-adapter approach allows us to generate genomic representations that includes fragments of <200 bp in size, previously not possible when using the standard approach of using a single adapter. By expanding the representation to smaller fragments using HpaII or MspI, we increase the representation by these isoschizomers to more than 1.32 million loci in the human genome, representing 98.5% of CpG islands and 91.1% of refSeq promoters. This advance allows the development of a new, high-resolution version of our HpaII-tiny fragment Enrichment by Ligation-mediated PCR (HELP) assay to study cytosine methylation. We also show that the MspI representation generates information about copy-number variation, that the assay can be used on as little as 10 ng of DNA and that massively parallel sequencing can be used as an alternative to microarrays to read the output of the assay, making this a powerful discovery platform for studies of genomic and epigenomic abnormalities.

Trophoblast Stem Cells

At the first cell fate decision in mammalian development, the origins of trophoblast and embryonic cell lineages are established as the trophectoderm and the inner cell mass (ICM) in the blastocyst. In the trophoblast cell lineage, a subset of the trophectoderm cells maintains the capacity to proliferate and contribute to the extraembryonic ectoderm, the ectoplacental cone, and the secondary giant cells of the early conceptus after implantation, and finally they produce the entire trophoblastic population in the mature placenta. The stem cell population of the trophectoderm lineage can be isolated and maintained in vitro in the presence of fibroblast growth factor 4, heparin, and a feeder layer of mouse embryonic fibroblast cells. These apparently immortal stem cells in culture are termed trophoblast stem (TS) cells, and exhibit the potential to differentiate into multiple trophoblastic cell types in vitro, as well as in vivo. Even after multiple passages, TS cells retain the ability to participate in the normal development of chimeras and contribute exclusively to the trophoblastic component of the placenta and of the parietal yolk sac. The fate of TS cells is strikingly in contrast to that of embryonic stem cells, which never contribute to these tissues. In this chapter, detailed protocols for the isolation and establishment of TS cell lines from blastocysts and their maintenance are described.

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome

Heterochromatin is believed to be associated with increased levels of cytosine methylation. With the recent availability of genome-wide, high-resolution molecular data reflecting chromatin organization and methylation, such relationships can be explored systematically. As well-defined surrogates for heterochromatin, we tested the relationship between DNA replication timing and DNase hypersensitivity with cytosine methylation in two human cell types, unexpectedly finding the later-replicating, more heterochromatic regions to be less methylated than early replicating regions. When we integrated gene-expression data into the study, we found that regions of increased gene expression were earlier replicating, as previously identified, and that transcription-targeted cytosine methylation in gene bodies contributes to the positive correlation with early replication. A self-organizing map (SOM) approach was able to identify genomic regions with early replication and increased methylation, but lacking annotated transcripts, loci missed in simple two variable analyses, possibly encoding unrecognized intergenic transcripts. We conclude that the relationship of cytosine methylation with heterochromatin is not simple and depends on whether the genomic context is tandemly repetitive sequences often found near centromeres, which are known to be heterochromatic and methylated, or the remaining majority of the genome, where cytosine methylation is targeted preferentially to the transcriptionally active, euchromatic compartment of the genome.

Violet Light Exposure Can Be a Preventive Strategy Against Myopia Progression

Prevalence of myopia is increasing worldwide. Outdoor activity is one of the most important environmental factors for myopia control. Here we show that violet light (VL, 360–400 nm wavelength) suppresses myopia progression. First, we confirmed that VL suppressed the axial length (AL) elongation in the chick myopia model. Expression microarray analyses revealed that myopia suppressive gene EGR1 was upregulated by VL exposure. VL exposure induced significantly higher upregulation of EGR1 in chick chorioretinal tissues than blue light under the same conditions. Next, we conducted clinical research retrospectively to compare the AL elongation among myopic children who wore eyeglasses (VL blocked) and two types of contact lenses (partially VL blocked and VL transmitting). The data showed the VL transmitting contact lenses suppressed myopia progression most. These results suggest that VL is one of the important outdoor environmental factors for myopia control. Since VL is apt to be excluded from our modern society due to the excessive UV protection, VL exposure can be a preventive strategy against myopia progression.

Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells

Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability and karyotype in culture. We previously showed that infrequent bursts of Zscan4 expression (Z4 events) are important for the maintenance of telomere length and genome stability in mESCs. However, the molecular details of Z4 events remain unclear. Here we show that Z4 events involve unexpected transcriptional derepression in heterochromatin regions that usually remain silent. During a Z4 event, we see rapid derepression and rerepression of heterochromatin leading to a burst of transcription that coincides with transient histone hyperacetylation and DNA demethylation, clustering of pericentromeric heterochromatin around the nucleolus, and accumulation of activating and repressive chromatin remodelling complexes. This heterochromatin-based transcriptional activity suggests that mESCs may maintain their extraordinary genome stability at least in part by transiently resetting their heterochromatin.

The Help Assay

Genomic representations using ligation-mediated PCR have been used successfully as the foundation for a number of high-throughput assays. HpaII tiny fragment enrichment by ligation-mediated PCR (HELP) is an example of the use of such representations to study cytosine methylation in the genome. The HELP assay differs from most other assays testing cytosine methylation because of its positive representation of hypomethylated DNA in the genome, whereas other assays infer the presence of hypomethylated sequences by the absence of signal, for which there can be confounding technical reasons. Hypomethylated sequences represent the minority of the genome and tend to be located at unique sequences with functionally interesting properties such as transcription start sites. By performing a comparative genomic hybridization using an MspI representation from the same DNA sample, we represent all potential loci that could be generated by HpaII in the situation of global hypomethylation; in practice, HpaII generates a subset of loci from this population, allowing us to discriminate hypomethylated loci (represented by both HpaII and MspI) from methylated loci (represented by MspI only).

Establishment of trophoblast stem cell lines from somatic cell nuclear-transferred embryos.

Placental abnormalities occur frequently in cloned animals. Here, we attempted to isolate trophoblast stem (TS) cells from mouse blastocysts produced by somatic cell nuclear transfer (NT) at the blastocyst stage (NT blastocysts). Despite the predicted deficiency of the trophoblast cell lineage, we succeeded in isolating cell colonies with typical morphology of TS cells and cell lines from the NT blastocysts (ntTS cell lines) with efficiency as high as that from native blastocysts. The established 10 ntTS cell lines could be maintained in the undifferentiated state and induced to differentiate into several trophoblast subtypes in vitro. A comprehensive analysis of the transcriptional and epigenetic traits demonstrated that ntTS cells were indistinguishable from control TS cells. In addition, ntTS cells contributed exclusively to the placenta and survived until term in chimeras, indicating that ntTS cells have developmental potential as stem cells. Taken together, our data show that NT blastocysts contain cells that can produce TS cells in culture, suggesting that proper commitment to the trophoblast cell lineage in NT embryos occurs by the blastocyst stage.

Trophoblast cell lineage in cloned mouse embryos

Most conceptuses derived by somatic cell nuclear transfer (SCNT) in mice undergo developmental arrest as a result of embryonic or extraembryonic defects. Even when fetuses survive to term, prominent placental overgrowth or placentomegaly is often present, indicating that SCNT affects the development of trophoblast cell lineage. The trophoblast cell lineage is established at the blastocyst stage when the stem cell population of the trophoblast cell lineage resides in the polar trophectoderm. Therefore, it is possible that the developmental arrest and placentomegaly that accompany SCNT are induced by insufficient reprogramming of the donor somatic nucleus to enable the cells to acquire full potency as stem cells of the trophoblast cell lineage. Despite the abnormalities of the extraembryonic tissues of SCNT embryos, trophoblast stem (TS) cell lines have been successfully isolated from SCNT blastocysts and their properties appear to be indistinguishable from those of TS cells derived from native blastocysts. This suggests that SCNT does not affect the emergence and autonomous properties of TS cells. In this review, we discuss specification of cell lineage and the extent of reprogramming of TS cells in SCNT blastocysts.