المؤلفون: Hidenori Akutsu, Koichiro Nishino, Akihiro Umezawa, Yoshikazu Arai, Mayu Yamazaki-Inoue, Masashi Toyoda, Ken Takasawa

المصدر: Human Cell. 31:78-86

مصطلحات موضوعية: 0301 basic medicine, Homeobox protein NANOG, Cancer Research, Transcription, Genetic, Induced Pluripotent Stem Cells, Gene Expression, Biology, Stem cell marker, Epigenesis, Genetic, 03 medical and health sciences, Humans, Telomerase reverse transcriptase, Epigenetics, Induced pluripotent stem cell, Telomerase, Cells, Cultured, Cell Biology, DNA Methylation, Cellular Reprogramming, Cell biology, 030104 developmental biology, embryonic structures, DNA methylation, Cancer research, Stem cell, Reprogramming

الوصف: During reprogramming into human induced pluripotent stem cells (iPSCs), several stem cell marker genes are induced, such as OCT-4, NANOG, SALL4, and TERT. OCT-4, NANOG, and SALL4 gene expression can be regulated by DNA methylation. Their promoters become hypomethylated in iPSCs during reprogramming, leading to their induced expression. However, epigenetic regulation of the TERT gene remains unclear. In this study, we focused on epigenetic regulation of the human TERT gene and identified a differentially methylated region (DMR) at a distal region in the TERT promoter between human iPSCs and their parental somatic cells. Interestingly, the TERT-DMR was highly methylated in iPSCs, but low-level methylation was observed in their parental somatic cells. Region-specific, methylated-promoter assays showed that the methylated TERT-DMR up-regulated the promoter activity in iPSCs. In addition, Lamin B1 accumulated at the TERT-DMR in iPSCs, but not in their parent somatic cells. These results suggested that the TERT transcription was enhanced by DNA methylation at the TERT-DMR via binding to nuclear lamina during reprogramming. Our findings shed light on a new functional aspect of DNA methylation in gene expression.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f8aa0d08f3fa9c4452042a553317a751Test
https://doi.org/10.1007/s13577-017-0190-xTest

المؤلفون: Mahito Nakanishi, Manami Ohtaka, Koichiro Nishino, Masashi Toyoda, Hidenori Akutsu, Tohru Sugawara, Yoshikazu Arai, Mayu Yamazaki-Inoue, Akihiro Umezawa, Ken Takasawa, Ken Nishimura

المصدر: Regenerative Therapy
Regenerative Therapy, Vol 9, Iss, Pp 71-78 (2018)

مصطلحات موضوعية: 0301 basic medicine, Human iPSCs, Biomedical Engineering, Biomaterials, 03 medical and health sciences, Retrovirus, SOX2, Epigenetics, lcsh:QH573-671, Aberrant methylation, Induced pluripotent stem cell, lcsh:R5-920, DNA methylation, biology, lcsh:Cytology, Human ESCs, biology.organism_classification, Embryonic stem cell, Sendai virus, Cell biology, 030104 developmental biology, Original Article, lcsh:Medicine (General), Reprogramming, Developmental Biology

الوصف: Human induced pluripotent stem cells (iPSCs) are established by introducing several reprogramming factors, such as OCT3/4, SOX2, KLF4, c-MYC. Because of their pluripotency and immortality, iPSCs are considered to be a powerful tool for regenerative medicine. To date, iPSCs have been established all over the world by various gene delivery methods. All methods induced high-quality iPSCs, but epigenetic analysis of abnormalities derived from differences in the gene delivery methods has not yet been performed. Here, we generated genetically matched human iPSCs from menstrual blood cells by using three kinds of vectors, i.e., retrovirus, Sendai virus, and episomal vectors, and compared genome-wide DNA methylation profiles among them. Although comparison of aberrant methylation revealed that iPSCs generated by Sendai virus vector have lowest number of aberrant methylation sites among the three vectors, the iPSCs generated by non-integrating methods did not show vector-specific aberrant methylation. However, the differences between the iPSC lines were determined to be the number of random aberrant hyper-methylated regions compared with embryonic stem cells. These random aberrant hyper-methylations might be a cause of the differences in the properties of each of the iPSC lines.

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8b9157e1b981a74af739f0bafe06369cTest
https://doi.org/10.1101/355099Test

المؤلفون: Hatsune Makino, Akihiro Umezawa, Kunio Hirano, Hajime Okita, Shogo Nagata, Yoshitaka Miyagawa, Masato Nakagawa, Masashi Toyoda, Shinpei Yamaguchi, Shinya Yamanaka, Hidenori Akutsu, Nobutaka Kiyokawa, Koichiro Nishino, Takashi Tada

المصدر: Genes to Cells. 14:1395-1404

مصطلحات موضوعية: Male, Pluripotent Stem Cells, Homeobox protein NANOG, Cellular differentiation, Mice, Transgenic, Biology, Immunoenzyme Techniques, Kruppel-Like Factor 4, Mice, Genetics, Animals, Humans, Amnion, RNA, Messenger, Induced pluripotent stem cell, Embryonic Stem Cells, Yolk Sac, Chimera, Reverse Transcriptase Polymerase Chain Reaction, Gene Expression Profiling, Infant, Newborn, Teratoma, Gene Expression Regulation, Developmental, Cell Differentiation, Cell Biology, DNA Methylation, Cellular Reprogramming, Molecular biology, Embryonic stem cell, KLF4, embryonic structures, DNA methylation, Female, Stem cell, Reprogramming, Biomarkers

الوصف: Practical clinical applications for current induced pluripotent stem cell (iPSC) technologies are hindered by very low generation efficiencies. Here, we demonstrate that newborn human (h) and mouse (m) extra-embryonic amnion (AM) and yolk-sac (YS) cells, in which endogenous KLF4/Klf4, c-MYC/c-Myc and RONIN/Ronin are expressed, can be reprogrammed to hiPSCs and miPSCs with efficiencies for AM cells of 0.02% and 0.1%, respectively. Both hiPSC and miPSCs are indistinguishable from embryonic stem cells in colony morphology, expression of pluripotency markers, global gene expression profile, DNA methylation status of OCT4 and NANOG, teratoma formation and, in the case of miPSCs, generation of germline transmissible chimeric mice. As copious amounts of human AM cells can be collected without invasion, and stored long term by conventional means without requirement for in vitro culture, they represent an ideal source for cell banking and subsequent 'on demand' generation of hiPSCs for personal regenerative and pharmaceutical applications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::27fb4cc8535a80736df1760dff065c0cTest
https://doi.org/10.1111/j.1365-2443.2009.01356.xTest

المؤلفون: Takuya Imamura, Jun Ohgane, Koichiro Nishino, Kunio Shiota, Satoshi Tanaka, Yasushi Kogo, Atsushi Urano, Naka Hattori

المصدر: Genes to Cells. 7:961-969

مصطلحات موضوعية: Differentially methylated regions, Epigenetics of physical exercise, CpG site, DNA methylation, Genetics, Cell Biology, Epigenetics, Biology, RNA-Directed DNA Methylation, Reprogramming, Molecular biology, Epigenomics

الوصف: Background: DNA methylation is involved in many gene functions such as gene-silencing, X-inactivation, imprinting and stability of the gene. We recently found that some CpG islands had a tissue-dependent and differentially methylated region (T-DMR) in normal tissues, raising the possibility that there may be more CpG islands capable of differential methylation. Results: We investigated the genome-wide DNA methylation pattern of CpG islands by restriction landmark genomic scanning (RLGS) in mouse stem cells (ES, EG and trophoblast stem) before and after differentiation, and sperm as well as somatic tissues. A total of 247 spots out of 1500 (16%) showed differences in the appearance of their RLGS profiles, indicating that CpG islands having T-DMR were numerous and widespread. The methylation pattern was specific, and varied in a precise manner according to cell lineage, tissue type and during cell differentiation. Conclusions: Genomic loci with altered methylation status seem to be more common than has hitherto been realized. The formation of DNA methylation patterns at CpG islands is one of the epigenetic events which underlies the production of various cell types in the body. These findings should have implications for the use of embryonic stem cells and cells derived from them therapeutically, and also for the cloning of animals by the transfer of somatic cell nuclei.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::422aff4a0b30ea4e2fd0542c718b718aTest
https://doi.org/10.1046/j.1365-2443.2002.00574.xTest

المؤلفون: Koichiro Nishino, Akihiro Umezawa, Tohru Sugawara, Hidenori Akutsu

المصدر: Stem Cell Research & Therapy

مصطلحات موضوعية: Induced stem cells, Induced Pluripotent Stem Cells, Cell- and Tissue-Based Therapy, Drug Evaluation, Preclinical, Medicine (miscellaneous), Cell Differentiation, Review, Cell Biology, Embryoid body, DNA Methylation, Biology, Biochemistry, Genetics and Molecular Biology (miscellaneous), Embryonic stem cell, Epigenesis, Genetic, Cell biology, MicroRNAs, Humans, Molecular Medicine, Stem cell, Induced pluripotent stem cell, Cell potency, Reprogramming, Embryonic Stem Cells, Adult stem cell

الوصف: Induced pluripotent stem (iPS) cells, obtained from reprogramming somatic cells by ectopic expression of a defined set of transcription factors or chemicals, are expected to be used as differentiated cells for drug screening or evaluations of drug toxicity and cell replacement therapies. As pluripotent stem cells, iPS cells are similar to embryonic stem (ES) cells in morphology and marker expression. Several types of iPS cells have been generated using combinations of reprogramming molecules and/or small chemical compounds from different types of tissues. A comprehensive approach, such as global gene or microRNA expression analysis and whole genomic DNA methylation profiling, has demonstrated that iPS cells are similar to their embryonic counterparts. Considering the substantial variation among iPS cell lines reported to date, the safety and therapeutic implications of these differences should be thoroughly evaluated before they are used in cell therapies. Here, we review recent research defining the concept of standardization for iPS cells, their ability to differentiate and the identity of the differentiated cells.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d55699e1de9ef79b4f5fbd85bb339a98Test
https://doi.org/10.1186/scrt99Test

المؤلفون: Akihiro Umezawa, Koichiro Nishino

المصدر: Stem Cells and Cancer Stem Cells, Volume 4 ISBN: 9789400728271

مصطلحات موضوعية: Cell type, Amnion, Cell, Biology, Embryonic stem cell, Cell biology, medicine.anatomical_structure, embryonic structures, DNA methylation, medicine, Epigenetics, Induced pluripotent stem cell, Reprogramming, reproductive and urinary physiology

الوصف: Epigenetic reprogramming is a critical event in the generation of induced pluripotent stem cells (iPSCs). Although the iPSCs from different sources are very similar to each other and to embryonic stem cells (ESCs), there are epigenetic differences in small fraction. iPSCs become epigenetically closer to each other with continuous passaging even though they have been derived from different cell types; human amnion, endometrium and menstrual blood cells. However, iPSCs exhibit distinct epigenetic distances from ESCs at early passages. Continuous passaging of the iPSCs diminishes the differences between iPSCs and ESCs via periodic aberrant hyper-methylation. This aberrant stochastic hyper-methylation and their convergence is a direct cause of the transgene-independent phases of iPS reprogramming. The number of passages for “convergence” of the aberrant hyper-methylation is dependent on the parental cell type. Interestingly, the amnion-derived-iPSCs show a more rapid decrease in the number of aberrant methylated sites during additional cultivation than endometrium-derived-iPSCs and menstrual blood cell-derived-iPSCs. Amnion cells offer additional benefits; they can be collected in a non-invasive manner and can be frozen and stored by conventional methods. Therefore, they are a strong candidate cell source for iPSC generation for clinical applications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::4e3500970da5cad7aeda3d9946bbe82cTest
https://doi.org/10.1007/978-94-007-2828-8_6Test

المؤلفون: Hidenori Akutsu, Yoshihiro Fukawatase, Masashi Toyoda, Hironari Sakaguchi, Emi Chikazawa, Mayu Yamazaki-Inoue, Akihiro Umezawa, Koichiro Nishino

المصدر: PLoS Genetics
PLoS Genetics, Vol 7, Iss 5, p e1002085 (2011)

مصطلحات موضوعية: Epigenomics, Cancer Research, Microarrays, Cellular differentiation, Gene Expression, Epigenesis, Genetic, Chromosomes, Human, Transgenes, Induced pluripotent stem cell, Genetics (clinical), reproductive and urinary physiology, Stem Cells, Cell Differentiation, Methylation, Genomics, Immunohistochemistry, Cell biology, DNA methylation, embryonic structures, RNA, Long Noncoding, Epigenetics, DNA modification, Reprogramming, Research Article, Genetic Markers, Cell type, lcsh:QH426-470, Cell Potency, Induced Pluripotent Stem Cells, Biology, Cell Line, Genetics, Genome-Wide Association Studies, Humans, Gene Silencing, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Embryonic Stem Cells, Genome, Human, Proteins, Computational Biology, Human Genetics, DNA Methylation, Comparative Genomics, Molecular biology, Embryonic stem cell, lcsh:Genetics, Karyotyping, Genome Expression Analysis, Developmental Biology

الوصف: Epigenetic reprogramming is a critical event in the generation of induced pluripotent stem cells (iPSCs). Here, we determined the DNA methylation profiles of 22 human iPSC lines derived from five different cell types (human endometrium, placental artery endothelium, amnion, fetal lung fibroblast, and menstrual blood cell) and five human embryonic stem cell (ESC) lines, and we followed the aberrant methylation sites in iPSCs for up to 42 weeks. The iPSCs exhibited distinct epigenetic differences from ESCs, which were caused by aberrant methylation at early passages. Multiple appearances and then disappearances of random aberrant methylation were detected throughout iPSC reprogramming. Continuous passaging of the iPSCs diminished the differences between iPSCs and ESCs, implying that iPSCs lose the characteristics inherited from the parent cells and adapt to very closely resemble ESCs over time. Human iPSCs were gradually reprogrammed through the “convergence” of aberrant hyper-methylation events that continuously appeared in a de novo manner. This iPS reprogramming consisted of stochastic de novo methylation and selection/fixation of methylation in an environment suitable for ESCs. Taken together, random methylation and convergence are driving forces for long-term reprogramming of iPSCs to ESCs.
Author Summary iPSCs change to resemble ESCs via two phases: the transgene-dependent phase, in which the transcription factors act to transform somatic cells into pluripotent stem cells, and the transgene-independent phase, in which the transcription factors are silenced. In this study, we established human iPSCs derived from 5 different cell types by retroviral infection of the Yamanaka 4 factors, and we identified 8 novel epigenetic markers (SALL4, EPHA1, PTPN6, RAB25, GBP4, LYST, SP100, and UBE1L) by comprehensive DNA methylation analysis. The aberrant hyper-methylation in iPSCs occurred stochastically throughout the genome and decreased during the long-term iPSC reprogramming, suggesting that the aberrant stochastic hyper-methylation and their convergence are a direct cause of the transgene-independent phase of iPS reprogramming. These results favor the stochastic model of the Yamanaka model rather than the elite model. In addition, the stem cell–specific methylation states and the epigenetic difference between iPSCs and ESCs are useful indices for evaluating human iPSCs in therapeutic applications.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::15e8199c324e8efde60a4059f3c9e964Test
https://pubmed.ncbi.nlm.nih.gov/21637780Test

المؤلفون: Masato Hiyama, Hiroyuki Imai, Koichiro Nishino, Kiyoshi Kano, Ken Takeshi Kusakabe, Shoichi Wakitani, Ken Takasawa, Wataru Fujii, Yasuo Kiso

المصدر: PLoS ONE
PLoS ONE, Vol 10, Iss 6, p e0130585 (2015)

مصطلحات موضوعية: lcsh:Medicine, Germ layer, Biology, Mice, Polyploid, Genes, Reporter, Animals, Epigenetics, lcsh:Science, Embryonic Stem Cells, Cell Proliferation, Genetics, Multidisciplinary, Tetraploid complementation assay, lcsh:R, fungi, food and beverages, Cell Differentiation, Embryo, DNA Methylation, Embryo, Mammalian, Embryonic stem cell, Cell biology, Tetraploidy, Blastocyst, embryonic structures, lcsh:Q, Female, Ploidy, Reprogramming, Germ Layers, Transcription Factors, Research Article

الوصف: Polyploid amphibians and fishes occur naturally in nature, while polyploid mammals do not. For example, tetraploid mouse embryos normally develop into blastocysts, but exhibit abnormalities and die soon after implantation. Thus, polyploidization is thought to be harmful during early mammalian development. However, the mechanisms through which polyploidization disrupts development are still poorly understood. In this study, we aimed to elucidate how genome duplication affects early mammalian development. To this end, we established tetraploid embryonic stem cells (TESCs) produced from the inner cell masses of tetraploid blastocysts using electrofusion of two-cell embryos in mice and studied the developmental potential of TESCs. We demonstrated that TESCs possessed essential pluripotency and differentiation potency to form teratomas, which differentiated into the three germ layers, including diploid embryonic stem cells. TESCs also contributed to the inner cell masses in aggregated chimeric blastocysts, despite the observation that tetraploid embryos fail in normal development soon after implantation in mice. In TESCs, stability after several passages, colony morphology, and alkaline phosphatase activity were similar to those of diploid ESCs. TESCs also exhibited sufficient expression and localization of pluripotent markers and retained the normal epigenetic status of relevant reprogramming factors. TESCs proliferated at a slower rate than ESCs, indicating that the difference in genomic dosage was responsible for the different growth rates. Thus, our findings suggested that mouse ESCs maintained intrinsic pluripotency and differentiation potential despite tetraploidization, providing insights into our understanding of developmental elimination in polyploid mammals.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cd0c35ff30da4889285f44be8342be60Test
https://doi.org/10.1371/journal.pone.0130585Test

المؤلفون: Masako Suzuki, Kunio Shiota, Jun Ohgane, Naka Hattori, Koichiro Nishino

مصطلحات موضوعية: Homeobox protein NANOG, Rex1, DNA methylation, Stem cell, Biology, Induced pluripotent stem cell, Reprogramming, Embryonic stem cell, Adult stem cell, Cell biology

الوصف: Stem cells raise the possibility of regenerating failing body parts with new tissue. Before stem cells can safely fulfill their promise, many technical problems, including understanding the stem cell phenotype, must be overcome. DNA methylation, which is responsible for gene silencing and is associated with chromatin remodeling, is an epigenetic system that determines the specific characteristic of a variety of cells, including stem cells. Each cell type has a unique DNA methylation profile produced by varied loci-specific methylation. Investigation of such DNA methylation profiles provides a way of identifying pluripotent stem cells. Further, it is likely that analysis of the epigenetic status of stem cells may provide novel information regarding "sternness" within these populations.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_________::a3734db3e1693ab23a86b9c22d6d14bcTest
https://doi.org/10.1385/1-59745-037-5:421Test

المؤلفون: Kunio Shiota, Naoko Hattori, Yeoung Gyu Ko, Koichiro Nishino, Satoshi Tanaka, Yoshikazu Arai

المصدر: The Journal of biological chemistry. 280(10)

مصطلحات موضوعية: DNA (Cytosine-5-)-Methyltransferase 1, Transcription, Genetic, Embryonic Development, Biology, Biochemistry, DNA methyltransferase, Mice, Epigenetics of physical exercise, Pregnancy, Histone methylation, Animals, DNA (Cytosine-5-)-Methyltransferases, Molecular Biology, RNA-Directed DNA Methylation, Epigenomics, DNA Primers, Base Sequence, Gene Expression Regulation, Developmental, Cell Biology, Exons, DNA Methylation, Molecular biology, Isoenzymes, Differentially methylated regions, embryonic structures, DNA methylation, Oocytes, Female, 5' Untranslated Regions, Reprogramming

الوصف: Methylation of DNA is involved in tissue-specific gene control, and establishment of DNA methylation pattern in the genome is thought to be essential for embryonic development. Three isoforms of Dnmt1 (DNA methyltransferase 1) transcripts, Dnmt1s, Dnmt1o, and Dnmt1p, are produced by alternative usage of multiple first exons. Dnmt1s is expressed in somatic cells. Dnmt1p is found only in pachytene spermatocytes, whereas Dnmt1o is specific to oocytes and preimplantation embryos. Here we determined that there is a tissue-dependent differentially methylated region (T-DMR) in the 5' region of Dnmt1o but not in that of the Dnmt1s/1p. The methylation status of the Dnmt1o T-DMR was distinctively different in the oocyte from that in the sperm and adult somatic tissues and changed at each stage from fertilization to blastocyst stage, suggesting that active methylation and demethylation occur during preimplantation development. The T-DMR was highly methylated in somatic cells and embryonic stem cells. Analysis using Dnmt-deficient embryonic stem cell lines revealed that Dnmt1, Dnmt3a, and Dnmt3b are each partially responsible for maintenance of methylation of Dnmt1o T-DMR. In particular, there are compensatory and cooperative roles between Dnmt3a and Dnmt3b. Thus, the regulatory region of Dnmt1o, but not of Dnmt1s/1p, appeared to be a target of DNA methylation. The present study also suggested that the DNA methylation status of the gene region dynamically changes during embryogenesis independently of the change in the bulk DNA methylation status.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9e433097ab0644639d116fbbddf8434bTest
https://pubmed.ncbi.nlm.nih.gov/15634679Test