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Rasmussen TP. Parallels between artificial reprogramming and the biogenesis of cancer stem cells: Involvement of lncRNAs. Semin Cancer Biol 2019; 57:36-44. [PMID: 30273656 DOI: 10.1016/j.semcancer.2018.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/12/2018] [Accepted: 09/26/2018] [Indexed: 02/08/2023]
Abstract
Cellular identity is established and maintained by the interplay of cell type-specific transcription factors and epigenetic regulation of the genome. During development in vivo and differentiation in vitro, transitions from one cell type to the next are triggered by cell signaling events culminating in modifications of chromatin that render genes accessible or inaccessible to the transcriptional apparatus. In recent years it has become apparent that cellular identity is plastic, and technological reprogramming methods such as somatic cell nuclear transfer and induced pluripotency can yield reprogrammed cells that have been restored to a state of developmental potency. Long noncoding RNAs (lncRNAs) are untranslated functional RNA molecules that are intimately involved in the regulation of the chromatin of protein-coding genes. In fact, recent evidence shows that there are more lncRNA species in the cell than mRNA species and that most protein-coding genes are likely to be under epigenetic regulation mediated by lncRNAs. This review examines lncRNA function in reprogrammed pluripotent cells and cancer stem cells. Because cancer stem cells arise from normal cells, their biogenesis can be viewed as a reprogramming process that occurs in vivo, and parallels between artificial reprogramming and cancer stem cell biogenesis are discussed.
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Affiliation(s)
- Theodore P Rasmussen
- University of Connecticut, Department of Pharmaceutical Sciences, 69 North Eagleville Road, Storrs, CT 06269, USA; University of Connecticut, Department of Molecular and Cell Biology, 91 North Eagleville Road, Storrs, CT 06269, USA; University of Connecticut, Institute for Systems Genomics, 181 Auditorium Road, Storrs, CT 06269, USA; University of Connecticut, UConn Stem Cell Institute, 400 Farmington Avenue Farmington, CT 06033, USA.
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Epigenetic modifications in the embryonic and induced pluripotent stem cells. Gene Expr Patterns 2018; 29:1-9. [PMID: 29625185 DOI: 10.1016/j.gep.2018.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/03/2018] [Accepted: 04/03/2018] [Indexed: 02/07/2023]
Abstract
Epigenetic modifications are involved in global reprogramming of the cell transcriptome. Therefore, synchronized major shifts in the expression of many genes could be achieved through epigenetic changes. The regulation of gene expression could be implemented by different epigenetic events including histone modifications, DNA methylation and chromatin remodelling. Interestingly, it has been documented that reprogramming of somatic cells to induced pluripotent stem (iPS) cells is also a typical example of epigenetic modifications. Additionally, epigenetic would determine the fates of almost all cells upon differentiation of stem cells into somatic cells. Currently, generation of iPS cells through epigenetic modifications is a routine laboratory practice. Despite all our knowledge, inconsistency in the results of reprogramming and differentiation of stem cells, highlight the need for more thorough investigation into the role of epigenetic modification in generation and maintenance of stem cells. Besides, subtle differences have been observed among different iPS cells and between iPS and ES cells. Although, a handful of detailed review regarding the status of epigenetics in stem cells has been published previously, in the current review, an abstracted and rather simplified view has been presented for those who want to gain a more general overview on this subject. However, almost all key references and ground breaking studies were included, which could be further explored to gain more in depth knowledge regarding this topic. The most dominant epigenetic changes have been presented followed by the impacts of such changes on the global gene expression. Epigenetic status in iPS and ES cells were compared. In addition to including the issues related to X-chromosome reactivation in the stem cells, we have also included loss of imprinting for some genes as a major drawback in generation of iPS cells. Finally, the overall impacts of epigenetic modifications on different aspects of stem cells has been discussed, including their use in cell therapy.
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Mao J, Zhao MT, Whitworth KM, Spate LD, Walters EM, O'Gorman C, Lee K, Samuel MS, Murphy CN, Wells K, Rivera RM, Prather RS. Oxamflatin treatment enhances cloned porcine embryo development and nuclear reprogramming. Cell Reprogram 2014; 17:28-40. [PMID: 25548976 DOI: 10.1089/cell.2014.0075] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Faulty epigenetic reprogramming of somatic nuclei is thought to be the main reason for low cloning efficiency by somatic cell nuclear transfer (SCNT). Histone deacetylase inhibitors (HDACi), such as Scriptaid, improve developmental competence of SCNT embryos in several species. Another HDACi, Oxamflatin, is about 100 times more potent than Scriptaid in the ability to inhibit nuclear-specific HDACs. The present study determined the effects of Oxamflatin treatment on embryo development, DNA methylation, and gene expression. Oxamflatin treatment enhanced blastocyst formation of SCNT embryos in vitro. Embryo transfer produced more pigs born and fewer mummies from the Oxamflatin-treated group compared to the Scriptaid-treated positive control. Oxamflatin also decreased DNA methylation of POU5F1 regulatory elements and centromeric repeat elements in day-7 blastocysts. When compared to in vitro-fertilized (IVF) embryos, the methylation status of POU5F1, NANOG, and centromeric repeat was similar in the cloned embryos, indicating these genes were successfully reprogrammed. However, compared to the lack of methylation of XIST in day-7 IVF embryos, a higher methylation level in day-7 cloned embryos was observed, implying that X chromosomes were activated in day-7 IVF blastocysts, but were not fully activated in cloned embryos, i.e., reprogramming of XIST was delayed. A time-course analysis of XIST DNA methylation on day-13, -15, -17, and -19 in vivo embryos revealed that XIST methylation initiated at about day 13 and was not completed by day 19. The methylation of the XIST gene in day-19 control cloned embryos was delayed again when compared to in vivo embryos. However, methylation of XIST in Oxamflatin-treated embryos was comparable with in vivo embryos, which further demonstrated that Oxamflatin could accelerate the delayed reprogramming of XIST gene and thus might improve cloning efficiency.
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Affiliation(s)
- Jiude Mao
- 1 National Swine Resource and Research Center, University of Missouri , Columbia, MO, 65211
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Kim JS, Choi HW, Araúzo-Bravo MJ, Schöler HR, Do JT. Reactivation of inactive X chromosome and post-transcriptional reprogramming of Xist in induced pluripotent stem cells. J Cell Sci 2014; 128:81-7. [DOI: 10.1242/jcs.154294] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Direct reprogramming of somatic cells to pluripotent stem cells entails the obliteration of somatic cell memory and the reestablishment of epigenetic events. Induced pluripotent stem (iPS) cells have been created by reprogramming somatic cells through the transduction of reprogramming factors. During cell reprogramming, female somatic cells must overcome at least one more barrier than male somatic cells in order to enter a pluripotent state, as they must reactivate an inactive X chromosome (Xi). In this study, we investigated whether the sex of somatic cells affects reprogramming efficiency, differentiation potential, and the post-transcriptional processing of Xist RNA after reprogramming. There were no differences between male and female iPS cells with respect to reprogramming efficiency or their differentiation potential in vivo. However, reactivating Xi took longer than reactivating pluripotency-related genes. We also found that direct reprogramming leads to gender appropriate posttranscriptional reprogramming: like male embryonic stem (ES) cells, male iPS cells expressed only the long Xist isoform, whereas female iPS cells, like female ES cells, expressed both the long and short isoforms.
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Han DW, Tapia N, Araúzo-Bravo MJ, Lim KT, Kim KP, Ko K, Lee HT, Schöler HR. Sox2 Level Is a Determinant of Cellular Reprogramming Potential. PLoS One 2013; 8:e67594. [PMID: 23825671 PMCID: PMC3688988 DOI: 10.1371/journal.pone.0067594] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 05/23/2013] [Indexed: 11/19/2022] Open
Abstract
Epiblast stem cells (EpiSCs) and embryonic stem cells (ESCs) differ in their in vivo differentiation potential. While ESCs form teratomas and efficiently contribute to the development of chimeras, EpiSCs form teratomas but very rarely chimeras. In contrast to their differentiation potential, the reprogramming potential of EpiSCs has not yet been investigated. Here we demonstrate that the epiblast-derived pluripotent stem cells EpiSCs and P19 embryonal carcinoma cells (ECCs) exhibit a lower reprogramming potential than ESCs and F9 ECCs. In addition, we show that the low reprogramming ability is due to the lower levels of Sox2 in epiblast-derived stem cells. Consistent with this observation, overexpression of Sox2 enhances reprogramming efficiency. In summary, these findings suggest that a low reprogramming potential is a general feature of epiblast-derived stem cells and that the Sox2 level is a determinant of the cellular reprogramming potential.
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Affiliation(s)
- Dong Wook Han
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Republic of Korea
- Institute of Functional Genomics, Konkuk University, Seoul, Republic of Korea
- * E-mail:
| | - Natalia Tapia
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marcos J. Araúzo-Bravo
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Kyung Tae Lim
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Kee Pyo Kim
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Kinarm Ko
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Republic of Korea
- Institute of Functional Genomics, Konkuk University, Seoul, Republic of Korea
| | - Hoon Taek Lee
- Department of Stem Cell Biology, School of Medicine, Konkuk University, Seoul, Republic of Korea
| | - Hans R. Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
- University of Münster, Medical Faculty, Münster, Germany
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Peri S, de Cicco RL, Santucci-Pereira J, Slifker M, Ross EA, Russo IH, Russo PA, Arslan AA, Belitskaya-Lévy I, Zeleniuch-Jacquotte A, Bordas P, Lenner P, Åhman J, Afanasyeva Y, Johansson R, Sheriff F, Hallmans G, Toniolo P, Russo J. Defining the genomic signature of the parous breast. BMC Med Genomics 2012; 5:46. [PMID: 23057841 PMCID: PMC3487939 DOI: 10.1186/1755-8794-5-46] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Accepted: 09/19/2012] [Indexed: 11/10/2022] Open
Abstract
Background It is accepted that a woman's lifetime risk of developing breast cancer after menopause is reduced by early full term pregnancy and multiparity. This phenomenon is thought to be associated with the development and differentiation of the breast during pregnancy. Methods In order to understand the underlying molecular mechanisms of pregnancy induced breast cancer protection, we profiled and compared the transcriptomes of normal breast tissue biopsies from 71 parous (P) and 42 nulliparous (NP) healthy postmenopausal women using Affymetrix Human Genome U133 Plus 2.0 arrays. To validate the results, we performed real time PCR and immunohistochemistry. Results We identified 305 differentially expressed probesets (208 distinct genes). Of these, 267 probesets were up- and 38 down-regulated in parous breast samples; bioinformatics analysis using gene ontology enrichment revealed that up-regulated genes in the parous breast represented biological processes involving differentiation and development, anchoring of epithelial cells to the basement membrane, hemidesmosome and cell-substrate junction assembly, mRNA and RNA metabolic processes and RNA splicing machinery. The down-regulated genes represented biological processes that comprised cell proliferation, regulation of IGF-like growth factor receptor signaling, somatic stem cell maintenance, muscle cell differentiation and apoptosis. Conclusions This study suggests that the differentiation of the breast imprints a genomic signature that is centered in the mRNA processing reactome. These findings indicate that pregnancy may induce a safeguard mechanism at post-transcriptional level that maintains the fidelity of the transcriptional process.
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Affiliation(s)
- Suraj Peri
- Breast Cancer Research Laboratory, Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Takehashi M, Tada M, Kanatsu-Shinohara M, Morimoto H, Kazuki Y, Oshimura M, Tada T, Shinohara T. Hybridization of Testis-Derived Stem Cells with Somatic Cells and Embryonic Stem Cells in Mice1. Biol Reprod 2012; 86:178. [DOI: 10.1095/biolreprod.112.098988] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Piccolo FM, Pereira CF, Cantone I, Brown K, Tsubouchi T, Soza-Ried J, Merkenschlager M, Fisher AG. Using heterokaryons to understand pluripotency and reprogramming. Philos Trans R Soc Lond B Biol Sci 2011; 366:2260-5. [PMID: 21727131 DOI: 10.1098/rstb.2011.0004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Reprogramming differentiated cells towards pluripotency can be achieved by different experimental strategies including the forced expression of specific 'inducers' and nuclear transfer. While these offer unparalleled opportunities to generate stem cells and advance disease modelling, the relatively low levels of successful reprogramming achieved (1-2%) makes a direct analysis of the molecular events associated with productive reprogramming very challenging. The generation of transient heterokaryons between human differentiated cells (such as lymphocytes or fibroblasts) and mouse pluripotent stem cell lines results in a much higher frequency of successful conversion (15% SSEA4 expressing cells) and provides an alternative approach to study early events during reprogramming. Under these conditions, differentiated nuclei undergo a series of remodelling events before initiating human pluripotent gene expression and silencing differentiation-associated genes. When combined with genetic or RNAi-based approaches and high-throughput screens, heterokaryon studies can provide important new insights into the factors and mechanisms required to reprogramme unipotent cells towards pluripotency.
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Affiliation(s)
- Francesco M Piccolo
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
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Do JT, Choi HW, Choi Y, Schöler HR. Pluripotent Hybrid Cells Contribute to Extraembryonic as well as Embryonic Tissues. Stem Cells Dev 2011; 20:1063-9. [DOI: 10.1089/scd.2010.0385] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Jeong Tae Do
- Laboratory of Stem Cell and Developmental Biology, CHA Stem Cell Institute, CHA University, Seoul, Republic of Korea
| | - Hyun Woo Choi
- Laboratory of Stem Cell and Developmental Biology, CHA Stem Cell Institute, CHA University, Seoul, Republic of Korea
| | - Youngsok Choi
- Department of Biomedical Science, CHA University, Seoul, Republic of Korea
| | - Hans R. Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
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Shafa M, Krawetz R, Rancourt DE. Returning to the stem state: Epigenetics of recapitulating pre-differentiation chromatin structure. Bioessays 2010; 32:791-9. [DOI: 10.1002/bies.201000033] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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