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Waisman A, Sevlever F, Saulnier D, Francia M, Blanco R, Amín G, Lombardi A, Biani C, Palma MB, Scarafía A, Smucler J, La Greca A, Moro L, Sevlever G, Guberman A, Miriuka S. The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network. Sci Rep 2024; 14:10420. [PMID: 38710730 PMCID: PMC11074312 DOI: 10.1038/s41598-024-59247-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
In the mouse embryo, the transition from the preimplantation to the postimplantation epiblast is governed by changes in the gene regulatory network (GRN) that lead to transcriptional, epigenetic, and functional changes. This transition can be faithfully recapitulated in vitro by the differentiation of mouse embryonic stem cells (mESCs) to epiblast-like cells (EpiLCs), that reside in naïve and formative states of pluripotency, respectively. However, the GRN that drives this conversion is not fully elucidated. Here we demonstrate that the transcription factor OCT6 is a key driver of this process. Firstly, we show that Oct6 is not expressed in mESCs but is rapidly induced as cells exit the naïve pluripotent state. By deleting Oct6 in mESCs, we find that knockout cells fail to acquire the typical morphological changes associated with the formative state when induced to differentiate. Additionally, the key naïve pluripotency TFs Nanog, Klf2, Nr5a2, Prdm14, and Esrrb were expressed at higher levels than in wild-type cells, indicating an incomplete dismantling of the naïve pluripotency GRN. Conversely, premature expression of Oct6 in naïve cells triggered a rapid morphological transformation mirroring differentiation, that was accompanied by the upregulation of the endogenous Oct6 as well as the formative genes Sox3, Zic2/3, Foxp1, Dnmt3A and FGF5. Strikingly, we found that OCT6 represses Nanog in a bistable manner and that this regulation is at the transcriptional level. Moreover, our findings also reveal that Oct6 is repressed by NANOG. Collectively, our results establish OCT6 as a key TF in the dissolution of the naïve pluripotent state and support a model where Oct6 and Nanog form a double negative feedback loop which could act as an important toggle mediating the transition to the formative state.
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Affiliation(s)
- Ariel Waisman
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
| | - Federico Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Denisse Saulnier
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Marcos Francia
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Renata Blanco
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Guadalupe Amín
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Antonella Lombardi
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Celeste Biani
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - María Belén Palma
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Agustina Scarafía
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Joaquín Smucler
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandro La Greca
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Lucía Moro
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Gustavo Sevlever
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina
| | - Alejandra Guberman
- Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Facultad de Ciencias Exactas y Naturales, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
- Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago Miriuka
- Laboratorio de Investigación Aplicada a Neurociencias (LIAN), Fundación Para la Lucha Contra las Enfermedades Neurológicas de la Infancia (FLENI), Instituto de Neurociencias (INEU), CONICET, Buenos Aires, Argentina.
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Yao H, Shao Q, Shao Y. Transcription Factor CTCFL Promotes Cell Proliferation, Migration, and Invasion in Gastric Cancer via Activating DPPA2. Comput Math Methods Med 2021; 2021:9097931. [PMID: 34721660 DOI: 10.1155/2021/9097931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/03/2021] [Indexed: 11/17/2022]
Abstract
Objective To explore the relationship between CTCFL and DPPA2 and validate the positive role of CTCFL/DPPA2 in cell malignant behaviors in gastric cancer. Methods We predicted gastric cancer-related transcription factors and corresponding target mRNAs through bioinformatics. Levels of CTCFL and DPPA2 were assessed via qRT-PCR and western blot. In vitro experiments were utilized to assay the cell biological behaviors. CHIP was utilized for the assessment of the targeted relationship between CTCFL and DPPA2. Results CTCFL and DPPA2 were both highly expressed in gastric cancer cells, and high CTCFLL and DPPA2 could promote cell malignant behaviors. CHIP validated that DPPA2 was a target of CTCFL. In addition, high DPPA2 rescued the repressive impact of CTCFL silencing on the cell proliferation, migration, and invasion in gastric cancer. Conclusion The transcription factor CTCFL fosters cell proliferative, migratory, and invasive properties via activating DPPA2 in gastric cancer.
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Wang J, Zhuang H, Zhang H, Li Q, Cao X, Lin Z, Lin T, Chen X, Ni X, Yang J, Zhao Y, Shen L, Wang H, Zhu J, Ye M, Jin X. SPOP suppresses testicular germ cell tumors progression through ubiquitination and degradation of DPPA2. Biochem Biophys Res Commun 2021; 557:55-61. [PMID: 33862460 DOI: 10.1016/j.bbrc.2021.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 10/21/2022]
Abstract
Dysregulation of the ubiquitin-proteasome pathway is strongly associated with cancer initiation and progression. Speckle-type POZ(pox virus and zinc finger protein) protein(SPOP) is an adapter protein of CUL3-based E3 ubiquitin ligase complexes. Gene expression profiling from the Cancer Genome Atlas (TCGA) suggests that SPOP is downregulated in testicular germ cell tumors (TGCTs), but the specific contribution of this protein remains to be explored. In this study, we show that the germ line-specific factor DPPA2 was identified as a proteolytic substrate for the SPOP-CUL3-RBX1 E3 ubiquitin-ligase complex. SPOP specifically binds to a SPOP-binding consensus (SBC) degron located in DPPA2 and targets DPPA2 for degradation via the ubiquitin-proteasome pathway. SPOP downregulation increases the expression of pluripotency markers OCT4 and Nanog but decreases that of early differentiation marker gene Fst. This effect is partly dependent on its activity toward DPPA2. In addition, the dysregulation of SPOP-DPPA2 axis contributes to the malignant transformation phenotypes of TGCT cells.
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Affiliation(s)
- Jian Wang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Hui Zhuang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Hui Zhang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Qian Li
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Xinyi Cao
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Zihan Lin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Ting Lin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Xiwei Chen
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Xiaoqi Ni
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Jianye Yang
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Yiting Zhao
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Liliang Shen
- Department of Urology, Yinzhou Renmin Hospital Affiliated to Medical School of Ningbo University, Ningbo, 315040, China
| | - Haibiao Wang
- Department of Hepato-biliary-pancreatic Surgery, The Affiliated Ningbo Medical Center of LiHuiLi Hospital of Medical School of Ningbo University, Ningbo, 315048, China
| | - Jie Zhu
- Department of Hepato-biliary-pancreatic Surgery, The Affiliated Ningbo Medical Center of LiHuiLi Hospital of Medical School of Ningbo University, Ningbo, 315048, China
| | - Meng Ye
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China
| | - Xiaofeng Jin
- The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo, 315211, China.
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Setthawong P, Phakdeedindan P, Techakumphu M, Tharasanit T. Molecular signature and colony morphology affect in vitro pluripotency of porcine induced pluripotent stem cells. Reprod Domest Anim 2021; 56:1104-1116. [PMID: 34013645 DOI: 10.1111/rda.13954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/17/2021] [Indexed: 12/29/2022]
Abstract
Overall efficiency of cell reprogramming for porcine fibroblasts into induced pluripotent stem cells (iPSCs) is currently poor, and few cell lines have been established. This study examined gene expression during early phase of cellular reprogramming in the relationship to the iPSC colony morphology and in vitro pluripotent characteristics. Fibroblasts were reprogrammed with OCT4, SOX2, KLF4 and c-MYC. Two different colony morphologies referred to either compact (n = 10) or loose (n = 10) colonies were further examined for proliferative activity, gene expression and in vitro pluripotency. A total of 1,697 iPSC-like colonies (2.34%) were observed after gene transduction. The compact colonies contained with tightly packed cells with a distinct-clear border between the colony and feeder cells, while loose colonies demonstrated irregular colony boundary. For quantitative expression of genes responsible for early phase cell reprogramming, the Dppa2 and EpCAM were significantly upregulated while NR0B1 was downregulated in compact colonies compared with loose phenotype (p < .05). Higher proportion of compact iPSC phenotype (5 of 10, 50%) could be maintained in undifferentiated state for more than 50 passages compared unfavourably with loose morphology (3 of 10, 30%). All iPS cell lines obtained from these two types of colony morphologies expressed pluripotent genes and proteins (OCT4, NANOG and E-cadherin). In addition, they could aggregate and form three-dimensional structure of embryoid bodies. However, only compact iPSC colonies differentiated into three germ layers. Molecular signature of early phase of cell reprogramming coupled with primary colony morphology reflected the in vitro pluripotency of porcine iPSCs. These findings can be simply applied for pre-screening selection of the porcine iPSC cell line.
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Affiliation(s)
- Piyathip Setthawong
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Praopilas Phakdeedindan
- Department of Animal Husbandry, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Mongkol Techakumphu
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Theerawat Tharasanit
- Department of Obstetrics, Gynaecology and Reproduction, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,CU-Animal Fertility Research Unit, Chulalongkorn University, Bangkok, Thailand
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Abstract
Zinc finger and SCAN domain containing 4 (Zscan4) is a gene that is specifically expressed during zygotic genome activation (ZGA) in mouse preimplantation embryos, and a
reduction of Zscan4 transcripts leads to developmental failure. In mouse embryonic stem cells (ESCs), Zscan4 is expressed transiently in as little as 1–5%
of the cell population. Zscan4 has also been shown to enhance the efficiency of mouse induced pluripotent stem cells (iPSCs) generation and their quality. Although ZSCAN4
plays important roles in murine embryos and stem cells, its expression and role in bovine embryos is unknown. This study examines ZSCAN4 transcripts in bovine embryos at
various developmental stages and attempts to elucidate the functions of ZSCAN4 during bovine preimplantation development. ZSCAN4 transcripts were found to be upregulated at
the 8- and 16-cell stages. We next attempted ZSCAN4 downregulation in bovine early embryos by RNA interference and evaluated developmental competency and transcripts levels
of genes involved in ZGA and iPSCs generation. Although the bovine embryos injected with ZSCAN4-siRNA could develop to the 8-cell stage, very few were developing beyond the
16-cell stage. PIWIL2 expression was reduced in ZSCAN4 downregulated embryos. It is possible that ZSCAN4 downregulated embryos fail to
regulate gene expression during ZGA. Our results indicate that ZSCAN4 is an important factor for the preimplantation development of bovine embryos.
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Affiliation(s)
- Kazuki Takahashi
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate 020-8550, Japan
| | - Pablo J Ross
- Department of Animal Science, University of California Davis, CA 95616, U. S. A
| | - Ken Sawai
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate 020-8550, Japan.,Faculty of Agriculture, Iwate University, Iwate 020-8550, Japan
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Li L, Wang Y, Wang Q, Qu J, Wei X, Xu J, Wang Y, Suo F, Zhang Y. High developmental pluripotency‑associated 4 expression promotes cell proliferation and glycolysis, and predicts poor prognosis in non‑small‑cell lung cancer. Mol Med Rep 2019; 20:445-454. [PMID: 31180527 PMCID: PMC6580026 DOI: 10.3892/mmr.2019.10272] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 03/15/2019] [Indexed: 12/22/2022] Open
Abstract
The developmental pluripotency‑associated 4 (Dppa4) gene serves critical roles in cell self‑renewal, as well as in cancer development and progression. However, the regulatory role of Dppa4 in non‑small‑cell lung cancer (NSCLC) and its underlying mechanisms remain elusive. The aim of the present study was to investigate the biological function of Dppa4 in NSCLC and its underlying mechanism of action. Dppa4 expression was measured in NSCLC tissue samples and cell lines, and its effect on cell proliferation and the expression of glycolytic enzymes was determined. In addition, the underlying mechanisms of Dppa4‑induced alterations in glycolysis were analyzed. Univariate and multivariate analyses were also performed to analyze the prognostic significance of clinicopathological characteristics. Dppa4 was found to be highly expressed in NSCLC tissues and cell lines. Furthermore, it was observed that Dppa4 was correlated with the degree of tumor differentiation and TNM stage. Univariate and multivariate analyses identified Dppa4 expression and clinical stage as prognostic factors for NSCLC patients. Kaplan‑Meier analysis further revealed that patients with lower Dppa4 expression exhibited a better prognosis. In NSCLC cells, Dppa4 knockdown inhibited cell proliferation, while Dppa4 overexpression enhanced cell proliferation, which was likely mediated by glycolysis promotion. Dppa4 knockdown had no evident effect on the majority of enzymes examined; however, glucose transporter type 4 (GLUT‑4) and pyruvate kinase isozyme M2 were significantly upregulated, and hexokinase II (HK‑II) and lactate dehydrogenase B (LDHB) were downregulated following Dppa4 knockdown. By contrast, Dppa4 overexpression resulted in downregulation of GLUT‑4, and upregulation of HK‑II, enolase and LDHB, whereas it had no effect on other enzymes. Since the most evident effect was observed on LDHB, further functional experiments demonstrated that this enzyme reversed the promoting effects of Dppa4 in NSCLC. In conclusion, Dppa4 promotes NSCLC progression, partly through glycolysis by LDHB. Thus, the Dppa4‑LDHB axis critically contributes to glycolysis in NSCLC cells, thereby promoting NSCLC development and progression.
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Affiliation(s)
- Longfei Li
- Department of Cardiothoracic Surgery, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Yufeng Wang
- Department of Nuclear Medicine, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Qiang Wang
- Department of Radiotherapy and Oncology, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Jingming Qu
- Department of Cardiothoracic Surgery, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Xiangju Wei
- Department of Cardiothoracic Surgery, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Jilei Xu
- Department of Cardiothoracic Surgery, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Yuanjin Wang
- Department of Cardiothoracic Surgery, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Feng Suo
- Department of Cardiothoracic Surgery, Xuzhou Cancer Hospital, Xuzhou, Jiangsu 221000, P.R. China
| | - Yangjie Zhang
- Department of Orthopedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
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Cheng S, Pei Y, He L, Peng G, Reinius B, Tam PP, Jing N, Deng Q. Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development. Cell Rep 2019; 26:2593-2607.e3. [DOI: 10.1016/j.celrep.2019.02.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/29/2018] [Accepted: 02/08/2019] [Indexed: 01/13/2023] Open
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Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell 2019; 176:816-830.e18. [PMID: 30595451 PMCID: PMC6546437 DOI: 10.1016/j.cell.2018.11.036] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/01/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023]
Abstract
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
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Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | | | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Marco Michalski
- Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nicolas P Holcomb
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jesse L Turner
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | | | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; UC San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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Dupont G, Yilmaz E, Loukas M, Macchi V, De Caro R, Tubbs RS. Human embryonic stem cells: Distinct molecular personalities and applications in regenerative medicine. Clin Anat 2018; 32:354-360. [PMID: 30521112 PMCID: PMC6850663 DOI: 10.1002/ca.23318] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 12/02/2018] [Indexed: 12/11/2022]
Abstract
The field of stem cell biology is exciting because it provides researchers and clinicians with seemingly unlimited applications for treating many human diseases. Stem cells are a renewable source of pluripotent cells that can differentiate into nearly all human cell types. In this article we focus particularly on human embryonic stem (hES) cells, derived from the inner cell mass of the blastocyst and cultured for expansion while remaining undifferentiated, to explore their unique molecular personalities and clinical applications. The aim of this literature review is to reflect the interest in hES cells and to provide a resource for researchers and clinicians interested in the molecular characteristics of such cells. Clin. Anat. 32:354–360, 2019. © 2018 The Authors. Clinical Anatomy published by Wiley Periodicals, Inc. on behalf of American Association of Clinical Anatomists.
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Affiliation(s)
| | - Emre Yilmaz
- Seattle Science Foundation, Seattle, Washington
| | - Marios Loukas
- Department of Anatomical Sciences, St. George's University, Grenada, West Indies
| | - Veronica Macchi
- Department of Neuroscience, Anatomy Institute, University of Padova, Padova, Italy
| | - Raffaele De Caro
- Department of Neuroscience, Anatomy Institute, University of Padova, Padova, Italy
| | - R Shane Tubbs
- Seattle Science Foundation, Seattle, Washington.,Department of Anatomical Sciences, St. George's University, Grenada, West Indies
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11
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Chen X, Han T, Fisher JE, Harrouk W, Tassinari MS, Merry GE, Sloper D, Fuscoe JC, Hansen DK, Inselman AL. Transcriptomics analysis of early embryonic stem cell differentiation under osteoblast culture conditions: Applications for detection of developmental toxicity. Reprod Toxicol 2017; 69:75-83. [PMID: 28189605 DOI: 10.1016/j.reprotox.2017.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/30/2016] [Accepted: 02/01/2017] [Indexed: 12/14/2022]
Abstract
The mouse embryonic stem cell test (mEST) is a promising in vitro assay for predicting developmental toxicity. In the current study, early differentiation of D3 mouse embryonic stem cells (mESCs) under osteoblast culture conditions and embryotoxicity of cadmium sulfate were examined. D3 mESCs were exposed to cadmium sulfate for 24, 48 or 72h, and whole genome transcriptional profiles were determined. The results indicate a track of differentiation was identified as mESCs differentiate. Biological processes that were associated with differentiation related genes included embryonic development and, specifically, skeletal system development. Cadmium sulfate inhibited mESC differentiation at all three time points. Functional pathway analysis indicated biological pathways affected included those related to skeletal development, renal and reproductive function. In summary, our results suggest that transcriptional profiles are a sensitive indicator of early mESC differentiation. Transcriptomics may improve the predictivity of the mEST by suggesting possible modes of action for tested chemicals.
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Affiliation(s)
- Xinrong Chen
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, United States.
| | - Tao Han
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, United States.
| | - J Edward Fisher
- Center for Drug Evaluation and Research, Food and Drug Administration, United States.
| | - Wafa Harrouk
- Center for Drug Evaluation and Research, Food and Drug Administration, United States.
| | - Melissa S Tassinari
- Center for Drug Evaluation and Research, Food and Drug Administration, United States.
| | - Gwenn E Merry
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, United States.
| | - Daniel Sloper
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, United States.
| | - James C Fuscoe
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, United States.
| | - Deborah K Hansen
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, United States.
| | - Amy L Inselman
- Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, United States.
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12
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Choi KH, Park JK, Son D, Hwang JY, Lee DK, Ka H, Park J, Lee CK. Reactivation of Endogenous Genes and Epigenetic Remodeling Are Barriers for Generating Transgene-Free Induced Pluripotent Stem Cells in Pig. PLoS One 2016; 11:e0158046. [PMID: 27336671 PMCID: PMC4918974 DOI: 10.1371/journal.pone.0158046] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/09/2016] [Indexed: 12/22/2022] Open
Abstract
Cellular reprogramming of committed cells into a pluripotent state can be induced by ectopic expression of genes such as OCT4, SOX2, KLF4, and MYC. Reprogrammed cells can be maintained by activating endogenous pluripotent networks without transgene expression. Although various research groups have attempted to generate pig induced pluripotent stem cells (iPSCs), authentic iPSCs have not be obtained, instead showing dependence on transgene expression. In this study, iPSCs were derived from porcine fetal fibroblasts via drug-inducible vectors carrying human transcription factors (OCT4, SOX2, KLF4, and MYC). Therefore, this study investigated characteristics of iPSCs and reprogramming mechanisms in pig. The iPSCs were stably maintained over an extended period with potential in vitro differentiation into three germ layers. In addition, the pluripotent state of iPSCs was regulated by modulating culture conditions. They showed naive- or primed-like pluripotent states in LIF or bFGF supplemented culture conditions, respectively. However, iPSCs could not be maintained without ectopic expression of transgenes. The cultured iPSCs expressed endogenous transcription factors such as OCT4 and SOX2, but not NANOG (a known gateway to complete reprogramming). Endogenous genes related to mesenchymal-to-epithelial transition (DPPA2, CDH1, EPCAM, and OCLN) were not sufficiently reactivated, as measured by qPCR. DNA methylation analysis for promoters of OCT4, NANOG, and XIST showed that epigenetic reprogramming did not occur in female iPSCs. Based on our results, expression of exogenous genes could not sufficiently activate the essential endogenous genes and remodel the epigenetic milieu to achieve faithful pluripotency in pig. Accordingly, investigating iPSCs could help us improve and develop reprogramming methods by understanding reprogramming mechanisms in pig.
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Affiliation(s)
- Kwang-Hwan Choi
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Jin-Kyu Park
- Division of Animal Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States of America
| | - Dongchan Son
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Jae Yeon Hwang
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Dong-Kyung Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
| | - Hakhyun Ka
- Department of Biological Resources and Technology, Yonsei University, Wonju, Korea
| | | | - Chang-Kyu Lee
- Department of Agricultural Biotechnology, Animal Biotechnology Major, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Korea
- Institute of Green Bio Science and Technology, Seoul National University, Pyeong Chang, Kangwon do, Korea
- * E-mail:
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13
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Shabestarian H, Ghodsi M, Mallak AJ, Jafarian AH, Montazer M, Forghanifard MM. DPPA2 Protein Expression is Associated with Gastric Cancer Metastasis. Asian Pac J Cancer Prev 2016; 16:8461-5. [DOI: 10.7314/apjcp.2015.16.18.8461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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Zhang M, Cui F, Lu S, Lu H, Xue Y, Wang J, Chen J, Zhao S, Ma S, Zhang Y, Yu Y, Peng Z, Tang H. Developmental pluripotency-associated 4: a novel predictor for prognosis and a potential therapeutic target for colon cancer. J Exp Clin Cancer Res 2015; 34:60. [PMID: 26063247 PMCID: PMC4466839 DOI: 10.1186/s13046-015-0176-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 05/27/2015] [Indexed: 12/12/2022]
Abstract
Backgrounds Developmental pluripotency-associated 4 (Dppa4) gene plays an important role in self-renewal and pluripotency sustainability in embryonic stem cells. It is re-expressed in several malignant tumors and is identified as a new pluripotency-related oncogene. The present study investigates the expression and clinical significance of Dppa4 in colon cancer. Methods Real-time polymerase chain reaction and Western blotting were used to evaluate Dppa4 mRNA and protein expression in 39 pairs of fresh-frozzen colon cancer samples, which were compared with adjacent normal mucosa. The Dppa4 protein was evaluated by immunohistochemical techniques using colon tissue microarrays (TMA). The sample included 185 cancer specimens and corresponding normal colorectal mucosa. The effect of Dppa4 knockdown on colorectal cancer cell proliferation was investigated using Cell Counting Kit-8 (CCK8) assays and colony-formation assays. Results Both the mRNA and protein level expression of Dppa4 gene was found to be upregulated in colon cancer tissues. Furthermore, the upregulated expression of Dppa4 was significantly correlated with the results of American Joint Committee on Cancer (AJCC) stage (P = 0.01), invasion depth (P = 0.028), nodal involvement (P = 0.012), distant metastasis (P = 0.003), and differentiation (P = 0.002). Dppa4 was also shown to be an independent prognostic indicator of disease-free survival (HR 6.118, 95 % CI 3.004–12.462) and overall survival (HR 6.348, 95 % CI 2.875–14.014) for patients with colon cancer. Knockdown of Dppa4 expression inhibited the proliferation of colorectal cancer cell lines through G1/S transition regulation. Conclusion The results indicate that Dppa4 might play an important role in colon cancer progression and function as a novel prognostic indicator and a potential therapeutic target.
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Affiliation(s)
- Meng Zhang
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Feifei Cui
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Su Lu
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Huijun Lu
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Yingming Xue
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Jingtao Wang
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Jian Chen
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Senlin Zhao
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Shaofei Ma
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Yu Zhang
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Yang Yu
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Zhihai Peng
- Departments of General Surgery, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
| | - Huamei Tang
- Departments of Pathology, Shanghai Jiaotong University Affiiated First People's Hospital, Shanghai, 200080, People's Republic of China.
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15
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Wang L, Zhao Y, Bao X, Zhu X, Kwok YKY, Sun K, Chen X, Huang Y, Jauch R, Esteban MA, Sun H, Wang H. LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. Cell Res 2015; 25:335-50. [PMID: 25686699 PMCID: PMC4349245 DOI: 10.1038/cr.2015.21] [Citation(s) in RCA: 193] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 11/01/2014] [Accepted: 11/18/2014] [Indexed: 12/17/2022] Open
Abstract
Emerging studies document the roles of long non-coding RNAs (LncRNAs) in regulating gene expression at chromatin level but relatively less is known how they regulate DNA methylation. Here we identify an lncRNA, Dum (developmental pluripotency-associated 2 (Dppa2) Upstream binding Muscle lncRNA) in skeletal myoblast cells. The expression of Dum is dynamically regulated during myogenesis in vitro and in vivo. It is also transcriptionally induced by MyoD binding upon myoblast differentiation. Functional analyses show that it promotes myoblast differentiation and damage-induced muscle regeneration. Mechanistically, Dum was found to silence its neighboring gene, Dppa2, in cis through recruiting Dnmt1, Dnmt3a and Dnmt3b. Furthermore, intrachromosomal looping between Dum locus and Dppa2 promoter is necessary for Dum/Dppa2 interaction. Collectively, we have identified a novel lncRNA that interacts with Dnmts to regulate myogenesis.
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Affiliation(s)
- Lijun Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yu Zhao
- Department of Obstetrics and Gynaecology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xichen Bao
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Xihua Zhu
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yvonne Ka-yin Kwok
- Department of Obstetrics and Gynaecology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Kun Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaona Chen
- Department of Obstetrics and Gynaecology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Yongheng Huang
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ralf Jauch
- Genome Regulation Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Miguel A Esteban
- Laboratory of Chromatin and Human Disease, Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
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16
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Ghodsi M, Jafarian AH, Montazer M, Sadeghian MH, Forghanifard MM. Diagnostic clinical relevance of developmental pluripotency-associated 2 (DPPA2) in colorectal cancer. Int J Surg 2015; 13:193-7. [DOI: 10.1016/j.ijsu.2014.11.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/22/2014] [Indexed: 12/17/2022]
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17
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Tung PY, Varlakhanova NV, Knoepfler PS. Identification of DPPA4 and DPPA2 as a novel family of pluripotency-related oncogenes. Stem Cells 2014; 31:2330-42. [PMID: 23963736 DOI: 10.1002/stem.1526] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 07/07/2013] [Accepted: 07/07/2013] [Indexed: 11/07/2022]
Abstract
In order to identify novel pluripotency-related oncogenes, an expression screen for oncogenic foci-inducing genes within a retroviral human embryonic stem cell cDNA library was conducted. From this screen, we identified not only known oncogenes but also intriguingly the key pluripotency factor, DPPA4 (developmental pluripotency-associated four) that encodes a DNA binding SAP domain-containing protein. DPPA4 has not been previously identified as an oncogene but is highly expressed in embryonal carcinomas, pluripotent germ cell tumors, and other cancers. DPPA4 is also mutated in some cancers. In direct transformation assays, we validated that DPPA4 is an oncogene in both mouse 3T3 cells and immortalized human dermal fibroblasts. Overexpression of DPPA4 generates oncogenic foci (sarcoma cells) and causes anchorage-independent growth. The in vitro transformed cells also give rise to tumors in immunodeficient mice. Furthermore, functional analyses indicate that both the DNA-binding SAP domain and the histone-binding C-terminal domain are critical for the oncogenic transformation activity of DPPA4. Downregulation of DPPA4 in E14 mouse embryonic stem cells and P19 mouse embryonic carcinoma cells causes decreased cell proliferation in each case. In addition, DPPA4 overexpression induces cell proliferation through genes related to regulation of G1/S transition. Interestingly, we observed similar findings for family member DPPA2. Thus, we have identified a new family of pluripotency-related oncogenes consisting of DPPA2 and DPPA4. Our findings have important implications for stem cell biology and tumorigenesis.
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Affiliation(s)
- Po-Yuan Tung
- Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, California, USA; University of California Davis Genome Center, University of California Davis, Davis, California, USA; UC Davis Comprehensive Cancer Center, Shriners Hospital For Children Northern California, Sacramento, California, USA; Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, California, USA
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Schmaltz-panneau B, Jouneau L, Osteil P, Tapponnier Y, Afanassieff M, Moroldo M, Jouneau A, Daniel N, Archilla C, Savatier P, Duranthon V. Contrasting transcriptome landscapes of rabbit pluripotent stem cells in vitro and in vivo. Anim Reprod Sci 2014; 149:67-79. [DOI: 10.1016/j.anireprosci.2014.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 05/26/2014] [Indexed: 01/25/2023]
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19
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Raeisossadati R, Abbaszadegan MR, Moghbeli M, Tavassoli A, Kihara AH, Forghanifard MM. Aberrant expression of DPPA2 and HIWI genes in colorectal cancer and their impacts on poor prognosis. Tumour Biol 2014; 35:5299-305. [PMID: 24532429 DOI: 10.1007/s13277-014-1690-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Accepted: 01/23/2014] [Indexed: 02/06/2023] Open
Abstract
Cancer cells have countless behaviors of pluripotent embryonic stem cells and germ line cells, such as unlimited proliferation, self-renewal, and migration. Expression of specific germ line and embryonic genes in tumor cells may be associated with indefinite growth and invasiveness of such cells. Developmental pluripotency factor 2 (DPPA2) and HIWI are two important developmental genes which are involved in embryonic and germ line stem cell properties. Deciphering the role of these genes seems to be necessary for understanding cancer initiation and progression. Tumoral and normal tissues from 46 colorectal cancer (CRC) patients were subjected to gene expression analysis using quantitative real-time reverse transcription-polymerase chain reaction, prior to any therapeutic intervention. Overexpression of DPPA2 and HIWI was detected in 26.1 and 34.8 % of specimens, respectively. Significant correlation between DPPA2 overexpression and lymph node metastasis of the tumor cells (P=0.049) was seen in the samples with advanced stages (III/IV) of the tumor development. HIWI mRNA expression was significantly associated to the depth of tumor invasion (P=0.020) and the stage of tumorigenesis progression (P=0.030). In samples with overexpression of at least one gene, DPPA2 mRNA expression was significantly correlated to the stage of tumor (P=0.017). In the same samples, a significant correlation was observed between mRNA expression of HIWI and the stage of tumor cells (P=0.034). These results documented the important role of HIWI and DPPA2 in tumorigenesis and also in lymph node metastasis of tumor cells. Further evaluation is required to uncover the detailed role of HIWI and DPPA2 and their interactions in tumorigenesis of CRC.
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Affiliation(s)
- Reza Raeisossadati
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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20
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Lee KC, Wong WK, Feng B. Decoding the Pluripotency Network: The Emergence of New Transcription Factors. Biomedicines 2013; 1:49-78. [PMID: 28548056 PMCID: PMC5423462 DOI: 10.3390/biomedicines1010049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Revised: 12/10/2013] [Accepted: 12/11/2013] [Indexed: 12/25/2022] Open
Abstract
Since the successful isolation of mouse and human embryonic stem cells (ESCs) in the past decades, massive investigations have been conducted to dissect the pluripotency network that governs the ability of these cells to differentiate into all cell types. Beside the core Oct4-Sox2-Nanog circuitry, accumulating regulators, including transcription factors, epigenetic modifiers, microRNA and signaling molecules have also been found to play important roles in preserving pluripotency. Among the various regulations that orchestrate the cellular pluripotency program, transcriptional regulation is situated in the central position and appears to be dominant over other regulatory controls. In this review, we would like to summarize the recent advancements in the accumulating findings of new transcription factors that play a critical role in controlling both pluripotency network and ESC identity.
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Affiliation(s)
- Kai Chuen Lee
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Room 105A, 1/F, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, N.T., Hong Kong, China.
| | - Wing Ki Wong
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Room 105A, 1/F, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, N.T., Hong Kong, China.
| | - Bo Feng
- Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, the Chinese University of Hong Kong, Room 105A, 1/F, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, Shatin, N.T., Hong Kong, China.
- SBS Core Laboratory, Shenzhen Research Institute, the Chinese University of Hong Kong, 4/F CUHK Shenzhen Research Institute Building, No.10, 2nd Yuexing Road, Nanshan District, Shenzhen 518057, China.
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Golipour A, David L, Liu Y, Jayakumaran G, Hirsch CL, Trcka D, Wrana JL. A late transition in somatic cell reprogramming requires regulators distinct from the pluripotency network. Cell Stem Cell 2013; 11:769-82. [PMID: 23217423 DOI: 10.1016/j.stem.2012.11.008] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 10/04/2012] [Accepted: 11/14/2012] [Indexed: 01/07/2023]
Abstract
Reprogramming of somatic cells to a pluripotent state via expression of Oct4, Klf4, Myc, and Sox2 is a multistep process involving phased changes in gene expression. Here, we focus on the later stages of reprogramming, termed maturation and stabilization. We show that the stabilization phase and the acquisition of pluripotency are dependent on the removal of transgene expression late in the maturation phase. Clonal analysis of cells undergoing reprogramming revealed subsets of stabilization-competent (SC) and stabilization-incompetent (SI) cells. SC clones acquire a competency gene-expression signature late in the maturation phase. Functional analysis of SC signature genes identified enhancers of the transition to the stabilization phase and a distinct subset of genes required for the maintenance of pluripotency. Thus, the acquisition and maintenance of pluripotency are regulated by distinct molecular networks, and a specific regulatory program not previously implicated in reprogramming is required for the transition to transgene independence.
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Affiliation(s)
- Azadeh Golipour
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
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22
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Soufi A, Zaret KS. Understanding impediments to cellular conversion to pluripotency by assessing the earliest events in ectopic transcription factor binding to the genome. Cell Cycle 2013; 12:1487-91. [PMID: 23603987 DOI: 10.4161/cc.24663] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In all known cases of transcription factor (TF)-based reprogramming, the process is relatively slow and inefficient. For example, it takes about a month for the ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) to fully reprogram human somatic cells to pluripotency. Furthermore, recent studies indicate that there is an initial stochastic phase, whereby random cells in the converting population begin to express a few genes of the new fate, followed by a so-called deterministic phase, whereby activation of a network for the new fate leads to homogeneous changes in gene expression patterns within a subset of the cell population. We recently mapped the initial interactions between OSKM factors and the human genome during the first 48 h of human fibroblast conversion to pluripotency. Unlike that reported in ES and iPS cells, distal enhancer sites in closed chromatin dominate the initial O, S, K and M binding distribution, showing that promoter occupancy is a later event in reprogramming. O, S and K act as pioneer factors for c-Myc, and c-Myc enhances the engagement of O, S and K. Despite the ability of OSKM to access closed chromatin, megabase-scale chromatin regions in somatic cells, referred to as "differentially bound regions" (DBRs), are remarkably refractory to OSKM binding at 48 h, though they become bound in pluripotent cells. These DBRs are highly enriched for the repressive H3K9me3 mark and span genes at the top of the deterministic hierarchy. Transient knockdown of the relevant chromatin modifiers allows access of OSKM to DBRs and a more rapid and efficient conversion to pluripotency. Thus, overcoming DBR barriers helps explain the conversion from a stochastic to a deterministic phase of transcription factor-mediated cell type conversion.
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Affiliation(s)
- Abdenour Soufi
- Institute for Regenerative Medicine, Epigenetics Program and Department of Cell and Developmental Biology, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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Abstract
Embryonic stem cell (ESC) markers are molecules specifically expressed in ES cells. Understanding of the functions of these markers is critical for characterization and elucidation for the mechanism of ESC pluripotent maintenance and self-renewal, therefore helping to accelerate the clinical application of ES cells. Unfortunately, different cell types can share single or sometimes multiple markers; thus the main obstacle in the clinical application of ESC is to purify ES cells from other types of cells, especially tumor cells. Currently, the marker-based flow cytometry (FCM) technique and magnetic cell sorting (MACS) are the most effective cell isolating methods, and a detailed maker list will help to initially identify, as well as isolate ESCs using these methods. In the current review, we discuss a wide range of cell surface and generic molecular markers that are indicative of the undifferentiated ESCs. Other types of molecules, such as lectins and peptides, which bind to ESC via affinity and specificity, are also summarized. In addition, we review several markers that overlap with tumor stem cells (TSCs), which suggest that uncertainty still exists regarding the benefits of using these markers alone or in various combinations when identifying and isolating cells.
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Affiliation(s)
- Wenxiu Zhao
- Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; (W.Z.); (X.J.); (F.Z.); (L.L.)
| | - Xiang Ji
- Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; (W.Z.); (X.J.); (F.Z.); (L.L.)
- Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
| | - Fangfang Zhang
- Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; (W.Z.); (X.J.); (F.Z.); (L.L.)
- Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
| | - Liang Li
- Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; (W.Z.); (X.J.); (F.Z.); (L.L.)
- Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing 100084, China
| | - Lan Ma
- Life Science Division, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China; (W.Z.); (X.J.); (F.Z.); (L.L.)
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Elliott AM, Hohenstein Elliott KA, Kammesheidt A. High-Resolution Genomic Profiling of Chromosomal Abnormalities in Human Stem Cells Using the 135 K StemArray. Stem Cells Int 2012; 2012:431534. [PMID: 22567024 DOI: 10.1155/2012/431534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Revised: 02/06/2012] [Accepted: 02/06/2012] [Indexed: 11/29/2022] Open
Abstract
Culturing stem cells for an extended period of time can lead to acquired chromosomal aberrations. Determining the copy number variant (CNV) profile of stem cell lines is critical since CNVs can have dramatic effects on gene expression and tumorigenic potential. Here, we describe an improved version of our StemArray, a stem-cell-focused comparative genomic hybridization (aCGH) microarray, which contains 135,000 probes and covers over 270 stem cell and cancer related genes at the exon level. We have dramatically increased the median probe spacing throughout the genome in order to obtain a higher resolution genetic profile of the cell lines. To illustrate the importance of using the StemArray, we describe a karyotypically normal iPSC line in which we detected acquired chromosomal variations that could affect the cellular phenotype of the cells. Identifying adaptive chromosomal aberrations in stem cell lines is essential if they are to be used in regenerative medicine.
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Wong CK, So WY, Law SK, Leung FP, Yau KL, Yao X, Huang Y, Li X, Tsang SY. Estrogen controls embryonic stem cell proliferation via store-operated calcium entry and the nuclear factor of activated T-cells (NFAT). J Cell Physiol 2012; 227:2519-30. [PMID: 21898397 DOI: 10.1002/jcp.22990] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Embryonic stem cells (ESCs) can self-renew indefinitely and differentiate into all cell lineages. Calcium is a universal second messenger which regulates a number of cellular pathways. Previous studies showed that store-operated calcium channels (SOCCs) but not voltage-operated calcium channels are present in mouse ESCs (mESCs). In this study, store-operated calcium entry (SOCE) was found to exist in mESCs using confocal microscopy. SOCC blockers lanthanum, 2-aminoethoxydiphenyl borate (2-APB) and SKF-96365 reduced mESC proliferation in a concentration-dependent manner, suggesting that SOCE is important for ESC proliferation. Pluripotent markers, Sox-2, Klf-4, and Nanog, were down-regulated by 2-APB, suggesting that self-renewal property of mESCs relies on SOCE. 17β-estradiol (E2) enhanced mESC proliferation. This enhanced proliferation was associated with an increment of SOCE. Both stimulated proliferation and increased SOCE could be reversed by SOCC blockers suggesting that E2 mediates its stimulatory effect on proliferation via enhancing SOCE. Also, cyclosporin A and INCA-6, inhibitors of calcineurin [phosphatase that de-phosphorylates and activates nuclear factor of activated T-cells (NFAT)], reversed the proliferative effect of E2, indicating that NFAT is involved in E2-stimulated proliferation. Interestingly, E2 caused the nuclear translocation of NFATc4, and this could be reversed by 2-APB. These results suggested that NFATc4 is the downstream target of E2-induced SOCE. The present investigation provides the first line of evidence that SOCE and NFAT are crucial for ESCs to maintain their unique characteristics. In addition, the present investigation also provides novel information on the mechanisms of how E2, an important female sex hormone, affects ESC proliferation.
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Affiliation(s)
- Chun-Kit Wong
- School of Life Sciences, Chinese University of Hong Kong, Hong Kong, China
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Abstract
Human embryonic stem cell (hESC) lines have been derived from the inner cell mass of blastocysts. Five hESC lines have been derived from 32 discarded blastocysts in Taiwan, and these lines have since been continuously cultured on mitotically inactivated mouse embryonic fibroblasts as feeder in the hESC medium for more than 44 passages and underwent freezing/thawing processes. All of five hESC lines expressed characteristic undifferentiated hESC markers such as SSEA-4, TRA-1-81, alkaline phosphatase, TERT, transcription factors POU5F1 (OCT4), and NANOG. The hESC lines T1 and T3 possess normal female karyotypes, whereas lines T4 and T5 are normal male, but line T2 is male trisomy 12 (47XY,+12). The hESC lines T1, T2, T3, and T5 were able to produce teratomas in SCID mice, and line T4 could only form embryoid bodies in vitro. Global gene expression profiles of single colonies of these five hESC lines were analyzed using Affymetrix human genome U133 plus 2.0 GeneChip. The results showed that 4,145 transcripts, including 19% of unknown functions, were detected in all five hESC lines. Comparison of the 4,145 genes commonly expressed in the five hESC lines with those genes expressed in teratoma produced by hESC line T1 and placenta revealed 40 genes exclusively expressed in all five hESC lines. These 40 genes include the previously reported stemness genes such as POU5F1 (OCT4), NANOG, TDGF1 (CRIPTO), SALL4, LECT1, and BUB1 responsible for self-renewal and pluripotent differentiation. The global gene expression analysis also indicated that the TGFβ/activin branch components inhibin BC, ACVR2A, ACVR1 (ALK2), TGFBR1 (ALK5), and SMAD2 were found to be highly expressed in undifferentiated states of these five hESC lines and decreased upon differentiation. The epigenetic states and expression of 32 known imprinted genes in these five hESC lines and/or differentiated derivatives were also investigated. In short, the hESC nature of these five hESC lines is supported by the undifferentiated state, extensive renewal capacity, and pluripotency, including the ability to form teratomas and/or embryoid bodies; and these cell lines will be useful for research on human embryonic stem cell biology and drug development/toxicity testing. The epigenetic states and expression of imprinted genes in hESC lines should be thoroughly studied after extended culture and upon differentiation in order to understand epigenetic stability in hESC lines before their clinical applications.
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Affiliation(s)
- Steven Shoei-Lung Li
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
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Nakamura T, Nakagawa M, Ichisaka T, Shiota A, Yamanaka S. Essential roles of ECAT15-2/Dppa2 in functional lung development. Mol Cell Biol 2011; 31:4366-78. [PMID: 21896782 DOI: 10.1128/MCB.05701-11] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Many transcription factors and DNA binding proteins play essential roles in the development of organs in which they are highly and/or specifically expressed. Embryonic stem cell (ESC)-associated transcript 15-1 (ECAT15-1) and ECAT15-2, also known as developmental pluripotency-associated 4 (Dppa4) and Dppa2, respectively, are enriched in mouse ESCs and preimplantation embryos, and their genes encode homologous proteins with a common DNA binding domain known as the SAP motif. Previously, ECAT15-1 was shown to be important in lung development, while it is dispensable in early development. In this study, we generated ECAT15-2 single and ECAT15-1 ECAT15-2 double knockout (double KO) mice and found that almost all mutants, like ECAT15-1 mutants, died around birth with respiratory defects. Paradoxically, the expression of neither ECAT15-1 nor ECAT15-2 was detected in lung organogenesis. Several genes, such as Nkx2-5, Gata4, and Pitx2, were downregulated in the ECAT15-2-null lung. On the other hand, genomic DNA of these genes showed inactive chromatin statuses in ECAT15-2-null ESCs, but not in wild-type ESCs. The chromatin immunoprecipitation (ChIP) assay revealed that ECAT15-2 binds to the regulatory region of Nkx2-5 in ESCs. These data suggest that ECAT15-2 has important roles in lung development, where it is no longer expressed, by leaving epigenetic marks from earlier developmental stages.
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Thompson PA, Brewster AM, Kim-Anh D, Baladandayuthapani V, Broom BM, Edgerton ME, Hahn KM, Murray JL, Sahin A, Tsavachidis S, Wang Y, Zhang L, Hortobagyi GN, Mills GB, Bondy ML. Selective genomic copy number imbalances and probability of recurrence in early-stage breast cancer. PLoS One 2011; 6:e23543. [PMID: 21858162 PMCID: PMC3155554 DOI: 10.1371/journal.pone.0023543] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 07/20/2011] [Indexed: 01/08/2023] Open
Abstract
A number of studies of copy number imbalances (CNIs) in breast tumors support associations between individual CNIs and patient outcomes. However, no pattern or signature of CNIs has emerged for clinical use. We determined copy number (CN) gains and losses using high-density molecular inversion probe (MIP) arrays for 971 stage I/II breast tumors and applied a boosting strategy to fit hazards models for CN and recurrence, treating chromosomal segments in a dose-specific fashion (-1 [loss], 0 [no change] and +1 [gain]). The concordance index (C-Index) was used to compare prognostic accuracy between a training (n = 728) and test (n = 243) set and across models. Twelve novel prognostic CNIs were identified: losses at 1p12, 12q13.13, 13q12.3, 22q11, and Xp21, and gains at 2p11.1, 3q13.12, 10p11.21, 10q23.1, 11p15, 14q13.2-q13.3, and 17q21.33. In addition, seven CNIs previously implicated as prognostic markers were selected: losses at 8p22 and 16p11.2 and gains at 10p13, 11q13.5, 12p13, 20q13, and Xq28. For all breast cancers combined, the final full model including 19 CNIs, clinical covariates, and tumor marker-approximated subtypes (estrogen receptor [ER], progesterone receptor, ERBB2 amplification, and Ki67) significantly outperformed a model containing only clinical covariates and tumor subtypes (C-Index(full model), train[test] = 0.72[0.71] ± 0.02 vs. C-Index(clinical + subtype model), train[test] = 0.62[0.62] ± 0.02; p<10(-6)). In addition, the full model containing 19 CNIs significantly improved prognostication separately for ER-, HER2+, luminal B, and triple negative tumors over clinical variables alone. In summary, we show that a set of 19 CNIs discriminates risk of recurrence among early-stage breast tumors, independent of ER status. Further, our data suggest the presence of specific CNIs that promote and, in some cases, limit tumor spread.
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Affiliation(s)
- Patricia A Thompson
- Department of Cellular and Molecular Medicine, Arizona Cancer Center, University of Arizona, Tucson, Arizona, United States of America.
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Kim M, Kang TW, Lee HC, Han YM, Kim H, Shin HD, Cheong HS, Lee D, Kim SY, Kim YS. Identification of DNA methylation markers for lineage commitment of in vitro hepatogenesis. Hum Mol Genet 2011; 20:2722-33. [DOI: 10.1093/hmg/ddr171] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Mali P, Chou BK, Yen J, Ye Z, Zou J, Dowey S, Brodsky RA, Ohm JE, Yu W, Baylin SB, Yusa K, Bradley A, Meyers DJ, Mukherjee C, Cole PA, Cheng L. Butyrate greatly enhances derivation of human induced pluripotent stem cells by promoting epigenetic remodeling and the expression of pluripotency-associated genes. Stem Cells 2010; 28:713-20. [PMID: 20201064 DOI: 10.1002/stem.402] [Citation(s) in RCA: 315] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report here that butyrate, a naturally occurring fatty acid commonly used as a nutritional supplement and differentiation agent, greatly enhances the efficiency of induced pluripotent stem (iPS) cell derivation from human adult or fetal fibroblasts. After transient butyrate treatment, the iPS cell derivation efficiency is enhanced by 15- to 51-fold using either retroviral or piggyBac transposon vectors expressing 4 to 5 reprogramming genes. Butyrate stimulation is more remarkable (>100- to 200-fold) on reprogramming in the absence of either KLF4 or MYC transgene. Butyrate treatment did not negatively affect properties of iPS cell lines established by either 3 or 4 retroviral vectors or a single piggyBac DNA transposon vector. These characterized iPS cell lines, including those derived from an adult patient with sickle cell disease by either the piggyBac or retroviral vectors, show normal karyotypes and pluripotency. To gain insights into the underlying mechanisms of butyrate stimulation, we conducted genome-wide gene expression and promoter DNA methylation microarrays and other epigenetic analyses on established iPS cells and cells from intermediate stages of the reprogramming process. By days 6 to 12 during reprogramming, butyrate treatment enhanced histone H3 acetylation, promoter DNA demethylation, and the expression of endogenous pluripotency-associated genes, including DPPA2, whose overexpression partially substitutes for butyrate stimulation. Thus, butyrate as a cell permeable small molecule provides a simple tool to further investigate molecular mechanisms of cellular reprogramming. Moreover, butyrate stimulation provides an efficient method for reprogramming various human adult somatic cells, including cells from patients that are more refractory to reprogramming.
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Affiliation(s)
- Prashant Mali
- Stem Cell Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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