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von Eyben FE, Kristiansen K, Kapp DS, Hu R, Preda O, Nogales FF. Epigenetic Regulation of Driver Genes in Testicular Tumorigenesis. Int J Mol Sci 2023; 24:ijms24044148. [PMID: 36835562 PMCID: PMC9966837 DOI: 10.3390/ijms24044148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/15/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
In testicular germ cell tumor type II (TGCT), a seminoma subtype expresses an induced pluripotent stem cell (iPSC) panel with four upregulated genes, OCT4/POU5F1, SOX17, KLF4, and MYC, and embryonal carcinoma (EC) has four upregulated genes, OCT4/POU5F1, SOX2, LIN28, and NANOG. The EC panel can reprogram cells into iPSC, and both iPSC and EC can differentiate into teratoma. This review summarizes the literature on epigenetic regulation of the genes. Epigenetic mechanisms, such as methylations of cytosines on the DNA string and methylations and acetylations of histone 3 lysines, regulate expression of these driver genes between the TGCT subtypes. In TGCT, the driver genes contribute to well-known clinical characteristics and the driver genes are also important for aggressive subtypes of many other malignancies. In conclusion, epigenetic regulation of the driver genes are important for TGCT and for oncology in general.
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Affiliation(s)
- Finn E. von Eyben
- Center for Tobacco Control Research, Birkevej 17, 5230 Odense, Denmark
- Correspondence: ; Tel.: +45-66145862
| | - Karsten Kristiansen
- Laboratory of Genomics and Molecular Biomedicine, August Krogh Building Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark
- BGI-Research, BGI-Shenzhen, Shenzhen 518120, China
- Institute of Metagenomics, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao 166555, China
| | - Daniel S. Kapp
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Rong Hu
- Department of Pathology, Laboratory Medicine, University of Wisconsin Hospital and Clinics, Madison, WI 53792, USA
| | - Ovidiu Preda
- Department of Pathology, San Cecilio University Hospital, 18071 Granada, CP, Spain
| | - Francisco F. Nogales
- Department of Pathology, School of Medicine, University Granada, 18071 Granada, CP, Spain
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2
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Jiao H, Walczak BE, Lee MS, Lemieux ME, Li WJ. GATA6 regulates aging of human mesenchymal stem/stromal cells. STEM CELLS (DAYTON, OHIO) 2020; 39:62-77. [PMID: 33252174 DOI: 10.1002/stem.3297] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 03/29/2020] [Accepted: 10/12/2020] [Indexed: 12/17/2022]
Abstract
Cellular reprogramming forcing the expression of pluripotency markers can reverse aging of cells, but how molecular mechanisms through which reprogrammed cells alter aging-related cellular activities still remains largely unclear. In this study, we reprogrammed human synovial fluid-derived mesenchymal stem cells (MSCs) into induced pluripotent stem cells (iPSCs) using six reprogramming factors and reverted the iPSCs back to MSCs, as an approach to cell rejuvenation. Using the parental and reprogrammed MSCs as control nonrejuvenated and rejuvenated cells, respectively, for comparative analysis, we found that aging-related activities were greatly reduced in reprogrammed MSCs compared with those in their parental lines, indicating reversal of cell aging. Global transcriptome analysis revealed differences in activities of regulatory networks associated with inflammation and proliferation. Mechanistically, we demonstrated that, compared with control cells, the expression of GATA binding protein 6 (GATA6) in reprogrammed cells was attenuated, resulting in an increase in the activity of sonic hedgehog signaling and the expression level of downstream forkhead box P1 (FOXP1), in turn ameliorating cellular hallmarks of aging. Lower levels of GATA6 expression were also found in cells harvested from younger mice or lower passage cultures. Our findings suggest that GATA6 is a critical regulator increased in aged MSCs that controls the downstream sonic hedgehog signaling and FOXP1 pathway to modulate cellular senescence and aging-related activities.
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Affiliation(s)
- Hongli Jiao
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Brian E Walczak
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ming-Song Lee
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Wan-Ju Li
- Department of Orthopedics and Rehabilitation, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
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3
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Zhou N, Zhang XB, Chen C, Chen XY, Kang B, He JQ, Gong GZ, Wang YJ, Zhou YW. Cellular context- and protein level-dependent interaction of pluripotency factor OCT4A with multiple octamer motifs of the same target gene. Life Sci 2020; 248:117461. [PMID: 32097665 DOI: 10.1016/j.lfs.2020.117461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 10/24/2022]
Abstract
AIMS To compare how OCT4A proteins interact with and regulate multiple OCT4A-octamer motifs (OMs) in different regions of the FOS gene expressed in somatic cancer cells versus pluripotent stem cells. MATERIALS AND METHODS Two FOS reporter gene systems harboring predicted OMs or their mutational counterparts were introduced into HeLa and NCCIT cells with varying OCT4A protein levels. The transcription of dsGFP reflecting FOS expression was quantitated by RT-qPCR, the OCT4A-OMs binding and the correlation between OCT4A and FOS transcription was determined by ChIP-PCR and RNA-Seq, respectively. KEY FINDINGS In NCCIT cells, abundant OCT4A proteins bound to and inhibited OM1 and OM2 at the promoter of the FOS gene. RA-induced OCT4A down-regulation transiently increased FOS transcription. In contrast, in HeLa cells that contain much lower levels of endogenous OCT4A proteins, OCT4A primarily bound to and activate OM1 thereby promoting FOS transcription. OCT4A KO significantly reduced FOS expression. Ectopically introduced OCT4A, at its leaked or induced expression level, promoted FOS transcription by binding to OM2/OM3 or OM1/OM3, respectively. Thus, the interaction of OCT4A proteins with different OMs is cellular context- and protein level-dependent, and such complicated OCT4A binding mode can only be reflected by a dsGFP-based reporter harboring the full-length FOS gene but not by that merely having the FOS promoter. SIGNIFICANCE Our findings unravel an additional layer of regulatory mechanisms that account for the cellular context- and dose-related versatile functions of OCT4A protein, and further underscore the importance of precise modulation of OCT4A in the regenerative medicine and anticancer therapies.
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Affiliation(s)
- Ning Zhou
- Department of Infectious Diseases, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xiao-Bing Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Cheng Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Xin-Yu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Jian-Qin He
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Guo-Zhong Gong
- Department of Infectious Diseases, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China
| | - Yan-Wen Zhou
- Department of Infectious Diseases, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China.
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The FGF, TGFβ and WNT axis Modulate Self-renewal of Human SIX2 + Urine Derived Renal Progenitor Cells. Sci Rep 2020; 10:739. [PMID: 31959818 PMCID: PMC6970988 DOI: 10.1038/s41598-020-57723-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 12/31/2019] [Indexed: 12/22/2022] Open
Abstract
Human urine is a non-invasive source of renal stem cells with regeneration potential. Urine-derived renal progenitor cells were isolated from 10 individuals of both genders and distinct ages. These renal progenitors express pluripotency-associated proteins- TRA-1-60, TRA-1-81, SSEA4, C-KIT and CD133, as well as the renal stem cell markers -SIX2, CITED1, WT1, CD24 and CD106. The transcriptomes of all SIX2+ renal progenitors clustered together, and distinct from the human kidney biopsy-derived epithelial proximal cells (hREPCs). Stimulation of the urine-derived renal progenitor cells (UdRPCs) with the GSK3β-inhibitor (CHIR99021) induced differentiation. Transcriptome and KEGG pathway analysis revealed upregulation of WNT-associated genes- AXIN2, JUN and NKD1. Protein interaction network identified JUN- a downstream target of the WNT pathway in association with STAT3, ATF2 and MAPK1 as a putative negative regulator of self-renewal. Furthermore, like pluripotent stem cells, self-renewal is maintained by FGF2-driven TGFβ-SMAD2/3 pathway. The urine-derived renal progenitor cells and the data presented should lay the foundation for studying nephrogenesis in human.
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Vlahova F, Hawkins KE, Ranzoni AM, Hau KL, Sagar R, De Coppi P, David AL, Adjaye J, Guillot PV. Human mid-trimester amniotic fluid (stem) cells lack expression of the pluripotency marker OCT4A. Sci Rep 2019; 9:8126. [PMID: 31148575 PMCID: PMC6544653 DOI: 10.1038/s41598-019-44572-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/20/2019] [Indexed: 02/07/2023] Open
Abstract
Expression of OCT4A is one of the hallmarks of pluripotency, defined as a stem cell's ability to differentiate into all the lineages of the three germ layers. Despite being defined as non-tumorigenic cells with high translational potential, human mid-trimester amniotic fluid stem cells (hAFSCs) are often described as sharing features with embryonic stem cells, including the expression of OCT4A, which could hinder their clinical potential. To clarify the OCT4A status of hAFSCs, we first undertook a systematic review of the literature. We then performed extensive gene and protein expression analyses to discover that neither frozen, nor fresh hAFSCs cultivated in multipotent stem cell culture conditions expressed OCT4A, and that the OCT4A positive results from the literature are likely to be attributed to the expression of pseudogenes or other OCT4 variants. To address this issue, we provide a robust protocol for the assessment of OCT4A in other stem cells.
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Affiliation(s)
- Filipa Vlahova
- University College London, Institute for Women's Health, Maternal and Fetal Medicine Department, London, UK
| | - Kate E Hawkins
- University College London, Institute for Women's Health, Maternal and Fetal Medicine Department, London, UK
| | - Anna Maria Ranzoni
- University College London, Institute for Women's Health, Maternal and Fetal Medicine Department, London, UK
| | - Kwan-Leong Hau
- University College London, Institute for Women's Health, Maternal and Fetal Medicine Department, London, UK
| | - Rachel Sagar
- University College London, Institute for Women's Health, Maternal and Fetal Medicine Department, London, UK
| | - Paolo De Coppi
- University College London, Great Ormond Street Institute for Child Health, London, UK.,Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium.,Specialist Neonatal and Paediatric Surgery, Great Ormond Street Hospital NHS Trust, London, UK
| | - Anna L David
- University College London, Institute for Women's Health, Maternal and Fetal Medicine Department, London, UK.,Department of Development and Regeneration, Katholieke Universiteit Leuven, Leuven, Belgium.,NIHR University College London Hospitals Biomedical Research Centre, Maple House, 149 Tottenham Court Road, London, W1T 7DN, UK
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty, Heinrich Heine University, Düsseldorf, Moorenstr. 5, 40225, Düsseldorf, Germany
| | - Pascale V Guillot
- University College London, Institute for Women's Health, Maternal and Fetal Medicine Department, London, UK.
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6
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Kuan II, Lee CC, Chen CH, Lu J, Kuo YS, Wu HC. The extracellular domain of epithelial cell adhesion molecule (EpCAM) enhances multipotency of mesenchymal stem cells through EGFR-LIN28-LET7 signaling. J Biol Chem 2019; 294:7769-7786. [PMID: 30926604 DOI: 10.1074/jbc.ra119.007386] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/19/2019] [Indexed: 11/06/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are widely considered to be an attractive cell source for regenerative therapies, but maintaining multipotency and self-renewal in cultured MSCs is especially challenging. Hence, the development and mechanistic description of strategies that help promote multipotency in MSCs will be vital to future clinical use. Here, using an array of techniques and approaches, including cell biology, RT-quantitative PCR, immunoblotting, immunofluorescence, flow cytometry, and ChIP assays, we show that the extracellular domain of epithelial cell adhesion molecule (EpCAM) (EpEX) significantly increases the levels of pluripotency factors through a signaling cascade that includes epidermal growth factor receptor (EGFR), signal transducer and activator of transcription 3 (STAT3), and Lin-28 homolog A (LIN28) and enhances the proliferation of human bone marrow MSCs. Moreover, we found that EpEX-induced LIN28 expression reduces the expression of the microRNA LET7 and up-regulates that of the transcription factor high-mobility group AT-hook 2 (HMGA2), which activates the transcription of pluripotency factors. Surprisingly, we found that EpEX treatment also enhances osteogenesis of MSCs under differentiation conditions, as evidenced by increases in osteogenic markers, including Runt-related transcription factor 2 (RUNX2). Taken together, our results indicate that EpEX stimulates EGFR signaling and thereby context-dependently controls MSC states and activities, promoting cell proliferation and multipotency under maintenance conditions and osteogenesis under differentiation conditions.
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Affiliation(s)
- I-I Kuan
- From the Institute of Cellular and Organismic Biology and
| | - Chi-Chiu Lee
- From the Institute of Cellular and Organismic Biology and
| | - Chien-Hsu Chen
- From the Institute of Cellular and Organismic Biology and
| | - Jean Lu
- Genomic Research Center, Academia Sinica, Taipei 115 and
| | - Yuan-Sung Kuo
- the Department of Surgery, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Han-Chung Wu
- From the Institute of Cellular and Organismic Biology and .,Genomic Research Center, Academia Sinica, Taipei 115 and
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7
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Jung J, Kim Y, Song J, Yoon YJ, Kim DE, Kim JA, Jin Y, Lee YJ, Kim S, Kwon BM, Han DC. KRIBB53 binds to OCT4 and enhances its degradation through the proteasome, causing apoptotic cell death of OCT4-positive testicular germ cell tumors. Carcinogenesis 2018; 39:838-849. [DOI: 10.1093/carcin/bgy054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/11/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Jiyae Jung
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Youngmi Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Jinhoi Song
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yae Jin Yoon
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Da-Eun Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Joo Ae Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yena Jin
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Yu-Jin Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Seokho Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Byoung-Mog Kwon
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
| | - Dong Cho Han
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
- University of Science and Technology in Korea, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, Korea
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8
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CpG Island Methylation Correlates with the Use of Alternative Promoters for USP44 Gene Expression in Human Pluripotent Stem Cells and Testes. Stem Cells Dev 2017; 26:1100-1110. [DOI: 10.1089/scd.2017.0057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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9
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Poursani EM, Mehravar M, Soltani BM, Mowla SJ. Novel variant of OCT4B4 is differentially expressed in human embryonic stem and embryonic carcinoma cells. Gene 2017. [PMID: 28633916 DOI: 10.1016/j.gene.2017.06.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
POU domain proteins are an important family of transcription factors that regulates cell type-specific gene expression. One of the most crucial members of this family that maintains pluripotency and self-renewal of embryonic stem cells is POU5F1/OCT4. The OCT4 gene can generate several variants under different situations/cell types includes OCT4A that is the major factor sustains pluripotency in embryonic stem and embryonic carcinoma cells, and also OCT4B and OCT4B1, which are transcribed from a different potential promoter located in intron1 and are expressed in various tissues and cell types. In present study, during expression check of OCT4B1 in embryonic carcinoma cells (NT2), we discovered a novel OCT4 transcript for the first time and designated it as OCT4B4. This variant is expressed in various human pluripotent cells and its expression is down-regulated upon induction of differentiation. Moreover, knocking down of OCT4B4 by shRNA resulted in increased accumulation of transfected cells in G0/G1 phase compared to the mock-transfected control cells.
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Affiliation(s)
- Ensieh M Poursani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Majid Mehravar
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahram Mohammad Soltani
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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10
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Han MH, Park SW, Do HJ, Chung HJ, Song H, Kim JH, Kim NH, Park KH, Kim JH. Growth and Differentiation Factor 3 Is Transcriptionally Regulated by OCT4 in Human Embryonic Carcinoma Cells. Biol Pharm Bull 2017; 39:1802-1808. [PMID: 27803451 DOI: 10.1248/bpb.b16-00299] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Growth and differentiation factor 3 (GDF3), a mammalian-specific transforming growth factor β ligand, and OCT4, one of key stem cell transcription factors, are expressed in testicular germ cell tumors (TGCTs) as well as pluripotent stem cells. To understand the molecular mechanism by which OCT4 and GDF3 function in tumorigenesis as well as stemness, we investigated the transcriptional regulation of GDF3 mediated by OCT4 in human embryonic carcinoma (EC) NCCIT cells, which are pluripotent stem cells of TGCTs. GDF3 and OCT4 was highly expressed in undifferentiated NCCIT cells and then significantly decreased upon retinoic acid-induced differentiation in a time-dependent manner. Moreover, GDF3 expression was reduced by short hairpin RNA-mediated knockdown of OCT4 and increased by OCT4 overexpression, suggesting that GDF3 and OCT4 have a functional relationship in pluripotent stem cells. A promoter-reporter assay revealed that the GDF3 promoter (-1721-Luc) activity was significantly activated by OCT4 in a dose-dependent manner. Moreover, the minimal promoter (-183-Luc) was sufficient for OCT4-mediated transcriptional activation and provided a potential binding site for the direct interaction with OCT4. Collectively, this study provides the evidence about the regulatory mechanism of GDF3 mediated by OCT4 in pluripotent EC cells.
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Affiliation(s)
- Mi-Hee Han
- Department of Biomedical Science, College of Life Science, CHA University
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11
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Matic I, Antunovic M, Brkic S, Josipovic P, Mihalic KC, Karlak I, Ivkovic A, Marijanovic I. Expression of OCT-4 and SOX-2 in Bone Marrow-Derived Human Mesenchymal Stem Cells during Osteogenic Differentiation. Open Access Maced J Med Sci 2016; 4:9-16. [PMID: 27275321 PMCID: PMC4884261 DOI: 10.3889/oamjms.2016.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 11/17/2022] Open
Abstract
AIM: Determine the levels of expression of pluripotency genes OCT-4 and SOX-2 before and after osteogenic differentiation of human mesenchymal stem cells (hMSCs). METHODS: Human MSCs were derived from the bone marrow and differentiated into osteoblasts. The analyses were performed on days 0 and 14 of the cell culture. In vitro differentiation was evaluated due to bone markers – alkaline phosphatase (AP) activity and the messenger RNA (mRNA) expression of AP and bone sialoprotein (BSP). The OCT-4 and SOX-2 expression was evaluated at mRNA level by real-time qPCR and at protein level by immunocytochemistry. RESULTS: In vitro cultures on day 14 showed an increase in AP activity and upregulation of AP and BSP gene expression. OCT-4 and SOX-2 in undifferentiated hMSCs on day 0 is detectable and very low compared to tumor cell lines as a positive control. Immunocytochemistry detected OCT-4 in the cell nuclei prior (day 0) and post differentiation (day 14). On the same time points, cultures were negative for SOX-2 protein. CONCLUSION: Messenger RNA for pluripotency markers OCT-4 and SOX-2 isolated from hMSCs was less present, while OCT-4 protein was detected in cell nuclei prior and post differentiation into osteoblast lineage.
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Affiliation(s)
- Igor Matic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Maja Antunovic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Sime Brkic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Pavle Josipovic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Katarina Caput Mihalic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivan Karlak
- Department of Traumatology, University Hospital Sestre Milosrdnice, Zagreb, Croatia
| | | | - Inga Marijanovic
- Division of Biology, Department of Molecular Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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12
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Yuan J, Li M, Torres YR, Galle CS, Meier JL. Differentiation-Coupled Induction of Human Cytomegalovirus Replication by Union of the Major Enhancer Retinoic Acid, Cyclic AMP, and NF-κB Response Elements. J Virol 2015; 89:12284-98. [PMID: 26423948 PMCID: PMC4665231 DOI: 10.1128/jvi.00965-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 09/08/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Triggers and regulatory pathways that effectively link human cytomegalovirus (HCMV) major immediate early (MIE) latent-lytic switch activation with progeny production are incompletely understood. In the quiescently infected human NTera2 cell model of primitive neural stem cells, we found that costimulation with vasoactive intestinal peptide (V) and phorbol ester (P) synergistically activated viral infection, but this effect waned over time. Coupling retinoic acid (R), an inducer of neuronal differentiation, to VP pulse stimulation attenuated the decline in viral activity and promoted the spread of the active infection through concentric layers of neighboring cells as cellular differentiation progressed. R stimulation alone was unable to activate the infection. The MIE enhancer cis-regulatory mechanisms responsible for this result were characterized by a strategy of combinatorial mutagenesis of five cis-acting element types (retinoic acid receptor binding elements [RARE], cyclic AMP [cAMP] response elements [CRE], NF-κB binding sites [kB], serum response element, and ETS/ELK-1 binding site) and multiple methods of assessment. We found that the CRE and kB combination sets the preinduction enhancer tone, is the major initiator and amplifier of RVP-induced MIE gene expression, and cooperates with RARE during cellular differentiation to enhance viral spread. In predifferentiated NTera2, we also found that the CRE-kB combination functions as initiator and amplifier of unstimulated HCMV MIE gene expression and cooperatively interacts with RARE to enhance viral spread. We conclude that RVP-stimulated signaling cascades and cellular differentiation operate through the enhancer CRE-kB-RARE core in strengthening induction of HCMV MIE gene expression in linkage with viral propagation. IMPORTANCE Cytomegalovirus-seropositive persons commonly lack detectable levels of cytomegalovirus replication, even when profoundly immunocompromised. In a human NTera2 cell model of primitive neural stem cells carrying resting cytomegalovirus genomes, we show that costimulation of protein kinase A and C-delta signaling cascades in conjunction with retinoic acid-induced neuronal differentiation brings about progeny virus propagation. Iterated DNA binding sites for retinoic acid receptor, CREB, and NF-κB family members in the cytomegalovirus major enhancer are at the crux in the pathway to HCMV activation. The stimulated CREB and NF-κB binding site combination vigorously initiates and amplifies the active cytomegalovirus infection and cooperates with activated retinoic acid receptor binding sites to further promote viral proliferation and spread between differentiated cells. These results support a paradigm in which a specific combination of stimuli coupled with cellular differentiation satisfies a core cis-activating code that unlocks enhancer silence to repower the cycle of cytomegalovirus propagation.
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Affiliation(s)
- Jinxiang Yuan
- University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Ming Li
- University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | | | - Courtney S Galle
- University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Jeffery L Meier
- Iowa City Veterans Affairs Medical Center, Iowa City, Iowa, USA University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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13
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Mojsin M, Topalovic V, Marjanovic Vicentic J, Stevanovic M. Transcription factor NF-Y inhibits cell growth and decreases SOX2 expression in human embryonal carcinoma cell line NT2/D1. BIOCHEMISTRY (MOSCOW) 2015; 80:202-7. [PMID: 25756534 DOI: 10.1134/s0006297915020066] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Transcription factor NF-Y belongs to the embryonic stem cell transcription factor circuitry due to its role in the regulation of cell proliferation. We investigated the role of NF-Y in pluripotency maintenance using NT2/D1 cells as one of the best-characterized human embryonal carcinoma cell line. We investigated the efficiency of protein transduction and analyzed the effects of forced expression of short isoform of NF-Y A-subunit (NF-YAs) on NT2/D1 cell growth and expression of SOX2. We found that protein transduction is an efficient method for NF-Y overexpression in NT2/D1 cells. Next, we analyzed the effect of NF-YAs overexpression on NT2/D1 cell viability and detected significant reduction in cell growth. The negative effect of NF-YAs overexpression on NT2/D1 cell pluripotency maintenance was confirmed by the decrease in the level of the pluripotency marker SOX2. Finally, we checked the p53 status and determined that the NF-Y-induced inhibition of NT2/D1 cell growth is p53-independent.
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Affiliation(s)
- M Mojsin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, 11010, Serbia.
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14
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Zeira E, Abramovitch R, Meir K, Ram SE, Gil Y, Bulvik B, Bromberg Z, Levkovitch O, Nahmansson N, Adar R, Reubinoff B, Galun E, Gropp M. The knockdown of H19lncRNA reveals its regulatory role in pluripotency and tumorigenesis of human embryonic carcinoma cells. Oncotarget 2015; 6:34691-703. [PMID: 26415227 PMCID: PMC4741483 DOI: 10.18632/oncotarget.5787] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 12/27/2022] Open
Abstract
The function of imprinted H19 long non-coding RNA is still controversial. It is highly expressed in early embryogenesis and decreases after birth and re-expressed in cancer. To study the role of H19 in oncogenesis and pluripotency, we down-regulated H19 expression in vitro and in vivo in pluripotent human embryonic carcinoma (hEC) and embryonic stem (hES) cells. H19 knockdown resulted in a decrease in the expression of the pluripotency markers Oct4, Nanog, TRA-1-60 and TRA-1-81, and in the up-regulation of SSEA1; it further attenuated cell proliferation, decreased cell-matrix attachment, and up-regulated E-Cadherin expression. SCID-Beige mice transplanted with H19 down-regulated hEC cells exhibited slower kinetics of tumor formation, resulting in an increased animal survival. Tumors derived from H19 down-regulated cells showed a decrease in the expression of pluripotency markers and up-regulation of SSEA-1 and E-cadherin. Our results suggest that H19 oncogenicity in hEC cells is mediated through the regulation of the pluripotency state.
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Affiliation(s)
- Evelyne Zeira
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Rinat Abramovitch
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Karen Meir
- The Department of Pathology, Hadassah University Hospital, Jerusalem, Israel
| | - Sharona Even Ram
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Yaniv Gil
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Baruch Bulvik
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Zohar Bromberg
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Or Levkovitch
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Nathalie Nahmansson
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Revital Adar
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Benjamin Reubinoff
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Eithan Galun
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
| | - Michal Gropp
- The Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Medical Center, Jerusalem, Israel
- The Sydney and Judy Swartz Human Embryonic Stem Cell Research Center, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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15
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Yun JH, Park YG, Lee KM, Kim J, Nho CW. Curcumin induces apoptotic cell death via Oct4 inhibition and GSK-3β activation in NCCIT cells. Mol Nutr Food Res 2015; 59:1053-62. [PMID: 25755051 DOI: 10.1002/mnfr.201400739] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 01/16/2015] [Accepted: 02/16/2015] [Indexed: 01/02/2023]
Abstract
SCOPE Octamer-binding transcription factor 4 (Oct4) is a key regulator of pluripotent embryonic stem cell maintenance. However, increasing evidence has suggested that Oct4 is also expressed in cancer stem cells (CSCs) and is associated with tumor progression and chemoresistance. Curcumin (CUR) is a widely used cancer chemopreventive agent, and it has been used to treat several diseases including cancers. Here, we investigated whether CUR-induced apoptotic cell death by inhibiting Oct4 levels and examining molecular mechanisms in NCCIT human embryonic carcinoma cells. METHODS AND RESULTS CUR significantly inhibited Oct4 transcription levels in a dose-dependent manner by dual luciferase experiment, also decreased mRNA and protein levels in NCCIT human embryonic carcinoma cells, which express high levels of endogenous Oct4. Interestingly, we found that CUR treatment increased apoptotic cell death including subG0/G1 contents, cleavage caspases, and pro-apoptotic protein, as confirmed with a series of loss-of-function experiments using Oct4 siRNA. Furthermore, CUR induced marked total level of glycogen synthase kinase 3 beta (GSK-3β), resulting in an increase in apoptotic cell death, was evaluated using chemical inhibitor of GSK3-3β. CONCLUSION These data suggest that CUR induces apoptotic cell death through Oct4 inhibition and GSK-3β activation. Thus, CUR may be a useful cancer chemopreventive agent to suppress tumor progression or to improve chemoresistance by eliminating CSCs.
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Affiliation(s)
- Ji Ho Yun
- Natural Products Research Center, KIST Gangneung Institute, Gangneung, Gangwon-do, Korea.,Department of Life Science, Sogang University, Seoul, Korea
| | - Young Gyun Park
- Natural Products Research Center, KIST Gangneung Institute, Gangneung, Gangwon-do, Korea.,Department of Chemistry, Gangneung-Wonju National University, Gangneung, Gangwon-do, Korea
| | - Kyung-Mi Lee
- Natural Products Research Center, KIST Gangneung Institute, Gangneung, Gangwon-do, Korea
| | - Jungho Kim
- Department of Life Science, Sogang University, Seoul, Korea
| | - Chu Won Nho
- Natural Products Research Center, KIST Gangneung Institute, Gangneung, Gangwon-do, Korea
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16
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Fuchs H, Theuser M, Wruck W, Adjaye J. miR-27 negatively regulates pluripotency-associated genes in human embryonal carcinoma cells. PLoS One 2014; 9:e111637. [PMID: 25369332 PMCID: PMC4219743 DOI: 10.1371/journal.pone.0111637] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Accepted: 10/03/2014] [Indexed: 02/07/2023] Open
Abstract
Human embryonic stem cells and human embryonal carcinoma cells have been studied extensively with respect to the transcription factors (OCT4, SOX2 and NANOG), epigenetic modulators and associated signalling pathways that either promote self-renewal or induce differentiation in these cells. The ACTIVIN/NODAL axis (SMAD2/3) of the TGFß signalling pathway coupled with FGF signalling maintains self-renewal in these cells, whilst the BMP (SMAD1,5,8) axis promotes differentiation. Here we show that miR-27, a somatic-enriched miRNA, is activated upon RNAi-mediated suppression of OCT4 function in human embryonic stem cells. We further demonstrate that miR-27 negatively regulates the expression of the pluripotency-associated ACTIVIN/NODAL axis (SMAD2/3) of the TGFß signalling pathway by targeting ACVR2A, TGFßR1 and SMAD2. Additionally, we have identified a number of pluripotency-associated genes such as NANOG, LIN28, POLR3G and NR5A2 as novel miR-27 targets. Transcriptome analysis revealed that miR-27 over-expression in human embryonal carcinoma cells leads indeed to a significant up-regulation of genes involved in developmental pathways such as TGFß- and WNT-signalling.
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Affiliation(s)
- Heiko Fuchs
- Institute for Stem Cell Research and Regenerative Medicine, Faculty of Medicine, Heinrich Heine University, Duesseldorf, Germany
| | - Matthias Theuser
- Department of Vertebrate Genomics, Molecular Embryology and Aging Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Faculty of Medicine, Heinrich Heine University, Duesseldorf, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Faculty of Medicine, Heinrich Heine University, Duesseldorf, Germany
- Department of Vertebrate Genomics, Molecular Embryology and Aging Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail:
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17
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Vencken SF, Sethupathy P, Blackshields G, Spillane C, Elbaruni S, Sheils O, Gallagher MF, O'Leary JJ. An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines. BMC Genomics 2014; 15:711. [PMID: 25156079 PMCID: PMC4162954 DOI: 10.1186/1471-2164-15-711] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 07/15/2014] [Indexed: 12/13/2022] Open
Abstract
Background SOX2 is a core component of the transcriptional network responsible for maintaining embryonal carcinoma cells (ECCs) in a pluripotent, undifferentiated state of self-renewal. As such, SOX2 is an oncogenic transcription factor and crucial cancer stem cell (CSC) biomarker in embryonal carcinoma and, as more recently found, in the stem-like cancer cell component of many other malignancies. SOX2 is furthermore a crucial factor in the maintenance of adult stem cell phenotypes and has additional roles in cell fate determination. The SOX2-linked microRNA (miRNA) transcriptome and regulome has not yet been fully defined in human pluripotent cells or CSCs. To improve our understanding of the SOX2-linked miRNA regulatory network as a contribution to the phenotype of these cell types, we used high-throughput differential miRNA and gene expression analysis combined with existing genome-wide SOX2 chromatin immunoprecipitation (ChIP) data to map the SOX2 miRNA transcriptome in two human embryonal carcinoma cell (hECC) lines. Results Whole-microRNAome and genome analysis of SOX2-silenced hECCs revealed many miRNAs regulated by SOX2, including several with highly characterised functions in both cancer and embryonic stem cell (ESC) biology. We subsequently performed genome-wide differential expression analysis and applied a Monte Carlo simulation algorithm and target prediction to identify a SOX2-linked miRNA regulome, which was strongly enriched with epithelial-to-mesenchymal transition (EMT) markers. Additionally, several deregulated miRNAs important to EMT processes had SOX2 binding sites in their promoter regions. Conclusion In ESC-like CSCs, SOX2 regulates a large miRNA network that regulates and interlinks the expression of crucial genes involved in EMT. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-711) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian F Vencken
- Department of Histopathology, Trinity College Dublin, Sir Patrick Dun Research Laboratory, St, James's Hospital, Dublin, Ireland.
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18
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Liu YR, Laghari ZA, Novoa CA, Hughes J, Webster JRM, Goodwin PE, Wheatley SP, Scotting PJ. Sox2 acts as a transcriptional repressor in neural stem cells. BMC Neurosci 2014; 15:95. [PMID: 25103589 PMCID: PMC4148960 DOI: 10.1186/1471-2202-15-95] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/30/2014] [Indexed: 12/30/2022] Open
Abstract
Background The transcription factor, Sox2, is central to the behaviour of neural stem cells. It is also one of the key embryonic stem cell factors that, when overexpressed can convert somatic cells into induced pluripotent cells. Although generally studied as a transcriptional activator, recent evidence suggests that it might also repress gene expression. Results We show that in neural stem cells Sox2 represses as many genes as it activates. We found that Sox2 interacts directly with members of the groucho family of corepressors and that repression of several target genes required this interaction. Strikingly, where many of the genes activated by Sox2 encode transcriptional regulators, no such genes were repressed. Finally, we found that a mutant form of Sox2 that was unable to bind groucho was no longer able to inhibit differentiation of neural stem cells to the same extent as the wild type protein. Conclusions These data reveal a major new mechanism of action for this key transcription factor. In the context of our understanding of endogenous stem cells, this highlights the need to determine how such a central regulator can distinguish which genes to activate and which to repress. Electronic supplementary material The online version of this article (doi:10.1186/1471-2202-15-95) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | - Paul J Scotting
- Centre for Genetics and Genomics, School of Life Sciences, Queen's Medical Centre, Nottingham NG7 2UH, England.
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19
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Nair R, Santos L, Awasthi S, von Erlach T, Chow LW, Bertazzo S, Stevens MM. Extracellular Vesicles Derived from Preosteoblasts Influence Embryonic Stem Cell Differentiation. Stem Cells Dev 2014; 23:1625-35. [DOI: 10.1089/scd.2013.0633] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rekha Nair
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Lívia Santos
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Siddhant Awasthi
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
| | - Thomas von Erlach
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Lesley W. Chow
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Sergio Bertazzo
- Department of Materials, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
| | - Molly M. Stevens
- Department of Materials, Imperial College London, London, United Kingdom
- Department of Bioengineering, Imperial College London, London, United Kingdom
- Institute of Biomedical Engineering, Imperial College London, London, United Kingdom
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20
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Tung PY, Knoepfler PS. Epigenetic mechanisms of tumorigenicity manifesting in stem cells. Oncogene 2014; 34:2288-96. [PMID: 24931168 PMCID: PMC4268091 DOI: 10.1038/onc.2014.172] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 01/04/2023]
Abstract
One of the biggest roadblocks to using stem cells as the basis for regenerative medicine therapies is the tumorigenicity of stem cells. Unfortunately, the unique abilities of stem cells to self-renew and differentiate into a variety of cell types are also mechanistically linked to their tumorigenic behaviors. Understanding the mechanisms underlying the close relationship between stem cells and cancer cells has therefore become a primary goal in the field. In addition, knowledge gained from investigating the striking parallels between mechanisms orchestrating normal embryogenesis and those that invoke tumorigenesis may well serve as the foundation for developing novel cancer treatments. Emerging discoveries have demonstrated that epigenetic regulatory machinery plays important roles in normal stem cell functions, cancer development, and cancer stem cell identity. These studies provide valuable insights into both the shared and distinct mechanisms by which pluripotency and oncogenicity are established and regulated. In this review, the cancer-related epigenetic mechanisms found in pluripotent stem cells and cancer stem cells will be discussed, focusing on both the similarities and the differences.
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Affiliation(s)
- P-Y Tung
- 1] Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA, USA [2] UC Davis Genome Center, University of California Davis, Davis, CA, USA [3] UC Davis Comprehensive Cancer Center, Sacramento, CA, USA [4] Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA, USA
| | - P S Knoepfler
- 1] Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA, USA [2] UC Davis Genome Center, University of California Davis, Davis, CA, USA [3] UC Davis Comprehensive Cancer Center, Sacramento, CA, USA [4] Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA, USA
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21
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Labeling of neuronal differentiation and neuron cells with biocompatible fluorescent nanodiamonds. Sci Rep 2014; 4:5004. [PMID: 24830447 PMCID: PMC4023134 DOI: 10.1038/srep05004] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 04/29/2014] [Indexed: 12/27/2022] Open
Abstract
Nanodiamond is a promising carbon nanomaterial developed for biomedical applications. Here, we show fluorescent nanodiamond (FND) with the biocompatible properties that can be used for the labeling and tracking of neuronal differentiation and neuron cells derived from embryonal carcinoma stem (ECS) cells. The fluorescence intensities of FNDs were increased by treatment with FNDs in both the mouse P19 and human NT2/D1 ECS cells. FNDs were taken into ECS cells; however, FNDs did not alter the cellular morphology and growth ability. Moreover, FNDs did not change the protein expression of stem cell marker SSEA-1 of ECS cells. The neuronal differentiation of ECS cells could be induced by retinoic acid (RA). Interestingly, FNDs did not affect on the morphological alteration, cytotoxicity and apoptosis during the neuronal differentiation. Besides, FNDs did not alter the cell viability and the expression of neuron-specific marker β-III-tubulin in these differentiated neuron cells. The existence of FNDs in the neuron cells can be identified by confocal microscopy and flow cytometry. Together, FND is a biocompatible and readily detectable nanomaterial for the labeling and tracking of neuronal differentiation process and neuron cells from stem cells.
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22
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Kole D, Ambady S, Page RL, Dominko T. Maintenance of multipotency in human dermal fibroblasts treated with Xenopus laevis egg extract requires exogenous fibroblast growth factor-2. Cell Reprogram 2014; 16:18-28. [PMID: 24405062 PMCID: PMC3920749 DOI: 10.1089/cell.2013.0066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Direct reprogramming of a differentiated somatic cell into a developmentally more plastic cell would offer an alternative to applications in regenerative medicine that currently depend on either embryonic stem cells (ESCs), adult stem cells, or induced pluripotent stem cells (iPSCs). Here we report the potential of select Xenopus laevis egg extract fractions, in combination with exogenous fibroblast growth factor-2 (FGF2), to affect life span, morphology, gene expression, protein translation, and cellular localization of OCT4 and NANOG transcription factors, and the developmental potential of human dermal fibroblasts in vitro. A gradual change in morphology is accompanied by translation of embryonic transcription factors and their nuclear localization and a life span exceeding 60 population doublings. Cells acquire the ability to follow adipogenic, neuronal, and osteogenic differentiation under appropriate induction conditions in vitro. Analysis of active extract fractions reveals that Xenopus egg protein and RNAs as well as exogenously supplemented FGF2 are required and sufficient for induction and maintenance of this phenotypic change. Factors so far identified in the active fractions include FGF2 itself, transforming growth factor-β, maskin, and nucleoplasmin. Identification of critical factors needed for reprogramming may allow for nonviral, chemically defined derivation of human-induced multipotent cells that can be maintained by exogenous FGF2.
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Affiliation(s)
- Denis Kole
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609
| | - Sakthikumar Ambady
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609
| | - Raymond L. Page
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609
- Bioengineering Institute, Worcester Polytechnic Institute, Worcester, MA, 01609
- CellThera, Inc., Worcester, MA, 01605
| | - Tanja Dominko
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, 01609
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, 01609
- Bioengineering Institute, Worcester Polytechnic Institute, Worcester, MA, 01609
- CellThera, Inc., Worcester, MA, 01605
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Mojsin M, Vicentic JM, Schwirtlich M, Topalovic V, Stevanovic M. Quercetin reduces pluripotency, migration and adhesion of human teratocarcinoma cell line NT2/D1 by inhibiting Wnt/β-catenin signaling. Food Funct 2014; 5:2564-73. [DOI: 10.1039/c4fo00484a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In human teratocarcinoma cell line NT2/D1 quercetin exerts its anticancer effect through the inhibition of Wnt signaling.
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Affiliation(s)
- Marija Mojsin
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11010 Belgrade, Serbia
| | | | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11010 Belgrade, Serbia
| | - Vladanka Topalovic
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11010 Belgrade, Serbia
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering
- University of Belgrade
- 11010 Belgrade, Serbia
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24
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Peterson H, Abu Dawud R, Garg A, Wang Y, Vilo J, Xenarios I, Adjaye J. Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells. Front Physiol 2013; 4:303. [PMID: 24194720 PMCID: PMC3809568 DOI: 10.3389/fphys.2013.00303] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 10/02/2013] [Indexed: 11/13/2022] Open
Abstract
Pluripotency in human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) is regulated by three transcription factors—OCT3/4, SOX2, and NANOG. To fully exploit the therapeutic potential of these cells it is essential to have a good mechanistic understanding of the maintenance of self-renewal and pluripotency. In this study, we demonstrate a powerful systems biology approach in which we first expand literature-based network encompassing the core regulators of pluripotency by assessing the behavior of genes targeted by perturbation experiments. We focused our attention on highly regulated genes encoding cell surface and secreted proteins as these can be more easily manipulated by the use of inhibitors or recombinant proteins. Qualitative modeling based on combining boolean networks and in silico perturbation experiments were employed to identify novel pluripotency-regulating genes. We validated Interleukin-11 (IL-11) and demonstrate that this cytokine is a novel pluripotency-associated factor capable of supporting self-renewal in the absence of exogenously added bFGF in culture. To date, the various protocols for hESCs maintenance require supplementation with bFGF to activate the Activin/Nodal branch of the TGFβ signaling pathway. Additional evidence supporting our findings is that IL-11 belongs to the same protein family as LIF, which is known to be necessary for maintaining pluripotency in mouse but not in human ESCs. These cytokines operate through the same gp130 receptor which interacts with Janus kinases. Our finding might explain why mESCs are in a more naïve cell state compared to hESCs and how to convert primed hESCs back to the naïve state. Taken together, our integrative modeling approach has identified novel genes as putative candidates to be incorporated into the expansion of the current gene regulatory network responsible for inducing and maintaining pluripotency.
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Affiliation(s)
- Hedi Peterson
- Quretec Ltd. Tartu, Estonia ; Faculty of Mathematics and Computer Science, Institute of Computer Science, University of Tartu Tartu, Estonia ; Faculty of Science and Technology, Institute of Molecular and Cellular Biology, University of Tartu Tartu, Estonia
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25
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Hasibeder A, Venkataramani V, Thelen P, Radzun HJ, Schweyer S. Phytoestrogens regulate the proliferation and expression of stem cell factors in cell lines of malignant testicular germ cell tumors. Int J Oncol 2013; 43:1385-94. [PMID: 23969837 PMCID: PMC3823397 DOI: 10.3892/ijo.2013.2060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/01/2013] [Indexed: 01/14/2023] Open
Abstract
Phytoestrogens have been shown to exert anti-proliferative effects on different cancer cells. In addition it could be demonstrated that inhibition of proliferation is associated with downregulation of the known stem cell factors NANOG, POU5F1 and SOX2 in tumor cells. We demonstrate the potential of Belamcanda chinensis extract (BCE) and tectorigenin as anticancer drugs in cell lines of malignant testicular germ cell tumor cells (TGCT) by inhibition of proliferation and regulating the expression of stem cell factors. The TGCT cell lines TCam-2 and NTera-2 were treated with BCE or tectorigenin and MTT assay was used to measure the proliferation of tumor cells. In addition, the expression of stem cell factors was analyzed by quantitative PCR and western blot analysis. Furthermore, global expression analysis was performed by microarray technique. BCE and tectorigenin inhibited proliferation and downregulated the stem cell factors NANOG and POU5F1 in TGCT cells. In addition, gene expression profiling revealed induction of genes important for the differentiation and inhibition of oncogenes. Utilizing connectivity map in an attempt to elucidate mechanism underlying BCE treatments we found highly positive association to histone deacetylase inhibitors (HDACi) amongst others. Causing no histone deacetylase inhibition, the effects of BCE on proliferation and stem cell factors may be based on histone-independent mechanisms such as direct hyperacetylation of transcription factors. Based on these findings, phytoestrogens may be useful as new agents in the treatment of TGCT.
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Affiliation(s)
- Astrid Hasibeder
- Department of Pathology, Georg August University, D-37075 Göttingen, Germany
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Kuo CL, Lam CM, Hewitt JE, Scotting PJ. Formation of the embryonic organizer is restricted by the competitive influences of Fgf signaling and the SoxB1 transcription factors. PLoS One 2013; 8:e57698. [PMID: 23469052 PMCID: PMC3585176 DOI: 10.1371/journal.pone.0057698] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 01/23/2013] [Indexed: 11/18/2022] Open
Abstract
The organizer is one of the earliest structures to be established during vertebrate development and is crucial to subsequent patterning of the embryo. We have previously shown that the SoxB1 transcription factor, Sox3, plays a central role as a transcriptional repressor of zebrafish organizer gene expression. Recent data suggest that Fgf signaling has a positive influence on organizer formation, but its role remains to be fully elucidated. In order to better understand how Fgf signaling fits into the complex regulatory network that determines when and where the organizer forms, the relationship between the positive effects of Fgf signaling and the repressive effects of the SoxB1 factors must be resolved. This study demonstrates that both fgf3 and fgf8 are required for expression of the organizer genes, gsc and chd, and that SoxB1 factors (Sox3, and the zebrafish specific factors, Sox19a and Sox19b) can repress the expression of both fgf3 and fgf8. However, we also find that these SoxB1 factors inhibit the expression of gsc and chd independently of their repression of fgf expression. We show that ectopic expression of organizer genes induced solely by the inhibition of SoxB1 function is dependent upon the activation of fgf expression. These data allow us to describe a comprehensive signaling network in which the SoxB1 factors restrict organizer formation by inhibiting Fgf, Nodal and Wnt signaling, as well as independently repressing the targets of that signaling. The organizer therefore forms only where Nodal-induced Fgf signaling overlaps with Wnt signaling and the SoxB1 proteins are absent.
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Affiliation(s)
- Cheng-Liang Kuo
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, QMC, Nottingham, United Kingdom
| | - Chi Man Lam
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, QMC, Nottingham, United Kingdom
| | - Jane E. Hewitt
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, QMC, Nottingham, United Kingdom
| | - Paul J. Scotting
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, QMC, Nottingham, United Kingdom
- * E-mail:
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Mouse Lymphoblastic Leukemias Induced by Aberrant Prdm14 Expression Demonstrate Widespread Copy Number Alterations Also Found in Human ALL. Cancers (Basel) 2012; 4:1050-1066. [PMID: 23487523 PMCID: PMC3593237 DOI: 10.3390/cancers4041050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Aberrant expression and activation of oncogenes in somatic cells has been associated with cancer initiation. Required for reacquisition of pluripotency in the developing germ cell, PRDM14 initiates lymphoblastic leukemia when misexpressed in murine bone marrow. Activation of pluripotency in somatic cells can lead to aneuploidy and copy number alterations during iPS cell generation, and we hypothesized that PRDM14-induced lymphoblastic leukemias would demonstrate significant chromosomal damage. High-resolution oligo array comparative genomic hybridization demonstrated infrequent aneuploidy but frequent amplification and deletion, with amplifications occurring in a 5:1 ratio with deletions. Many deletions (i.e., Cdkn2a, Ebf1, Pax5, Ikzf1) involved B-cell development genes and tumor suppressor genes, recapitulating deletions occurring in human leukemia. Pathways opposing senescence were frequently deactivated via Cdkn2a deletion or Tbx2 amplification, with corollary gene expression. Additionally, gene expression studies of abnormal pre-leukemic B-precursors showed downregulation of genes involved in chromosomal stability (i.e., Xrcc6) and failure to upregulate DNA repair pathways. We propose a model of leukemogenesis, triggered by pluripotency genes like Prdm14, which involves ongoing DNA damage and failure to activate non-homologous end-joining secondary to aberrant gene expression.
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Abu Dawud R, Schreiber K, Schomburg D, Adjaye J. Human embryonic stem cells and embryonal carcinoma cells have overlapping and distinct metabolic signatures. PLoS One 2012; 7:e39896. [PMID: 22768158 PMCID: PMC3387229 DOI: 10.1371/journal.pone.0039896] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/28/2012] [Indexed: 11/17/2022] Open
Abstract
While human embryonic stem cells (hESCs) and human embryonal carcinoma cells (hECCs) have been studied extensively at the levels of the genome, transcriptome, proteome and epigenome our knowledge of their corresponding metabolomes is limited. Here, we present the metabolic signatures of hESCs and hESCs obtained by untargeted gas chromatography coupled to mass spectrometry (GC-MS). Whilst some metabolites are common to both cell types, representing the self-renewal and house-keeping signatures, others were either higher (e.g., octadecenoic acid, glycerol-3-phosphate, 4-hydroxyproline) or lower (e.g., glutamic acid, mannitol, malic acid, GABA) in hESCs (H9) compared to hECCs (NTERA2), these represent cell type specific signatures. Further, our combined results of GC-MS and microarray based gene expression profiling of undifferentiated and OCT4-depleted hESCs are consistent with the Warburg effect which is increased glycolysis in embryonic cells and tumor cells in the presence of O2 while oxidative phosphorylation (OXPHOS) is impaired or even shut down. RNAi-based OCT4 knock down mediated differentiation resulted in the activation of the poised OXPHOS machinery by expressing missing key proteins such as NDUFC1, UQCRB and COX, increase in TCA cycle activity and decreased lactate metabolism. These results shed light on the metabolite layer of pluripotent stem cells and could potentially establish novel metabolic markers of self renewal and pluripotency.
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Affiliation(s)
- Raed Abu Dawud
- Department of Vertebrate Genomics, Max-Planck-Institute for Molecular Genetics, Berlin, Germany
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Ushida H, Chano T, Minami K, Kita H, Kawakami T, Okabe H, Okada Y, Okamoto K. Therapeutic Potential of SOX2 Inhibition for Embryonal Carcinoma. J Urol 2012; 187:1876-81. [DOI: 10.1016/j.juro.2011.12.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Indexed: 01/26/2023]
Affiliation(s)
- Hiroshi Ushida
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Tokuhiro Chano
- Department of Clinical Laboratory Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Kahori Minami
- Department of Clinical Laboratory Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Hiroko Kita
- Department of Clinical Laboratory Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Takahiro Kawakami
- Department of Clinical Laboratory Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Hidetoshi Okabe
- Department of Clinical Laboratory Medicine, Shiga University of Medical Science, Shiga, Japan
| | - Yusaku Okada
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Keisei Okamoto
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
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Som A, Luštrek M, Singh NK, Fuellen G. Derivation of an interaction/regulation network describing pluripotency in human. Gene 2012; 502:99-107. [PMID: 22548825 DOI: 10.1016/j.gene.2012.04.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 03/21/2012] [Accepted: 04/09/2012] [Indexed: 01/08/2023]
Abstract
Identification of the key genes/proteins of pluripotency and their interrelationships is an important step in understanding the induction and maintenance of pluripotency. Experimental approaches have accumulated large amounts of interaction/regulation data in mouse. We investigate how far such information can be transferred to human, the species of maximum interest, for which experimental data are much more limited. To address this issue, we mapped an existing mouse pluripotency network (the PluriNetWork) to human. We transferred interaction and regulation links between genes/proteins from mouse to human on the basis of orthologous relationship of the genes/proteins (called interolog mapping). To reduce the number of false positives, we used four different methods: phylogenetic profiling, Gene Ontology semantic similarity, gene co-expression, and RNA interference (RNAi) data. The methods and the resulting networks were evaluated by a novel approach using the information about the genes known to be involved in pluripotency from the literature. The RNAi method proved best for filtering out unlikely interactions, so it was used to construct the final human pluripotency network. The RNAi data are based on human embryonic stem cells (hESCs) that are generally considered to be in a (primed) epiblast stem cell state. Therefore, we assume that the final human network may reflect the (primed) epiblast stem cell state more closely, while the mouse network reflects the (unprimed/naïve) embryonic stem cell state more closely.
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Affiliation(s)
- Anup Som
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University of Rostock, Ernst-Heydemann-Str. 8, 18057, Rostock, Germany
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Westerman BA, Braat AK, Taub N, Potman M, Vissers JHA, Blom M, Verhoeven E, Stoop H, Gillis A, Velds A, Nijkamp W, Beijersbergen R, Huber LA, Looijenga LHJ, van Lohuizen M. A genome-wide RNAi screen in mouse embryonic stem cells identifies Mp1 as a key mediator of differentiation. ACTA ACUST UNITED AC 2011; 208:2675-89. [PMID: 22143885 PMCID: PMC3244037 DOI: 10.1084/jem.20102037] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite intense investigation of intrinsic and extrinsic factors that regulate pluripotency, the process of initial fate commitment of embryonic stem (ES) cells is still poorly understood. We used a genome-wide short hairpin RNA screen in mouse ES cells to identify genes that are essential for initiation of differentiation. Knockdown of the scaffolding protein Mek binding protein 1 (Mp1, also known as Lamtor3 or Map2k1ip1) stimulated self-renewal of ES cells, blocked differentiation, and promoted proliferation. Fibroblast growth factor 4 (FGF4) signaling is required for initial fate commitment of ES cells. Knockdown of Mp1 inhibited FGF4-induced differentiation but did not alter FGF4-driven proliferation. This uncoupling of differentiation and proliferation was also observed when oncogenic Ras isoforms were overexpressed in ES cells. Knockdown of Mp1 redirected FGF4 signaling from differentiation toward pluripotency and up-regulated the pluripotency-related genes Esrrb, Rex1, Tcl1, and Sox2. We also found that human germ cell tumors (GCTs) express low amounts of Mp1 in the invasive embryonic carcinoma and seminoma histologies and higher amounts of Mp1 in the noninvasive carcinoma in situ precursor and differentiated components. Knockdown of Mp1 in invasive GCT cells resulted in resistance to differentiation, thereby showing a functional role for Mp1 both in normal differentiation of ES cells and in germ cell cancer.
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Affiliation(s)
- Bart A Westerman
- Division of Molecular Genetics, the Netherlands Cancer Institute, 1066 CX Amsterdam, Netherlands
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Zoldan J, Lytton-Jean AKR, Karagiannis ED, Deiorio-Haggar K, Bellan LM, Langer R, Anderson DG. Directing human embryonic stem cell differentiation by non-viral delivery of siRNA in 3D culture. Biomaterials 2011; 32:7793-800. [PMID: 21835461 DOI: 10.1016/j.biomaterials.2011.06.057] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/24/2011] [Indexed: 12/19/2022]
Abstract
Human embryonic stem cells (hESCs) hold great potential as a resource for regenerative medicine. Before achieving therapeutic relevancy, methods must be developed to control stem cell differentiation. It is clear that stem cells can respond to genetic signals, such as those imparted by nucleic acids, to promote lineage-specific differentiation. Here we have developed an efficient system for delivering siRNA to hESCs in a 3D culture matrix using lipid-like materials. We show that non-viral siRNA delivery in a 3D scaffolds can efficiently knockdown 90% of GFP expression in GFP-hESCs. We further show that this system can be used as a platform for directing hESC differentiation. Through siRNA silencing of the KDR receptor gene, we achieve concurrent downregulation (60-90%) in genes representative of the endoderm germ layer and significant upregulation of genes representative of the mesoderm germ layer (27-90 fold). This demonstrates that siRNA can direct stem cell differentiation by blocking genes representative of one germ layer and also provides a particularly powerful means to isolate the endoderm germ layer from the mesoderm and ectoderm. This ability to inhibit endoderm germ layer differentiation could allow for improved control over hESC differentiation to desired cell types.
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Affiliation(s)
- Janet Zoldan
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
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Peng S, Chen LL, Lei XX, Yang L, Lin H, Carmichael GG, Huang Y. Genome-wide studies reveal that Lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells. Stem Cells 2011; 29:496-504. [PMID: 21425412 DOI: 10.1002/stem.591] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Lin28 inhibits the expression of let-7 microRNAs but also exhibits let-7-independent functions. Using immunoprecipitation and deep sequencing, we show here that Lin28 preferentially associates with a small subset of cellular mRNAs. Of particular interest are those for ribosomal proteins and metabolic enzymes, the expression levels of which are known to be coupled to cell growth and survival. Polysome profiling and reporter analyses suggest that Lin28 stimulates the translation of many or most of these targets. Moreover, Lin28-responsive elements were found within the coding regions of all target genes tested. Finally, a mutant Lin28 that still binds RNA but fails to interact with RNA helicase A (RHA), acts as a dominant-negative inhibitor of Lin28-dependent stimulation of translation. We suggest that Lin28, working in concert with RHA, enhances the translation of genes important for the growth and survival of human embryonic stem cells.
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Affiliation(s)
- Shuping Peng
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut, USA
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Nie J, Stewart R, Zhang H, Thomson JA, Ruan F, Cui X, Wei H. TF-Cluster: a pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). BMC SYSTEMS BIOLOGY 2011; 5:53. [PMID: 21496241 PMCID: PMC3101171 DOI: 10.1186/1752-0509-5-53] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 04/15/2011] [Indexed: 12/24/2022]
Abstract
BACKGROUND Identifying the key transcription factors (TFs) controlling a biological process is the first step toward a better understanding of underpinning regulatory mechanisms. However, due to the involvement of a large number of genes and complex interactions in gene regulatory networks, identifying TFs involved in a biological process remains particularly difficult. The challenges include: (1) Most eukaryotic genomes encode thousands of TFs, which are organized in gene families of various sizes and in many cases with poor sequence conservation, making it difficult to recognize TFs for a biological process; (2) Transcription usually involves several hundred genes that generate a combination of intrinsic noise from upstream signaling networks and lead to fluctuations in transcription; (3) A TF can function in different cell types or developmental stages. Currently, the methods available for identifying TFs involved in biological processes are still very scarce, and the development of novel, more powerful methods is desperately needed. RESULTS We developed a computational pipeline called TF-Cluster for identifying functionally coordinated TFs in two steps: (1) Construction of a shared coexpression connectivity matrix (SCCM), in which each entry represents the number of shared coexpressed genes between two TFs. This sparse and symmetric matrix embodies a new concept of coexpression networks in which genes are associated in the context of other shared coexpressed genes; (2) Decomposition of the SCCM using a novel heuristic algorithm termed "Triple-Link", which searches the highest connectivity in the SCCM, and then uses two connected TF as a primer for growing a TF cluster with a number of linking criteria. We applied TF-Cluster to microarray data from human stem cells and Arabidopsis roots, and then demonstrated that many of the resulting TF clusters contain functionally coordinated TFs that, based on existing literature, accurately represent a biological process of interest. CONCLUSIONS TF-Cluster can be used to identify a set of TFs controlling a biological process of interest from gene expression data. Its high accuracy in recognizing true positive TFs involved in a biological process makes it extremely valuable in building core GRNs controlling a biological process. The pipeline implemented in Perl can be installed in various platforms.
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Affiliation(s)
- Jeff Nie
- Morgridge Institute for Research, 330 N. Orchard St., Madison, WI 53715, USA
| | - Ron Stewart
- Morgridge Institute for Research, 330 N. Orchard St., Madison, WI 53715, USA
| | - Hang Zhang
- Department of Computer Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - James A Thomson
- Morgridge Institute for Research, 330 N. Orchard St., Madison, WI 53715, USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin, 600 Highland Ave., Madison, WI 53792, USA
- Department of Cell & Regenerative Biology, University of Wisconsin, 1300 University Ave., Madison, WI 53705, USA
- Department of Molecular, Cellular, & Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Fang Ruan
- Program of Computing Science and Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Xiaoqi Cui
- Department of Mathematics, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Hairong Wei
- School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
- Biotechnology Research Center, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
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Trueb B. Biology of FGFRL1, the fifth fibroblast growth factor receptor. Cell Mol Life Sci 2011; 68:951-64. [PMID: 21080029 PMCID: PMC11115071 DOI: 10.1007/s00018-010-0576-3] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2010] [Revised: 10/20/2010] [Accepted: 10/22/2010] [Indexed: 01/08/2023]
Abstract
FGFRL1 (fibroblast growth factor receptor like 1) is the most recently discovered member of the FGFR family. It contains three extracellular Ig-like domains similar to the classical FGFRs, but it lacks the protein tyrosine kinase domain and instead contains a short intracellular tail with a peculiar histidine-rich motif. The gene for FGFRL1 is found in all metazoans from sea anemone to mammals. FGFRL1 binds to FGF ligands and heparin with high affinity. It exerts a negative effect on cell proliferation, but a positive effect on cell differentiation. Mice with a targeted deletion of the Fgfrl1 gene die perinatally due to alterations in their diaphragm. These mice also show bilateral kidney agenesis, suggesting an essential role for Fgfrl1 in kidney development. A human patient with a frameshift mutation exhibits craniosynostosis, arguing for an additional role of FGFRL1 during bone formation. FGFRL1 contributes to the complexity of the FGF signaling system.
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Affiliation(s)
- Beat Trueb
- Department of Clinical Research, University of Bern, Switzerland.
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Park SJ, Nakai K. A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns. BMC Bioinformatics 2011; 12 Suppl 1:S50. [PMID: 21342583 PMCID: PMC3044308 DOI: 10.1186/1471-2105-12-s1-s50] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background To understand the gene regulatory system that governs the self-renewal and pluripotency of embryonic stem cells (ESCs) is an important step for promoting regenerative medicine. In it, the role of several core transcription factors (TFs), such as Oct4, Sox2 and Nanog, has been intensively investigated, details of their involvement in the genome-wide gene regulation are still not well clarified. Methods We constructed a predictive model of genome-wide gene expression in mouse ESCs from publicly available ChIP-seq data of 12 core TFs. The tag sequences were remapped on the genome by various alignment tools. Then, the binding density of each TF is calculated from the genome-wide bona fide TF binding sites. The TF-binding data was combined with the data of several epigenetic states (DNA methylation, several histone modifications, and CpG island) of promoter regions. These data as well as the ordinary peak intensity data were used as predictors of a simple linear regression model that predicts absolute gene expression. We also developed a pipeline for analyzing the effects of predictors and their interactions. Results Through our analysis, we identified two classes of genes that are either well explained or inefficiently explained by our model. The latter class seems to be genes that are not directly regulated by the core TFs. The regulatory regions of these gene classes show apparently distinct patterns of DNA methylation, histone modifications, existence of CpG islands, and gene ontology terms, suggesting the relative importance of epigenetic effects. Furthermore, we identified statistically significant TF interactions correlated with the epigenetic modification patterns. Conclusions Here, we proposed an improved prediction method in explaining the ESC-specific gene expression. Our study implies that the majority of genes are more or less directly regulated by the core TFs. In addition, our result is consistent with the general idea of relative importance of epigenetic effects in ESCs.
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Affiliation(s)
- Sung-Joon Park
- Human Genome Center, Institute of Medical Science, University of Tokyo, Japan.
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Coyle DE, Li J, Baccei M. Regional differentiation of retinoic acid-induced human pluripotent embryonic carcinoma stem cell neurons. PLoS One 2011; 6:e16174. [PMID: 21283767 PMCID: PMC3024414 DOI: 10.1371/journal.pone.0016174] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 12/08/2010] [Indexed: 11/18/2022] Open
Abstract
The NTERA2 cl D1 (NT2) cell line, derived from human teratocarcinoma, exhibits similar properties as embryonic stem (ES) cells or very early neuroepithelial progenitors. NT2 cells can be induced to become postmitotic central nervous system neurons (NT2N) with retinoic acid. Although neurons derived from pluripotent cells, such as NT2N, have been characterized for their neurotransmitter phenotypes, their potential suitability as a donor source for neural transplantation also depends on their ability to respond to localized environmental cues from a specific region of the CNS. Therefore, our study aimed to characterize the regional transcription factors that define the rostocaudal and dorsoventral identity of NT2N derived from a monolayer differentiation paradigm using quantitative PCR (qPCR). Purified NT2N mainly expressed both GABAergic and glutamatergic phenotypes and were electrically active but did not form functional synapses. The presence of immature astrocytes and possible radial glial cells was noted. The NT2N expressed a regional transcription factor code consistent with forebrain, hindbrain and spinal cord neural progenitors but showed minimal expression of midbrain phenotypes. In the dorsoventral plane NT2N expressed both dorsal and ventral neural progenitors. Of major interest was that even under the influence of retinoic acid, a known caudalization factor, the NT2N population maintained a rostral phenotype subpopulation which expressed cortical regional transcription factors. It is proposed that understanding the regional differentiation bias of neurons derived from pluripotent stem cells will facilitate their successful integration into existing neuronal networks within the CNS.
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Affiliation(s)
- Dennis E Coyle
- Department of Anesthesiology, University of Cincinnati, Cincinnati, Ohio, United States of America.
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Philonenko ES, Shutova MV, Chestkov IV, Lagarkova MA, Kiselev SL. Current progress and potential practical application for human pluripotent stem cells. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 292:153-96. [PMID: 22078961 DOI: 10.1016/b978-0-12-386033-0.00004-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Pluripotent stem cells are able to give rise to all cell types of the organism. There are two sources for human pluripotent stem cells: embryonic stem cells (ESCs) derived from surplus blastocysts created for in vitro fertilization and induced pluripotent stem cells (iPSCs) generated by reprogramming of somatic cells. ESCs have been an area of intense research during the past decade, and two clinical trials have been recently approved. iPSCs were created only recently, and most of the research has been focused on the iPSC generation protocols and investigation of mechanisms of direct reprogramming. The iPSC technology makes possible to derive pluripotent stem cells from any patient. However, there are a number of hurdles to be overcome before iPSCs will find a niche in practice. In this review, we discuss differences and similarities of the two pluripotent cell types and assess prospects for application of these cells in biomedicine.
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Jung M, Peterson H, Chavez L, Kahlem P, Lehrach H, Vilo J, Adjaye J. A data integration approach to mapping OCT4 gene regulatory networks operative in embryonic stem cells and embryonal carcinoma cells. PLoS One 2010; 5:e10709. [PMID: 20505756 PMCID: PMC2873957 DOI: 10.1371/journal.pone.0010709] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 04/25/2010] [Indexed: 01/06/2023] Open
Abstract
It is essential to understand the network of transcription factors controlling self-renewal of human embryonic stem cells (ESCs) and human embryonal carcinoma cells (ECs) if we are to exploit these cells in regenerative medicine regimes. Correlating gene expression levels after RNAi-based ablation of OCT4 function with its downstream targets enables a better prediction of motif-specific driven expression modules pertinent for self-renewal and differentiation of embryonic stem cells and induced pluripotent stem cells.We initially identified putative direct downstream targets of OCT4 by employing CHIP-on-chip analysis. A comparison of three peak analysis programs revealed a refined list of OCT4 targets in the human EC cell line NCCIT, this list was then compared to previously published OCT4 CHIP-on-chip datasets derived from both ES and EC cells. We have verified an enriched POU-motif, discovered by a de novo approach, thus enabling us to define six distinct modules of OCT4 binding and regulation of its target genes.A selection of these targets has been validated, like NANOG, which harbours the evolutionarily conserved OCT4-SOX2 binding motif within its proximal promoter. Other validated targets, which do not harbour the classical HMG motif are USP44 and GADD45G, a key regulator of the cell cycle. Over-expression of GADD45G in NCCIT cells resulted in an enrichment and up-regulation of genes associated with the cell cycle (CDKN1B, CDKN1C, CDK6 and MAPK4) and developmental processes (BMP4, HAND1, EOMES, ID2, GATA4, GATA5, ISL1 and MSX1). A comparison of positively regulated OCT4 targets common to EC and ES cells identified genes such as NANOG, PHC1, USP44, SOX2, PHF17 and OCT4, thus further confirming their universal role in maintaining self-renewal in both cell types. Finally we have created a user-friendly database (http://biit.cs.ut.ee/escd/), integrating all OCT4 and stem cell related datasets in both human and mouse ES and EC cells.In the current era of systems biology driven research, we envisage that our integrated embryonic stem cell database will prove beneficial to the booming field of ES, iPS and cancer research.
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Affiliation(s)
- Marc Jung
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (JA); (MJ)
| | - Hedi Peterson
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
- Quretec Ltd., Tartu, Estonia
| | - Lukas Chavez
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Pascal Kahlem
- EMBL - European Bioinformatics Institute, Cambridge, United Kingdom
| | - Hans Lehrach
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Jaak Vilo
- Quretec Ltd., Tartu, Estonia
- Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - James Adjaye
- Molecular Embryology and Aging Group, Department of Vertebrate Genomics, Max-Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail: (JA); (MJ)
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Lorenz P, Dietmann S, Wilhelm T, Koczan D, Autran S, Gad S, Wen G, Ding G, Li Y, Rousseau-Merck MF, Thiesen HJ. The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues. BMC Genomics 2010; 11:206. [PMID: 20346131 PMCID: PMC2865497 DOI: 10.1186/1471-2164-11-206] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 03/26/2010] [Indexed: 11/17/2022] Open
Abstract
Background Expansion of multi-C2H2 domain zinc finger (ZNF) genes, including the Krüppel-associated box (KRAB) subfamily, paralleled the evolution of tetrapodes, particularly in mammalian lineages. Advances in their cataloging and characterization suggest that the functions of the KRAB-ZNF gene family contributed to mammalian speciation. Results Here, we characterized the human 8q24.3 ZNF cluster on the genomic, the phylogenetic, the structural and the transcriptome level. Six (ZNF7, ZNF34, ZNF250, ZNF251, ZNF252, ZNF517) of the seven locus members contain exons encoding KRAB domains, one (ZNF16) does not. They form a paralog group in which the encoded KRAB and ZNF protein domains generally share more similarities with each other than with other members of the human ZNF superfamily. The closest relatives with respect to their DNA-binding domain were ZNF7 and ZNF251. The analysis of orthologs in therian mammalian species revealed strong conservation and purifying selection of the KRAB-A and zinc finger domains. These findings underscore structural/functional constraints during evolution. Gene losses in the murine lineage (ZNF16, ZNF34, ZNF252, ZNF517) and potential protein truncations in primates (ZNF252) illustrate ongoing speciation processes. Tissue expression profiling by quantitative real-time PCR showed similar but distinct patterns for all tested ZNF genes with the most prominent expression in fetal brain. Based on accompanying expression signatures in twenty-six other human tissues ZNF34 and ZNF250 revealed the closest expression profiles. Together, the 8q24.3 ZNF genes can be assigned to a cerebellum, a testis or a prostate/thyroid subgroup. These results are consistent with potential functions of the ZNF genes in morphogenesis and differentiation. Promoter regions of the seven 8q24.3 ZNF genes display common characteristics like missing TATA-box, CpG island-association and transcription factor binding site (TFBS) modules. Common TFBS modules partly explain the observed expression pattern similarities. Conclusions The ZNF genes at human 8q24.3 form a relatively old mammalian paralog group conserved in eutherian mammals for at least 130 million years. The members persisted after initial duplications by undergoing subfunctionalizations in their expression patterns and target site recognition. KRAB-ZNF mediated repression of transcription might have shaped organogenesis in mammalian ontogeny.
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Affiliation(s)
- Peter Lorenz
- Institute of Immunology, University of Rostock, Schillingallee 70, 18055 Rostock, Germany
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Fernández IS, Cuevas P, Angulo J, López-Navajas P, Canales-Mayordomo A, González-Corrochano R, Lozano RM, Valverde S, Jiménez-Barbero J, Romero A, Giménez-Gallego G. Gentisic acid, a compound associated with plant defense and a metabolite of aspirin, heads a new class of in vivo fibroblast growth factor inhibitors. J Biol Chem 2010; 285:11714-29. [PMID: 20145243 DOI: 10.1074/jbc.m109.064618] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Fibroblast growth factors are key proteins in many intercellular signaling networks. They normally remain attached to the extracellular matrix, which confers on them a considerable stability. The unrestrained accumulation of fibroblast growth factors in the extracellular milieu, either due to uncontrolled synthesis or enzymatic release, contributes to the pathology of many diseases. Consequently, the neutralization of improperly mobilized fibroblast growth factors is of clear therapeutic interest. In pursuing described rules to identify potential inhibitors of these proteins, gentisic acid, a plant pest-controlling compound, an aspirin and vegetarian diet common catabolite, and a component of many traditional liquors and herbal remedies, was singled out as a powerful inhibitor of fibroblast growth factors. Gentisic acid was used as a lead to identify additional compounds with better inhibitory characteristics generating a new chemical class of fibroblast growth factor inhibitors that includes the agent responsible for alkaptonuria. Through low and high resolution approaches, using representative members of the fibroblast growth factor family and their cell receptors, it was shown that this class of inhibitors may employ two different mechanisms to interfere with the assembly of the signaling complexes that trigger fibroblast growth factor-driven mitogenesis. In addition, we obtained evidence from in vivo disease models that this group of inhibitors may be of interest to treat cancer and angiogenesis-dependent diseases.
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Affiliation(s)
- Israel S Fernández
- Departamento de Biología Físico-Química, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
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Busch W, Kühnel D, Schirmer K, Scholz S. Tungsten carbide cobalt nanoparticles exert hypoxia-like effects on the gene expression level in human keratinocytes. BMC Genomics 2010; 11:65. [PMID: 20105288 PMCID: PMC2824725 DOI: 10.1186/1471-2164-11-65] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 01/27/2010] [Indexed: 01/07/2023] Open
Abstract
Background Tungsten carbide (WC) and tungsten carbide cobalt (WC-Co) nanoparticles are of occupational health relevance because of the increasing usage in hard metal industries. Earlier studies showed an enhanced toxic potential for WC-Co compared to WC or cobalt ions alone. Therefore, we investigated the impact of these particles, compared to cobalt ions applied as CoCl2, on the global gene expression level in human keratinocytes (HaCaT) in vitro. Results WC nanoparticles exerted very little effects on the transcriptomic level after 3 hours and 3 days of exposure. In contrast, WC-Co nanoparticles caused significant transcriptional changes that were similar to those provoked by CoCl2. However, CoCl2 exerted even more pronounced changes in the transcription patterns. Gene set enrichment analyses revealed that the differentially expressed genes were related to hypoxia response, carbohydrate metabolism, endocrine pathways, and targets of several transcription factors. The role of the transcription factor HIF1 (hypoxia inducible factor 1) is particularly highlighted and aspects of downstream events as well as the role of other transcription factors related to cobalt toxicity are considered. Conclusions This study provides extensive data useful for the understanding of nanoparticle and cobalt toxicity. It shows that WC nanoparticles caused low transcriptional responses while WC-Co nanoparticles are able to exert responses similar to that of free cobalt ions, particularly the induction of hypoxia-like effects via interactions with HIF1α in human keratinocytes. However, the enhanced toxicity of WC-Co particles compared to CoCl2 could not be explained by differences in gene transcription.
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Affiliation(s)
- Wibke Busch
- UFZ - Helmholtz-Centre for Environmental Research Leipzig, Department of Bioanalytical Ecotoxicology, 04318 Leipzig, Germany.
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Page RL, Ambady S, Holmes WF, Vilner L, Kole D, Kashpur O, Huntress V, Vojtic I, Whitton H, Dominko T. Induction of stem cell gene expression in adult human fibroblasts without transgenes. CLONING AND STEM CELLS 2009; 11:417-26. [PMID: 19622035 DOI: 10.1089/clo.2009.0015] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Reprogramming of differentiated somatic cells into induced pluripotent stem (iPS) cells has potential for derivation of patient-specific cells for therapy as well as for development of models with which to study disease progression. Derivation of iPS cells from human somatic cells has been achieved by viral transduction of human fibroblasts with early developmental genes. Because forced expression of these genes by viral transduction results in transgene integration with unknown and unpredictable potential mutagenic effects, identification of cell culture conditions that can induce endogenous expression of these genes is desirable. Here we show that primary adult human fibroblasts have basal expression of mRNA for OCT4, SOX2, and NANOG. However, translation of these messages into detectable proteins and their subcellular localization depends on cell culture conditions. Manipulation of oxygen concentration and FGF2 supplementation can modulate expression of some pluripotency related genes at the transcriptional, translational, and cellular localization level. Changing cell culture condition parameters led to expression of REX1, potentiation of expression of LIN28, translation of OCT4, SOX2, and NANOG, and translocation of these transcription factors to the cell nucleus. We also show that culture conditions affect the in vitro lifespan of dermal fibroblasts, nearly doubling the number of population doublings before the cells reach replicative senescence. Our results suggest that it is possible to induce and manipulate endogenous expression of stem cell genes in somatic cells without genetic manipulation, but this short-term induction may not be sufficient for acquisition of true pluripotency. Further investigation of the factors involved in inducing this response could lead to discovery of defined culture conditions capable of altering cell fate in vitro. This would alleviate the need for forced expression by transgenesis, thus eliminating the risk of mutagenic effects due to genetic manipulation.
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Gene silencing in human embryonic stem cells by RNA interference. Biochem Biophys Res Commun 2009; 390:1106-10. [DOI: 10.1016/j.bbrc.2009.10.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Accepted: 10/08/2009] [Indexed: 12/27/2022]
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Korkola JE, Houldsworth J, Bosl GJ, Chaganti RSK. Molecular events in germ cell tumours: linking chromosome-12 gain, acquisition of pluripotency and response to cisplatin. BJU Int 2009; 104:1334-8. [PMID: 19840009 DOI: 10.1111/j.1464-410x.2009.08855.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Germ cell tumours (GCTs) represent the leading cause of cancer-related morbidity and mortality in young men aged 18-35 years. Transformation of the cell of origin results in tumours with several unique properties. GCTs are characterized by gain of the short arm of chromosome 12 in almost all cases, a frequency of genomic alteration not seen in any other solid tumours. GCTs are truly pluripotent, giving rise to cells of somatic and extra-embryonic lineages, which results in tumours with a spectrum of differentiation that rivals that seen in normal embryogenesis and development. Despite the presence of genomic instability and many oncogenic changes, GCTs are highly curable, even in the metastatic setting, due to their extreme sensitivity to cisplatin-based chemotherapy. In this review we highlight some of the molecular events associated with the genesis, differentiation and chemotherapeutic response of these tumours, and discuss how these alterations are linked with biological features unique to germ cells.
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Affiliation(s)
- James E Korkola
- Cell Biology Division, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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Wang X, Lin G, Martins-Taylor K, Zeng H, Xu RH. Inhibition of caspase-mediated anoikis is critical for basic fibroblast growth factor-sustained culture of human pluripotent stem cells. J Biol Chem 2009; 284:34054-64. [PMID: 19828453 DOI: 10.1074/jbc.m109.052290] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Apoptosis and proliferation are two dynamically and tightly regulated processes that together maintain the homeostasis of renewable tissues. Anoikis is a subtype of apoptosis induced by detachment of adherent cells from the extracellular matrix. By using the defined mTeSR1 medium and collecting freshly detached cells, we found here that human pluripotent stem (PS) cells including embryonic stem (ES) cells and induced pluripotent stem cells are subject to constant anoikis in culture, which is escalated in the absence of basic fibroblast growth factor (bFGF). Withdrawal of bFGF also promotes apoptosis and differentiation of the remaining adherent cells without affecting their cell cycle progression. Insulin-like growth factor 2 (IGF2) has previously been reported to act downstream of FGF signaling to support self-renewal of human ES cells. However, we found that IGF2 cannot substitute bFGF in the TeSR1-supported culture, although endogenous IGF signaling is required to sustain self-renewal of human ES cells. On the other hand, all of the bFGF withdrawal effects observed here can be markedly prevented by the caspase inhibitor z-VAD-FMK. We further demonstrated that the bFGF-repressed anoikis is dependent on activation of ERK and AKT and associated with inhibition of Bcl-2-interacting mediator of cell death and the caspase-ROCK1-myosin signaling. Anoikis is independent of pre-detachment apoptosis and differentiation of the cells. Because previous studies of human PS cells have been focused on attached cells, our findings revealed a neglected role of bFGF in sustaining self-renewal of human PS cells: preventing them from anoikis via inhibition of caspase activation.
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Affiliation(s)
- Xiaofang Wang
- University of Connecticut Stem Cell Institute, Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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Pascal LE, Vêncio RZN, Goo YA, Page LS, Shadle CP, Liu AY. Temporal expression profiling of the effects of secreted factors from prostate stromal cells on embryonal carcinoma stem cells. Prostate 2009; 69:1353-65. [PMID: 19455603 DOI: 10.1002/pros.20982] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND There is a growing body of evidence indicating that epigenetic influences originating from stromal cells in the immediate microenvironment may play a role in carcinogenesis. Determining the molecular mechanisms involved in stromal-stem cell interaction could provide critical insight into prostate development and disease progression, particularly with regard to their relationship to and influence on the putative cancer stem cell. METHODS Prostate and bladder stromal cells prepared from tissue specimens were co-cultured with the pluripotent embryonal carcinoma cell line NCCIT. Transcriptome analysis was used to characterize NCCIT cell response to prostate or bladder signaling. RESULTS A systems approach demonstrated that prostate stromal cells were capable of inducing gene expression changes in NCCIT through secreted factors. Induction led to a loss of embryonic stem cell markers, with concurrent up-regulation of many genes characteristic of stromal mesenchyme cells as well as some of epithelial and cancer stem cells. Bladder stromal signaling produced gene expression changes different from those of prostate signaling. CONCLUSIONS This study indicates that paracrine stromal cell signaling can affect cancer stem cell response in an organ-specific manner and may provide insight for future development of treatment strategies such as differentiation therapy.
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Affiliation(s)
- Laura E Pascal
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA.
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You JS, Kang JK, Seo DW, Park JH, Park JW, Lee JC, Jeon YJ, Cho EJ, Han JW. Depletion of embryonic stem cell signature by histone deacetylase inhibitor in NCCIT cells: involvement of Nanog suppression. Cancer Res 2009; 69:5716-25. [PMID: 19567677 DOI: 10.1158/0008-5472.can-08-4953] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The embryonic stem cell-like gene expression signature has been shown to be associated with poorly differentiated aggressive human tumors and has attracted great attention as a potential target for future cancer therapies. Here, we investigate the potential of the embryonic stem cell signature as molecular target for the therapy and the strategy to suppress the embryonic stem cell signature. The core stemness gene Nanog is abnormally overexpressed in human embryonic carcinoma NCCIT cells showing gene expression profiles similar to embryonic stem cells. Down-regulation of the gene by either small interfering RNAs targeting Nanog or histone deacetylase inhibitor apicidin causes reversion of expression pattern of embryonic stem cell signature including Oct4, Sox2, and their target genes, leading to cell cycle arrest, inhibition of colony formation in soft agar, and induction of differentiation into all three germ layers. These effects are antagonized by reintroduction of Nanog. Interestingly, embryonic carcinoma cells (NCCIT, NTERA2, and P19) exhibit a higher sensitivity to apicidin in down-regulation of Nanog compared with embryonic stem cells. Furthermore, the down-regulation of Nanog expression by apicidin is mediated by a coordinated change in recruitment of epigenetic modulators and transcription factors to the promoter region. These findings indicate that overexpression of stemness gene Nanog in NCCIT cells is associated with maintaining stem cell-like phenotype and suggest that targeting Nanog might be an approach for improved therapy of poorly differentiated tumors.
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Affiliation(s)
- Jueng Soo You
- Department of Biochemistry and Molecular Biology, College of Pharmacy, Sungkyunkwan University, Suwon, Korea
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Greber B, Lehrach H, Adjaye J. Control of early fate decisions in human ES cells by distinct states of TGFbeta pathway activity. Stem Cells Dev 2009; 17:1065-77. [PMID: 18393632 DOI: 10.1089/scd.2008.0035] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mechanisms controlling self-renewal versus lineage commitment in human embryonic stem (hES) cells are not well understood. Nonetheless, current knowledge suggests a crucial role for TGFbeta signaling in controlling these early fate decisions. We have investigated the effects of TGFbeta pathway activation and inhibition on gene expression in hES cells. Our data reveal that SMAD 2/3 signaling directly supports NANOG expression, while SMAD 1/5/8 activation moderately represses SOX2. In addition, genes encoding key developmentally relevant signaling molecules and transcription factors appear to be immediately downstream of SMAD 1/5/8 signaling, or require both SMAD 1/5/8 and 2/3 activation, or inactivation of TGFbeta signaling for their induction. Defined stimulation/inhibition of the two TGFbeta branches appeared to control early fate decisions in accordance with these downstream transcriptional effects. Our results therefore help to better understand how pluripotency is mediated at the transcriptional level.
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Affiliation(s)
- Boris Greber
- Max Planck Institute for Molecular Genetics, Department of Vertebrate Genomics, Berlin, Germany.
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50
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Regenbrecht CRA, Lehrach H, Adjaye J. Stemming cancer: functional genomics of cancer stem cells in solid tumors. ACTA ACUST UNITED AC 2009; 4:319-28. [PMID: 18561035 PMCID: PMC2758383 DOI: 10.1007/s12015-008-9034-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cancer stem cells (CSCs) were discovered about 15 years ago in hematopoietic cancers. Subsequently, cancer stem cells were discovered in various solid tumors. Based on parallels with normal stem cells, a developmental process of cancer stem cells follows paths of organized, hierarchical structure of cells with different degrees of maturity. While some investigators have reported particular markers as identification of cancer stem cells, these markers require further research. In this review, we focus on the functional genomics of cancer stem cells. Functional genomics provides useful information on the signaling pathways which are consecutively activated or inactivated amongst those cells. This information is of particular importance for cancer research and clinical treatment in many respects. (1) Understanding of self-renewal mechanisms crucial to tumor growth. (2) Allow the identification of new, more specific marker for CSCs, and (3) pathways that are suitable as future targets for anti-cancer drugs. This is of particular importance, because today's chemotherapy targets the proliferating cancer cells sparing the relatively slow dividing cancer stem cells. The first step on this long road therefore is to analyze genome-wide expression-profiles within the same type of cancer and then between different types of cancer, encircling those target genes and pathways, which are specific to these cells.
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Affiliation(s)
- C R A Regenbrecht
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics (Molecular Embryology and Aging group), Ihnestrasse 73, 14195 Berlin, Germany
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