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Moqbel MS, Alhaider AK, Almathen F, Amor NNB, Al-Ramadan SY. Osteopontin expression in dromedary camel's conceptuses during the peri-implantation period. Reprod Domest Anim 2024; 59:e14694. [PMID: 39075937 DOI: 10.1111/rda.14694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/31/2024]
Abstract
The reproductive efficiency of dromedary camels is hindered by challenges such as early embryonic mortality, which may be attributed to a lack of synchronization between conceptus signalling and uterine receptivity. Understanding the intricate biological processes involved in feto-maternal interactions during implantation is crucial to address these limitations. Osteopontin (OPN) is a protein involved in cell signalling and adhesion, playing a crucial role in embryonic implantation. Previous studies have shown the presence of OPN in the uterine endometrium of various mammalian species including dromedary camels. However, the expression pattern of OPN in dromedary conceptuses remains unexplored. Thus, the current study aimed, for the first time, to investigate the temporospatial expression of OPN in dromedary conceptuses during the peri-implantation period at Days 8, 10, and 12 of pregnancy. Twelve conceptuses were recovered non-surgically from pregnant females on Days 8, 10, 12 of pregnancy. Quantitative real-time PCR (qrt-PCR), immunohistochemistry (IHC), and immunofluorescence (IF) were employed for analysis of the expression of OPN mRNA and protein. The results revealed significant increases in both OPN mRNA and protein expression started on Day 10 and peaked at Day 12 of pregnancy. Immuno-localization confirmed the presence of OPN protein in the trophectoderm and endoderm of dromedary conceptuses. In conclusion, the expression and localization of OPN during the peri-implantation period in dromedary conceptuses imply its involvement as a crucial reproductive factor and its upregulation during this period, with a pronounced increase close to attachment time (Day 12 of pregnancy) further supports its role in embryo adhesion, implantation, and placentation.
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Affiliation(s)
- Mohammed Salem Moqbel
- Department of Anatomy, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Abdulraman Khalid Alhaider
- Department of Clinical Studies, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Faisal Almathen
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Nidhal Neji Ben Amor
- Department of Veterinary Public Health, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Saeed Yaseen Al-Ramadan
- Department of Anatomy, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
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2
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Singleton KS, Silva-Rodriguez P, Cunningham DD, Silva EM. Xenopus Sox11 Partner Proteins and Functional Domains in Neurogenesis. Genes (Basel) 2024; 15:243. [PMID: 38397232 PMCID: PMC10887758 DOI: 10.3390/genes15020243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Sox11, a member of the SoxC family of transcription factors, has distinct functions at different times in neural development. Studies in mouse, frog, chick, and zebrafish show that Sox11 promotes neural fate, neural differentiation, and neuron maturation in the central nervous system. These diverse roles are controlled in part by spatial and temporal-specific protein interactions. However, the partner proteins and Sox11-interaction domains underlying these diverse functions are not well defined. Here, we identify partner proteins and the domains of Xenopus laevis Sox11 required for protein interaction and function during neurogenesis. Our data show that Sox11 co-localizes and interacts with Pou3f2 and Neurog2 in the anterior neural plate and in early neurons, respectively. We also demonstrate that Sox11 does not interact with Neurog1, a high-affinity partner of Sox11 in the mouse cortex, suggesting that Sox11 has species-specific partner proteins. Additionally, we determined that the N-terminus including the HMG domain of Sox11 is necessary for interaction with Pou3f2 and Neurog2, and we established a novel role for the N-terminal 46 amino acids in the specification of placodal progenitors. This is the first identification of partner proteins for Sox11 and of domains required for partner-protein interactions and distinct roles in neurogenesis.
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Affiliation(s)
- Kaela S. Singleton
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
| | - Pablo Silva-Rodriguez
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Doreen D. Cunningham
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Elena M. Silva
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
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3
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Nazarov IB, Zilov DS, Gordeev MN, Potapenko EV, Yeremenko N, Tomilin AN. Transcriptional Coactivator BOB1 (OBF1, OCA-B) Modulates the Specificity of DNA Recognition by the POU-Domain Factors OCT1 and OCT2 in a Monomeric Configuration. Biomolecules 2024; 14:123. [PMID: 38254723 PMCID: PMC10812921 DOI: 10.3390/biom14010123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/24/2024] Open
Abstract
BOB1, a mammalian lymphocyte-specific transcriptional coactivator of the transcription factors OCT1 and OCT2 (OCT1/2), plays important roles in normal immune responses, autoimmunity, and hematologic malignancies. The issue of a DNA sequence preference change imposed by BOB1 was raised more than two decades ago but remains unresolved. In this paper, using the EMSA-SELEX-Seq approach, we have reassessed the intrinsic ability of BOB1 to modulate the specificity of DNA recognition by OCT1 and OCT2. Our results have reaffirmed previous conclusions regarding BOB1 selectivity towards the dimer configuration of OCT1/2. However, they suggest that the monomeric configuration of these factors, assembled on the classical octamer ATGCAAAT and related motifs, are the primary targets of BOB1. Our data further specify the DNA sequence preference imposed by BOB1 and predict the probability of ternary complex formation. These results provide an additional insight into the action of BOB1-an essential immune regulator and a promising molecular target for the treatment of autoimmune diseases and hematologic malignancies.
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Affiliation(s)
- Igor B. Nazarov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Danil S. Zilov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Mikhail N. Gordeev
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
| | - Evgenii V. Potapenko
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel;
- University of Haifa, Haifa 3498838, Israel
| | - Nataliya Yeremenko
- Center for Research in Transplantation and Translational Immunology UMR1064, 30 Bd Jean Monnet, Nantes University, CEDEX 01, 44093 Nantes, France;
| | - Alexey N. Tomilin
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (D.S.Z.); (M.N.G.)
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4
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Betzler AC, Brunner C. The Role of the Transcriptional Coactivator BOB.1/OBF.1 in Adaptive Immunity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1459:53-77. [PMID: 39017839 DOI: 10.1007/978-3-031-62731-6_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
BOB.1/OBF.1 is a transcriptional coactivator involved in octamer-dependent transcription. Thereby, BOB.1/OBF.1 is involved in the transcriptional regulation of genes important for lymphocyte physiology. BOB.1/OBF.1-deficient mice reveal multiple B- and T-cell developmental defects. The most prominent defect of these mice is the complete absence of germinal centers (GCs) resulting in severely impaired T-cell-dependent immune responses. In humans, BOB.1/OBF.1 is associated with several autoimmune and inflammatory diseases but also linked to liquid and solid tumors. Although its role for B-cell development is relatively well understood, its exact role for the GC reaction and T-cell biology has long been unclear. Here, the contribution of BOB.1/OBF.1 for B-cell maturation is summarized, and recent findings regarding its function in GC B- as well as in various T-cell populations are discussed. Finally, a detailed perspective on how BOB.1/OBF.1 contributes to different pathologies is provided.
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Affiliation(s)
- Annika C Betzler
- Department of Oto-Rhino-Larnygology, Ulm University Medical Center, Ulm, Germany
- Core Facility Immune Monitoring, Ulm University, Ulm, Germany
| | - Cornelia Brunner
- Department of Oto-Rhino-Larnygology, Ulm University Medical Center, Ulm, Germany.
- Core Facility Immune Monitoring, Ulm University, Ulm, Germany.
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5
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Zhao Y, Li J, Lian Y, Zhou Q, Wu Y, Kang J. METTL3-Dependent N6-Methyladenosine Modification Programs Human Neural Progenitor Cell Proliferation. Int J Mol Sci 2023; 24:15535. [PMID: 37958523 PMCID: PMC10647291 DOI: 10.3390/ijms242115535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
METTL3, a methyltransferase responsible for N6-methyladenosine (m6A) modification, plays key regulatory roles in mammal central neural system (CNS) development. However, the specific epigenetic mechanisms governing human CNS development remain poorly elucidated. Here, we generated small-molecule-assisted shut-off (SMASh)-tagged hESC lines to reduce METTL3 protein levels, and found that METTL3 is not required for human neural progenitor cell (hNPC) formation and neuron differentiation. However, METTL3 deficiency inhibited hNPC proliferation by reducing SLIT2 expression. Mechanistic studies revealed that METTL3 degradation in hNPCs significantly decreased the enrichment of m6A in SLIT2 mRNA, consequently reducing its expression. Our findings reveal a novel functional target (SLIT2) for METTL3 in hNPCs and contribute to a better understanding of m6A-dependent mechanisms in hNPC proliferation.
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Affiliation(s)
- Yuan Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Z.); (J.L.); (Y.L.); (Q.Z.)
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center of Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jianguo Li
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Z.); (J.L.); (Y.L.); (Q.Z.)
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center of Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yilin Lian
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Z.); (J.L.); (Y.L.); (Q.Z.)
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center of Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qian Zhou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Z.); (J.L.); (Y.L.); (Q.Z.)
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center of Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yukang Wu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Z.); (J.L.); (Y.L.); (Q.Z.)
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center of Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; (Y.Z.); (J.L.); (Y.L.); (Q.Z.)
- Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center of Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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6
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Tan DS, Cheung SL, Gao Y, Weinbuch M, Hu H, Shi L, Ti SC, Hutchins AP, Cojocaru V, Jauch R. The homeodomain of Oct4 is a dimeric binder of methylated CpG elements. Nucleic Acids Res 2023; 51:1120-1138. [PMID: 36631980 PMCID: PMC9943670 DOI: 10.1093/nar/gkac1262] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 01/13/2023] Open
Abstract
Oct4 is essential to maintain pluripotency and has a pivotal role in establishing the germline. Its DNA-binding POU domain was recently found to bind motifs with methylated CpG elements normally associated with epigenetic silencing. However, the mode of binding and the consequences of this capability has remained unclear. Here, we show that Oct4 binds to a compact palindromic DNA element with a methylated CpG core (CpGpal) in alternative states of pluripotency and during cellular reprogramming towards induced pluripotent stem cells (iPSCs). During cellular reprogramming, typical Oct4 bound enhancers are uniformly demethylated, with the prominent exception of the CpGpal sites where DNA methylation is often maintained. We demonstrate that Oct4 cooperatively binds the CpGpal element as a homodimer, which contrasts with the ectoderm-expressed POU factor Brn2. Indeed, binding to CpGpal is Oct4-specific as other POU factors expressed in somatic cells avoid this element. Binding assays combined with structural analyses and molecular dynamic simulations show that dimeric Oct4-binding to CpGpal is driven by the POU-homeodomain whilst the POU-specific domain is detached from DNA. Collectively, we report that Oct4 exerts parts of its regulatory function in the context of methylated DNA through a DNA recognition mechanism that solely relies on its homeodomain.
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Affiliation(s)
- Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Shun Lai Cheung
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Maike Weinbuch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China,Institute for Molecular Medicine, Ulm University, Ulm, Germany
| | - Haoqing Hu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Liyang Shi
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Shih-Chieh Ti
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Andrew P Hutchins
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Vlad Cojocaru
- STAR-UBB Institute, Babeş-Bolyai University, Cluj-Napoca, Romania,Computational Structural Biology Group, Utrecht University, The Netherlands,Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf Jauch
- To whom correspondence should be addressed. Tel: +852 3917 9511; Fax: +852 28559730;
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7
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Zhu Z, Huang F, Jiang Y, Ruan S, Liu M, Zhang Y, Li Y, Chen J, Cui Y, Chen Z, Chen H, Zeng F. OLMALINC/OCT4/BMP2 axis enhances osteogenic-like phenotype of renal interstitial fibroblasts to participate in Randall's plaque formation. Mol Med 2022; 28:162. [PMID: 36581839 PMCID: PMC9798568 DOI: 10.1186/s10020-022-00576-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/15/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Randall's plaques (RP) are identified as anchored sites for kidney calcium oxalate stones, but the mechanism remains unclear. Given the importance of osteogenic-like cells in RP formation and OCT4 in reprogramming differentiated cells to osteoblasts, the current study explored the potential role of OCT4 in RP formation. METHODS OCT4 and biomineralization were evaluated in RP, and immunofluorescence co-staining was performed to identify these cells with alteration of OCT4 and osteogenic markers. Based on the analysis of tissue, we further investigated the mechanism of OCT4 in regulating osteogenic-like differentiation of primary human renal interstitial fibroblasts (hRIFs) in vitro and vivo. RESULTS We identified the upregulated OCT4 in RP, with a positive correlation to osteogenic markers. Interestingly, fibroblast marker Vimentin was partially co-localized with upregulated OCT4 and osteogenic markers in RP. Further investigations revealed that OCT4 significantly enhanced the osteogenic-like phenotype of hRIFs in vitro and in vivo. Mechanically, OCT4 directly bound to BMP2 promoter and facilitated its CpG island demethylation to transcriptionally promote BMP2 expression. Furthermore, combination of RIP and RNA profiling uncovered that lncRNA OLMALINC physically interacted with OCT4 to promote its stabilization via disrupting the ubiquitination. Additionally, OLMALINC was upregulated in fibroblasts in RP visualized by FISH, and a positive correlation was revealed between OLMALINC and OCT4 in RP. CONCLUSIONS The upregulation of OCT4 in hRIFs was a pathological feature of RP formation, and OLMALINC/OCT4/BMP2 axis facilitated hRIFs to acquire osteogenic-like phenotype under osteogenic conditions, through which the pathway might participate in RP formation. Our findings opened up a new avenue to better understand RP formation in which osteogenic-like process was partially triggered by lncRNAs and pluripotency maintenance related genes.
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Affiliation(s)
- Zewu Zhu
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China ,grid.47100.320000000419368710Department of Internal Medicine, Section Endocrinology, Yale University School of Medicine, New Haven, CT USA
| | - Fang Huang
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Yingcheng Jiang
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Shuhao Ruan
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Minghui Liu
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Youjie Zhang
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Yongchao Li
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Jinbo Chen
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Yu Cui
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Zhiyong Chen
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Hequn Chen
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
| | - Feng Zeng
- grid.216417.70000 0001 0379 7164Department of Urology, Xiangya Hospital, Central South University, Changsha, 410008 Hunan China
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8
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Rios ÁFL, Tirapelli DPDC, Cirino MLDA, Rodrigues AR, Ramos ES, Carlotti CG. Expression of pluripotency-related genes in human glioblastoma. Neurooncol Adv 2022; 4:vdab163. [PMID: 35274101 PMCID: PMC8903226 DOI: 10.1093/noajnl/vdab163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Cancer is a group of heterogeneous diseases characterized by several disruptions of the genetic and epigenetic components of cell biology. Some types of cancer have been shown to be constituted by a mosaic of cells with variable differentiation states, with more aggressive tumors being more undifferentiated. In most cases, undifferentiated tumor cells express associated embryonic markers such as the OCT4, NANOG, SOX2, and CARM1 genes. The ectopic or reminiscent expression of some master regulator genes of pluripotency has been indicated as the cause of the poorly differentiated state of tumors, and based on the evidence of some reports, can be used as a possible therapeutic target. Considering this information, a more detailed investigation of the expression of pluripotency-associated genes is necessary to evaluate the roles of these genes in the etiology of some tumors and their use targets of therapy. Methods The expression of four pluripotency-related genes was investigated (OCT4, NANOG, SOX2, and CARM1) in the most malignant primary human brain tumor, glioblastoma (GBM). Results and Conclusion The results demonstrated a signature of OCT4/SOX2/CARM1 genes and a significant increase of CARM1 expression in GBM cases.
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Affiliation(s)
- Álvaro Fabrício Lopes Rios
- Laboratory of Biotechnology, Center for Biosciences and Biotechnology, North Fluminense State University, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | | | - Mucio Luiz de Assis Cirino
- Department of Surgery and Anatomy, Ribeirão Preto Faculty of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Andressa Romualdo Rodrigues
- Laboratory of Morphofunctional and Integrated Practices, Franca Medical School, University of Franca, Franca, São Paulo, Brazil
| | - Ester S Ramos
- Department of Genetics, Ribeirão Preto Faculty of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Carlos Gilberto Carlotti
- Department of Surgery and Anatomy, Ribeirão Preto Faculty of Medicine, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
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9
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Bakhmet EI, Tomilin AN. Key features of the POU transcription factor Oct4 from an evolutionary perspective. Cell Mol Life Sci 2021; 78:7339-7353. [PMID: 34698883 PMCID: PMC11072838 DOI: 10.1007/s00018-021-03975-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/16/2021] [Accepted: 10/12/2021] [Indexed: 01/06/2023]
Abstract
Oct4, a class V POU-domain protein that is encoded by the Pou5f1 gene, is thought to be a key transcription factor in the early development of mammals. This transcription factor plays indispensable roles in pluripotent stem cells as well as in the acquisition of pluripotency during somatic cell reprogramming. Oct4 has also been shown to play a role as a pioneer transcription factor during zygotic genome activation (ZGA) from zebrafish to human. However, during the past decade, several studies have brought these conclusions into question. It was clearly shown that the first steps in mouse development are not affected by the loss of Oct4. Subsequently, the role of Oct4 as a genome activator was brought into doubt. It was also found that the reprogramming of somatic cells into induced pluripotent stem cells (iPSCs) could proceed without Oct4. In this review, we summarize recent findings, reassess the role of Oct4 in reprogramming and ZGA, and point to structural features that may underlie this role. We speculate that pluripotent stem cells resemble neural stem cells more closely than previously thought. Oct4 orthologs within the POUV class hold key roles in genome activation during early development of species with late ZGA. However, in Placentalia, eutherian-specific proteins such as Dux overtake Oct4 in ZGA and endow them with the formation of an evolutionary new tissue-the placenta.
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Affiliation(s)
- Evgeny I Bakhmet
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia.
| | - Alexey N Tomilin
- Laboratory of the Molecular Biology of Stem Cells, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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10
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Kramer AC, Erikson DW, McLendon BA, Seo H, Hayashi K, Spencer TE, Bazer FW, Burghardt RC, Johnson GA. SPP1 expression in the mouse uterus and placenta: Implications for implantation. Biol Reprod 2021; 105:892-904. [PMID: 34165144 DOI: 10.1093/biolre/ioab125] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/10/2021] [Accepted: 06/22/2021] [Indexed: 11/14/2022] Open
Abstract
Secreted phosphoprotein 1 [SPP1, also known as osteopontin (OPN)] binds integrins to mediate cell-cell and cell-extracellular matrix communication to promote cell adhesion, migration, and differentiation. Considerable evidence links SPP1 to pregnancy in several species. Current evidence suggests that SPP1 is involved in implantation and placentation in mice, but in vivo localization of SPP1 and in vivo mechanistic studies to substantiate these roles are incomplete and contradictory. We localized Spp1 mRNA and protein in the endometrium and placenta of mice throughout gestation, and utilized delayed implantation of mouse blastocysts to link SPP1 expression to the implantation chamber. Spp1 mRNA and protein localized to the endometrial luminal (LE), but not glandular epithelia (GE) in interimplantation regions of the uterus throughout gestation. Spp1 mRNA and protein also localized to uterine naturel killer (uNK) cells of the decidua. Within the implantation chamber, Spp1 mRNA localized only to intermittent LE cells, and to the inner cell mass. SPP1 protein localized to intermittent trophoblast cells, and to the parietal endoderm. These results suggest that SPP1: 1) is secreted by the LE at interimplantation sites for closure of the uterine lumen to form the implantation chamber; 2) is secreted by LE adjacent to the attaching trophoblast cells for attachment and invasion of the blastocyst; and 3) is not a component of histotroph secreted from the GE, but is secreted from uNK cells in the decidua to increase angiogenesis within the decidua to augment hemotrophic support of embryonic/fetal development of the conceptus.
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Affiliation(s)
- Avery C Kramer
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
| | - David W Erikson
- Endocrine Technologies Core, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA
| | - Bryan A McLendon
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
| | - Heewon Seo
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
| | - Kanako Hayashi
- School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Thomas E Spencer
- Department of Animal Science, University of Missouri, Columbia, MO, USA
| | - Fuller W Bazer
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Robert C Burghardt
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
| | - Greg A Johnson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, College Station, TX, USA
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11
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Dan S, Song Y, Duan X, Pan X, Chen C, She S, Su T, Li J, Chen X, Zhou Y, Chen W, Zhang X, Pan X, Wang YJ, Kang B. LSD1-mediated demethylation of OCT4 safeguards pluripotent stem cells by maintaining the transcription of PORE-motif-containing genes. Sci Rep 2021; 11:10285. [PMID: 33986438 PMCID: PMC8119428 DOI: 10.1038/s41598-021-89734-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 04/30/2021] [Indexed: 11/09/2022] Open
Abstract
Reversible lysine methylation is essential for regulating histones and emerges to critically regulate non-histone proteins as well. Here we show that the master transcription factor OCT4 in pluripotent stem cells (PSCs) was methylated at multiple lysine residues. LSD1 that is highly expressed in PSCs can directly interact with and demethylate OCT4 at lysine 222 (K222) in the flexible linker region. Reduced LSD1 activity led to the methylation of OCT4-K222 that diminished the differentiation potential of PSCs while facilitating proteasome-independent degradation of OCT4 proteins. Furthermore, site-specifically replacing K222 with phenylalanine to mimic the constitutively methylated lysine promoted the 'locked-in' mode engagement of the OCT4 PORE-homodimers that tightly bind to and block the transcription of multiple PORE-motif-containing target genes regulating cell fate determination and cell junction organization, and thereby reducing the pluripotency of PSCs. Thus, LSD1-mediated demethylation of OCT4 plays a crucial role in restricting the 'locked-in' mode binding of OCT4 PORE-homodimers to the PORE-motif-containing genes and thereby maintaining their transcription to safeguard the pluripotency of PSCs.
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Affiliation(s)
- Songsong Dan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Yuelin Song
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Xiaotao Duan
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiao Pan
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Cheng Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Shiqi She
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Tong Su
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Jingchao Li
- College of Life Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Xinyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Yanwen Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Wenjie Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Xiaobing Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Xiaoyun Pan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
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12
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Yeremenko N, Danger R, Baeten D, Tomilin A, Brouard S. Transcriptional regulator BOB.1: Molecular mechanisms and emerging role in chronic inflammation and autoimmunity. Autoimmun Rev 2021; 20:102833. [PMID: 33864944 DOI: 10.1016/j.autrev.2021.102833] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 11/19/2022]
Abstract
Lymphocytes constitute an essential and potent effector compartment of the immune system. Therefore, their development and functions must be strictly regulated to avoid inappropriate immune responses, such as autoimmune reactions. Several lines of evidence from genetics (e.g. association with multiple sclerosis and primary biliary cirrhosis), human expression studies (e.g. increased expression in target tissues and draining lymph nodes of patients with autoimmune diseases), animal models (e.g. loss of functional protein protects animals from the development of collagen-induced arthritis, experimental autoimmune encephalomyelitis, type 1 diabetes, bleomycin-induced fibrosis) strongly support a causal link between the aberrant expression of the lymphocyte-restricted transcriptional regulator BOB.1 and the development of autoimmune diseases. In this review, we summarize the current knowledge of unusual structural and functional plasticity of BOB.1, stringent regulation of its expression, and the pivotal role that BOB.1 plays in shaping B- and T-cell responses. We discuss recent developments highlighting the significant contribution of BOB.1 to the pathogenesis of autoimmune diseases and how to leverage our knowledge to target this regulator to treat autoimmune tissue inflammation.
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Affiliation(s)
- Nataliya Yeremenko
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France; Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.
| | - Richard Danger
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
| | - Dominique Baeten
- Amsterdam Rheumatology and Immunology Center, Department of Clinical Immunology and Rheumatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands; Department of Experimental Immunology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Alexey Tomilin
- Institute of Cytology, Russian Academy of Sciences, St-Petersburg, Russian Federation
| | - Sophie Brouard
- CHU Nantes, Université de Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes, France
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13
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Tan DS, Chen Y, Gao Y, Bednarz A, Wei Y, Malik V, Ho DHH, Weng M, Ho SY, Srivastava Y, Velychko S, Yang X, Fan L, Kim J, Graumann J, Stormo GD, Braun T, Yan J, Schöler HR, Jauch R. Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering. Mol Biol Evol 2021; 38:2854-2868. [PMID: 33720298 PMCID: PMC8233511 DOI: 10.1093/molbev/msab075] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factor-driven cell fate engineering in pluripotency induction, transdifferentiation, and forward reprogramming requires efficiency, speed, and maturity for widespread adoption and clinical translation. Here, we used Oct4, Sox2, Klf4, and c-Myc driven pluripotency reprogramming to evaluate methods for enhancing and tailoring cell fate transitions, through directed evolution with iterative screening of pooled mutant libraries and phenotypic selection. We identified an artificially evolved and enhanced POU factor (ePOU) that substantially outperforms wild-type Oct4 in terms of reprogramming speed and efficiency. In contrast to Oct4, not only can ePOU induce pluripotency with Sox2 alone, but it can also do so in the absence of Sox2 in a three-factor ePOU/Klf4/c-Myc cocktail. Biochemical assays combined with genome-wide analyses showed that ePOU possesses a new preference to dimerize on palindromic DNA elements. Yet, the moderate capacity of Oct4 to function as a pioneer factor, its preference to bind octamer DNA and its capability to dimerize with Sox2 and Sox17 proteins remain unchanged in ePOU. Compared with Oct4, ePOU is thermodynamically stabilized and persists longer in reprogramming cells. In consequence, ePOU: 1) differentially activates several genes hitherto not implicated in reprogramming, 2) reveals an unappreciated role of thyrotropin-releasing hormone signaling, and 3) binds a distinct class of retrotransposons. Collectively, these features enable ePOU to accelerate the establishment of the pluripotency network. This demonstrates that the phenotypic selection of novel factor variants from mammalian cells with desired properties is key to advancing cell fate conversions with artificially evolved biomolecules.
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Affiliation(s)
- Daisylyn Senna Tan
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yanpu Chen
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Ya Gao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Anastasia Bednarz
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Department of Biology, Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Yuanjie Wei
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Vikas Malik
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Medicine, Columbia Center for Human Development, Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Derek Hoi-Hang Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Sik Yin Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yogesh Srivastava
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Xiaoxiao Yang
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Ligang Fan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.,School of Medicine, Northwest University, Xi'an, China
| | - Johnny Kim
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Johannes Graumann
- Max Planck Institute for Heart and Lung Research, Mass Spectrometry Service Group, Bad Nauheim, Germany
| | - Gary D Stormo
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, USA
| | - Thomas Braun
- Department of Cardiac Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Jian Yan
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China.,School of Medicine, Northwest University, Xi'an, China
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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14
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Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat Genet 2021; 53:354-366. [PMID: 33603233 PMCID: PMC8812996 DOI: 10.1038/s41588-021-00782-6] [Citation(s) in RCA: 257] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 01/07/2021] [Indexed: 01/30/2023]
Abstract
The arrangement (syntax) of transcription factor (TF) binding motifs is an important part of the cis-regulatory code, yet remains elusive. We introduce a deep learning model, BPNet, that uses DNA sequence to predict base-resolution chromatin immunoprecipitation (ChIP)-nexus binding profiles of pluripotency TFs. We develop interpretation tools to learn predictive motif representations and identify soft syntax rules for cooperative TF binding interactions. Strikingly, Nanog preferentially binds with helical periodicity, and TFs often cooperate in a directional manner, which we validate using clustered regularly interspaced short palindromic repeat (CRISPR)-induced point mutations. Our model represents a powerful general approach to uncover the motifs and syntax of cis-regulatory sequences in genomics data.
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Affiliation(s)
- Žiga Avsec
- Department of Informatics, Technical University of Munich, Garching, Germany,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, Munich, Germany,Currently at DeepMind, London, UK
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Avanti Shrikumar
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Amr Alexandari
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Khyati Dalal
- Stowers Institute for Medical Research, Kansas City, MO, USA,The University of Kansas Medical Center, Kansas City, KS, USA
| | - Robin Fropf
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Charles McAnany
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Julien Gagneur
- Department of Informatics, Technical University of Munich, Garching, Germany
| | - Anshul Kundaje
- Department of Computer Science, Stanford University, Stanford, CA, USA,Department of Genetics, Stanford University, Stanford, CA, USA,correspondence: ,
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO, USA,The University of Kansas Medical Center, Kansas City, KS, USA,correspondence: ,
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15
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Morii A, Katayama S, Inazu T. Establishment of a Simple Method for Inducing Neuronal Differentiation of P19 EC Cells without Embryoid Body Formation and Analysis of the Role of Histone Deacetylase 8 Activity in This Differentiation. Biol Pharm Bull 2020; 43:1096-1103. [PMID: 32612072 DOI: 10.1248/bpb.b20-00091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
P19 pluripotent embryonic carcinoma (EC) stem cells are derived from pluripotent germ cell tumours and can differentiate into three germ layers. Treatment of these cells in suspension culture with retinoic acid induces their differentiation into neurons and glial cells. Hence, these cells are an excellent in vitro model to study the transition from the upper blastoderm to the neuroectoderm. However, because of the complex nature of the techniques involved, the results are highly dependent on the skills of the experimenter. Herein, we developed a simple method to induce neuronal differentiation of adherent P19 EC cells in TaKaRa NDiff® 227 serum-free medium (originally N2B27 medium). This medium markedly induced neuronal differentiation of P19 EC cells. The addition of retinoic acid to the NDiff® 227 medium further enhanced differentiation. Furthermore, cells differentiated by the conventional method, as well as the new method, showed identical expression of the mature neuronal marker, neuronal nuclei. To determine whether our approach could be applied for neuronal studies, we measured histone deacetylase 8 (HDAC8) activity using an HDAC8 inhibitor and HDAC8-knockout P19 EC cells. Inhibition of HDAC8 activity suppressed neuronal maturation. Additionally, HDAC8-knockout cell lines showed immature differentiation compared to the wild-type cell line. These results indicate that HDAC8 directly regulates the neuronal differentiation of P19 EC cells. Thus, our method involving P19 EC cells can be used as an experimental system to study the nervous system. Moreover, this method is suitable for screening drugs that affect the nervous system and cell differentiation.
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Affiliation(s)
- Atsushi Morii
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University
| | - Syouichi Katayama
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University
| | - Tetsuya Inazu
- Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University
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16
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Hori N, Kubo S, Sakasegawa T, Sakurai C, Hatsuzawa K. OCT3/4-binding sequence-dependent maintenance of the unmethylated state of CTCF-binding sequences with DNA demethylation and suppression of de novo DNA methylation in the H19 imprinted control region. Gene 2020; 743:144606. [DOI: 10.1016/j.gene.2020.144606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 03/16/2020] [Accepted: 03/18/2020] [Indexed: 11/25/2022]
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17
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Malik V, Glaser LV, Zimmer D, Velychko S, Weng M, Holzner M, Arend M, Chen Y, Srivastava Y, Veerapandian V, Shah Z, Esteban MA, Wang H, Chen J, Schöler HR, Hutchins AP, Meijsing SH, Pott S, Jauch R. Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2. Nat Commun 2019; 10:3477. [PMID: 31375664 PMCID: PMC6677745 DOI: 10.1038/s41467-019-11054-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 06/19/2019] [Indexed: 12/21/2022] Open
Abstract
Oct4, along with Sox2 and Klf4 (SK), can induce pluripotency but structurally similar factors like Oct6 cannot. To decode why Oct4 has this unique ability, we compare Oct4-binding, accessibility patterns and transcriptional waves with Oct6 and an Oct4 mutant defective in the dimerization with Sox2 (Oct4defSox2). We find that initial silencing of the somatic program proceeds indistinguishably with or without Oct4. Oct6 mitigates the mesenchymal-to-epithelial transition and derails reprogramming. These effects are a consequence of differences in genome-wide binding, as the early binding profile of Oct4defSox2 resembles Oct4, whilst Oct6 does not bind pluripotency enhancers. Nevertheless, in the Oct6-SK condition many otherwise Oct4-bound locations become accessible but chromatin opening is compromised when Oct4defSox2 occupies these sites. We find that Sox2 predominantly facilitates chromatin opening, whilst Oct4 serves an accessory role. Formation of Oct4/Sox2 heterodimers is essential for pluripotency establishment; however, reliance on Oct4/Sox2 heterodimers declines during pluripotency maintenance. Oct4, along with Sox2 and Klf4 can induce pluripotency, but structurally similar factors like Oct6 cannot. Here, using pluripotency competent and incompetent factors, the authors show that Sox2 plays a dominant role in facilitating chromatin opening at Oct4 bound DNA early during reprogramming to pluripotency.
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Affiliation(s)
- Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Laura V Glaser
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Dennis Zimmer
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Sergiy Velychko
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149, Münster, Germany
| | - Mingxi Weng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Markus Holzner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Marius Arend
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Yanpu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Yogesh Srivastava
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Veeramohan Veerapandian
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China.,University of Chinese Academy of Sciences, 100049, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China.,Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, 510515, Guangzhou, Guangdong, China
| | - Zahir Shah
- University of Chinese Academy of Sciences, 100049, Beijing, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China
| | - Miguel A Esteban
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China.,Laboratory of RNA, Chromatin, and Human Disease, Key Laboratory of Regenerative Biology and Guangdong Provincial Key Laboratory of Stem Cells and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 510005, Guangzhou, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Prince of Wales Hospital, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), 510005, Guangzhou, China
| | - Hans R Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, 48149, Münster, Germany.,Medical Faculty, University of Münster, 48149, Münster, Germany
| | - Andrew P Hutchins
- Department of Biology, Southern University of Science and Technology, 518055, Shenzhen, Guangdong, China
| | - Sebastiaan H Meijsing
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Sebastian Pott
- Department of Human Genetics, The University of Chicago, Chicago, IL, 60637, USA
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, 510530, Guangzhou, China. .,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine; Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530, Guangzhou, China. .,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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18
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Makoukji J. Chromatin Immunoprecipitation Assay for Analyzing Transcription Factor Activity at the Level of Peripheral Myelin Gene Promoters. Methods Mol Biol 2019; 2011:647-658. [PMID: 31273726 DOI: 10.1007/978-1-4939-9554-7_37] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
Disruption of epigenetic regulators of transcription is a central mechanism of oncogenesis. Differential gene expression is facilitated by transcriptional regulatory mechanisms and chromatin modifications through DNA-protein interactions. One of the widely used assays to study this is chromatin immunoprecipitation (ChIP) assay, which enables the analysis of association between regulatory molecules, specific promoters, and histone modifications within the context of the cell. This is of immense value as ChIP assays can provide a glimpse of the regulatory mechanisms involved in gene expression in vivo. It is also a powerful technique for analyzing histone modifications as well as binding sites for proteins that bind either directly or indirectly to DNA. The basic steps in this protocol are fixation, sonication, immunoprecipitation, and analysis of the immunoprecipitated DNA. Although ChIP is a versatile tool, this procedure requires the optimization of the various reaction conditions. Here, we present a detailed application of the ChIP assay to study the differential recruitment of transcriptional factors at the level of peripheral myelin gene promoters.
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Affiliation(s)
- Joelle Makoukji
- Neurogenetics Program, Division of Pediatric Neurology, Department of Pediatrics and Adolescent Medicine, AUBMC Special Kids Clinic, American University of Beirut Medical Center, Beirut, Lebanon.
- Department of Biochemistry, Faculty of Medicine, American University of Beirut, Beirut, Lebanon.
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19
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Tang X, Engström Y. Regulation of immune and tissue homeostasis by Drosophila POU factors. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 109:24-30. [PMID: 30954681 DOI: 10.1016/j.ibmb.2019.04.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 03/17/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
The innate immune system of insects deploys both cellular and humoral reactions in immunocompetent tissues for protection of insects against a variety of infections, including bacteria, fungi, and viruses. Transcriptional regulation of genes encoding antimicrobial peptides (AMPs), cytokines, and other immune effectors plays a pivotal role in maintenance of immune homeostasis both prior to and after infections. The POU/Oct transcription factor family is a subclass of the homeodomain proteins present in all metazoans. POU factors are involved in regulation of development, metabolism and immunity. Their role in regulation of immune functions has recently become evident, and involves control of tissue-specific, constitutive expression of immune effectors in barrier epithelia as well as positive and negative control of immune responses in gut and fat body. In addition, they have been shown to affect the composition of gut microbiota and play a role in regulation of intestinal stem cell activities. In this review, we summarize the current knowledge of how POU transcription factors control Drosophila immune homeostasis in healthy and infected insects. The role of POU factor isoform specific regulation of stem cell activities in Drosophila and mammals is also discussed.
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Affiliation(s)
- Xiongzhuo Tang
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691, Stockholm, Sweden
| | - Ylva Engström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE-10691, Stockholm, Sweden.
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20
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Ince S, Erdogan M, Demirel HH, Agca Y, Dal G, Uguz C. Boron enhances early embryonic gene expressions and improves fetal development of rats. J Trace Elem Med Biol 2018; 50:34-46. [PMID: 30262302 DOI: 10.1016/j.jtemb.2018.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/30/2018] [Accepted: 06/01/2018] [Indexed: 01/01/2023]
Abstract
Boron is present as several different components in nature. Besides its industrial use, it is an essential element and is playing a very important role in the metabolism. In this study, it was aimed to determine the in vivo effects of boron on mRNA expression of HEX, NANOG, and OCT-3/4 genes in embryo and histological changes during fetal development. Therefore, totally 60 female rats were allocated into 5 equal groups. Experimental groups are as the followings; positive control (fed with standart rat diet), negative control (fed with boron free diet), low boron group (fed with boron free diet and given 0.04 μg boron/ml via gastric gavage), marginal boron group (fed with boron free diet and given 0.3 μg boron/ml via gastric gavage) and normal boron group (fed with boron free diet and given 2 μg boron/ml via gastric gavage). Experimental period was performed for 14 days. Embryos were collected after 4 days of mating and the expression and protein levels of early embryonic genes namely HEX, NANOG, and OCT-3/4 were determined by using Real-Time PCR. Also, 10-20 day embryo and fetus development were histologically determined. According to the results, mRNA expression and protein levels of early embryonic genes were increased in boron groups while decreased in boron deficient group. Histopathologically, tissue and organ developments were definitely observed in the boron groups. In conclusion, mRNA expression levels of early embryonic genes decreased in boron deficient group and boron has an important role for fetal development.
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Affiliation(s)
- Sinan Ince
- Department of Pharmacology and Toxicology, Faculty of Veterinary Medicine, Afyon Kocatepe University, Afyonkarahisar, Turkey.
| | - Metin Erdogan
- Department of Medical Biology and Genetics, Faculty of Veterinary Medicine, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - Hasan Huseyin Demirel
- Department of Laboratory and Veterinary Health, Bayat Vocational School, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - Yuksel Agca
- Department of Veterinary Pathobiology, University of Missouri College of Veterinary Medicine, Columbia, MO, USA
| | - Gamze Dal
- Department of Medical Biology and Genetics, Faculty of Veterinary Medicine, Afyon Kocatepe University, Afyonkarahisar, Turkey
| | - Cevdet Uguz
- Department of Medical Biology and Genetics, Faculty of Veterinary Medicine, Afyon Kocatepe University, Afyonkarahisar, Turkey
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21
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Pesta M, Cedikova M, Dvorak P, Dvorakova J, Kulda V, Srbecka K, Muller L, Bouchalova V, Kralickova M, Babuska V, Kuncova J, Mullerova D. Trends in gene expression changes during adipogenesis in human adipose derived mesenchymal stem cells under dichlorodiphenyldichloroethylene exposure. Mol Cell Toxicol 2018. [DOI: 10.1007/s13273-018-0041-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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22
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Constable S, Lim JM, Vaidyanathan K, Wells L. O-GlcNAc transferase regulates transcriptional activity of human Oct4. Glycobiology 2018; 27:927-937. [PMID: 28922739 DOI: 10.1093/glycob/cwx055] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/10/2017] [Indexed: 01/06/2023] Open
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) is a single sugar modification found on many different classes of nuclear and cytoplasmic proteins. Addition of this modification, by the enzyme O-linked N-acetylglucosamine transferase (OGT), is dynamic and inducible. One major class of proteins modified by O-GlcNAc is transcription factors. O-GlcNAc regulates transcription factor properties through a variety of different mechanisms including localization, stability and transcriptional activation. Maintenance of embryonic stem (ES) cell pluripotency requires tight regulation of several key transcription factors, many of which are modified by O-GlcNAc. Octamer-binding protein 4 (Oct4) is one of the key transcription factors required for pluripotency of ES cells and more recently, the generation of induced pluripotent stem (iPS) cells. The action of Oct4 is modulated by the addition of several post-translational modifications, including O-GlcNAc. Previous studies in mice found a single site of O-GlcNAc addition responsible for transcriptional regulation. This study was designed to determine if this mechanism is conserved in humans. We mapped 10 novel sites of O-GlcNAc attachment on human Oct4, and confirmed a role for OGT in transcriptional activation of Oct4 at a site distinct from that found in mouse that allows distinction between different Oct4 target promoters. Additionally, we uncovered a potential new role for OGT that does not include its catalytic function. These results confirm that human Oct4 activity is being regulated by OGT by a mechanism that is distinct from mouse Oct4.
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Affiliation(s)
- Sandii Constable
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Jae-Min Lim
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.,Department of Chemistry, Changwon National University, Changwon, Gyeongnam 641-773, South Korea
| | - Krithika Vaidyanathan
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Lance Wells
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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23
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Makrides N, Panayiotou E, Fanis P, Karaiskos C, Lapathitis G, Malas S. Sequential Role of SOXB2 Factors in GABAergic Neuron Specification of the Dorsal Midbrain. Front Mol Neurosci 2018; 11:152. [PMID: 29867344 PMCID: PMC5952183 DOI: 10.3389/fnmol.2018.00152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/17/2018] [Indexed: 12/23/2022] Open
Abstract
Studies proposed a model for embryonic neurogenesis where the expression levels of the SOXB2 and SOXB1 factors regulate the differentiation status of the neural stem cells. However, the precise role of the SOXB2 genes remains controversial. Therefore, this study aims to investigate the effects of individual deletions of the SOX21 and SOX14 genes during the development of the dorsal midbrain. We show that SOX21 and SOX14 function distinctly during the commitment of the GABAergic lineage. More explicitly, deletion of SOX21 reduced the expression of the GABAergic precursor marker GATA3 and BHLHB5 while the expression of GAD6, which marks GABAergic terminal differentiation, was not affected. In contrast deletion of SOX14 alone was sufficient to inhibit terminal differentiation of the dorsal midbrain GABAergic neurons. Furthermore, we demonstrate through gain-of-function experiments, that despite the homology of SOX21 and SOX14, they have unique gene targets and cannot compensate for the loss of each other. Taken together, these data do not support a pan-neurogenic function for SOXB2 genes in the dorsal midbrain, but instead they influence, sequentially, the specification of GABAergic neurons.
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Affiliation(s)
- Neoklis Makrides
- Developmental and Functional Genetics Group, The Cyprus Institute of Neurology & Genetics and Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Elena Panayiotou
- Neurologic Clinic A, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Pavlos Fanis
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Christos Karaiskos
- Neuroscience Laboratory, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - George Lapathitis
- Neuroscience Laboratory, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Stavros Malas
- Developmental and Functional Genetics Group, The Cyprus Institute of Neurology & Genetics and Cyprus School of Molecular Medicine, Nicosia, Cyprus
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24
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Malik V, Zimmer D, Jauch R. Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming. Cell Mol Life Sci 2018; 75:1587-1612. [PMID: 29335749 PMCID: PMC11105716 DOI: 10.1007/s00018-018-2748-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 12/23/2017] [Accepted: 01/08/2018] [Indexed: 12/28/2022]
Abstract
The POU (Pit-Oct-Unc) protein family is an evolutionary ancient group of transcription factors (TFs) that bind specific DNA sequences to direct gene expression programs. The fundamental importance of POU TFs to orchestrate embryonic development and to direct cellular fate decisions is well established, but the molecular basis for this activity is insufficiently understood. POU TFs possess a bipartite 'two-in-one' DNA binding domain consisting of two independently folding structural units connected by a poorly conserved and flexible linker. Therefore, they represent a paradigmatic example to study the molecular basis for the functional versatility of TFs. Their modular architecture endows POU TFs with the capacity to accommodate alternative composite DNA sequences by adopting different quaternary structures. Moreover, associations with partner proteins crucially influence the selection of their DNA binding sites. The plentitude of DNA binding modes confers the ability to POU TFs to regulate distinct genes in the context of different cellular environments. Likewise, different binding modes of POU proteins to DNA could trigger alternative regulatory responses in the context of different genomic locations of the same cell. Prominent POU TFs such as Oct4, Brn2, Oct6 and Brn4 are not only essential regulators of development but have also been successfully employed to reprogram somatic cells to pluripotency and neural lineages. Here we review biochemical, structural, genomic and cellular reprogramming studies to examine how the ability of POU TFs to select regulatory DNA, alone or with partner factors, is tied to their capacity to epigenetically remodel chromatin and drive specific regulatory programs that give cells their identities.
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Affiliation(s)
- Vikas Malik
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Dennis Zimmer
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 511436, China.
- Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
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25
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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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26
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Abstract
Chromatin immunoprecipitation (ChIP) is an invaluable method to characterize interactions between proteins and genomic DNA, such as the genomic localization of transcription factors and posttranslational modification of histones. DNA and proteins are reversibly and covalently crosslinked using formaldehyde. Then the cells are lysed to release the chromatin. The chromatin is fragmented into smaller sizes either by micrococcal nuclease (MNase) or sonication and then purified from other cellular components. The protein-DNA complexes are enriched by immunoprecipitation (IP) with antibodies that target the epitope of interest. The DNA is released from the proteins by heat and protease treatment, followed by degradation of contaminating RNAs with RNase. The resulting DNA is analyzed using various methods, including PCR, qPCR, or sequencing. This protocol outlines each of these steps for both yeast and human cells.
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27
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Kijewska M, Kocyk M, Kloss M, Stepniak K, Korwek Z, Polakowska R, Dabrowski M, Gieryng A, Wojtas B, Ciechomska IA, Kaminska B. The embryonic type of SPP1 transcriptional regulation is re-activated in glioblastoma. Oncotarget 2017; 8:16340-16355. [PMID: 28030801 PMCID: PMC5369967 DOI: 10.18632/oncotarget.14092] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 12/16/2016] [Indexed: 11/25/2022] Open
Abstract
Osteopontin (SPP1, a secreted phosphoprotein 1) is primarily involved in immune responses, tissue remodelling and biomineralization. However, it is also overexpressed in many cancers and regulates tumour progression by increasing migration, invasion and cancer stem cell self-renewal. Mechanisms of SPP1 overexpression in gliomas are poorly understood. We demonstrate overexpression of two out of five SPP1 isoforms in glioblastoma (GBM) and differential isoform expression in glioma cell lines. Up-regulated SPP1 expression is associated with binding of the GLI1 transcription factor to the promoter and OCT4 (octamer-binding transcription factor 4) to the first SPP1 intron of the SPP1 gene in human glioma cells but not in non-transformed astrocytes. GLI1 knockdown reduced SPP1 mRNA and protein levels in glioma cells. GLI1 and OCT4 are known regulators of stem cell pluripotency. GBMs contain rare cells that express stem cell markers and display ability to self-renew. We reveal that SPP1 is overexpressed in glioma initiating cells defined by high rhodamine 123 efflux, sphere forming capacity and stemness marker expression. Forced differentiation of human glioma spheres reduced SPP1 expression. Knockdown of SPP1, GLI1 or CD44 with siRNAs diminished sphere formation. C6 glioma cells stably depleted of Spp1 displayed reduced sphere forming capacity and downregulated stemness marker expression. Overexpression of the wild type Spp1, but not Spp1 lacking a Cd44 binding domain, rescued cell ability to form spheres. Our findings show re-activation of the embryonic-type transcriptional regulation of SPP1 in malignant gliomas and point to the importance of SPP1-CD44 interactions in self-renewal and pluripotency glioma initiating cells.
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Affiliation(s)
- Magdalena Kijewska
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Marta Kocyk
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Michal Kloss
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Karolina Stepniak
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Korwek
- Laboratory of Molecular Bases of Aging, The Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
| | | | - Michal Dabrowski
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Anna Gieryng
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Bartosz Wojtas
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Iwona A Ciechomska
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
| | - Bozena Kaminska
- Laboratory of Molecular Neurobiology, The Nencki Institute of Experimental Biology of the Polish Academy of Sciences, Warsaw, Poland
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28
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Kelly GM, Gatie MI. Mechanisms Regulating Stemness and Differentiation in Embryonal Carcinoma Cells. Stem Cells Int 2017; 2017:3684178. [PMID: 28373885 PMCID: PMC5360977 DOI: 10.1155/2017/3684178] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/10/2017] [Accepted: 02/08/2017] [Indexed: 02/06/2023] Open
Abstract
Just over ten years have passed since the seminal Takahashi-Yamanaka paper, and while most attention nowadays is on induced, embryonic, and cancer stem cells, much of the pioneering work arose from studies with embryonal carcinoma cells (ECCs) derived from teratocarcinomas. This original work was broad in scope, but eventually led the way for us to focus on the components involved in the gene regulation of stemness and differentiation. As the name implies, ECCs are malignant in nature, yet maintain the ability to differentiate into the 3 germ layers and extraembryonic tissues, as well as behave normally when reintroduced into a healthy blastocyst. Retinoic acid signaling has been thoroughly interrogated in ECCs, especially in the F9 and P19 murine cell models, and while we have touched on this aspect, this review purposely highlights how some key transcription factors regulate pluripotency and cell stemness prior to this signaling. Another major focus is on the epigenetic regulation of ECCs and stem cells, and, towards that end, this review closes on what we see as a new frontier in combating aging and human disease, namely, how cellular metabolism shapes the epigenetic landscape and hence the pluripotency of all stem cells.
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Affiliation(s)
- Gregory M. Kelly
- Department of Biology, Molecular Genetics Unit, Western University, London, ON, Canada
- Collaborative Program in Developmental Biology, Western University, London, ON, Canada
- Department of Paediatrics and Department of Physiology and Pharmacology, Western University, London, ON, Canada
- Child Health Research Institute, London, ON, Canada
- Ontario Institute for Regenerative Medicine, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohamed I. Gatie
- Department of Biology, Molecular Genetics Unit, Western University, London, ON, Canada
- Collaborative Program in Developmental Biology, Western University, London, ON, Canada
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29
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Jerabek S, Ng CK, Wu G, Arauzo-Bravo MJ, Kim KP, Esch D, Malik V, Chen Y, Velychko S, MacCarthy CM, Yang X, Cojocaru V, Schöler HR, Jauch R. Changing POU dimerization preferences converts Oct6 into a pluripotency inducer. EMBO Rep 2016; 18:319-333. [PMID: 28007765 PMCID: PMC5286379 DOI: 10.15252/embr.201642958] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 11/03/2016] [Accepted: 11/08/2016] [Indexed: 11/25/2022] Open
Abstract
The transcription factor Oct4 is a core component of molecular cocktails inducing pluripotent stem cells (iPSCs), while other members of the POU family cannot replace Oct4 with comparable efficiency. Rather, group III POU factors such as Oct6 induce neural lineages. Here, we sought to identify molecular features determining the differential DNA‐binding and reprogramming activity of Oct4 and Oct6. In enhancers of pluripotency genes, Oct4 cooperates with Sox2 on heterodimeric SoxOct elements. By re‐analyzing ChIP‐Seq data and performing dimerization assays, we found that Oct6 homodimerizes on palindromic OctOct more cooperatively and more stably than Oct4. Using structural and biochemical analyses, we identified a single amino acid directing binding to the respective DNA elements. A change in this amino acid decreases the ability of Oct4 to generate iPSCs, while the reverse mutation in Oct6 does not augment its reprogramming activity. Yet, with two additional amino acid exchanges, Oct6 acquires the ability to generate iPSCs and maintain pluripotency. Together, we demonstrate that cell type‐specific POU factor function is determined by select residues that affect DNA‐dependent dimerization.
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Affiliation(s)
- Stepan Jerabek
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Calista Kl Ng
- Institute of Medical Biology, Singapore City, Singapore
| | - Guangming Wu
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Marcos J Arauzo-Bravo
- Biodonostia Health Research Institute, San Sebastián, Spain.,IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Kee-Pyo Kim
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Daniel Esch
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | - Vikas Malik
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Yanpu Chen
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Sergiy Velychko
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
| | | | - Xiaoxiao Yang
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Vlad Cojocaru
- Max Planck Institute for Molecular Biomedicine, Münster, Germany.,Center for Multiscale Theory and Computation, University of Münster, Münster, Germany
| | - Hans R Schöler
- Max Planck Institute for Molecular Biomedicine, Münster, Germany .,Medical Faculty, University of Münster, Münster, Germany
| | - Ralf Jauch
- Genome Regulation Laboratory, Drug Discovery Pipeline, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China .,Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
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30
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Manipulation of OCT4 Levels in Human Embryonic Stem Cells Results in Induction of Differential Cell Types. Exp Biol Med (Maywood) 2016; 232:1368-80. [DOI: 10.3181/0703-rm-63] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
To fully understand self-renewal and pluripotency and their regulation in human embryonic stem cells (hESCs), it is necessary to generate genetically modified cells and analyze the consequences of elevated and reduced expression of genes. Genes expressed in hESCs using plasmid vectors, however, are subject to silencing. Moreover, hESCs have a low plating efficiency when dissociated to single cells, making creation of subcloned lines inefficient. In addition to overexpression experiments, it is important to perform loss-of-function studies, which can be achieved rapidly using RNA interference (RNAi). We report stable long-term expression of enhanced green fluorescent protein (eGFP) in hESCs using a lentiviral vector, and establishment of an eGFP-expressing subline (RG6) using manual dissection. To demonstrate the efficacy of RNAi in hESCs, an RNAi expression vector was used to achieve reduced expression of eGFP in hESCs. To evaluate the role of OCT4 in the regulation of hESC self-renewal and differentiation, a vector expressing a hairpin RNA targeting endogenous expression of OCT4 was constructed. In a novel experiment in hESCs, the OCT4 cDNA sequence was cloned into an expression vector to allow for the transient upregulation of OCT4 in hESCs. The ability to manipulate levels of OCT4 above and below enodogenous levels allows the determination of OCT4 function in hESCs. Specifically, reduced expression of OCT4 in hESCs promoted upregulation of markers indicative of mesoderm and endoderm differentiation, and elevated levels of OCT4 in hESCs promoted upregulation of markers indicative of endoderm derivatives. Thus, both upregulation and downregulation of Oct4 in hESCs results in differentiation, but with patterns distinct from parallel experiments in mice.
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31
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Singh VK, Saini A, Kalsan M, Kumar N, Chandra R. Describing the Stem Cell Potency: The Various Methods of Functional Assessment and In silico Diagnostics. Front Cell Dev Biol 2016; 4:134. [PMID: 27921030 PMCID: PMC5118841 DOI: 10.3389/fcell.2016.00134] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/02/2016] [Indexed: 12/11/2022] Open
Abstract
Stem cells are defined by their capabilities to self-renew and give rise to various types of differentiated cells depending on their potency. They are classified as pluripotent, multipotent, and unipotent as demonstrated through their potential to generate the variety of cell lineages. While pluripotent stem cells may give rise to all types of cells in an organism, Multipotent and Unipotent stem cells remain restricted to the particular tissue or lineages. The potency of these stem cells can be defined by using a number of functional assays along with the evaluation of various molecular markers. These molecular markers include diagnosis of transcriptional, epigenetic, and metabolic states of stem cells. Many reports are defining the particular set of different functional assays, and molecular marker used to demonstrate the developmental states and functional capacities of stem cells. The careful evaluation of all these methods could help in generating standard identifying procedures/markers for them.
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Affiliation(s)
- Vimal K Singh
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Abhishek Saini
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Manisha Kalsan
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Neeraj Kumar
- Stem Cell Research Laboratory, Department of Biotechnology, Delhi Technological University Delhi, India
| | - Ramesh Chandra
- Department of Chemistry, University of Delhi Delhi, India
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Vázquez-Arreguín K, Tantin D. The Oct1 transcription factor and epithelial malignancies: Old protein learns new tricks. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1859:792-804. [PMID: 26877236 PMCID: PMC4880489 DOI: 10.1016/j.bbagrm.2016.02.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/06/2016] [Accepted: 02/09/2016] [Indexed: 01/29/2023]
Abstract
The metazoan-specific POU domain transcription factor family comprises activities underpinning developmental processes such as embryonic pluripotency and neuronal specification. Some POU family proteins efficiently bind an 8-bp DNA element known as the octamer motif. These proteins are known as Oct transcription factors. Oct1/POU2F1 is the only widely expressed POU factor. Unlike other POU factors it controls no specific developmental or organ system. Oct1 was originally described to operate at target genes associated with proliferation and immune modulation, but more recent results additionally identify targets associated with oxidative and cytotoxic stress resistance, metabolic regulation, stem cell function and other unexpected processes. Oct1 is pro-oncogenic in multiple contexts, and several recent reports provide broad evidence that Oct1 has prognostic and therapeutic value in multiple epithelial tumor settings. This review focuses on established and emerging roles of Oct1 in epithelial tumors, with an emphasis on mechanisms of transcription regulation by Oct1 that may underpin these findings. This article is part of a Special Issue entitled: The Oct Transcription Factor Family, edited by Dr. Dean Tantin.
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Affiliation(s)
- Karina Vázquez-Arreguín
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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Activation of the pluripotency factor OCT4 in smooth muscle cells is atheroprotective. Nat Med 2016; 22:657-65. [PMID: 27183216 PMCID: PMC4899256 DOI: 10.1038/nm.4109] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 04/13/2016] [Indexed: 01/18/2023]
Abstract
There are controversial claims that the embryonic stem cell (ESC) pluripotency factor OCT4 is activated in somatic cells, but there is no evidence it plays a functional role in these cells. Herein we demonstrate that smooth muscle cell (SMC)-specific conditional knockout of Oct4 within Apoe−/− mice resulted in increased lesion size and changes consistent with decreased plaque stability including a thinner fibrous cap, increased necrotic core, and increased intra-plaque hemorrhage. Results of SMC-lineage tracing studies showed that these changes were likely due to marked reductions in SMC number within lesions including impaired SMC migration and investment within the fibrous cap. Re-activation of Oct4 within SMCs was associated with hydroxymethylation of the Oct4 promoter and was HIF1α- and KLF4-dependent. Results provide the first direct evidence that OCT4 plays a functional role in somatic cells and highlight the importance of further investigation of possible OCT4 functions in normal and diseased somatic cells.
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Mistri TK, Devasia AG, Chu LT, Ng WP, Halbritter F, Colby D, Martynoga B, Tomlinson SR, Chambers I, Robson P, Wohland T. Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells. EMBO Rep 2015; 16:1177-91. [PMID: 26265007 PMCID: PMC4576985 DOI: 10.15252/embr.201540467] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 07/06/2015] [Indexed: 12/19/2022] Open
Abstract
Embryonic stem cell (ESC) identity is orchestrated by co-operativity between the transcription factors (TFs) Sox2 and the class V POU-TF Oct4 at composite Sox/Oct motifs. Neural stem cells (NSCs) lack Oct4 but express Sox2 and class III POU-TFs Oct6, Brn1 and Brn2. This raises the question of how Sox2 interacts with POU-TFs to transcriptionally specify ESCs versus NSCs. Here, we show that Oct4 alone binds the Sox/Oct motif and the octamer-containing palindromic MORE equally well. Sox2 binding selectively increases the affinity of Oct4 for the Sox/Oct motif. In contrast, Oct6 binds preferentially to MORE and is unaffected by Sox2. ChIP-Seq in NSCs shows the MORE to be the most enriched motif for class III POU-TFs, including MORE subtypes, and that the Sox/Oct motif is not enriched. These results suggest that in NSCs, co-operativity between Sox2 and class III POU-TFs may not occur and that POU-TF-driven transcription uses predominantly the MORE cis architecture. Thus, distinct interactions between Sox2 and POU-TF subclasses distinguish pluripotent ESCs from multipotent NSCs, providing molecular insight into how Oct4 alone can convert NSCs to pluripotency.
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Affiliation(s)
- Tapan Kumar Mistri
- Department of Chemistry, National University of Singapore, Singapore, Singapore Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore, Singapore MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Arun George Devasia
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore, Singapore
| | - Lee Thean Chu
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore, Singapore
| | - Wei Ping Ng
- Department of Chemistry, National University of Singapore, Singapore, Singapore
| | - Florian Halbritter
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Douglas Colby
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Ben Martynoga
- Division of Molecular Neurobiology, MRC-National Institute for Medical Research, Mill Hill, London, UK
| | - Simon R Tomlinson
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Ian Chambers
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Paul Robson
- Developmental Cellomics Laboratory, Genome Institute of Singapore, Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore, Singapore The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Thorsten Wohland
- Department of Chemistry, National University of Singapore, Singapore, Singapore Department of Biological Sciences, National University of Singapore, Singapore, Singapore Centre for Bioimaging Sciences, National University of Singapore, Singapore, Singapore
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Sokolik C, Liu Y, Bauer D, McPherson J, Broeker M, Heimberg G, Qi LS, Sivak DA, Thomson M. Transcription factor competition allows embryonic stem cells to distinguish authentic signals from noise. Cell Syst 2015; 1:117-129. [PMID: 26405695 DOI: 10.1016/j.cels.2015.08.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Stem cells occupy variable environments where they must distinguish stochastic fluctuations from developmental cues. Here, we use optogenetics to investigate how the pluripotency network in embryonic stem (ES) cells achieves a robust response to differentiation cues but not to gene expression fluctuations. We engineered ES cells in which we could quantitatively ontrol the endogenous mechanism of neural differentiation through a light-inducible Brn2 transgene and monitor differentiation status through a genome-integrated Nanog-GFP reporter. By exposing cells to pulses of Brn2, we find that the pluripotency network rejects Brn2 inputs that are below specific magnitude or duration thresholds, but allows rapid differentiation when both thresholds are satisfied. The filtering properties of the network arise through its positive feedback architecture and the intrinsic half-life of Nanog, which determines the duration threshold in the network. Together our results suggest that the dynamic properties of positive-feedback networks might determine how inputs are classified as signal or noise by stem cells.
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Affiliation(s)
- Cameron Sokolik
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA ; Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - Yanxia Liu
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - David Bauer
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA ; Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - Jade McPherson
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA ; Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - Michael Broeker
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA ; Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - Graham Heimberg
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - Lei S Qi
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - David A Sivak
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA
| | - Matt Thomson
- Center for Systems and Synthetic Biology, University of California, San Francisco; San Francisco, California, 94158. USA ; Department of Cellular and Molecular Pharmacology, University of California, San Francisco; San Francisco, California, 94158. USA
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Lamour V, Henry A, Kroonen J, Nokin MJ, von Marschall Z, Fisher LW, Chau TL, Chariot A, Sanson M, Delattre JY, Turtoi A, Peulen O, Rogister B, Castronovo V, Bellahcène A. Targeting osteopontin suppresses glioblastoma stem-like cell character and tumorigenicityin vivo. Int J Cancer 2015; 137:1047-57. [DOI: 10.1002/ijc.29454] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/24/2014] [Accepted: 12/10/2014] [Indexed: 01/08/2023]
Affiliation(s)
- Virginie Lamour
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège; Belgium
| | - Aurélie Henry
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège; Belgium
| | - Jérôme Kroonen
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liège; Belgium
| | - Marie-Julie Nokin
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège; Belgium
| | | | - Larry W. Fisher
- Craniofacial and Skeletal Diseases Branch, NIDCR, NIH, DHHS; Bethesda MD
| | - Tieu-Lan Chau
- Laboratory of Medical Chemistry, GIGA-Signal Transduction, University of Liège; Belgium
| | - Alain Chariot
- Laboratory of Medical Chemistry, GIGA-Signal Transduction, University of Liège; Belgium
| | - Marc Sanson
- UMR 975, INSERM-UPMC, GH Pitié-Salpêtrière; Paris
| | | | - Andrei Turtoi
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège; Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège; Belgium
| | - Bernard Rogister
- Laboratory of Developmental Neurobiology, GIGA-Neurosciences, University of Liège; Belgium
- Stem Cells and Regenerative Medicine, GIGA-Development, University of Liège; Belgium
| | - Vincent Castronovo
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège; Belgium
| | - Akeila Bellahcène
- Metastasis Research Laboratory, GIGA-Cancer, University of Liège; Belgium
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Urban S, Kobi D, Ennen M, Langer D, Le Gras S, Ye T, Davidson I. A Brn2-Zic1 axis specifies the neuronal fate of retinoic-acid-treated embryonic stem cells. J Cell Sci 2015; 128:2303-18. [PMID: 25991548 DOI: 10.1242/jcs.168849] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/13/2015] [Indexed: 12/19/2022] Open
Abstract
Mouse embryonic stem cells (ESCs) treated with all-trans retinoic acid differentiate into a homogenous population of glutamatergic neurons. Although differentiation is initiated through activation of target genes by the retinoic acid receptors, the downstream transcription factors specifying neuronal fate are less well characterised. Here, we show that the transcription factor Brn2 (also known as Pou3f2) is essential for the neuronal differentiation programme. By integrating results from RNA-seq following Brn2 silencing with results from Brn2 ChIP-seq, we identify a set of Brn2 target genes required for the neurogenic programme. Further integration of Brn2 ChIP-seq data from retinoic-acid-treated ESCs and P19 cells with data from ESCs differentiated into neuronal precursors by Fgf2 treatment and that from fibroblasts trans-differentiated into neurons by ectopic Brn2 expression showed that Brn2 occupied a distinct but overlapping set of genomic loci in these differing conditions. However, a set of common binding sites and target genes defined the core of the Brn2-regulated neuronal programme, among which was that encoding the transcription factor Zic1. Small hairpin RNA (shRNA)-mediated silencing of Zic1 prevented ESCs from differentiating into neuronal precursors, thus defining a hierarchical Brn2-Zic1 axis that is essential to specify neural fate in retinoic-acid-treated ESCs.
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Affiliation(s)
- Sylvia Urban
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France
| | - Dominique Kobi
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France
| | - Marie Ennen
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France
| | - Diana Langer
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France
| | - Stéphanie Le Gras
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France
| | - Tao Ye
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France
| | - Irwin Davidson
- Department of Functional Genomics and Cancer, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France Equipe Labellisée of the Ligue Nationale Contre le Cancer, CNRS/INSERM/UDS, 1 Rue Laurent Fries, Illkirch, Cédex 67404, France
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Hawkins K, Joy S, McKay T. Cell signalling pathways underlying induced pluripotent stem cell reprogramming. World J Stem Cells 2014; 6:620-628. [PMID: 25426259 PMCID: PMC4178262 DOI: 10.4252/wjsc.v6.i5.620] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/03/2014] [Accepted: 09/17/2014] [Indexed: 02/07/2023] Open
Abstract
Induced pluripotent stem (iPS) cells, somatic cells reprogrammed to the pluripotent state by forced expression of defined factors, represent a uniquely valuable resource for research and regenerative medicine. However, this methodology remains inefficient due to incomplete mechanistic understanding of the reprogramming process. In recent years, various groups have endeavoured to interrogate the cell signalling that governs the reprogramming process, including LIF/STAT3, BMP, PI3K, FGF2, Wnt, TGFβ and MAPK pathways, with the aim of increasing our understanding and identifying new mechanisms of improving safety, reproducibility and efficiency. This has led to a unified model of reprogramming that consists of 3 stages: initiation, maturation and stabilisation. Initiation of reprogramming occurs in almost all cells that receive the reprogramming transgenes; most commonly Oct4, Sox2, Klf4 and cMyc, and involves a phenotypic mesenchymal-to-epithelial transition. The initiation stage is also characterised by increased proliferation and a metabolic switch from oxidative phosphorylation to glycolysis. The maturation stage is considered the major bottleneck within the process, resulting in very few “stabilisation competent” cells progressing to the final stabilisation phase. To reach this stage in both mouse and human cells, pre-iPS cells must activate endogenous expression of the core circuitry of pluripotency, comprising Oct4, Sox2, and Nanog, and thus reach a state of transgene independence. By the stabilisation stage, iPS cells generally use the same signalling networks that govern pluripotency in embryonic stem cells. These pathways differ between mouse and human cells although recent work has demonstrated that this is context dependent. As iPS cell generation technologies move forward, tools are being developed to interrogate the process in more detail, thus allowing a greater understanding of this intriguing biological phenomenon.
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Osteopontin is expressed in the oviduct and promotes fertilization and preimplantation embryo development of mouse. ZYGOTE 2014; 23:622-30. [DOI: 10.1017/s0967199414000483] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SummaryOsteopontin (OPN) is a multifunctional phosphoprotein that is detected in various tissues, including male and female reproductive tracts. In this study, we evaluated OPN expression in mouse oviducts during the estrus cycle, and at days 1–5 of pregnancy and pseudopregnancy by reverse transcription polymerase chain reaction (RT-PCR) and immunohistochemistry. The mice oocytes, sperm and embryos were treated with different concentrations of anti-OPN antibody in vitro to detect the function of OPN in fertilization and preimplantation embryo development. OPN mRNA and protein expression in mouse oviducts were cyclic dependent throughout the estrous cycle, which was highest at estrous and lowest at diestrous. Such a phenomenon was consistent with the change in estrogen level in mice. The expression levels of OPN in mice oviduct of normal pregnancy and pseudopregnancy were significantly different, which indicated that OPN expression in mouse oviducts was depend on estrogen and preimplantation embryo. Furthermore, anti-OPN antibody treatment could reduce the rates of fertilization, cleavage and blastocyst formation in vitro in a dose-dependent way. Overall, our results indicated that the expression of OPN in mouse oviducts during the estrous cycle and early pregnancy is likely regulated by estrogen and the embryo, and OPN may play a vital role in oocyte fertilization and preimplantation embryo development.
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Rijlaarsdam MA, Looijenga LHJ. An oncofetal and developmental perspective on testicular germ cell cancer. Semin Cancer Biol 2014; 29:59-74. [PMID: 25066859 DOI: 10.1016/j.semcancer.2014.07.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 07/17/2014] [Indexed: 12/19/2022]
Abstract
Germ cell tumors (GCTs) represent a diverse group of tumors presumably originating from (early fetal) developing germ cells. Most frequent are the testicular germ cell cancers (TGCC). Overall, TGCC is the most frequent malignancy in Caucasian males (20-40 years) and remains an important cause of (treatment related) mortality in these young men. The strong association between the phenotype of TGCC stem cell components and their totipotent ancestor (fetal primordial germ cell or gonocyte) makes these tumors highly relevant from an onco-fetal point of view. This review subsequently discusses the evidence for the early embryonic origin of TGCCs, followed by an overview of the crucial association between TGCC pathogenesis, genetics, environmental exposure and the (fetal) testicular micro-environment (genvironment). This culminates in an evaluation of three genvironmentally modulated hallmarks of TGCC directly related to the oncofetal pathogenesis of TGCC: (1) maintenance of pluripotency, (2) cell cycle control/cisplatin sensitivity and (3) regulation of proliferation/migration/apoptosis by KIT-KITL mediated receptor tyrosine kinase signaling. Briefly, TGCC exhibit identifiable stem cell components (seminoma and embryonal carcinoma) and progenitors that show large and consistent similarities to primordial/embryonic germ cells, their presumed totipotent cells of origin. TGCC pathogenesis depends crucially on a complex interaction of genetic and (micro-)environmental, i.e. genvironmental risk factors that have only been partly elucidated despite significant effort. TGCC stem cell components also show a high degree of similarity with embryonic stem/germ cells (ES) in the regulation of pluripotency and cell cycle control, directly related to their exquisite sensitivity to DNA damaging agents (e.g. cisplatin). Of note, (ES specific) micro-RNAs play a pivotal role in the crossover between cell cycle control, pluripotency and chemosensitivity. Moreover, multiple consistent observations reported TGCC to be associated with KIT-KITL mediated receptor tyrosine kinase signaling, a pathway crucially implicated in proliferation, migration and survival during embryogenesis including germ cell development. In conclusion, TGCCs are a fascinating model for onco-fetal developmental processes especially with regard to studying cell cycle control, pluripotency maintenance and KIT-KITL signaling. The knowledge presented here contributes to better understanding of the molecular characteristics of TGCC pathogenesis, translating to identification of at risk individuals and enhanced quality of care for TGCC patients (diagnosis, treatment and follow-up).
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Affiliation(s)
- Martin A Rijlaarsdam
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Leendert H J Looijenga
- Department of Pathology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands.
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Cobalt and nickel stabilize stem cell transcription factor OCT4 through modulating its sumoylation and ubiquitination. PLoS One 2014; 9:e86620. [PMID: 24497960 PMCID: PMC3908935 DOI: 10.1371/journal.pone.0086620] [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: 11/03/2013] [Accepted: 12/15/2013] [Indexed: 01/13/2023] Open
Abstract
Stem cell research can lead to the development of treatments for a wide range of ailments including diabetes, heart disease, aging, neurodegenerative diseases, spinal cord injury, and cancer. OCT4 is a master regulator of self-renewal of undifferentiated embryonic stem cells. OCT4 also plays a crucial role in reprogramming of somatic cells into induced pluripotent stem (iPS) cells. Given known vivo reproductive toxicity of cobalt and nickel metals, we examined the effect of these metals on expression of several stem cell factors in embryonic Tera-1 cells, as well as stem cells. Cobalt and nickel induced a concentration-dependent increase of OCT4 and HIF-1α, but not NANOG or KLF4. OCT4 induced by cobalt and nickel was due primarily to protein stabilization because MG132 stabilized OCT4 in cells treated with either metals and because neither nickel nor cobalt significantly modulated its steady-state mRNA level. OCT4 stabilization by cobalt and nickel was mediated largely through reactive oxygen species (ROS) as co-treatment with ascorbic acid abolished OCT4 increase. Moreover, nickel and cobalt treatment increased sumoylation and mono-ubiquitination of OCT4 and K123 was crucial for mediating these modifications. Combined, our observations suggest that nickel and cobalt may exert their reproductive toxicity through perturbing OCT4 activity in the stem cell compartment.
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Transcriptional protein-protein cooperativity in POU/HMG/DNA complexes revealed by normal mode analysis. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:854710. [PMID: 24324527 PMCID: PMC3845252 DOI: 10.1155/2013/854710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 09/22/2013] [Indexed: 11/26/2022]
Abstract
Biomolecular cooperativity is of great scientific interest due to its role in biological processes. Two transcription factors (TFs), Oct-4 and Sox-2, are crucial in transcriptional regulation of embryonic stem cells. In this paper, we analyze how Oct-1 (a similar POU factor) and Sox-2, interact cooperatively at their enhancer binding sites in collective motions. Normal mode analysis (NMA) is implemented to study the collective motions of two complexes with each involving these TFs and an enhancer. The special structure of Oct proteins is analyzed comprehensively, after which each Oct/Sox group is reassembled into two protein pairs. We subsequently propose a segmentation idea to extract the most correlated segments in each pair, using correlations of motion magnitude curves. The median analysis on these correlation values shows the intimacy of subunit POUS (Oct-1) and Sox-2. Using those larger-than-median correlation values, we conduct statistical studies and propose several protein-protein cooperative modes (S and D) coupled with their subtypes. Additional filters are applied and similar results are obtained. A supplementary study on the rotation angle curves reaches an agreement with these modes. Overall, these proposed cooperative modes provide useful information for us to understand the complicated interaction mechanism in the POU/HMG/DNA complexes.
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Hosseinpour B, Bakhtiarizadeh MR, Khosravi P, Ebrahimie E. Predicting distinct organization of transcription factor binding sites on the promoter regions: a new genome-based approach to expand human embryonic stem cell regulatory network. Gene 2013; 531:212-9. [DOI: 10.1016/j.gene.2013.09.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 09/01/2013] [Accepted: 09/04/2013] [Indexed: 12/23/2022]
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Jerabek S, Merino F, Schöler HR, Cojocaru V. OCT4: dynamic DNA binding pioneers stem cell pluripotency. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2013; 1839:138-54. [PMID: 24145198 DOI: 10.1016/j.bbagrm.2013.10.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/02/2013] [Accepted: 10/06/2013] [Indexed: 12/12/2022]
Abstract
OCT4 was discovered more than two decades ago as a transcription factor specific to early embryonic development. Early studies with OCT4 were descriptive and looked at determining the functional roles of OCT4 in the embryo as well as in pluripotent cell lines derived from embryos. Later studies showed that OCT4 was one of the transcription factors in the four-factor cocktail required for reprogramming somatic cells into induced pluripotent stem cells (iPSCs) and that it is the only factor that cannot be substituted in this process by other members of the same protein family. In recent years, OCT4 has emerged as a master regulator of the induction and maintenance of cellular pluripotency, with crucial roles in the early stages of differentiation. Currently, mechanistic studies look at elucidating the molecular details of how OCT4 contributes to establishing selective gene expression programs that define different developmental stages of pluripotent cells. OCT4 belongs to the POU family of proteins, which have two conserved DNA-binding domains connected by a variable linker region. The functions of OCT4 depend on its ability to recognize and bind to DNA regulatory regions alone or in cooperation with other transcription factors and on its capacity to recruit other factors required to regulate the expression of specific sets of genes. Undoubtedly, future iPSC-based applications in regenerative medicine will benefit from understanding how OCT4 functions. Here we provide an integrated view of OCT4 research conducted to date by reviewing the different functional roles for OCT4 and discussing the current progress in understanding their underlying molecular mechanisms. This article is part of a Special Issue entitled: Chromatin and epigenetic regulation of animal development.
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Affiliation(s)
- Stepan Jerabek
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Felipe Merino
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany
| | - Hans Robert Schöler
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany.
| | - Vlad Cojocaru
- Department of Cell and Developmental Biology, Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, 48149 Münster, Germany.
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Epigenetic control of cytokine gene expression: regulation of the TNF/LT locus and T helper cell differentiation. Adv Immunol 2013; 118:37-128. [PMID: 23683942 DOI: 10.1016/b978-0-12-407708-9.00002-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Epigenetics encompasses transient and heritable modifications to DNA and nucleosomes in the native chromatin context. For example, enzymatic addition of chemical moieties to the N-terminal "tails" of histones, particularly acetylation and methylation of lysine residues in the histone tails of H3 and H4, plays a key role in regulation of gene transcription. The modified histones, which are physically associated with gene regulatory regions that typically occur within conserved noncoding sequences, play a functional role in active, poised, or repressed gene transcription. The "histone code" defined by these modifications, along with the chromatin-binding acetylases, deacetylases, methylases, demethylases, and other enzymes that direct modifications resulting in specific patterns of histone modification, shows considerable evolutionary conservation from yeast to humans. Direct modifications at the DNA level, such as cytosine methylation at CpG motifs that represses promoter activity, are another highly conserved epigenetic mechanism of gene regulation. Furthermore, epigenetic modifications at the nucleosome or DNA level can also be coupled with higher-order intra- or interchromosomal interactions that influence the location of regulatory elements and that can place them in an environment of specific nucleoprotein complexes associated with transcription. In the mammalian immune system, epigenetic gene regulation is a crucial mechanism for a range of physiological processes, including the innate host immune response to pathogens and T cell differentiation driven by specific patterns of cytokine gene expression. Here, we will review current findings regarding epigenetic regulation of cytokine genes important in innate and/or adaptive immune responses, with a special focus upon the tumor necrosis factor/lymphotoxin locus and cytokine-driven CD4+ T cell differentiation into the Th1, Th2, and Th17 lineages.
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Xie QZ, Qi QR, Chen YX, Xu WM, Liu Q, Yang J. Uterine micro-environment and estrogen-dependent regulation of osteopontin expression in mouse blastocyst. Int J Mol Sci 2013; 14:14504-17. [PMID: 23852023 PMCID: PMC3742256 DOI: 10.3390/ijms140714504] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 06/10/2013] [Accepted: 07/01/2013] [Indexed: 12/23/2022] Open
Abstract
Embryo implantation is a highly synchronized bioprocess between an activated blastocyst and a receptive uterus. In mice, successful implantation relies on the dynamic interplay of estrogen and progesterone; however, the key mediators downstream of these hormones that act on blastocyst competency and endometrium receptivity acquisition are largely unknown. In this study, we showed that the expression of osteopontin (OPN) in mouse blastocysts is regulated by ovarian estrogen and uterine micro-environment. OPN mRNA is up-regulated in mouse blastocyst on day 4 of pregnancy, which is associated with ovarian estrogen secretion peak. Hormone treatment in vivo demonstrated that OPN expression in a blastocyst is regulated by estrogen through an estrogen receptor (ER). Our results of the delayed and activated implantation model showed that OPN expression is induced after estrogen injection. While estrogen treatment during embryo culture in vitro showed less effect on OPN expression, the tubal ligation model on day 3 of pregnancy confirmed that the regulation of estrogen on OPN expression in blastocyst might, through some specific cytokines, have existed in a uterine micro-environment. Collectively, our study presents that estrogen regulates OPN expression and it may play an important role during embryo implantation by activating blastocyst competence and facilitating the endometrium acceptable for active blastocyst.
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Affiliation(s)
- Qing-Zhen Xie
- Center for Reproductive Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China; E-Mails: (Q.-R.Q.); (Y.-X.C.); (W.-M.X.); (Q.L.); (J.Y.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-27-8804-1919 (ext. 123); Fax: +86-27-8808-0749
| | - Qian-Rong Qi
- Center for Reproductive Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China; E-Mails: (Q.-R.Q.); (Y.-X.C.); (W.-M.X.); (Q.L.); (J.Y.)
| | - Ying-Xian Chen
- Center for Reproductive Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China; E-Mails: (Q.-R.Q.); (Y.-X.C.); (W.-M.X.); (Q.L.); (J.Y.)
- Department of Obstetrics and Gynecology, Taihe Hospital, Shiyan 441000, Hubei, China
| | - Wang-Ming Xu
- Center for Reproductive Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China; E-Mails: (Q.-R.Q.); (Y.-X.C.); (W.-M.X.); (Q.L.); (J.Y.)
| | - Qian Liu
- Center for Reproductive Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China; E-Mails: (Q.-R.Q.); (Y.-X.C.); (W.-M.X.); (Q.L.); (J.Y.)
| | - Jing Yang
- Center for Reproductive Medicine, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, China; E-Mails: (Q.-R.Q.); (Y.-X.C.); (W.-M.X.); (Q.L.); (J.Y.)
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Acetylated histone H3K56 interacts with Oct4 to promote mouse embryonic stem cell pluripotency. Proc Natl Acad Sci U S A 2013; 110:11493-8. [PMID: 23798425 DOI: 10.1073/pnas.1309914110] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The presence of acetylated histone H3K56 (H3K56ac) in human ES cells (ESCs) correlates positively with the binding of Nanog, Sox2, and Oct4 (NSO) transcription factors at their target gene promoters. However, the function of H3K56ac there has been unclear. We now report that Oct4 interacts with H3K56ac in mouse ESC nuclear extracts and that perturbing H3K56 acetylation decreases Oct4-H3 binding. This interaction is likely to be direct because it can be recapitulated in vitro in an H3K56ac-dependent manner and is functionally important because H3K56ac combines with NSO factors in chromatin immunoprecipitation sequencing to mark the regions associated with pluripotency better than NSO alone. Moreover, reducing H3K56ac by short hairpin Asf1a decreases expression of pluripotency-related markers and increases expression of differentiation-related ones. Therefore, our data suggest that H3K56ac plays a central role in binding to Oct4 to promote the pluripotency of ESCs.
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Beltrão-Braga PCB, Pignatari GC, Russo FB, Fernandes IR, Muotri AR. In-a-dish: induced pluripotent stem cells as a novel model for human diseases. Cytometry A 2013; 83:11-7. [PMID: 23281003 DOI: 10.1002/cyto.a.22231] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 09/20/2012] [Accepted: 10/24/2012] [Indexed: 12/12/2022]
Abstract
Human pluripotent stem cells bring promise in regenerative medicine due to their self-renewing ability and the potential to become any cell type in the body. Moreover, pluripotent stem cells can produce specialized cell types that are affected in certain diseases, generating a new way to study cellular and molecular mechanisms involved in the disease pathology under the controlled conditions of a scientific laboratory. Thus, induced pluripotent stem cells (iPSC) are already being used to gain insights into the biological mechanisms of several human disorders. Here we review the use of iPSC as a novel tool for disease modeling in the lab.
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Affiliation(s)
- P C B Beltrão-Braga
- Stem Cell Laboratory, Surgery Department, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil.
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Frum T, Halbisen MA, Wang C, Amiri H, Robson P, Ralston A. Oct4 cell-autonomously promotes primitive endoderm development in the mouse blastocyst. Dev Cell 2013; 25:610-22. [PMID: 23747191 DOI: 10.1016/j.devcel.2013.05.004] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 04/10/2013] [Accepted: 05/06/2013] [Indexed: 01/18/2023]
Abstract
In embryonic stem (ES) cells and in early mouse embryos, the transcription factor Oct4 is an essential regulator of pluripotency. Oct4 transcriptional targets have been described in ES cell lines; however, the molecular mechanisms by which Oct4 regulates establishment of pluripotency in the epiblast (EPI) have not been fully elucidated. Here, we show that neither maternal nor zygotic Oct4 is required for the formation of EPI cells in the blastocyst. Rather, Oct4 is first required for development of the primitive endoderm (PE), an extraembryonic lineage. EPI cells promote PE fate in neighboring cells by secreting Fgf4, and Oct4 is required for expression of Fgf4, but we show that Oct4 promotes PE development cell-autonomously, downstream of Fgf4 and Mapk. Finally, we show that Oct4 is required for the expression of multiple EPI and PE genes as well as multiple metabolic pathways essential for the continued growth of the preimplantation embryo.
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Affiliation(s)
- Tristan Frum
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Li R, Bai Y, Liu T, Wang X, Wu Q. Induced pluripotency and direct reprogramming: a new window for treatment of neurodegenerative diseases. Protein Cell 2013; 4:415-24. [PMID: 23686735 DOI: 10.1007/s13238-013-2089-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Accepted: 01/09/2013] [Indexed: 12/11/2022] Open
Abstract
Human embryonic stem cells (hESCs) are pluripotent cells that have the ability of unlimited self-renewal and can be differentiated into different cell lineages, including neural stem (NS) cells. Diverse regulatory signaling pathways of neural stem cells differentiation have been discovered, and this will be of great benefit to uncover the mechanisms of neuronal differentiation in vivo and in vitro. However, the limitations of hESCs resource along with the religious and ethical concerns impede the progress of ESCs application. Therefore, the induced pluripotent stem cells (iPSCs) via somatic cell reprogramming have opened up another new territory for regenerative medicine. iPSCs now can be derived from a number of lineages of cells, and are able to differentiate into certain cell types, including neurons. Patient-specifi c iPSCs are being used in human neurodegenerative disease modeling and drug screening. Furthermore, with the development of somatic direct reprogramming or lineage reprogramming technique, a more effective approach for regenerative medicine could become a complement for iPSCs.
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Affiliation(s)
- Rui Li
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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