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Mil J, Soto JA, Matulionis N, Krall A, Day F, Stiles L, Montales KP, Azizad DJ, Gonzalez CE, Nano PR, Martija AA, Perez-Ramirez CA, Nguyen CV, Kan RL, Andrews MG, Christofk HR, Bhaduri A. Metabolic Atlas of Early Human Cortex Identifies Regulators of Cell Fate Transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.10.642470. [PMID: 40161647 PMCID: PMC11952424 DOI: 10.1101/2025.03.10.642470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Characterization of cell type emergence during human cortical development, which enables unique human cognition, has focused primarily on anatomical and transcriptional characterizations. Metabolic processes in the human brain that allow for rapid expansion, but contribute to vulnerability to neurodevelopmental disorders, remain largely unexplored. We performed a variety of metabolic assays in primary tissue and stem cell derived cortical organoids and observed dynamic changes in core metabolic functions, including an unexpected increase in glycolysis during late neurogenesis. By depleting glucose levels in cortical organoids, we increased outer radial glia, astrocytes, and inhibitory neurons. We found the pentose phosphate pathway (PPP) was impacted in these experiments and leveraged pharmacological and genetic manipulations to recapitulate these radial glia cell fate changes. These data identify a new role for the PPP in modulating radial glia cell fate specification and generate a resource for future exploration of additional metabolic pathways in human cortical development.
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Affiliation(s)
- Jessenya Mil
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jose A. Soto
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Nedas Matulionis
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Abigail Krall
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Francesca Day
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Linsey Stiles
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, California, USA
| | - Katrina P. Montales
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Daria J. Azizad
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Carlos E. Gonzalez
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Patricia R. Nano
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Antoni A. Martija
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Cesar A. Perez-Ramirez
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Claudia V. Nguyen
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ryan L. Kan
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Madeline G. Andrews
- School of Biological and Health Systems Engineering, Arizona State University, Phoenix, AZ, United States
| | - Heather R. Christofk
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
| | - Aparna Bhaduri
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, United States
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Niharika, Ureka L, Roy A, Patra SK. Dissecting SOX2 expression and function reveals an association with multiple signaling pathways during embryonic development and in cancer progression. Biochim Biophys Acta Rev Cancer 2024; 1879:189136. [PMID: 38880162 DOI: 10.1016/j.bbcan.2024.189136] [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: 05/09/2023] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
SRY (Sex Determining Region) box 2 (SOX2) is an essential transcription factor that plays crucial roles in activating genes involved in pre- and post-embryonic development, adult tissue homeostasis, and lineage specifications. SOX2 maintains the self-renewal property of stem cells and is involved in the generation of induced pluripotency stem cells. SOX2 protein contains a particular high-mobility group domain that enables SOX2 to achieve the capacity to participate in a broad variety of functions. The information about the involvement of SOX2 with gene regulatory elements, signaling networks, and microRNA is gradually emerging, and the higher expression of SOX2 is functionally relevant to various cancer types. SOX2 facilitates the oncogenic phenotype via cellular proliferation and enhancement of invasive tumor properties. Evidence are accumulating in favor of three dimensional (higher order) folding of chromatin and epigenetic control of the SOX2 gene by chromatin modifications, which implies that the expression level of SOX2 can be modulated by epigenetic regulatory mechanisms, specifically, via DNA methylation and histone H3 modification. In view of this, and to focus further insights into the roles SOX2 plays in physiological functions, involvement of SOX2 during development, precisely, the advances of our knowledge in pre- and post-embryonic development, and interactions of SOX2 in this scenario with various signaling pathways in tumor development and cancer progression, its potential as a therapeutic target against many cancers are summarized and discussed in this article.
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Affiliation(s)
- Niharika
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lina Ureka
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ankan Roy
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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3
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Mercurio S, Serra L, Pagin M, Nicolis SK. Deconstructing Sox2 Function in Brain Development and Disease. Cells 2022; 11:cells11101604. [PMID: 35626641 PMCID: PMC9139651 DOI: 10.3390/cells11101604] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 02/04/2023] Open
Abstract
SOX2 is a transcription factor conserved throughout vertebrate evolution, whose expression marks the central nervous system from the earliest developmental stages. In humans, SOX2 mutation leads to a spectrum of CNS defects, including vision and hippocampus impairments, intellectual disability, and motor control problems. Here, we review how conditional Sox2 knockout (cKO) in mouse with different Cre recombinases leads to very diverse phenotypes in different regions of the developing and postnatal brain. Surprisingly, despite the widespread expression of Sox2 in neural stem/progenitor cells of the developing neural tube, some regions (hippocampus, ventral forebrain) appear much more vulnerable than others to Sox2 deletion. Furthermore, the stage of Sox2 deletion is also a critical determinant of the resulting defects, pointing to a stage-specificity of SOX2 function. Finally, cKOs illuminate the importance of SOX2 function in different cell types according to the different affected brain regions (neural precursors, GABAergic interneurons, glutamatergic projection neurons, Bergmann glia). We also review human genetics data regarding the brain defects identified in patients carrying mutations within human SOX2 and examine the parallels with mouse mutants. Functional genomics approaches have started to identify SOX2 molecular targets, and their relevance for SOX2 function in brain development and disease will be discussed.
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4
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Chen F, Chen, Wang J, Zhang S, Chen M, Zhang X, Wu Z. Overexpression of SSR2 promotes proliferation of liver cancer cells and predicts prognosis of patients with hepatocellular carcinoma. J Cell Mol Med 2022; 26:3169-3182. [PMID: 35481617 PMCID: PMC9170819 DOI: 10.1111/jcmm.17314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/22/2022] [Accepted: 03/23/2022] [Indexed: 11/30/2022] Open
Abstract
Signal Sequence Receptor Subunit 2 (SSR2) is a key endoplasmic reticulum gene involved in protein folding and processing. Previous studies found that it was upregulated in several cancers, but its precise role in hepatocellular carcinoma (HCC) remains unclear. To have a better understanding of this gene in HCC, we examined the expression of SSR2 in HCC tissues by analysing The Cancer Genome Atlas (TCGA) data and immunohistochemistry. We also assessed the association between SSR2 expression and clinicopathological characteristics of HCC patients and patient survival. Potential function of SSR2 was predicted through GSEA and protein–protein interaction analysis. MTT, flowcytometry, transwell and a nude mice xenograft model were employed to investigate the biological functions in vivo and in vitro. The results showed that the expression of SSR2 was significantly increased in HCC tissues, and SSR2 expression was associated with several clinical characteristics. In addition, patients with higher SSR2 expression had poorer survival. Enrichment analysis suggested that SSR2 was probably involved in biological process or signalling pathways related to G2/M checkpoint, passive transmembrane transporter activity, ATF2_S_UP. V1_UP and ncRNA metabolic process. Further experimental study showed that SSR2 knockdown inhibited cell proliferation, migration and invasion ability and promoted apoptosis and cell cycle arrest in vitro. Moreover, downregulation of SSR2 also repressed the growth of HepG2 cells in vivo. In conclusion, our study suggests that SSR2 may act as an oncogene in HCC.
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Affiliation(s)
- Fengsui Chen
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China.,Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Chen
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Jielong Wang
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Shi'an Zhang
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China
| | - Mengxue Chen
- Fuzhou Hospital of Traditional Chinese Medicine, Fuzhou, Fujian, P.R. China
| | - Xia Zhang
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China.,Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
| | - Zhixian Wu
- Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force, Fujian Medical University, Fuzhou, Fujian, P.R. China.,Department of Hepatobiliary Disease, 900 Hospital of the Joint Logistics Support Force (Dongfang Hospital), Xiamen University, Fuzhou, Fujian, P.R. China
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5
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Mahlokozera T, Patel B, Chen H, Desouza P, Qu X, Mao DD, Hafez D, Yang W, Taiwo R, Paturu M, Salehi A, Gujar AD, Dunn GP, Mosammaparast N, Petti AA, Yano H, Kim AH. Competitive binding of E3 ligases TRIM26 and WWP2 controls SOX2 in glioblastoma. Nat Commun 2021; 12:6321. [PMID: 34732716 PMCID: PMC8566473 DOI: 10.1038/s41467-021-26653-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
The pluripotency transcription factor SOX2 is essential for the maintenance of glioblastoma stem cells (GSC), which are thought to underlie tumor growth, treatment resistance, and recurrence. To understand how SOX2 is regulated in GSCs, we utilized a proteomic approach and identified the E3 ubiquitin ligase TRIM26 as a direct SOX2-interacting protein. Unexpectedly, we found TRIM26 depletion decreased SOX2 protein levels and increased SOX2 polyubiquitination in patient-derived GSCs, suggesting TRIM26 promotes SOX2 protein stability. Accordingly, TRIM26 knockdown disrupted the SOX2 gene network and inhibited both self-renewal capacity as well as in vivo tumorigenicity in multiple GSC lines. Mechanistically, we found TRIM26, via its C-terminal PRYSPRY domain, but independent of its RING domain, stabilizes SOX2 protein by directly inhibiting the interaction of SOX2 with WWP2, which we identify as a bona fide SOX2 E3 ligase in GSCs. Our work identifies E3 ligase competition as a critical mechanism of SOX2 regulation, with functional consequences for GSC identity and maintenance. SOX2 is required for the maintenance of glioblastoma stem cells (GSCs). Here the authors identify that the RING family E3 ubiquitin ligase TRIM26 promotes SOX2 stability in a non-canonical ligase-independent manner and thus, increases the tumorigenicity of GSCs.
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Affiliation(s)
- Tatenda Mahlokozera
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Bhuvic Patel
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Hao Chen
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Desouza
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Xuan Qu
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Diane D Mao
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Hafez
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Yang
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - Rukayat Taiwo
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Mounica Paturu
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Afshin Salehi
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Amit D Gujar
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Allegra A Petti
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA.,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA. .,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA. .,The Brain Tumor Center, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA. .,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA.
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6
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Reactive oxygen species (ROS): Critical roles in breast tumor microenvironment. Crit Rev Oncol Hematol 2021; 160:103285. [DOI: 10.1016/j.critrevonc.2021.103285] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/18/2021] [Accepted: 02/27/2021] [Indexed: 02/06/2023] Open
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7
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Saenz-Antoñanzas A, Moncho-Amor V, Auzmendi-Iriarte J, Elua-Pinin A, Rizzoti K, Lovell-Badge R, Matheu A. CRISPR/Cas9 Deletion of SOX2 Regulatory Region 2 ( SRR2) Decreases SOX2 Malignant Activity in Glioblastoma. Cancers (Basel) 2021; 13:cancers13071574. [PMID: 33805518 PMCID: PMC8037847 DOI: 10.3390/cancers13071574] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/12/2021] [Accepted: 03/17/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Understanding how SOX2, a major driver of cancer stem cells, is regulated in cancer cells is relevant to tackle tumorigenesis. In this study, we deleted the SRR2 regulatory region in glioblastoma cells. Our data confirm that the SRR2 enhancer regulates SOX2 expression in cancer and reveal that SRR2 deletion halts malignant activity of SOX2. Abstract SOX2 is a transcription factor associated with stem cell activity in several tissues. In cancer, SOX2 expression is increased in samples from several malignancies, including glioblastoma, and high SOX2 levels are associated with the population of tumor-initiating cells and with poor patient outcome. Therefore, understanding how SOX2 is regulated in cancer cells is relevant to tackle tumorigenesis. The SOX2 regulatory region 2(SRR2) is located downstream of the SOX2 coding region and mediates SOX2 expression in embryonic and adult stem cells. In this study, we deleted SRR2 using CRISPR/Cas9 in glioblastoma cells. Importantly, SRR2-deleted glioblastoma cells presented reduced SOX2 expression and decreased proliferative activity and self-renewal capacity in vitro. In line with these results, SRR2-deleted glioblastoma cells displayed decreased tumor initiation and growth in vivo. These effects correlated with an elevation of p21CIP1 cell cycle and p27KIP1 quiescence regulators. In conclusion, our data reveal that SRR2 deletion halts malignant activity of SOX2 and confirms that the SRR2 enhancer regulates SOX2 expression in cancer.
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Affiliation(s)
- Ander Saenz-Antoñanzas
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
| | - Veronica Moncho-Amor
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London NW1 1AT, UK; (V.M.-A.); (K.R.); (R.L.-B.)
| | - Jaione Auzmendi-Iriarte
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
| | - Alejandro Elua-Pinin
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
- Donostia Hospital, 20014 San Sebastian, Spain
| | - Karine Rizzoti
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London NW1 1AT, UK; (V.M.-A.); (K.R.); (R.L.-B.)
| | - Robin Lovell-Badge
- Stem Cell Biology and Developmental Genetics Lab, The Francis Crick Institute, London NW1 1AT, UK; (V.M.-A.); (K.R.); (R.L.-B.)
| | - Ander Matheu
- Cellular Oncology Group, Biodonostia Health Research Institute, 20014 San Sebastian, Spain; (A.S.-A.); (J.A.-I.); (A.E.-P.)
- CIBER of Frailty and Healthy Aging (CIBERfes), Carlos III Institute, 28029 Madrid, Spain
- IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain
- Correspondence:
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8
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Batool S, Kayani MA, Valis M, Kuca K. Neural Differentiation of Mouse Embryonic Stem Cells-An in vitro Approach to Profile DNA Methylation of Reprogramming Factor Sox2-SRR2. Front Genet 2021; 12:641095. [PMID: 33828585 PMCID: PMC8019947 DOI: 10.3389/fgene.2021.641095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/02/2021] [Indexed: 12/30/2022] Open
Abstract
Sox2 is one of the core transcription factors maintaining the embryonic stem cells (ES) pluripotency and, also indispensable for cellular reprogramming. However, limited data is available about the DNA methylation of pluripotency genes during lineage-specific differentiations. This study investigated the DNA methylation of Sox2 regulatory region 2 (SRR2) during directed differentiation of mouse ES into neural lineage. ES cells were first grown to form embryoid bodies in suspension which were then dissociated, and cultured in defined medium to promote neural differentiation. Typical neuronal morphology together with the up-regulation of Pax6, neuroepithelial stem cell intermediate filament and β-tubulin III and, down-regulation of pluripotency genes Oct4, Nanog and Sox2 showed the existence of neural phenotype in cells undergoing differentiation. Three CpGs in the core enhancer region of neural-specific SRR2 were individually investigated by direct DNA sequencing post-bisulfite treatment and, found to be unmethylated in differentiated cells at time-points chosen for analysis. This analysis does not limit the possibility of methylation at other CpG sites than those profiled here and/or transient methylation. Hence, similar analyses exploring the DNA methylation at other regions of the Sox2 gene could unravel the onset and transitions of epigenetic signatures influencing the outcome of differentiation pathways and neural development. The data presented here shows that in vitro neural differentiation of embryonic stem cells can be employed to study and characterize molecular regulatory mechanisms governing neurogenesis by applying diverse pharmacological and toxicological agents.
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Affiliation(s)
- Sajida Batool
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Martin Valis
- Department of Neurology of the Medical Faculty of Charles University and University Hospital in Hradec Kralove, Hradec Kralove, Czechia
| | - Kamil Kuca
- Department of Chemistry, University of Hradec Kralove, Hradec Kralove, Czechia
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9
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NF-YA transcriptionally activates the expression of SOX2 in cervical cancer stem cells. PLoS One 2019; 14:e0215494. [PMID: 31365524 PMCID: PMC6668781 DOI: 10.1371/journal.pone.0215494] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 07/08/2019] [Indexed: 01/06/2023] Open
Abstract
Roles for SOX2 have been extensively studied in several types of cancer, including colorectal cancer, glioblastoma and breast cancer, with particular emphasis placed on the roles of SOX2 in cancer stem cell. Our previous study identified SOX2 as a marker in cervical cancer stem cells driven by a full promoter element of SOX2 EGFP reporter. Here, dual-luciferase reporter and mutagenesis analyses were employed, identifying key cis-elements in the SOX2 promoter, including binding sites for SOX2, OCT4 and NF-YA factors in SOX2 promoter. Mutagenesis analysis provided additional evidence to show that one high affinity-binding domain CCAAT box was precisely recognized and bound by the transcription factor NF-YA. Furthermore, overexpression of NF-YA in primitive cervical cancer cells SiHa and C33A significantly activated the transcription and the protein expression of SOX2. Collectively, our data identified NF-YA box CCAAT as a key cis-element in the SOX2 promoter, suggesting that NF-YA is a potent cellular regulator in the maintenance of SOX2-positive cervical cancer stem cell by specific transcriptional activation of SOX2.
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10
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Modrek AS, Golub D, Khan T, Bready D, Prado J, Bowman C, Deng J, Zhang G, Rocha PP, Raviram R, Lazaris C, Stafford JM, LeRoy G, Kader M, Dhaliwal J, Bayin NS, Frenster JD, Serrano J, Chiriboga L, Baitalmal R, Nanjangud G, Chi AS, Golfinos JG, Wang J, Karajannis MA, Bonneau RA, Reinberg D, Tsirigos A, Zagzag D, Snuderl M, Skok JA, Neubert TA, Placantonakis DG. Low-Grade Astrocytoma Mutations in IDH1, P53, and ATRX Cooperate to Block Differentiation of Human Neural Stem Cells via Repression of SOX2. Cell Rep 2018; 21:1267-1280. [PMID: 29091765 DOI: 10.1016/j.celrep.2017.10.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/24/2017] [Accepted: 10/02/2017] [Indexed: 02/07/2023] Open
Abstract
Low-grade astrocytomas (LGAs) carry neomorphic mutations in isocitrate dehydrogenase (IDH) concurrently with P53 and ATRX loss. To model LGA formation, we introduced R132H IDH1, P53 shRNA, and ATRX shRNA into human neural stem cells (NSCs). These oncogenic hits blocked NSC differentiation, increased invasiveness in vivo, and led to a DNA methylation and transcriptional profile resembling IDH1 mutant human LGAs. The differentiation block was caused by transcriptional silencing of the transcription factor SOX2 secondary to disassociation of its promoter from a putative enhancer. This occurred because of reduced binding of the chromatin organizer CTCF to its DNA motifs and disrupted chromatin looping. Our human model of IDH mutant LGA formation implicates impaired NSC differentiation because of repression of SOX2 as an early driver of gliomagenesis.
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Affiliation(s)
- Aram S Modrek
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Danielle Golub
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Themasap Khan
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Devin Bready
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Jod Prado
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Christopher Bowman
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Jingjing Deng
- Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Guoan Zhang
- Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Pedro P Rocha
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Ramya Raviram
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Charalampos Lazaris
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Center, NYU School of Medicine, New York, NY 10016, USA
| | - James M Stafford
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Gary LeRoy
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Michael Kader
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - Joravar Dhaliwal
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA
| | - N Sumru Bayin
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Joshua D Frenster
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Jonathan Serrano
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Luis Chiriboga
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Rabaa Baitalmal
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Gouri Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew S Chi
- Department of Neurology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - John G Golfinos
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jing Wang
- Department of Anesthesiology, NYU School of Medicine, New York, NY 10016, USA
| | - Matthias A Karajannis
- Department of Pediatrics, NYU School of Medicine, New York, NY 10016, USA; Department of Otolaryngology, NYU School of Medicine, New York, NY 10016, USA
| | - Richard A Bonneau
- Department of Biology, New York University, New York, New York, 10003, USA; Department of Computer Science, New York University, New York, New York, 10003, USA; Simons Center for Data Analysis, New York, NY 10010, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Aristotelis Tsirigos
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Applied Bioinformatics Center, NYU School of Medicine, New York, NY 10016, USA
| | - David Zagzag
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - Matija Snuderl
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA; Department of Neurology, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jane A Skok
- Department of Pathology, NYU School of Medicine, New York, NY 10016, USA
| | - Thomas A Neubert
- Department of Cell Biology, NYU School of Medicine, New York, NY 10016, USA
| | - Dimitris G Placantonakis
- Department of Neurosurgery, NYU School of Medicine, New York, NY 10016, USA; Kimmel Center for Stem Cell Biology, NYU School of Medicine, New York, NY 10016, USA; Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA; Brain Tumor Center, NYU School of Medicine, New York, NY 10016, USA; Neuroscience Institute, NYU School of Medicine, New York, NY 10016, USA.
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11
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Epigenetic modifications in the embryonic and induced pluripotent stem cells. Gene Expr Patterns 2018; 29:1-9. [PMID: 29625185 DOI: 10.1016/j.gep.2018.04.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 03/03/2018] [Accepted: 04/03/2018] [Indexed: 02/07/2023]
Abstract
Epigenetic modifications are involved in global reprogramming of the cell transcriptome. Therefore, synchronized major shifts in the expression of many genes could be achieved through epigenetic changes. The regulation of gene expression could be implemented by different epigenetic events including histone modifications, DNA methylation and chromatin remodelling. Interestingly, it has been documented that reprogramming of somatic cells to induced pluripotent stem (iPS) cells is also a typical example of epigenetic modifications. Additionally, epigenetic would determine the fates of almost all cells upon differentiation of stem cells into somatic cells. Currently, generation of iPS cells through epigenetic modifications is a routine laboratory practice. Despite all our knowledge, inconsistency in the results of reprogramming and differentiation of stem cells, highlight the need for more thorough investigation into the role of epigenetic modification in generation and maintenance of stem cells. Besides, subtle differences have been observed among different iPS cells and between iPS and ES cells. Although, a handful of detailed review regarding the status of epigenetics in stem cells has been published previously, in the current review, an abstracted and rather simplified view has been presented for those who want to gain a more general overview on this subject. However, almost all key references and ground breaking studies were included, which could be further explored to gain more in depth knowledge regarding this topic. The most dominant epigenetic changes have been presented followed by the impacts of such changes on the global gene expression. Epigenetic status in iPS and ES cells were compared. In addition to including the issues related to X-chromosome reactivation in the stem cells, we have also included loss of imprinting for some genes as a major drawback in generation of iPS cells. Finally, the overall impacts of epigenetic modifications on different aspects of stem cells has been discussed, including their use in cell therapy.
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Ribecco-Lutkiewicz M, Sodja C, Haukenfrers J, Haqqani AS, Ly D, Zachar P, Baumann E, Ball M, Huang J, Rukhlova M, Martina M, Liu Q, Stanimirovic D, Jezierski A, Bani-Yaghoub M. A novel human induced pluripotent stem cell blood-brain barrier model: Applicability to study antibody-triggered receptor-mediated transcytosis. Sci Rep 2018; 8:1873. [PMID: 29382846 PMCID: PMC5789839 DOI: 10.1038/s41598-018-19522-8] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 12/27/2017] [Indexed: 12/21/2022] Open
Abstract
We have developed a renewable, scalable and transgene free human blood-brain barrier model, composed of brain endothelial cells (BECs), generated from human amniotic fluid derived induced pluripotent stem cells (AF-iPSC), which can also give rise to syngeneic neural cells of the neurovascular unit. These AF-iPSC-derived BECs (i-BEC) exhibited high transendothelial electrical resistance (up to 1500 Ω cm2) inducible by astrocyte-derived molecular cues and retinoic acid treatment, polarized expression of functional efflux transporters and receptor mediated transcytosis triggered by antibodies against specific receptors. In vitro human BBB models enable pre-clinical screening of central nervous system (CNS)-targeting drugs and are of particular importance for assessing species-specific/selective transport mechanisms. This i-BEC human BBB model discriminates species-selective antibody- mediated transcytosis mechanisms, is predictive of in vivo CNS exposure of rodent cross-reactive antibodies and can be implemented into pre-clinical CNS drug discovery and development processes.
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Affiliation(s)
- Maria Ribecco-Lutkiewicz
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Caroline Sodja
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Julie Haukenfrers
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Arsalan S Haqqani
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Dao Ly
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Peter Zachar
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Ewa Baumann
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Marguerite Ball
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Jez Huang
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Marina Rukhlova
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Marzia Martina
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Qing Liu
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Danica Stanimirovic
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
| | - Anna Jezierski
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada.
| | - Mahmud Bani-Yaghoub
- Human Health Therapeutics Portfolio, National Research Council of Canada, Ottawa, ON, K1A 0R6, Canada
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13
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Topalovic V, Krstic A, Schwirtlich M, Dolfini D, Mantovani R, Stevanovic M, Mojsin M. Epigenetic regulation of human SOX3 gene expression during early phases of neural differentiation of NT2/D1 cells. PLoS One 2017; 12:e0184099. [PMID: 28886103 PMCID: PMC5590877 DOI: 10.1371/journal.pone.0184099] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 08/17/2017] [Indexed: 01/09/2023] Open
Abstract
Sox3/SOX3 is one of the earliest neural markers in vertebrates. Together with the Sox1/SOX1 and Sox2/SOX2 genes it is implicated in the regulation of stem cell identity. In the present study, we performed the first analysis of epigenetic mechanisms (DNA methylation and histone marks) involved in the regulation of the human SOX3 gene expression during RA-induced neural differentiation of NT2/D1 cells. We show that the promoter of the human SOX3 gene is extremely hypomethylated both in undifferentiated NT2/D1 cells and during the early phases of RA-induced neural differentiation. By employing chromatin immunoprecipitation, we analyze several histone modifications across different regions of the SOX3 gene and their dynamics following initiation of differentiation. In the same timeframe we investigate profiles of selected histone marks on the promoters of human SOX1 and SOX2 genes. We demonstrate differences in histone signatures of SOX1, SOX2 and SOX3 genes. Considering the importance of SOXB1 genes in the process of neural differentiation, the present study contributes to a better understanding of epigenetic mechanisms implicated in the regulation of pluripotency maintenance and commitment towards the neural lineage.
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Affiliation(s)
- Vladanka Topalovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Diletta Dolfini
- Department of Biosciences, University of Milan, Milan, Italy
| | | | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Marija Mojsin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- * E-mail:
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14
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Mandalos NP, Remboutsika E. Sox2: To crest or not to crest? Semin Cell Dev Biol 2016; 63:43-49. [PMID: 27592260 DOI: 10.1016/j.semcdb.2016.08.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 08/29/2016] [Accepted: 08/30/2016] [Indexed: 12/12/2022]
Abstract
Precise control of neural progenitor transformation into neural crest stem cells ensures proper craniofacial and head development. In the neural progenitor pool, SoxB factors play an essential role as cell fate determinants of neural development, whereas during neural crest stem cell formation, Sox2 plays a predominant role as a guardian of the developmental clock that ensures precision of cell flow in the developing head.
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Affiliation(s)
- Nikolaos Panagiotis Mandalos
- National University of Athens Medical School, Department of Pediatrics, 75 Mikras Asias Str., 115 27, Athens, Greece; Stem Cell Biology Laboratory, Biomedical Sciences Research Centre "Alexander Fleming", 34 Fleming Str., 16672 Vari-Attica, Greece; Adjunct Faculty, The Lieber Institute for Brain Development, Basic Sciences Division, Johns Hopkins Medical Campus, 855 North Wolfe Str., Suite 300, 3rd Floor, Baltimore, MD 21205, USA
| | - Eumorphia Remboutsika
- National University of Athens Medical School, Department of Pediatrics, 75 Mikras Asias Str., 115 27, Athens, Greece; Stem Cell Biology Laboratory, Biomedical Sciences Research Centre "Alexander Fleming", 34 Fleming Str., 16672 Vari-Attica, Greece; Adjunct Faculty, The Lieber Institute for Brain Development, Basic Sciences Division, Johns Hopkins Medical Campus, 855 North Wolfe Str., Suite 300, 3rd Floor, Baltimore, MD 21205, USA.
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15
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Mao DD, Gujar AD, Mahlokozera T, Chen I, Pan Y, Luo J, Brost T, Thompson EA, Turski A, Leuthardt EC, Dunn GP, Chicoine MR, Rich KM, Dowling JL, Zipfel GJ, Dacey RG, Achilefu S, Tran DD, Yano H, Kim AH. A CDC20-APC/SOX2 Signaling Axis Regulates Human Glioblastoma Stem-like Cells. Cell Rep 2015; 11:1809-21. [PMID: 26074073 DOI: 10.1016/j.celrep.2015.05.027] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 02/28/2015] [Accepted: 05/12/2015] [Indexed: 11/29/2022] Open
Abstract
Glioblastoma harbors a dynamic subpopulation of glioblastoma stem-like cells (GSCs) that can propagate tumors in vivo and is resistant to standard chemoradiation. Identification of the cell-intrinsic mechanisms governing this clinically important cell state may lead to the discovery of therapeutic strategies for this challenging malignancy. Here, we demonstrate that the mitotic E3 ubiquitin ligase CDC20-anaphase-promoting complex (CDC20-APC) drives invasiveness and self-renewal in patient tumor-derived GSCs. Moreover, CDC20 knockdown inhibited and CDC20 overexpression increased the ability of human GSCs to generate brain tumors in an orthotopic xenograft model in vivo. CDC20-APC control of GSC invasion and self-renewal operates through pluripotency-related transcription factor SOX2. Our results identify a CDC20-APC/SOX2 signaling axis that controls key biological properties of GSCs, with implications for CDC20-APC-targeted strategies in the treatment of glioblastoma.
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Affiliation(s)
- Diane D Mao
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Amit D Gujar
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Tatenda Mahlokozera
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Program in Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ishita Chen
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yanchun Pan
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jingqin Luo
- Division of Biostatistics, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Taylor Brost
- Program in Molecular Cell Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elizabeth A Thompson
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alice Turski
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eric C Leuthardt
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael R Chicoine
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Keith M Rich
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Joshua L Dowling
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gregory J Zipfel
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ralph G Dacey
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Samuel Achilefu
- Molecular Imaging Center, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David D Tran
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Hiroko Yano
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Albert H Kim
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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16
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Montalbán-Loro R, Domingo-Muelas A, Bizy A, Ferrón SR. Epigenetic regulation of stemness maintenance in the neurogenic niches. World J Stem Cells 2015; 7:700-710. [PMID: 26029342 PMCID: PMC4444611 DOI: 10.4252/wjsc.v7.i4.700] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/12/2014] [Accepted: 03/20/2015] [Indexed: 02/06/2023] Open
Abstract
In the adult mouse brain, the subventricular zone lining the lateral ventricles and the subgranular zone in the dentate gyrus of the hippocampus are two zones that contain neural stem cells (NSCs) with the capacity to give rise to neurons and glia during the entire life of the animal. Spatial and temporal regulation of gene expression in the NSCs population is established and maintained by the coordinated interaction between transcription factors and epigenetic regulators which control stem cell fate. Epigenetic mechanisms are heritable alterations in genome function that do not involve changes in DNA sequence itself but that modulate gene expression, acting as mediators between the environment and the genome. At the molecular level, those epigenetic mechanisms comprise chemical modifications of DNA such as methylation, hydroxymethylation and histone modifications needed for the maintenance of NSC identity. Genomic imprinting is another normal epigenetic process leading to parental-specific expression of a gene, known to be implicated in the control of gene dosage in the neurogenic niches. The generation of induced pluripotent stem cells from NSCs by expression of defined transcription factors, provide key insights into fundamental principles of stem cell biology. Epigenetic modifications can also occur during reprogramming of NSCs to pluripotency and a better understanding of this process will help to elucidate the mechanisms required for stem cell maintenance. This review takes advantage of recent studies from the epigenetic field to report knowledge regarding the mechanisms of stemness maintenance of neural stem cells in the neurogenic niches.
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17
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Sarlak G, Vincent B. The Roles of the Stem Cell-Controlling Sox2 Transcription Factor: from Neuroectoderm Development to Alzheimer's Disease? Mol Neurobiol 2015; 53:1679-1698. [PMID: 25691455 DOI: 10.1007/s12035-015-9123-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 02/04/2015] [Indexed: 12/23/2022]
Abstract
Sox2 is a component of the core transcriptional regulatory network which maintains the totipotency of the cells during embryonic preimplantation period, the pluripotency of embryonic stem cells, and the multipotency of neural stem cells. This maintenance is controlled by internal loops between Sox2 and other transcription factors of the core such as Oct4, Nanog, Dax1, and Klf4, downstream proteins of extracellular ligands, epigenetic modifiers, and miRNAs. As Sox2 plays an important role in the balance between stem cells maintenance and commitment to differentiated lineages throughout the lifetime, it is supposed that Sox2 could regulate stem cells aging processes. In this review, we provide an update concerning the involvement of Sox2 in neurogenesis during normal aging and discuss its possible role in Alzheimer's disease.
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Affiliation(s)
- Golmaryam Sarlak
- Research Center for Neuroscience, Mahidol University, Nakhon Pathom, 73170, Thailand.,Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand
| | - Bruno Vincent
- Research Center for Neuroscience, Mahidol University, Nakhon Pathom, 73170, Thailand. .,Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, 73170, Thailand. .,Centre National de la Recherche Scientifique, 2 rue Michel Ange, 75016, Paris, France.
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18
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Stolzenburg S, Beltran AS, Swift-Scanlan T, Rivenbark AG, Rashwan R, Blancafort P. Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer. Oncogene 2015; 34:5427-35. [PMID: 25684141 PMCID: PMC4633433 DOI: 10.1038/onc.2014.470] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 11/15/2014] [Accepted: 12/09/2014] [Indexed: 12/16/2022]
Abstract
With the recent comprehensive mapping of cancer genomes, there is now a need for functional approaches to edit the aberrant epigenetic state of key cancer drivers to reprogram the epi-pathology of the disease. In this study we utilized a programmable DNA-binding methyltransferase to induce targeted incorporation of DNA methylation (DNAme) in the SOX2 oncogene in breast cancer through a six zinc finger (ZF) protein linked to DNA methyltransferase 3A (ZF-DNMT3A). We demonstrated long-lasting oncogenic repression, which was maintained even after suppression of ZF-DNMT3A expression in tumor cells. The de novo DNAme was faithfully propagated and maintained through cell generations even after the suppression of the expression of the chimeric methyltransferase in the tumor cells. Xenograft studies in NUDE mice demonstrated stable SOX2 repression and long-term breast tumor growth inhibition, which lasted for >100 days post implantation of the tumor cells in mice. This was accompanied with a faithful maintenance of DNAme in the breast cancer implants. In contrast, downregulation of SOX2 by ZF domains engineered with the Krueppel-associated box repressor domain resulted in a transient and reversible suppression of oncogenic gene expression. Our results indicated that targeted de novo DNAme of the SOX2 oncogenic promoter was sufficient to induce long-lasting epigenetic silencing, which was not only maintained during cell division but also significantly delayed the tumorigenic phenotype of cancer cells in vivo, even in the absence of treatment. Here, we outline a genome-based targeting approach to long-lasting tumor growth inhibition with potential applicability to many other oncogenic drivers that are currently refractory to drug design.
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Affiliation(s)
- S Stolzenburg
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Western Australia & School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Nedlands, Western Australia, Australia.,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - A S Beltran
- Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - T Swift-Scanlan
- Lineberger Comprehensive Cancer Center/School of Nursing, University of North Carolina, Chapel Hill, NC, USA
| | - A G Rivenbark
- Department of Pathology and Laboratory Medicine, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - R Rashwan
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Western Australia & School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Nedlands, Western Australia, Australia
| | - P Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Western Australia & School of Anatomy, Physiology and Human Biology, M309, The University of Western Australia, Nedlands, Western Australia, Australia.,Department of Pharmacology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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19
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Yamamizu K, Schlessinger D, Ko MSH. SOX9 accelerates ESC differentiation to three germ layer lineages by repressing SOX2 expression through P21 (WAF1/CIP1). Development 2015; 141:4254-66. [PMID: 25371362 DOI: 10.1242/dev.115436] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Upon removal of culture conditions that maintain an undifferentiated state, mouse embryonic stem cells (ESCs) differentiate into various cell types. Differentiation can be facilitated by forced expression of certain transcription factors (TFs), each of which can generally specify a particular developmental lineage. We previously established 137 mouse ESC lines, each of which carried a doxycycline-controllable TF. Among them, Sox9 has unique capacity: its forced expression accelerates differentiation of mouse ESCs into cells of all three germ layers. With the additional use of specific culture conditions, overexpression of Sox9 facilitated the generation of endothelial cells, hepatocytes and neurons from ESCs. Furthermore, Sox9 action increases formation of p21 (WAF1/CIP1), which then binds to the SRR2 enhancer of pluripotency marker Sox2 and inhibits its expression. Knockdown of p21 abolishes inhibition of Sox2 and Sox9-accelerated differentiation, and reduction of Sox2 2 days after the beginning of ESC differentiation can comparably accelerate mouse ESC formation of cells of three germ layers. These data implicate the involvement of the p21-Sox2 pathway in the mechanism of accelerated ESC differentiation by Sox9 overexpression. The molecular cascade could be among the first steps to program ESC differentiation.
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Affiliation(s)
- Kohei Yamamizu
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - David Schlessinger
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Minoru S H Ko
- Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA Department of Systems Medicine, Sakaguchi Laboratory, Keio University School of Medicine, Tokyo 160-8582, Japan
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20
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Chen YH, Yu J. Epigenetic disruptions of histone signatures for the trophectoderm and inner cell mass in mouse parthenogenetic embryos. Stem Cells Dev 2014; 24:550-64. [PMID: 25315067 DOI: 10.1089/scd.2014.0310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Epigenetic asymmetry has been shown to be associated with the first lineage allocation event in preimplantation development, that is, the formation of the trophectoderm (TE) and inner cell mass (ICM) lineages in the blastocyst. Since parthenogenesis causes aberrant segregation between the TE and ICM lineages, we examined several development-associated histone modifications in parthenotes, including those involved in (i) transcriptional activation [acetylated histone H3 lysine 9 (H3K9Ac) and lysine 14 (H3K14Ac), trimethylated histone H3 lysine 4 (H3K4Me3), and dimethylated histone H3 arginine 26 (H3R26Me2)] and (ii) transcriptional repression [trimethylated histone H3 lysine 9 (H3K9Me3) and lysine 27 (H3K27Me3), and mono-ubiquitinated histone H2A lysine 119 (H2AK119u1)]. Here, we report that in parthenotes, H3R26Me2 expression decreased from the morula stage, while expression patterns and levels of H3K9Ac, H3K27Me3, and H2AK119u1 were unchanged until the blastocyst stage; whereas H3K14Ac, H3K4Me3, and H3K9Me3 showed normal patterns and levels of expressions. Relative to the decrease of H3K9Ac in the ICM and increase in the TE of parthenotes, we detected reduced expression of TAT-interactive protein 60 acetyltransferase and histone deacetylase 1 deacetylase in the ICM and TE of parthenotes, respectively. Relative to the decrease of H3R26Me2, we also observed decreased expression of coactivator-associated arginine methyltransferase 1 methyltransferase and increased expression of the Wnt effector transcription factor 7L2 and miR-181c microRNA in parthenotes. Furthermore, relative to the decrease in H3K27Me3 and H2AK119u1, we found increased phosphorylation of Akt1 and enhancer of zeste homolog 2 in parthenogenetic TE. Therefore, our findings that histone signatures are impaired in parthenotes provide a mechanistic explanation for aberrant lineage segregation and TE defects.
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Affiliation(s)
- Yi-Hui Chen
- 1 Graduate Institute of Aerospace and Undersea Medicine, National Defense Medical Center , Taipei, Taiwan
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21
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Yang J, Tang Y, Liu H, Guo F, Ni J, Le W. Suppression of histone deacetylation promotes the differentiation of human pluripotent stem cells towards neural progenitor cells. BMC Biol 2014; 12:95. [PMID: 25406762 PMCID: PMC4254204 DOI: 10.1186/s12915-014-0095-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 10/29/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Emerging studies of human pluripotent stem cells (hPSCs) raise new prospects for neurodegenerative disease modeling and cell replacement therapies. Therefore, understanding the mechanisms underlying the commitment of neural progenitor cells (NPCs) is important for the application of hPSCs in neurodegenerative disease therapies. It has been reported that epigenetic modifications of histones play important roles in neural differentiation, but the exact mechanisms in regulating hPSC differentiation towards NPCs are not fully elucidated. RESULTS We demonstrated that suppression of histone deacetylases (HDACs) promoted the differentiation of hPSCs towards NPCs. Application of HDAC inhibitors (HDACi) increased the expression of neuroectodermal markers and enhanced the neuroectodermal specification once neural differentiation was initiated, thereby leading to more NPC generation. Similarly, the transcriptome analysis showed that HDACi increased the expression levels of ectodermal markers and triggered the NPC differentiation related pathways, while decreasing the expression levels of endodermal and mesodermal markers. Furthermore, we documented that HDAC3 but not HDAC1 or HDAC2 was the critical regulator participating in NPC differentiation, and knockdown of HDAC3's cofactor SMRT exhibited a similar effect as HDAC3 on NPC generation. CONCLUSIONS Our study reveals that HDACs, especially HDAC3, negatively regulate the differentiation of hPSCs towards NPCs at an earlier stage of neural differentiation. Moreover, HDAC3 might function by forming a repressor complex with its cofactor SMRT during this process. Thus, our findings uncover an important epigenetic mechanism of HDAC3 in the differentiation of hPSCs towards NPCs.
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Affiliation(s)
- Juan Yang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yu Tang
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hui Liu
- Center for Translational Research of Neurology Disease, The 1st Affiliated Hospital, Dalian Medical University, Dalian, China.
| | - Fang Guo
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jun Ni
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Weidong Le
- Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences/Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Center for Translational Research of Neurology Disease, The 1st Affiliated Hospital, Dalian Medical University, Dalian, China.
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22
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Vencken SF, Sethupathy P, Blackshields G, Spillane C, Elbaruni S, Sheils O, Gallagher MF, O'Leary JJ. An integrated analysis of the SOX2 microRNA response program in human pluripotent and nullipotent stem cell lines. BMC Genomics 2014; 15:711. [PMID: 25156079 PMCID: PMC4162954 DOI: 10.1186/1471-2164-15-711] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 07/15/2014] [Indexed: 12/13/2022] Open
Abstract
Background SOX2 is a core component of the transcriptional network responsible for maintaining embryonal carcinoma cells (ECCs) in a pluripotent, undifferentiated state of self-renewal. As such, SOX2 is an oncogenic transcription factor and crucial cancer stem cell (CSC) biomarker in embryonal carcinoma and, as more recently found, in the stem-like cancer cell component of many other malignancies. SOX2 is furthermore a crucial factor in the maintenance of adult stem cell phenotypes and has additional roles in cell fate determination. The SOX2-linked microRNA (miRNA) transcriptome and regulome has not yet been fully defined in human pluripotent cells or CSCs. To improve our understanding of the SOX2-linked miRNA regulatory network as a contribution to the phenotype of these cell types, we used high-throughput differential miRNA and gene expression analysis combined with existing genome-wide SOX2 chromatin immunoprecipitation (ChIP) data to map the SOX2 miRNA transcriptome in two human embryonal carcinoma cell (hECC) lines. Results Whole-microRNAome and genome analysis of SOX2-silenced hECCs revealed many miRNAs regulated by SOX2, including several with highly characterised functions in both cancer and embryonic stem cell (ESC) biology. We subsequently performed genome-wide differential expression analysis and applied a Monte Carlo simulation algorithm and target prediction to identify a SOX2-linked miRNA regulome, which was strongly enriched with epithelial-to-mesenchymal transition (EMT) markers. Additionally, several deregulated miRNAs important to EMT processes had SOX2 binding sites in their promoter regions. Conclusion In ESC-like CSCs, SOX2 regulates a large miRNA network that regulates and interlinks the expression of crucial genes involved in EMT. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-711) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sebastian F Vencken
- Department of Histopathology, Trinity College Dublin, Sir Patrick Dun Research Laboratory, St, James's Hospital, Dublin, Ireland.
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23
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Ma Q, Deng P, Zhu G, Liu C, Zhang L, Zhou Z, Luo X, Li M, Zhong M, Yu Z, Chen C, Zhang Y. Extremely low-frequency electromagnetic fields affect transcript levels of neuronal differentiation-related genes in embryonic neural stem cells. PLoS One 2014; 9:e90041. [PMID: 24595264 PMCID: PMC3940726 DOI: 10.1371/journal.pone.0090041] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 01/27/2014] [Indexed: 12/18/2022] Open
Abstract
Previous studies have reported that extremely low-frequency electromagnetic fields (ELF-EMF) can affect the processes of brain development, but the underlying mechanism is largely unknown. The proliferation and differentiation of embryonic neural stem cells (eNSCs) is essential for brain development during the gestation period. To date, there is no report about the effects of ELF-EMF on eNSCs. In this paper, we studied the effects of ELF-EMF on the proliferation and differentiation of eNSCs. Primary cultured eNSCs were treated with 50 Hz ELF-EMF; various magnetic intensities and exposure times were applied. Our data showed that there was no significant change in cell proliferation, which was evaluated by cell viability (CCK-8 assay), DNA synthesis (Edu incorporation), average diameter of neurospheres, cell cycle distribution (flow cytometry) and transcript levels of cell cycle related genes (P53, P21 and GADD45 detected by real-time PCR). When eNSCs were induced to differentiation, real-time PCR results showed a down-regulation of Sox2 and up-regulation of Math1, Math3, Ngn1 and Tuj1 mRNA levels after 50 Hz ELF-EMF exposure (2 mT for 3 days), but the percentages of neurons (Tuj1 positive cells) and astrocytes (GFAP positive cells) were not altered when detected by immunofluorescence assay. Although cell proliferation and the percentages of neurons and astrocytes differentiated from eNSCs were not affected by 50 Hz ELF-EMF, the expression of genes regulating neuronal differentiation was altered. In conclusion, our results support that 50 Hz ELF-EMF induce molecular changes during eNSCs differentiation, which might be compensated by post-transcriptional mechanisms to support cellular homeostasis.
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Affiliation(s)
- Qinlong Ma
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Ping Deng
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Gang Zhu
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Chuan Liu
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Lei Zhang
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Zhou Zhou
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Xue Luo
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Min Li
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Min Zhong
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Zhengping Yu
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
| | - Chunhai Chen
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
- * E-mail: (CC); (YZ)
| | - Yanwen Zhang
- Department of Occupational Health, Faculty of Preventive Medicine, Third Military Medical University, Chongqing, People's Republic of China
- * E-mail: (CC); (YZ)
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24
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Darby MM, Sabunciyan S. Repetitive Elements and Epigenetic Marks in Behavior and Psychiatric Disease. ADVANCES IN GENETICS 2014; 86:185-252. [DOI: 10.1016/b978-0-12-800222-3.00009-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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25
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Chou YT, Lee CC, Hsiao SH, Lin SE, Lin SC, Chung CH, Chung CH, Kao YR, Wang YH, Chen CT, Wei YH, Wu CW. The emerging role of SOX2 in cell proliferation and survival and its crosstalk with oncogenic signaling in lung cancer. Stem Cells 2013; 31:2607-2619. [PMID: 23940081 DOI: 10.1002/stem.1518] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 07/15/2013] [Indexed: 01/24/2023]
Abstract
Tumor cells have long been observed to share several biological characteristics with normal stem/progenitor cells; however, the oncogenic mechanisms underlying the lung stem/progenitor cell signaling remain elusive. Here, we report that SOX2, a self-renewal factor in lung stem/progenitor cells, is highly expressed in a subclass of lung cancer cells, the proliferation, survival, and chemoresistance of which are dependent on SOX2 signaling. Overexpression of SOX2 promotes oncogenic phenotypes in lung cancer cells; knockdown of SOX2 attenuated cell proliferation. We observed that SOX2 increased the expression of epidermal growth factor receptor (EGFR), and EGFR activation further upregulated SOX2 levels, forming a positive feedback loop. SOX2 expression promoted chemoresistance, and silencing of SOX2 perturbed mitochondrial function, causing marked apoptosis and autophagy. SOX2 induced BCL2L1, the ectopic expression of which rescued the effects of SOX2 silencing on apoptosis, autophagy, and mitochondrial function. SOX2 promoted tumor formation, along with increased cell proliferation in a xenograft mouse model. SOX2 expression is associated with poor prognosis in lung cancer patients; moreover, SOX2, EGFR, and BCL2L1 expression levels were significantly correlated in lung tumors. Our findings support the emerging role of SOX2 in cell proliferation and survival by eliciting oncogenic EGFR and BCL2L1 signaling with potential applications as a prognosis marker and a therapeutic target in lung cancer.
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Affiliation(s)
- Yu-Ting Chou
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan
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26
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Li H, Collado M, Villasante A, Matheu A, Lynch CJ, Cañamero M, Rizzoti K, Carneiro C, Martínez G, Vidal A, Lovell-Badge R, Serrano M. p27(Kip1) directly represses Sox2 during embryonic stem cell differentiation. Cell Stem Cell 2013; 11:845-52. [PMID: 23217425 PMCID: PMC3549496 DOI: 10.1016/j.stem.2012.09.014] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 08/08/2012] [Accepted: 09/17/2012] [Indexed: 11/06/2022]
Abstract
The mechanisms responsible for the transcriptional silencing of pluripotency genes in differentiated cells are poorly understood. We have observed that cells lacking the tumor suppressor p27 can be reprogrammed into induced pluripotent stem cells (iPSCs) in the absence of ectopic Sox2. Interestingly, cells and tissues from p27 null mice, including brain, lung, and retina, present an elevated basal expression of Sox2, suggesting that p27 contributes to the repression of Sox2. Furthermore, p27 null iPSCs fail to fully repress Sox2 upon differentiation. Mechanistically, we have found that upon differentiation p27 associates to the SRR2 enhancer of the Sox2 gene together with a p130-E2F4-SIN3A repressive complex. Finally, Sox2 haploinsufficiency genetically rescues some of the phenotypes characteristic of p27 null mice, including gigantism, pituitary hyperplasia, pituitary tumors, and retinal defects. Collectively, these results demonstrate an unprecedented connection between p27 and Sox2 relevant for reprogramming and cancer and for understanding human pathologies associated with p27 germline mutations.
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Affiliation(s)
- Han Li
- Tumor Suppression Group, Spanish National Cancer Research Centre, Madrid, E28029, Spain
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27
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Liang S, Furuhashi M, Nakane R, Nakazawa S, Goudarzi H, Hamada JI, Iizasa H. Isolation and characterization of human breast cancer cells with SOX2 promoter activity. Biochem Biophys Res Commun 2013; 437:205-11. [PMID: 23796710 DOI: 10.1016/j.bbrc.2013.06.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Accepted: 06/12/2013] [Indexed: 01/23/2023]
Abstract
Sex determining region Y-box 2 (SOX2) is well known as one of the "stemness" factors and is often expressed in cancers including breast cancer. In this study, we developed a reporter system using fluorescent protein driven by the promoter for SOX2 gene to detect and isolate living SOX2-positive cells. Using this system, we determined that SOX2 promoter activities were well correlated with SOX2 mRNA expression levels in 5 breast cancer cell lines, and that the cell population with positive SOX2 promoter activity (pSp-T(+)) isolated from one of the 5 cell lines, MCF-7 cells, showed a high SOX2 protein expression and high sphere-forming activity compared with very low promoter activity (pSp-T(low/-)). The pSp-T(+) population expressed higher mRNA levels of several stemness-related genes such as CD44, ABCB1, NANOG and TWIST1 than the pSp-T(low/-) population whereas the two populations expressed CD24 at similar levels. These results suggest that the cell population with SOX2 promoter activity contains cancer stem cell (CSC)-like cells which show different expression profiles from those of CSC-marker genes previously recognized in human breast cancers.
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Affiliation(s)
- Shanshan Liang
- Division of Stem Cell Biology, Institute for Genetic Medicine, Hokkaido University, Kita 15, Nishi 7, Sapporo 060-0815, Japan
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28
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Sarkar A, Hochedlinger K. The sox family of transcription factors: versatile regulators of stem and progenitor cell fate. Cell Stem Cell 2013; 12:15-30. [PMID: 23290134 DOI: 10.1016/j.stem.2012.12.007] [Citation(s) in RCA: 713] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Sox family transcription factors are well-established regulators of cell fate decisions during development. Accumulating evidence documents that they play additional roles in adult tissue homeostasis and regeneration. Remarkably, forced expression of Sox factors, in combination with other synergistic factors, reprograms differentiated cells into somatic or pluripotent stem cells. Dysregulation of Sox factors has been further implicated in diseases including cancer. Here, we review molecular and functional evidence linking Sox proteins with stem cell biology, cellular reprogramming, and disease with an emphasis on Sox2.
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Affiliation(s)
- Abby Sarkar
- Howard Hughes Medical Institute at Massachusetts General Hospital Cancer Center and Center for Regenerative Medicine, Boston, MA 02114, USA
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29
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Gapp K, Woldemichael BT, Bohacek J, Mansuy IM. Epigenetic regulation in neurodevelopment and neurodegenerative diseases. Neuroscience 2012; 264:99-111. [PMID: 23256926 DOI: 10.1016/j.neuroscience.2012.11.040] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 11/08/2012] [Accepted: 11/21/2012] [Indexed: 01/25/2023]
Abstract
From fertilization throughout development and until death, cellular programs in individual cells are dynamically regulated to fulfill multiple functions ranging from cell lineage specification to adaptation to internal and external stimuli. Such regulation is of major importance in brain cells, because the brain continues to develop long after birth and incorporates information from the environment across life. When compromised, these regulatory mechanisms can have detrimental consequences on neurodevelopment and lead to severe brain pathologies and neurodegenerative diseases in the adult individual. Elucidating these processes is essential to better understand their implication in disease etiology. Because they are strongly influenced by environmental factors, they have been postulated to depend on epigenetic mechanisms. This review describes recent studies that have identified epigenetic dysfunctions in the pathophysiology of several neurodevelopmental and neurodegenerative diseases. It discusses currently known pathways and molecular targets implicated in pathologies including imprinting disorders, Rett syndrome, and Alzheimer's, Parkinson's and Hungtinton's disease, and their relevance to these diseases.
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Affiliation(s)
- K Gapp
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - B T Woldemichael
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - J Bohacek
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland
| | - I M Mansuy
- Brain Research Institute, Medical Faculty of the University of Zürich and Swiss Federal Institute of Technology, Neuroscience Center Zürich, Zürich, Switzerland.
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30
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Mandalos N, Saridaki M, Harper JL, Kotsoni A, Yang P, Economides AN, Remboutsika E. Application of a novel strategy of engineering conditional alleles to a single exon gene, Sox2. PLoS One 2012; 7:e45768. [PMID: 23029233 PMCID: PMC3459942 DOI: 10.1371/journal.pone.0045768] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2012] [Accepted: 08/20/2012] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The Conditional by Inversion (COIN) method for engineering conditional alleles relies on an invertible optimized gene trap-like element, the COIN module, for imparting conditionality. The COIN module contains an optimized 3' splice site-polyadenylation signal pair, but is inserted antisense to the target gene and therefore does not alter transcription, until it is inverted by Cre recombinase. In order to make COIN applicable to all protein-coding genes, the COIN module has been engineered within an artificial intron, enabling insertion into an exon. METHODOLOGY/PRINCIPAL FINDINGS Therefore, theoretically, the COIN method should be applicable to single exon genes, and to test this idea we engineered a COIN allele of Sox2. This single exon gene presents additional design challenges, in that its proximal promoter and coding region are entirely contained within a CpG island, and are also spanned by an overlapping transcript, Sox2Ot, which contains mmu-miR1897. Here, we show that despite disruption of the CpG island by the COIN module intron, the COIN allele of Sox2 (Sox2(COIN)) is phenotypically wild type, and also does not interfere with expression of Sox2Ot and miR1897. Furthermore, the inverted COIN allele of Sox2, Sox2(INV) is functionally null, as homozygotes recapitulate the phenotype of Sox2(βgeo/βgeo) mice, a well-characterized Sox2 null. Lastly, the benefit of the eGFP marker embedded in the COIN allele is demonstrated as it mirrors the expression pattern of Sox2. CONCLUSIONS/SIGNIFICANCE Our results demonstrate the applicability of the COIN technology as a method of choice for targeting single exon genes.
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Affiliation(s)
- Nikolaos Mandalos
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
| | - Marannia Saridaki
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
| | - Jessica Lea Harper
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, United States of America
| | - Anastasia Kotsoni
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
| | - Peter Yang
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, United States of America
| | - Aris N. Economides
- Regeneron Pharmaceuticals Inc., Tarrytown, New York, United States of America
| | - Eumorphia Remboutsika
- Stem Cell Biology Laboratory, Institute of Molecular Biology and Genetics, Biomedical Sciences Research Centre “Alexander Fleming”, Vari, Greece
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López-Juárez A, Remaud S, Hassani Z, Jolivet P, Pierre Simons J, Sontag T, Yoshikawa K, Price J, Morvan-Dubois G, Demeneix BA. Thyroid hormone signaling acts as a neurogenic switch by repressing Sox2 in the adult neural stem cell niche. Cell Stem Cell 2012; 10:531-43. [PMID: 22560077 DOI: 10.1016/j.stem.2012.04.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 01/12/2012] [Accepted: 04/09/2012] [Indexed: 02/02/2023]
Abstract
The subventricular zone (SVZ) neural stem cell niche contains mixed populations of stem cells, transit-amplifying cells, and migrating neuroblasts. Deciphering how endogenous signals, such as hormones, affect the balance between these cell types is essential for understanding the physiology of niche plasticity and homeostasis. We show that Thyroid Hormone (T(3)) and its receptor, TRα1, are directly involved in maintaining this balance. TRα1 is expressed in amplifying and migrating cells. In vivo gain- and loss-of-function experiments demonstrate first, that T(3)/TRα1 directly repress Sox2 expression, and second, that TRα1 overexpression in the niche favors the appearance of DCX+ migrating neuroblasts. Lack of TRα increases numbers of SOX2+ cells in the SVZ. Hypothyroidism increases proportions of cells in interphase. Thus, in the adult SVZ, T(3)/TRα1 together favor neural stem cell commitment and progression toward a migrating neuroblast phenotype; this transition correlates with T(3)/TRα1-dependent transcriptional repression of Sox2.
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Affiliation(s)
- Alejandra López-Juárez
- UMR CNRS 7221, Evolution des Régulations Endocriniennes, Département Régulations, Développement et Diversité Moléculaire, Muséum National d'Histoire Naturelle, 75231 Paris, France
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32
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Stolzenburg S, Rots MG, Beltran AS, Rivenbark AG, Yuan X, Qian H, Strahl BD, Blancafort P. Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer. Nucleic Acids Res 2012; 40:6725-40. [PMID: 22561374 PMCID: PMC3413152 DOI: 10.1093/nar/gks360] [Citation(s) in RCA: 125] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The transcription factor (TF) SOX2 is essential for the maintenance of pluripotency and self-renewal in embryonic stem cells. In addition to its normal stem cell function, SOX2 over-expression is associated with cancer development. The ability to selectively target this and other oncogenic TFs in cells, however, remains a significant challenge due to the ‘undruggable’ characteristics of these molecules. Here, we employ a zinc finger (ZF)-based artificial TF (ATF) approach to selectively suppress SOX2 gene expression in cancer cells. We engineered four different proteins each composed of 6ZF arrays designed to bind 18 bp sites in the SOX2 promoter and enhancer region, which controls SOX2 methylation. The 6ZF domains were linked to the Kruppel Associated Box (SKD) repressor domain. Three engineered proteins were able to bind their endogenous target sites and effectively suppress SOX2 expression (up to 95% repression efficiencies) in breast cancer cells. Targeted down-regulation of SOX2 expression resulted in decreased tumor cell proliferation and colony formation in these cells. Furthermore, induced expression of an ATF in a mouse model inhibited breast cancer cell growth. Collectively, these findings demonstrate the effectiveness and therapeutic potential of engineered ATFs to mediate potent and long-lasting down-regulation of oncogenic TF expression in cancer cells.
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Affiliation(s)
- Sabine Stolzenburg
- Epigenetic Editing, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
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33
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Waldhaus J, Cimerman J, Gohlke H, Ehrich M, Müller M, Löwenheim H. Stemness of the organ of Corti relates to the epigenetic status of Sox2 enhancers. PLoS One 2012; 7:e36066. [PMID: 22570694 PMCID: PMC3343037 DOI: 10.1371/journal.pone.0036066] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 03/30/2012] [Indexed: 12/11/2022] Open
Abstract
In the adult mammalian auditory epithelium, the organ of Corti, loss of sensory hair cells results in permanent hearing loss. The underlying cause for the lack of regenerative response is the depletion of otic progenitors in the cell pool of the sensory epithelium. Here, we show that an increase in the sequence-specific methylation of the otic Sox2 enhancers NOP1 and NOP2 is correlated with a reduced self-renewal potential in vivo and in vitro; additionally, the degree of methylation of NOP1 and NOP2 is correlated with the dedifferentiation potential of postmitotic supporting cells into otic stem cells. Thus, the stemness the organ of Corti is related to the epigenetic status of the otic Sox2 enhancers. These observations validate the continued exploration of treatment strategies for dedifferentiating or reprogramming of differentiated supporting cells into progenitors to regenerate the damaged organ of Corti.
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Affiliation(s)
- Jörg Waldhaus
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
| | - Jelka Cimerman
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
| | | | - Mathias Ehrich
- SEQUENOM Inc., San Diego, California, United States of America
| | - Marcus Müller
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
| | - Hubert Löwenheim
- Department of Otorhinolaryngology, Head and Neck Surgery, Hearing Research Center Tübingen, University of Tübingen Medical Center, Tübingen, Germany
- * E-mail:
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34
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Chen CY, Morris Q, Mitchell JA. Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics 2012; 13:152. [PMID: 22537144 PMCID: PMC3406964 DOI: 10.1186/1471-2164-13-152] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 04/26/2012] [Indexed: 11/21/2022] Open
Abstract
Background Epigenetic modifications, transcription factor (TF) availability and differences in chromatin folding influence how the genome is interpreted by the transcriptional machinery responsible for gene expression. Enhancers buried in non-coding regions are found to be associated with significant differences in histone marks between different cell types. In contrast, gene promoters show more uniform modifications across cell types. Here we used histone modification and chromatin-associated protein ChIP-Seq data sets in mouse embryonic stem (ES) cells as well as genomic features to identify functional enhancer regions. Using co-bound sites of OCT4, SOX2 and NANOG (co-OSN, validated enhancers) and co-bound sites of MYC and MYCN (limited enhancer activity) as enhancer positive and negative training sets, we performed multinomial logistic regression with LASSO regularization to identify key features. Results Cross validations reveal that a combination of p300, H3K4me1, MED12 and NIPBL features to be top signatures of co-OSN regions. Using a model from 10 signatures, 83% of top 1277 putative 1 kb enhancer regions (probability greater than or equal to 0.8) overlapped with at least one TF peak from 7 mouse ES cell ChIP-Seq data sets. These putative enhancers are associated with increased gene expression of neighbouring genes and significantly enriched in multiple TF bound loci in agreement with combinatorial models of TF binding. Furthermore, we identified several motifs of known TFs significantly enriched in putative enhancer regions compared to random promoter regions and background. Comparison with an active H3K27ac mark in various cell types confirmed cell type-specificity of these enhancers. Conclusions The top enhancer signatures we identified (p300, H3K4me1, MED12 and NIPBL) will allow for the identification of cell type-specific enhancer regions in diverse cell types.
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Affiliation(s)
- Chih-yu Chen
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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Rivenbark AG, Stolzenburg S, Beltran AS, Yuan X, Rots MG, Strahl BD, Blancafort P. Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 2012; 7:350-60. [PMID: 22419067 DOI: 10.4161/epi.19507] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
An obstacle in the treatment of human diseases such as cancer is the inability to selectively and effectively target historically undruggable targets such as transcription factors. Here, we employ a novel technology using artificial transcription factors (ATFs) to epigenetically target gene expression in cancer cells. We show that site-specific DNA methylation and long-term stable repression of the tumor suppressor Maspin and the oncogene SOX2 can be achieved in breast cancer cells via zinc-finger ATFs targeting DNA methyltransferase 3a (DNMT3a) to the promoters of these genes. Using this approach, we show Maspin and SOX2 downregulation is more significant as compared with transient knockdown, which is also accompanied by stable phenotypic reprogramming of the cancer cell. These findings indicate that multimodular Zinc Finger Proteins linked to epigenetic editing domains can be used as novel cell resources to selectively and heritably alter gene expression patterns to stably reprogram cell fate.
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Affiliation(s)
- Ashley G Rivenbark
- Department of Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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36
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Kolovos P, Knoch TA, Grosveld FG, Cook PR, Papantonis A. Enhancers and silencers: an integrated and simple model for their function. Epigenetics Chromatin 2012; 5:1. [PMID: 22230046 PMCID: PMC3281776 DOI: 10.1186/1756-8935-5-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Accepted: 01/09/2012] [Indexed: 12/27/2022] Open
Abstract
Regulatory DNA elements such as enhancers, silencers and insulators are embedded in metazoan genomes, and they control gene expression during development. Although they fulfil different roles, they share specific properties. Herein we discuss some examples and a parsimonious model for their function is proposed. All are transcription units that tether their target promoters close to, or distant from, transcriptional hot spots (or 'factories').
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Affiliation(s)
- Petros Kolovos
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK.
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Alonso MM, Diez-Valle R, Manterola L, Rubio A, Liu D, Cortes-Santiago N, Urquiza L, Jauregi P, de Munain AL, Sampron N, Aramburu A, Tejada-Solís S, Vicente C, Odero MD, Bandrés E, García-Foncillas J, Idoate MA, Lang FF, Fueyo J, Gomez-Manzano C. Genetic and epigenetic modifications of Sox2 contribute to the invasive phenotype of malignant gliomas. PLoS One 2011; 6:e26740. [PMID: 22069467 PMCID: PMC3206066 DOI: 10.1371/journal.pone.0026740] [Citation(s) in RCA: 173] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 10/02/2011] [Indexed: 11/18/2022] Open
Abstract
We undertook this study to understand how the transcription factor Sox2 contributes to the malignant phenotype of glioblastoma multiforme (GBM), the most aggressive primary brain tumor. We initially looked for unbalanced genomic rearrangements in the Sox2 locus in 42 GBM samples and found that Sox2 was amplified in 11.5% and overexpressed in all the samples. These results prompted us to further investigate the mechanisms involved in Sox2 overexpression in GBM. We analyzed the methylation status of the Sox2 promoter because high CpG density promoters are associated with key developmental genes. The Sox2 promoter presented a CpG island that was hypomethylated in all the patient samples when compared to normal cell lines. Treatment of Sox2-negative glioma cell lines with 5-azacitidine resulted in the re-expression of Sox2 and in a change in the methylation status of the Sox2 promoter. We further confirmed these results by analyzing data from GBM cases generated by The Cancer Genome Atlas project. We observed Sox2 overexpression (86%; N = 414), Sox2 gene amplification (8.5%; N = 492), and Sox 2 promoter hypomethylation (100%; N = 258), suggesting the relevance of this factor in the malignant phenotype of GBMs. To further explore the role of Sox2, we performed in vitro analysis with brain tumor stem cells (BTSCs) and established glioma cell lines. Downmodulation of Sox2 in BTSCs resulted in the loss of their self-renewal properties. Surprisingly, ectopic expression of Sox2 in established glioma cells was not sufficient to support self-renewal, suggesting that additional factors are required. Furthermore, we observed that ectopic Sox2 expression was sufficient to induce invasion and migration of glioma cells, and knockdown experiments demonstrated that Sox2 was essential for maintaining these properties. Altogether, our data underscore the importance of a pleiotropic role of Sox2 and suggest that it could be used as a therapeutic target in GBM.
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Affiliation(s)
- Marta M. Alonso
- Department of Neuro-oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Oncology, University Hospital of Navarra, Pamplona, Spain
| | - Ricardo Diez-Valle
- Department of Neurosurgery, University Hospital of Navarra, Pamplona, Spain
| | - Lorea Manterola
- Division of Oncology, BioDonostia Institute, San Sebastian, Spain
| | - Angel Rubio
- Department of Biostatistics, Centro de Estudios e Investigaciones Técnicas de Guipuzcoa (CEIT), San Sebastian, Spain
| | - Dan Liu
- Department of Oncology, University Hospital of Navarra, Pamplona, Spain
| | - Nahir Cortes-Santiago
- Department of Neuro-oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Leire Urquiza
- Division of Oncology, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Patricia Jauregi
- Department of Oncology, University Hospital of Navarra, Pamplona, Spain
| | | | - Nicolás Sampron
- Division of Oncology, BioDonostia Institute, San Sebastian, Spain
| | - Ander Aramburu
- Department of Biostatistics, Centro de Estudios e Investigaciones Técnicas de Guipuzcoa (CEIT), San Sebastian, Spain
| | - Sonia Tejada-Solís
- Department of Neurosurgery, University Hospital of Navarra, Pamplona, Spain
| | - Carmen Vicente
- Division of Oncology, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - María D. Odero
- Division of Oncology, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
| | - Eva Bandrés
- Department of Oncology, University Hospital of Navarra, Pamplona, Spain
| | | | - Miguel A. Idoate
- Department of Pathology, University Hospital of Navarra, Pamplona, Spain
| | - Frederick F. Lang
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Juan Fueyo
- Department of Neuro-oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Candelaria Gomez-Manzano
- Department of Neuro-oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
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Du L, Yang Y, Xiao X, Wang C, Zhang X, Wang L, Zhang X, Li W, Zheng G, Wang S, Dong Z. Sox2 nuclear expression is closely associated with poor prognosis in patients with histologically node-negative oral tongue squamous cell carcinoma. Oral Oncol 2011; 47:709-13. [PMID: 21689966 DOI: 10.1016/j.oraloncology.2011.05.017] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 05/23/2011] [Accepted: 05/31/2011] [Indexed: 12/25/2022]
Abstract
Sox2 is a marker of embryonic stem cell pluripotency and plays an important role in tumor progression. However, Sox2 expression in oral tongue squamous cell carcinoma (OTSCC) and its correlation with patients' prognosis have not been investigated so far. In this study, we detected the expression of Sox2 in 82 patients with histologically node-negative (pN0) OTSCC by immunohistochemistry, and evaluated its correlation with clinicopatologic factors and disease prognosis. Sox2 positive expression was detected in 62.2% patients and showed a significant association with large tumor size. Survival analysis showed that patients with Sox2 positive expression had significantly poorer overall, cancer-specific and disease-free survivals than those with Sox2 negative expression at 5years after operation (P=0.004, 0.004 and 0.001, respectively). Multivariate analysis demonstrated that Sox2 positive expression was an independent prognosticator of unfavorable overall, cancer-specific and disease-free survivals (P=0.032, 0.035 and 0.011, respectively). According to our results, Sox2 positive expression was frequent in pN0 OTSCC and involved in tumor progression. The measurement of Sox2 expression may be helpful in predicting relapse and prognosis of patients with pN0 OTSCC.
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Affiliation(s)
- Lutao Du
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, PR China
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Struckmann S, Esch D, Schöler H, Fuellen G. Visualization and exploration of conserved regulatory modules using ReXSpecies 2. BMC Evol Biol 2011; 11:267. [PMID: 21942985 PMCID: PMC3203875 DOI: 10.1186/1471-2148-11-267] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 09/24/2011] [Indexed: 11/10/2022] Open
Abstract
Background The prediction of transcription factor binding sites is difficult for many reasons. Thus, filtering methods are needed to enrich for biologically relevant (true positive) matches in the large amount of computational predictions that are frequently generated from promoter sequences. Results ReXSpecies 2 filters predictions of transcription factor binding sites and generates a set of figures displaying them in evolutionary context. More specifically, it uses position specific scoring matrices to search for motifs that specify transcription factor binding sites. It removes redundant matches and filters the remaining matches by the phylogenetic group that the matrices belong to. It then identifies potential transcriptional modules, and generates figures that highlight such modules, taking evolution into consideration. Module formation, scoring by evolutionary criteria and visual clues reduce the amount of predictions to a manageable scale. Identification of transcription factor binding sites of particular functional importance is left to expert filtering. ReXSpecies 2 interacts with genome browsers to enable scientists to filter predictions together with other sequence-related data. Conclusions Based on ReXSpecies 2, we derive plausible hypotheses about the regulation of pluripotency. Our tool is designed to analyze transcription factor binding site predictions considering their common pattern of occurrence, highlighting their evolutionary history.
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Affiliation(s)
- Stephan Struckmann
- University of Rostock, Institute for Biostatistics and Informatics in Medicine and Ageing Research, Heydemannstrasse 8, 18057 Rostock, Germany.
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Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Cell 2011; 145:875-89. [PMID: 21663792 DOI: 10.1016/j.cell.2011.05.017] [Citation(s) in RCA: 416] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 03/03/2011] [Accepted: 05/16/2011] [Indexed: 02/06/2023]
Abstract
Cell fate decisions are fundamental for development, but we do not know how transcriptional networks reorganize during the transition from a pluripotent to a differentiated cell state. Here, we asked how mouse embryonic stem cells (ESCs) leave the pluripotent state and choose between germ layer fates. By analyzing the dynamics of the transcriptional circuit that maintains pluripotency, we found that Oct4 and Sox2, proteins that maintain ESC identity, also orchestrate germ layer fate selection. Oct4 suppresses neural ectodermal differentiation and promotes mesendodermal differentiation; Sox2 inhibits mesendodermal differentiation and promotes neural ectodermal differentiation. Differentiation signals continuously and asymmetrically modulate Oct4 and Sox2 protein levels, altering their binding pattern in the genome, and leading to cell fate choice. The same factors that maintain pluripotency thus also integrate external signals and control lineage selection. Our study provides a framework for understanding how complex transcription factor networks control cell fate decisions in progenitor cells.
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Lee ST, Chu K, Jung KH, Song YM, Jeon D, Kim SU, Kim M, Lee SK, Roh JK. Direct generation of neurosphere-like cells from human dermal fibroblasts. PLoS One 2011; 6:e21801. [PMID: 21765916 PMCID: PMC3135606 DOI: 10.1371/journal.pone.0021801] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2011] [Accepted: 06/07/2011] [Indexed: 01/19/2023] Open
Abstract
Neural stem cell (NSC) transplantation replaces damaged brain cells and provides disease-modifying effects in many neurological disorders. However, there has been no efficient way to obtain autologous NSCs in patients. Given that ectopic factors can reprogram somatic cells to be pluripotent, we attempted to generate human NSC-like cells by reprograming human fibroblasts. Fibroblasts were transfected with NSC line-derived cellular extracts and grown in neurosphere culture conditions. The cells were then analyzed for NSC characteristics, including neurosphere formation, gene expression patterns, and ability to differentiate. The obtained induced neurosphere-like cells (iNS), which formed daughter neurospheres after serial passaging, expressed neural stem cell markers, and had demethylated SOX2 regulatory regions, all characteristics of human NSCs. The iNS had gene expression patterns that were a combination of the patterns of NSCs and fibroblasts, but they could be differentiated to express neuroglial markers and neuronal sodium channels. These results show for the first time that iNS can be directly generated from human fibroblasts. Further studies on their application in neurological diseases are warranted.
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Affiliation(s)
- Soon-Tae Lee
- Department of Neurology, Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea
- Program in Neuroscience, Neuroscience Research Institute of SNUMRC, Seoul National University, Seoul, South Korea
| | - Kon Chu
- Department of Neurology, Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea
- Program in Neuroscience, Neuroscience Research Institute of SNUMRC, Seoul National University, Seoul, South Korea
| | - Keun-Hwa Jung
- Department of Neurology, Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea
- Program in Neuroscience, Neuroscience Research Institute of SNUMRC, Seoul National University, Seoul, South Korea
| | - Young-Mi Song
- Department of Neurology, Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Daejong Jeon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Seung U. Kim
- Division of Neurology, Department of Medicine, UBC Hospital, University of British Columbia, Vancouver, Canada
- Medical Research Institute, Chungang University School of Medicine, Seoul, South Korea
| | - Manho Kim
- Department of Neurology, Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea
- Program in Neuroscience, Neuroscience Research Institute of SNUMRC, Seoul National University, Seoul, South Korea
| | - Sang Kun Lee
- Department of Neurology, Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea
- Program in Neuroscience, Neuroscience Research Institute of SNUMRC, Seoul National University, Seoul, South Korea
| | - Jae-Kyu Roh
- Department of Neurology, Clinical Research Institute, Seoul National University Hospital, Seoul, South Korea
- Program in Neuroscience, Neuroscience Research Institute of SNUMRC, Seoul National University, Seoul, South Korea
- * E-mail:
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Gräff J, Kim D, Dobbin MM, Tsai LH. Epigenetic regulation of gene expression in physiological and pathological brain processes. Physiol Rev 2011; 91:603-49. [PMID: 21527733 DOI: 10.1152/physrev.00012.2010] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Over the past decade, it has become increasingly obvious that epigenetic mechanisms are an integral part of a multitude of brain functions that range from the development of the nervous system over basic neuronal functions to higher order cognitive processes. At the same time, a substantial body of evidence has surfaced indicating that several neurodevelopmental, neurodegenerative, and neuropsychiatric disorders are in part caused by aberrant epigenetic modifications. Because of their inherent plasticity, such pathological epigenetic modifications are readily amenable to pharmacological interventions and have thus raised justified hopes that the epigenetic machinery provides a powerful new platform for therapeutic approaches against these diseases. In this review, we give a detailed overview of the implication of epigenetic mechanisms in both physiological and pathological brain processes and summarize the state-of-the-art of "epigenetic medicine" where applicable. Despite, or because of, these new and exciting findings, it is becoming apparent that the epigenetic machinery in the brain is highly complex and intertwined, which underscores the need for more refined studies to disentangle brain-region and cell-type specific epigenetic codes in a given environmental condition. Clearly, the brain contains an epigenetic "hotspot" with a unique potential to not only better understand its most complex functions, but also to treat its most vicious diseases.
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Affiliation(s)
- Johannes Gräff
- Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
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Fuellen G, Struckmann S. Evolution of gene regulation of pluripotency--the case for wiki tracks at genome browsers. Biol Direct 2010; 5:67. [PMID: 21190561 PMCID: PMC3024949 DOI: 10.1186/1745-6150-5-67] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 12/29/2010] [Indexed: 12/23/2022] Open
Abstract
Background Experimentally validated data on gene regulation are hard to obtain. In particular, information about transcription factor binding sites in regulatory regions are scattered around in the literature. This impedes their systematic in-context analysis, e.g. the inference of their conservation in evolutionary history. Results We demonstrate the power of integrative bioinformatics by including curated transcription factor binding site information into the UCSC genome browser, using wiki and custom tracks, which enable easy publication of annotation data. Data integration allows to investigate the evolution of gene regulation of the pluripotency-associated genes Oct4, Sox2 and Nanog. For the first time, experimentally validated transcription factor binding sites in the regulatory regions of all three genes were assembled together based on manual curation of data from 39 publications. Using the UCSC genome browser, these data were then visualized in the context of multi-species conservation based on genomic alignment. We confirm previous hypotheses regarding the evolutionary age of specific regulatory patterns, establishing their "deep homology". We also confirm some other principles of Carroll's "Genetic theory of Morphological Evolution", such as "mosaic pleiotropy", exemplified by the dual role of Sox2 reflected in its regulatory region. Conclusions We were able to elucidate some aspects of the evolution of gene regulation for three genes associated with pluripotency. Based on the expected return on investment for the community, we encourage other scientists to contribute experimental data on gene regulation (original work as well as data collected for reviews) to the UCSC system, to enable studies of the evolution of gene regulation on a large scale, and to report their findings. Reviewers This article was reviewed by Dr. Gustavo Glusman and Dr. Juan Caballero, Institute for Systems Biology, Seattle, USA (nominated by Dr. Doron Lancet, Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel), Dr. Niels Grabe, TIGA Center (BIOQUANT) and Medical Systems Biology Group, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, Germany (nominated by Dr. Mikhail Gelfand, Department of Bioinformatics, Institute of Information Transfer Problems, Russian Academy of Science, Moscow, Russian Federation) and Dr. Franz-Josef Müller, Center for Regenerative Medicine, The Scripps Research Institute, La Jolla, CA, USA and University Hospital for Psychiatry and Psychotherapy (part of ZIP gGmbH), University of Kiel, Germany (nominated by Dr. Trey Ideker, University of California, San Diego, La Jolla CA, United States).
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Affiliation(s)
- Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research - IBIMA, University of Rostock, Medical Faculty, Ernst-Heydemann-Str. 8, 18057 Rostock, Germany.
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Jezierski A, Gruslin A, Tremblay R, Ly D, Smith C, Turksen K, Sikorska M, Bani-Yaghoub M. Probing stemness and neural commitment in human amniotic fluid cells. Stem Cell Rev Rep 2010; 6:199-214. [PMID: 20221716 DOI: 10.1007/s12015-010-9116-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recently, human amniotic fluid (AF) cells have attracted a great deal of attention as an alternative cell source for transplantation and tissue engineering. AF contains a variety of cell types derived from fetal tissues, of which a small percentage is believed to represent stem cell sub-population(s). In contrast to human embryonic stem (ES) cells, AF cells are not subject to extensive legal or ethical considerations; nor are they limited by lineage commitment characteristic of adult stem cells. However, to become therapeutically valuable, better protocols for the isolation of AF stem cell sub-populations need to be developed. This study was designed to examine the molecular components involved in self-renewal, neural commitment and differentiation of AF cells obtained at different gestational ages. Our results showed that, although morphologically heterogeneous, AF cells derived from early gestational periods ubiquitously expressed KERATIN 8 (K8), suggesting that the majority of these cells may have an epithelial origin. In addition, AF cells expressed various components of NOTCH signaling (ligands, receptors and target genes), a pathway involved in stem cell maintenance, determination and differentiation. A sub-population of K8 positive cells (<10%) co-expressed NESTIN, a marker detected in the neuroepithelium, neural stem cells and neural progenitors. Throughout the gestational periods, a much smaller AF cell sub-population (<1%) expressed pluripotency markers, OCT4a, NANOG and SOX2, from which SOX2 positive AF cells could be isolated through single cell cloning. The SOX2 expressing AF clones showed the capacity to give rise to a neuron-like phenotype in culture, expressing neuronal markers such as MAP2, NFL and NSE. Taken together, our findings demonstrated the presence of fetal cells with stem cell characteristics in the amniotic fluid, highlighting the need for further research on their biology and clinical applications.
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Affiliation(s)
- Anna Jezierski
- Neurogenesis and Brain Repair, Neurobiology Program, Institute for Biological Sciences, National Research Council Canada, 1200 Montreal Road, Ottawa, Canada
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Unrestricted somatic stem cells (USSC) from human umbilical cord blood display uncommitted epigenetic signatures of the major stem cell pluripotency genes. Stem Cell Res 2010; 6:60-9. [PMID: 20933485 DOI: 10.1016/j.scr.2010.08.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Revised: 08/19/2010] [Accepted: 08/20/2010] [Indexed: 12/12/2022] Open
Abstract
Unrestricted somatic stem cells (USSC) from human cord blood display a broad differentiation potential for ectodermal, mesodermal, and endodermal cell types. The molecular basis for these stem cell properties is unclear and unlike embryonic stem cells (ESC) none of the major stem cell factors OCT4, SOX2, and NANOG exhibits significant expression in USSC. Here, we report that these key stem cell genes hold an epigenetic state in between that of an ESC and a terminally differentiated cell type. DNA methylation analysis exhibits partial demethylation of the regulatory region of OCT4 and a demethylated state of the NANOG and SOX2 promoter/enhancer regions. Further genome-wide DNA methylation profiling identified a partially demethylated state of the telomerase gene hTERT. Moreover, none of the pluripotency factors exhibited a repressive histone signature. Notably, SOX2 exhibits a bivalent histone signature consisting of the opposing histone marks dimeH3K4 and trimeH3K27, which is typically found on genes that are "poised" for transcription. Consequently, ectopic expression of OCT4 in USSC led to rapid induction of expression of its known target gene SOX2. Our data suggest that incomplete epigenetic repression and a "poised" epigenetic status of pluripotency genes preserves the USSC potential to be able to react adequately to distinct differentiation and reprogramming cues.
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Sox2 protein expression is an independent poor prognostic indicator in stage I lung adenocarcinoma. Am J Surg Pathol 2010; 34:1193-8. [PMID: 20631605 DOI: 10.1097/pas.0b013e3181e5e024] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Many patients with stage I nonsmall cell lung carcinoma will develop recurrence after surgical excision. Sox2 is a marker of embryonic stem cell pluripotency that is associated with aggressive tumor behavior and is expressed in a subset of lung adenocarcinomas. We hypothesized that Sox2 expression may provide prognostic information in early stage lung adenocarcinomas. We evaluated formalin-fixed, paraffin-embedded tissue from 104 stage I lung adenocarcinomas resected between 1997 and 2000. Sox2 expression was analyzed by immunohistochemistry and compared with clinicopathologic features, time-to-progression, and overall survival (OS). Sox2 expression was detected in 50% of the cases and was more frequent in tumors from older and male patients but not significantly associated with smoking status, tumor stage, grade, or histologic subtype. Compared with Sox2-negative tumors, Sox2 expression predicted a shorter time-to-progression (49% vs. 82% at 5 y; P=0.0006) and shorter OS (54% vs. 79% at 5 y; P=0.004). By multivariate analysis, Sox2 expression predicted a greater risk of progression among men [hazard ratio (HR) 5.6; 95% confidence interval (CI) 2.3-13.8] and women (HR 2.1; 95% CI 0.8-5.7). Sox2 expression was associated with significantly shorter OS among men (HR 2.5; 95% CI 1.2-5.1), but not in women. Sox2 seems to be an independent predictor of poor outcome in stage I lung adenocarcinomas and may help stratify patients at increased risk for recurrence.
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Barrand S, Collas P. Chromatin states of core pluripotency-associated genes in pluripotent, multipotent and differentiated cells. Biochem Biophys Res Commun 2009; 391:762-7. [PMID: 19944068 DOI: 10.1016/j.bbrc.2009.11.134] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Accepted: 11/19/2009] [Indexed: 12/19/2022]
Abstract
Oct4, Nanog and Sox2 constitute a core of transcription factors controlling pluripotency. Differentiation and reprogramming studies have unraveled a few epigenetic modifications associated in relation to the expression state of OCT4, NANOG and SOX2. There is, however, no comprehensive map of chromatin states on these genes in human primary cells at different stages of differentiation. We report here a profile of DNA methylation and of 10 histone modifications on regulatory regions of OCT4, NANOG and SOX2 in embryonal carcinoma cells, mesenchymal stem cells and fibroblasts. Bisulfite sequencing reveals correlation between promoter CpG methylation and repression of OCT4, but not NANOG or SOX2, suggesting distinct repression mechanisms. Whereas none of these genes, even when inactive, harbor repressive trimethylated H3K9, CpG hypomethylated NANOG and SOX2, but not CpG methylated OCT4, are enriched in repressive H3K27me3. H3K79me1 and H3K79me3 tend to parallel each other and are linked to repression. Moreover, we highlight an inverse relationship between H3K27me3 occupancy on promoters and H3K36me3 occupancy on coding regions of OCT4, NANOG and SOX2, suggesting a cross-talk between K27 and K36 methylation. Establishment of distinct repression mechanisms for pluripotency-associated genes may constitute a safeguard system to prevent promiscuous reactivation during development or differentiation.
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Affiliation(s)
- Sanna Barrand
- Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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Amaral PP, Neyt C, Wilkins SJ, Askarian-Amiri ME, Sunkin SM, Perkins AC, Mattick JS. Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA (NEW YORK, N.Y.) 2009; 15:2013-2027. [PMID: 19767420 PMCID: PMC2764477 DOI: 10.1261/rna.1705309] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 08/18/2009] [Indexed: 05/28/2023]
Abstract
The Sox2 gene is a key regulator of pluripotency embedded within an intron of a long noncoding RNA (ncRNA), termed Sox2 overlapping transcript (Sox2ot), which is transcribed in the same orientation. However, this ncRNA remains uncharacterized. Here we show that Sox2ot has multiple transcription start sites associated with genomic features that indicate regulated expression, including highly conserved elements (HCEs) and chromatin marks characteristic of gene promoters. To identify biological processes in which Sox2ot may be involved, we analyzed its expression in several developmental systems, compared to expression of Sox2. We show that Sox2ot is a stable transcript expressed in mouse embryonic stem cells, which, like Sox2, is down-regulated upon induction of embryoid body (EB) differentiation. However, in contrast to Sox2, Sox2ot is up-regulated during EB mesoderm-lineage differentiation. In adult mouse, Sox2ot isoforms were detected in tissues where Sox2 is expressed, as well as in different tissues, supporting independent regulation of expression of the ncRNA. Sox2dot, an isoform of Sox2ot transcribed from a distal HCE located >500 kb upstream of Sox2, was detected exclusively in the mouse brain, with enrichment in regions of adult neurogenesis. In addition, Sox2ot isoforms are transcribed from HCEs upstream of Sox2 in other vertebrates, including in several regions of the human brain. We also show that Sox2ot is dynamically regulated during chicken and zebrafish embryogenesis, consistently associated with central nervous system structures. These observations provide insight into the structure and regulation of the Sox2ot gene, and suggest conserved roles for Sox2ot orthologs during vertebrate development.
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Affiliation(s)
- Paulo P Amaral
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia,QLD 4072, Australia
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Wen S, Li H, Liu J. Epigenetic background of neuronal fate determination. Prog Neurobiol 2008; 87:98-117. [PMID: 19007844 DOI: 10.1016/j.pneurobio.2008.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 09/03/2008] [Accepted: 10/15/2008] [Indexed: 01/07/2023]
Abstract
The development of the central nervous system (CNS) starts from neural stem cells (NSCs). During this process, NSCs are specified in space- and time-related fashions, becoming spatially heterogeneous and generating a progressively restricted repertoire of cell types: neurons, astrocytes and oligodendrocytes. The processes of neurodevelopment are determined reciprocally by intrinsic and external factors which interface to program and re-program the profiling of fate-determination gene expression. Multiple signaling pathways act in a dynamic web mode to determine the fate of NSCs through modulating the activity of a distinct set of transcription factors which in turn trigger the transcription of neural fate-determination genes. Accumulating evidence reveals that during CNS development, multiple epigenetic factors regulate the activities of extracellular signaling and corresponding transcription factors in a coordinative manner, leading to the formation of a system with sophisticated structure and magic functions. This review aims to introduce recent advances in the epigenetic background of neural cell fate determination.
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Affiliation(s)
- Shu Wen
- Department of Cell Biology, College of Basic Medical Sciences, Dalian Medical University, 116044 Dalian, Liaoning, PR China
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