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Singleton KS, Silva-Rodriguez P, Cunningham DD, Silva EM. Xenopus Sox11 Partner Proteins and Functional Domains in Neurogenesis. Genes (Basel) 2024; 15:243. [PMID: 38397232 PMCID: PMC10887758 DOI: 10.3390/genes15020243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/03/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Sox11, a member of the SoxC family of transcription factors, has distinct functions at different times in neural development. Studies in mouse, frog, chick, and zebrafish show that Sox11 promotes neural fate, neural differentiation, and neuron maturation in the central nervous system. These diverse roles are controlled in part by spatial and temporal-specific protein interactions. However, the partner proteins and Sox11-interaction domains underlying these diverse functions are not well defined. Here, we identify partner proteins and the domains of Xenopus laevis Sox11 required for protein interaction and function during neurogenesis. Our data show that Sox11 co-localizes and interacts with Pou3f2 and Neurog2 in the anterior neural plate and in early neurons, respectively. We also demonstrate that Sox11 does not interact with Neurog1, a high-affinity partner of Sox11 in the mouse cortex, suggesting that Sox11 has species-specific partner proteins. Additionally, we determined that the N-terminus including the HMG domain of Sox11 is necessary for interaction with Pou3f2 and Neurog2, and we established a novel role for the N-terminal 46 amino acids in the specification of placodal progenitors. This is the first identification of partner proteins for Sox11 and of domains required for partner-protein interactions and distinct roles in neurogenesis.
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Affiliation(s)
- Kaela S. Singleton
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
| | - Pablo Silva-Rodriguez
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Doreen D. Cunningham
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
| | - Elena M. Silva
- Interdisciplinary Program in Neuroscience, Georgetown University Medical Center, Washington, DC 200057, USA
- Department of Biology, Georgetown University, Washington, DC 20057, USA; (P.S.-R.); (D.D.C.)
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2
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Ju LF, Xu HJ, Yang YG, Yang Y. Omics Views of Mechanisms for Cell Fate Determination in Early Mammalian Development. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:950-961. [PMID: 37075831 PMCID: PMC10928378 DOI: 10.1016/j.gpb.2023.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/18/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
During mammalian preimplantation development, a totipotent zygote undergoes several cell cleavages and two rounds of cell fate determination, ultimately forming a mature blastocyst. Along with compaction, the establishment of apicobasal cell polarity breaks the symmetry of an embryo and guides subsequent cell fate choice. Although the lineage segregation of the inner cell mass (ICM) and trophectoderm (TE) is the first symbol of cell differentiation, several molecules have been shown to bias the early cell fate through their inter-cellular variations at much earlier stages, including the 2- and 4-cell stages. The underlying mechanisms of early cell fate determination have long been an important research topic. In this review, we summarize the molecular events that occur during early embryogenesis, as well as the current understanding of their regulatory roles in cell fate decisions. Moreover, as powerful tools for early embryogenesis research, single-cell omics techniques have been applied to both mouse and human preimplantation embryos and have contributed to the discovery of cell fate regulators. Here, we summarize their applications in the research of preimplantation embryos, and provide new insights and perspectives on cell fate regulation.
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Affiliation(s)
- Lin-Fang Ju
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Heng-Ji Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yun-Gui Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ying Yang
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China; University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China; Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
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3
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Islam KN, Ajao A, Venkataramani K, Rivera J, Pathania S, Henke K, Siegfried KR. The RNA-binding protein Adad1 is necessary for germ cell maintenance and meiosis in zebrafish. PLoS Genet 2023; 19:e1010589. [PMID: 37552671 PMCID: PMC10437952 DOI: 10.1371/journal.pgen.1010589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 08/18/2023] [Accepted: 07/06/2023] [Indexed: 08/10/2023] Open
Abstract
The double stranded RNA binding protein Adad1 (adenosine deaminase domain containing 1) is a member of the adenosine deaminase acting on RNAs (Adar) protein family with germ cell-specific expression. In mice, Adad1 is necessary for sperm differentiation, however its function outside of mammals has not been investigated. Here, through an N-ethyl-N-nitrosourea (ENU) based forward genetic screen, we identified an adad1 mutant zebrafish line that develops as sterile males. Further histological examination revealed complete lack of germ cells in adult mutant fish, however germ cells populated the gonad, proliferated, and entered meiosis in larval and juvenile fish. Although meiosis was initiated in adad1 mutant testes, the spermatocytes failed to progress beyond the zygotene stage. Thus, Adad1 is essential for meiosis and germline maintenance in zebrafish. We tested if spermatogonial stem cells were affected using nanos2 RNA FISH and a label retaining cell (LRC) assay, and found that the mutant testes had fewer LRCs and nanos2-expressing cells compared to wild-type siblings, suggesting that failure to maintain the spermatogonial stem cells resulted in germ cell loss by adulthood. To identify potential molecular processes regulated by Adad1, we sequenced bulk mRNA from mutants and wild-type testes and found mis-regulation of genes involved in RNA stability and modification, pointing to a potential broader role in post-transcriptional regulation. Our findings suggest that the RNA regulatory protein Adad1 is required for fertility through regulation of spermatogonial stem cell maintenance in zebrafish.
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Affiliation(s)
- Kazi Nazrul Islam
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Anuoluwapo Ajao
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Kavita Venkataramani
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Joshua Rivera
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Shailja Pathania
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | - Katrin Henke
- Department of Orthopaedics, Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Kellee Renee Siegfried
- Biology Department, University of Massachusetts Boston, Boston, Massachusetts, United States of America
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4
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Eenjes E, Benthem F, Boerema-de Munck A, Buscop-van Kempen M, Tibboel D, Rottier RJ. Distinct roles for SOX2 and SOX21 in differentiation, distribution and maturation of pulmonary neuroendocrine cells. Cell Mol Life Sci 2023; 80:79. [PMID: 36867267 PMCID: PMC9984344 DOI: 10.1007/s00018-023-04731-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023]
Abstract
Pulmonary neuroendocrine (NE) cells represent a small population in the airway epithelium, but despite this, hyperplasia of NE cells is associated with several lung diseases, such as congenital diaphragmatic hernia and bronchopulmonary dysplasia. The molecular mechanisms causing the development of NE cell hyperplasia remains poorly understood. Previously, we showed that the SOX21 modulates the SOX2-initiated differentiation of epithelial cells in the airways. Here, we show that precursor NE cells start to develop in the SOX2 + SOX21 + airway region and that SOX21 suppresses the differentiation of airway progenitors to precursor NE cells. During development, clusters of NE cells start to form and NE cells mature by expressing neuropeptide proteins, such as CGRP. Deficiency in SOX2 resulted in decreased clustering, while deficiency in SOX21 increased both the numbers of NE ASCL1 + precursor cells early in development, and the number of mature cell clusters at E18.5. In addition, at the end of gestation (E18.5), a number of NE cells in Sox2 heterozygous mice, did not yet express CGRP suggesting a delay in maturation. In conclusion, SOX2 and SOX21 function in the initiation, migration and maturation of NE cells.
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Affiliation(s)
- Evelien Eenjes
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Floor Benthem
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Anne Boerema-de Munck
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Marjon Buscop-van Kempen
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Robbert J Rottier
- Department of Pediatric Surgery, Erasmus Medical Center-Sophia Children's Hospital, Wytemaweg 80, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands.
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.
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5
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Zang K, Yu ZH, Wang M, Huang Y, Zhu XX, Yao B. SOX2 como posible biomarcador pronóstico y diana molecular en el cáncer de pulmón: metaanálisis. Rev Clin Esp 2022; 222:584-592. [PMID: 35941044 DOI: 10.1016/j.rceng.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 05/30/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVE To determine the association of SOX2 with the prognosis in lung cancer, studies providing survival information were selected based on multivariate Cox regression analysis. MATERIAL AND METHODS PubMed, Embase, and Web of Science databases were searched to identify eligible studies before June 19, 2021. The hazard ratios (HR) with 95% confidence intervals (CI) were calculated to assess the prognostic impact of SOX2 based on multivariate Cox regression analysis. Publication bias was used to assess the risk of bias. Functional analysis of SOX2 was also conducted. RESULTS 13 studies with a total of 2008 patients with lung cancer were included. SOX2 expression was not correlated with overall survival in lung cancer (10 studies with 1591 cases). Between-study heterogeneity was noted (I2=85.6%, p<0.0001). Subgroup analysis suggested that no correlation was found between SOX2 expression and overall survival in non-small cell lung cancer (NSCLC: eight studies with 1319 cases) and small-cell lung cancer (SCLC: two studies with 272 cases). SOX2 expression was significantly associated with worse time-to-progression (two studies with 104 cases: HR=3.50, 95% CI=1.34-9.15) and recurrence-free survival (two studies with 335 cases: HR=1.45, 95% CI=1.12-1.87) in NSCLC. Function analysis demonstrated that SOX2 was involved in DNA repair, cell cycle, regulation of stem cell population maintenance, and Hippo signaling pathway. CONCLUSION SOX2 may be an independent prognostic factor in time-to-progression and recurrence-free survival and may become a promising therapeutic target. More studies are essential to further our findings.
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Affiliation(s)
- K Zang
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an City, China
| | - Z-H Yu
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an City, China.
| | - M Wang
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an City, China
| | - Y Huang
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an City, China
| | - X-X Zhu
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an City, China
| | - B Yao
- Department of ICU, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an City, China
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6
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Fan W, Huang T, Wu T, Bai H, Kawahara M, Takahashi M. Zona pellucida removal by acid Tyrode's solution affects pre- and post-implantation development and gene expression in mouse embryos. Biol Reprod 2022; 107:1228-1241. [PMID: 35948000 DOI: 10.1093/biolre/ioac155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/07/2022] [Accepted: 07/26/2022] [Indexed: 11/15/2022] Open
Abstract
The zona pellucida (ZP) plays a crucial role in the process of fertilization to early embryonic development, including cellular arrangement and communication between blastomeres. However, little is known regarding the role of the ZP in pre- and post-implantation embryonic development associated with gene expression. We investigated the effect of zona pellucida removal (ZPR) on pre- and post-implantation development of mouse embryos. After ZPR of 2-cell stage embryos was performed by acid Tyrode's solution, which is commonly used for ZP treatment, compaction occurred earlier in ZP-free (ZF) than ZP-intact (ZI) embryos. In addition, the expression of differentiation-related genes in the inner cell mass (ICM) and trophectoderm (TE) was significantly altered in ZF blastocyst compared with ZI embryos. After embryo transfer, the rate of implantation and live fetuses was lower in ZF embryos than in control embryos, whereas the fetal weight at E17.5 was not different. However, placental weight significantly increased in ZF embryos. RNA-seq analysis of the placenta showed that a total of 473 differentially expressed genes (DEGs) significantly influenced the biological process. The present study suggests that ZPR by acid Tyrode's solution at the 2-cell stage not only disturbs the expression pattern of ICM/TE-related genes but affects the post-implantation development of mouse embryos. Overall, this study provides deeper insight into the role of the ZP during early embryonic development and the viability of post-implantation development.
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Affiliation(s)
- Weihong Fan
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Tengda Huang
- Department of Liver Surgery & Liver Transplantation, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Tian Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, P.R. China
| | - Hanako Bai
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.,Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Manabu Kawahara
- Graduate School of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.,Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan
| | - Masashi Takahashi
- Research Faculty of Agriculture, Hokkaido University, Hokkaido 060-8589, Japan.,Graduate School of Global Food Resources, Hokkaido University, Hokkaido 060-8589, Japan
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7
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SOX2 como posible biomarcador pronóstico y diana molecular en el cáncer de pulmón: metaanálisis. Rev Clin Esp 2022. [DOI: 10.1016/j.rce.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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8
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Allègre N, Chauveau S, Dennis C, Renaud Y, Meistermann D, Estrella LV, Pouchin P, Cohen-Tannoudji M, David L, Chazaud C. NANOG initiates epiblast fate through the coordination of pluripotency genes expression. Nat Commun 2022; 13:3550. [PMID: 35729116 PMCID: PMC9213552 DOI: 10.1038/s41467-022-30858-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 05/24/2022] [Indexed: 12/20/2022] Open
Abstract
The epiblast is the source of all mammalian embryonic tissues and of pluripotent embryonic stem cells. It differentiates alongside the primitive endoderm in a “salt and pepper” pattern from inner cell mass (ICM) progenitors during the preimplantation stages through the activity of NANOG, GATA6 and the FGF pathway. When and how epiblast lineage specification is initiated is still unclear. Here, we show that the coordinated expression of pluripotency markers defines epiblast identity. Conversely, ICM progenitor cells display random cell-to-cell variability in expression of various pluripotency markers, remarkably dissimilar from the epiblast signature and independently from NANOG, GATA6 and FGF activities. Coordination of pluripotency markers expression fails in Nanog and Gata6 double KO (DKO) embryos. Collectively, our data suggest that NANOG triggers epiblast specification by ensuring the coordinated expression of pluripotency markers in a subset of cells, implying a stochastic mechanism. These features are likely conserved, as suggested by analysis of human embryos. Pluripotent epiblast cells segregate from primitive endoderm in the blastocyst inner cell mass (ICM). Here the authors show that mosaic epiblast differentiation during mouse and human preimplantation development initiates stochastically in ICM progenitors, independently of the FGF pathway, and requires NANOG activity
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Affiliation(s)
- Nicolas Allègre
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Sabine Chauveau
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Cynthia Dennis
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France.,Byonet, 19 rue du courait, F-63200, Riom, France
| | - Dimitri Meistermann
- Université de Nantes, CHU Nantes, INSERM, CR2TI, UMR 1064, ITUN, F-44000, Nantes, France.,Université de Nantes, CNRS, LS2N, CNRS UMR 6004, F-44000, Nantes, France
| | - Lorena Valverde Estrella
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Pierre Pouchin
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France
| | - Michel Cohen-Tannoudji
- Institut Pasteur, Université Paris Cité, CNRS UMR3738, Epigenomics, Proliferation, and the Identity of Cells, Department of Developmental and Stem Cell Biology, F-75015, Paris, France
| | - Laurent David
- Université de Nantes, CHU Nantes, INSERM, CR2TI, UMR 1064, ITUN, F-44000, Nantes, France.,Université de Nantes, CHU Nantes, INSERM, CNRS, UMS Biocore, INSERM UMS 016, CNRS UMS 3556, F-44000, Nantes, France
| | - Claire Chazaud
- Université Clermont Auvergne, CNRS, INSERM, GReD Institute, Faculté de Médecine, F-63000, Clermont-Ferrand, France.
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9
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Metz EP, Wilder PJ, Popay TM, Wang J, Liu Q, Kalluchi A, Rowley MJ, Tansey WP, Rizzino A. Elevating SOX2 Downregulates MYC through a SOX2:MYC Signaling Axis and Induces a Slowly Cycling Proliferative State in Human Tumor Cells. Cancers (Basel) 2022; 14:1946. [PMID: 35454854 PMCID: PMC9025961 DOI: 10.3390/cancers14081946] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 02/05/2023] Open
Abstract
Slowly cycling/infrequently proliferating tumor cells present a clinical challenge due to their ability to evade treatment. Previous studies established that high levels of SOX2 in both fetal and tumor cells restrict cell proliferation and induce a slowly cycling state. However, the mechanisms through which elevated SOX2 levels inhibit tumor cell proliferation have not been identified. To identify common mechanisms through which SOX2 elevation restricts tumor cell proliferation, we initially performed RNA-seq using two diverse tumor cell types. SOX2 elevation in both cell types downregulated MYC target genes. Consistent with these findings, elevating SOX2 in five cell lines representing three different human cancer types decreased MYC expression. Importantly, the expression of a dominant-negative MYC variant, omomyc, recapitulated many of the effects of SOX2 on proliferation, cell cycle, gene expression, and biosynthetic activity. We also demonstrated that rescuing MYC activity in the context of elevated SOX2 induces cell death, indicating that the downregulation of MYC is a critical mechanistic step necessary to maintain survival in the slowly cycling state induced by elevated SOX2. Altogether, our findings uncover a novel SOX2:MYC signaling axis and provide important insights into the molecular mechanisms through which SOX2 elevation induces a slowly cycling proliferative state.
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Affiliation(s)
- Ethan P. Metz
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (E.P.M.); (P.J.W.)
| | - Phillip J. Wilder
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (E.P.M.); (P.J.W.)
| | - Tessa M. Popay
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (T.M.P.); (W.P.T.)
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.W.); (Q.L.)
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.W.); (Q.L.)
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Achyuth Kalluchi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (A.K.); (M.J.R.)
| | - M. Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; (A.K.); (M.J.R.)
| | - William P. Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (T.M.P.); (W.P.T.)
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; (E.P.M.); (P.J.W.)
- Department of Pathology and Microbiology, University of Nebraska Medical Center Fred & Pamela Buffett Cancer Center, Omaha, NE 68198, USA
- Department of Biochemistry and Molecular Biology, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
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10
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Chen W, Chen X, Zhang X, Chen C, Dan S, Hu J, Kang B, Wang YJ. DNA repair proteins cooperate with SOX2 in regulating the transition of human embryonic stem cells to neural progenitor cells. Biochem Biophys Res Commun 2022; 586:163-170. [PMID: 34852960 DOI: 10.1016/j.bbrc.2021.11.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/14/2021] [Accepted: 11/14/2021] [Indexed: 11/02/2022]
Abstract
SOX2, a well-established pluripotency factor supporting the self-renewal of pluripotent stem cells (PSCs), is also a crucial factor for maintaining the properties and functionalities of neural progenitor cells (NPCs). It regulates the transcription of target genes by forming complexes with its partner factors, but systematic comparison of SOX2 binding partners in human PSCs versus NPCs is lacking. Here, by deciphering and comparing the SOX2-protein interactomes in human embryonic stem cells (hESCs) versus the NPCs derived from them, we identified 23 proteins with high reproducibility that are most differentially associated with SOX2, of which 9 are DNA repair proteins (PARP1, PARP2, PRKDC, XRCC1, XRCC5, XRCC6, RPA1, LIG3, DDB1). Genetic knocking-down or pharmacological inhibiting two of the DNA repair proteins (PARP1 and PRKDC) significantly up-regulated certain NPC or ectodermal biomarkers that are transcriptionally-suppressed by the SOX2/DNA repair protein complexes. These findings point to a crucial role of DNA repair proteins in pluripotent state transition and neural induction.
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Affiliation(s)
- Wenjie Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Xinyu Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Xiaobing Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Cheng Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Songsong Dan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Jianwen Hu
- Shanghai Bioprofile Technology Co., Ltd., Shanghai, 200241, China
| | - Bo Kang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Ying-Jie Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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11
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Yu NK, McClatchy DB, Diedrich JK, Romero S, Choi JH, Martínez-Bartolomé S, Delahunty CM, Muotri AR, Yates JR. Interactome analysis illustrates diverse gene regulatory processes associated with LIN28A in human iPS cell-derived neural progenitor cells. iScience 2021; 24:103321. [PMID: 34816099 PMCID: PMC8593586 DOI: 10.1016/j.isci.2021.103321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 09/07/2021] [Accepted: 10/19/2021] [Indexed: 12/02/2022] Open
Abstract
A single protein can be multifaceted depending on the cellular contexts and interacting molecules. LIN28A is an RNA-binding protein that governs developmental timing, cellular proliferation, differentiation, stem cell pluripotency, and metabolism. In addition to its best-known roles in microRNA biogenesis, diverse molecular roles have been recognized. In the nervous system, LIN28A is known to play critical roles in proliferation and differentiation of neural progenitor cells (NPCs). We profiled the endogenous LIN28A-interacting proteins in NPCs differentiated from human induced pluripotent stem (iPS) cells using immunoprecipitation and liquid chromatography-tandem mass spectrometry. We identified over 500 LIN28A-interacting proteins, including 156 RNA-independent interactors. Functions of these proteins span a wide range of gene regulatory processes. Prompted by the interactome data, we revealed that LIN28A may impact the subcellular distribution of its interactors and stress granule formation upon oxidative stress. Overall, our analysis opens multiple avenues for elaborating molecular roles and characteristics of LIN28A.
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Affiliation(s)
- Nam-Kyung Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Daniel B. McClatchy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jolene K. Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sarah Romero
- Department of Pediatrics/Rady Children’s Hospital San Diego, Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA 92037, USA
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Claire M. Delahunty
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Alysson R. Muotri
- Department of Pediatrics/Rady Children’s Hospital San Diego, Department of Cellular & Molecular Medicine, School of Medicine, University of California, San Diego, San Diego, CA 92037, USA
- Stem Cell Program, Center for Academic Research and Training in Anthropogeny (CARTA), Archealization Center (ArchC), Kavli Institute for Brain and Mind, La Jolla, CA 92037, USA
| | - John R. Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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12
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Aminu AJ, Petkova M, Atkinson AJ, Yanni J, Morris AD, Simms RT, Chen W, Yin Z, Kuniewicz M, Holda MK, Kuzmin VS, Perde F, Molenaar P, Dobrzynski H. Further insights into the molecular complexity of the human sinus node - The role of 'novel' transcription factors and microRNAs. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 166:86-104. [PMID: 34004232 DOI: 10.1016/j.pbiomolbio.2021.04.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023]
Abstract
RESEARCH PURPOSE The sinus node (SN) is the heart's primary pacemaker. Key ion channels (mainly the funny channel, HCN4) and Ca2+-handling proteins in the SN are responsible for its function. Transcription factors (TFs) regulate gene expression through inhibition or activation and microRNAs (miRs) do this through inhibition. There is high expression of macrophages and mast cells within the SN connective tissue. 'Novel'/unexplored TFs and miRs in the regulation of ion channels and immune cells in the SN are not well understood. Using RNAseq and bioinformatics, the expression profile and predicted interaction of key TFs and cell markers with key miRs in the adult human SN vs. right atrial tissue (RA) were determined. PRINCIPAL RESULTS 68 and 60 TFs significantly more or less expressed in the SN vs. RA respectively. Among those more expressed were ISL1 and TBX3 (involved in embryonic development of the SN) and 'novel' RUNX1-2, CEBPA, GLI1-2 and SOX2. These TFs were predicted to regulate HCN4 expression in the SN. Markers for different cells: fibroblasts (COL1A1), fat (FABP4), macrophages (CSF1R and CD209), natural killer (GZMA) and mast (TPSAB1) were significantly more expressed in the SN vs. RA. Interestingly, RUNX1-3, CEBPA and GLI1 also regulate expression of these cells. MiR-486-3p inhibits HCN4 and markers involved in immune response. MAJOR CONCLUSIONS In conclusion, RUNX1-2, CSF1R, TPSAB1, COL1A1 and HCN4 are highly expressed in the SN but not miR-486-3p. Their complex interactions can be used to treat SN dysfunction such as bradycardia. Interestingly, another research group recently reported miR-486-3p is upregulated in blood samples from severe COVID-19 patients who suffer from bradycardia.
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Affiliation(s)
- Abimbola J Aminu
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Maria Petkova
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Andrew J Atkinson
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Joseph Yanni
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Alex D Morris
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Robert T Simms
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Weixuan Chen
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Zeyuan Yin
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom
| | - Marcin Kuniewicz
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom; Department of Anatomy, Jagiellonian University Medical College, Krakow, Poland
| | - Mateusz K Holda
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom; Department of Anatomy, Jagiellonian University Medical College, Krakow, Poland
| | - Vladislav S Kuzmin
- Department of Human and Animal Physiology, Lomonosov Moscow State University, Moscow, Russia
| | - Filip Perde
- National Institute of Legal Medicine, Bucharest, Romania
| | - Peter Molenaar
- School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia; Cardiovascular Molecular & Therapeutics Translational Research Group, University of Queensland, The Prince Charles Hospital, Brisbane, Australia
| | - Halina Dobrzynski
- The Division of Cardiovascular Sciences, University of Manchester, United Kingdom; Department of Anatomy, Jagiellonian University Medical College, Krakow, Poland.
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13
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Newly characterized bovine mammary stromal region with epithelial properties supports representative epithelial outgrowth development from transplanted stem cells. Cell Tissue Res 2021; 387:39-61. [PMID: 34698917 DOI: 10.1007/s00441-021-03545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 10/13/2021] [Indexed: 10/20/2022]
Abstract
Limited outgrowth development of bovine mammary epithelial stem cells transplanted into de-epithelialized mouse fat pads restricts advanced studies on this productive organ's development and renewal. We challenged the mouse-bovine incompatibility by implanting parenchymal adjacent or distant bovine stromal layers (close and far stroma, respectively) into the mouse fat pad to serve as an endogenous niche for transplanted stem cells. The close stroma better supported stem cell take rate and outgrowth development. The diameter of these open duct-like structures represented and occasionally exceeded that of the endogenous ducts and appeared 8.3-fold wider than the capsule-like structures developed in the mouse fat pad after similar cell transplantation. RNA-Seq revealed lower complement activity in this layer, associated with secretion of specific laminins and WNT proteins favoring epithelial outgrowth development. The close stroma appeared genetically more similar to the parenchyma than to the far stroma due to epithelial characteristics, mainly of fibroblasts, including expression of epithelial markers, milk protein genes, and functional mammary claudins. Gene markers and activators of the mesenchymal-to-epithelial transition were highly enriched in the epithelial gene cluster and may contribute to the acquired epithelial properties of this stromal layer.
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14
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Eenjes E, Buscop-van Kempen M, Boerema-de Munck A, Edel GG, Benthem F, de Kreij-de Bruin L, Schnater M, Tibboel D, Collins J, Rottier RJ. SOX21 modulates SOX2-initiated differentiation of epithelial cells in the extrapulmonary airways. eLife 2021; 10:57325. [PMID: 34286693 PMCID: PMC8331192 DOI: 10.7554/elife.57325] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 07/20/2021] [Indexed: 12/23/2022] Open
Abstract
SOX2 expression levels are crucial for the balance between maintenance and differentiation of airway progenitor cells during development and regeneration. Here, we describe patterning of the mouse proximal airway epithelium by SOX21, which coincides with high levels of SOX2 during development. Airway progenitor cells in this SOX2+/SOX21+ zone show differentiation to basal cells, specifying cells for the extrapulmonary airways. Loss of SOX21 showed an increased differentiation of SOX2+ progenitor cells to basal and ciliated cells during mouse lung development. We propose a mechanism where SOX21 inhibits differentiation of airway progenitors by antagonizing SOX2-induced expression of specific genes involved in airway differentiation. Additionally, in the adult tracheal epithelium, SOX21 inhibits basal to ciliated cell differentiation. This suppressing function of SOX21 on differentiation contrasts SOX2, which mainly drives differentiation of epithelial cells during development and regeneration after injury. Furthermore, using human fetal lung organoids and adult bronchial epithelial cells, we show that SOX2+/SOX21+ regionalization is conserved. Lastly, we show that the interplay between SOX2 and SOX21 is context and concentration dependent leading to regulation of differentiation of the airway epithelium.
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Affiliation(s)
- Evelien Eenjes
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Marjon Buscop-van Kempen
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Anne Boerema-de Munck
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Gabriela G Edel
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Floor Benthem
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Lisette de Kreij-de Bruin
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Marco Schnater
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Dick Tibboel
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Jennifer Collins
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands
| | - Robbert J Rottier
- Department of Pediatric Surgery, Erasmus Medical Center - Sophia Children's Hospital, Rotterdam, Netherlands.,Department of Cell biology, Erasmus Medical Center, Rotterdam, Netherlands
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15
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Alternate Roles of Sox Transcription Factors beyond Transcription Initiation. Int J Mol Sci 2021; 22:ijms22115949. [PMID: 34073089 PMCID: PMC8198692 DOI: 10.3390/ijms22115949] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/19/2022] Open
Abstract
Sox proteins are known as crucial transcription factors for many developmental processes and for a wide range of common diseases. They were believed to specifically bind and bend DNA with other transcription factors and elicit transcriptional activation or repression activities in the early stage of transcription. However, their functions are not limited to transcription initiation. It has been showed that Sox proteins are involved in the regulation of alternative splicing regulatory networks and translational control. In this review, we discuss the current knowledge on how Sox transcription factors such as Sox2, Sry, Sox6, and Sox9 allow the coordination of co-transcriptional splicing and also the mechanism of SOX4-mediated translational control in the context of RNA polymerase III.
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16
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Niu CM, Xia MM, Zhong YN, Zheng Y. Mus musculus Barrier-To-Autointegration Factor 2 (Banf2) is Not Essential for Spermatogenesis or Fertility. Cytogenet Genome Res 2021; 161:167-177. [PMID: 33951625 DOI: 10.1159/000513850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 12/16/2020] [Indexed: 11/19/2022] Open
Abstract
The barrier-to-autointegration factor (BAF) is widely expressed in most human tissues and plays a critical role in chromatin organization, nuclear envelope assembly, gonadal development, and embryonic stem cell self-renewal. Complete loss of BAF has been shown to lead to embryonic lethality and gonadal defects. The BAF paralog, namely, barrier-to-autointegration factor 2 (BANF2), exhibits a testis-predominant expression pattern in both humans and mice. Unlike BAF, it may cause isolated male infertility. Therefore, we used the CRISPR/Cas9 system to generate Banf2-knockout mice to further study its function in spermatogenesis. Unexpectedly, knockout mice did not show any detectable abnormalities in histological structure of the testis, epididymis, ovary, and other tissues, and exhibited normal fertility, indicating that Banf2 is not essential for mouse spermatogenesis and fertility.
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Affiliation(s)
- Chang-Min Niu
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou, China
| | - Meng-Meng Xia
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou, China
| | - Ya-Nan Zhong
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou, China
| | - Ying Zheng
- Department of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Experimental and Translational Noncoding RNA Research, Yangzhou, China
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17
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Larrigan S, Shah S, Fernandes A, Mattar P. Chromatin Remodeling in the Brain-a NuRDevelopmental Odyssey. Int J Mol Sci 2021; 22:ijms22094768. [PMID: 33946340 PMCID: PMC8125410 DOI: 10.3390/ijms22094768] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 04/27/2021] [Indexed: 01/07/2023] Open
Abstract
During brain development, the genome must be repeatedly reconfigured in order to facilitate neuronal and glial differentiation. A host of chromatin remodeling complexes facilitates this process. At the genetic level, the non-redundancy of these complexes suggests that neurodevelopment may require a lexicon of remodelers with different specificities and activities. Here, we focus on the nucleosome remodeling and deacetylase (NuRD) complex. We review NuRD biochemistry, genetics, and functions in neural progenitors and neurons.
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Affiliation(s)
- Sarah Larrigan
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Alex Fernandes
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
| | - Pierre Mattar
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (S.L.); (S.S.); (A.F.)
- Ottawa Health Research Institute (OHRI), Ottawa, ON K1H 8L6, Canada
- Correspondence:
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18
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Stevanovic M, Drakulic D, Lazic A, Ninkovic DS, Schwirtlich M, Mojsin M. SOX Transcription Factors as Important Regulators of Neuronal and Glial Differentiation During Nervous System Development and Adult Neurogenesis. Front Mol Neurosci 2021; 14:654031. [PMID: 33867936 PMCID: PMC8044450 DOI: 10.3389/fnmol.2021.654031] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/11/2021] [Indexed: 12/11/2022] Open
Abstract
The SOX proteins belong to the superfamily of transcription factors (TFs) that display properties of both classical TFs and architectural components of chromatin. Since the cloning of the Sox/SOX genes, remarkable progress has been made in illuminating their roles as key players in the regulation of multiple developmental and physiological processes. SOX TFs govern diverse cellular processes during development, such as maintaining the pluripotency of stem cells, cell proliferation, cell fate decisions/germ layer formation as well as terminal cell differentiation into tissues and organs. However, their roles are not limited to development since SOX proteins influence survival, regeneration, cell death and control homeostasis in adult tissues. This review summarized current knowledge of the roles of SOX proteins in control of central nervous system development. Some SOX TFs suspend neural progenitors in proliferative, stem-like state and prevent their differentiation. SOX proteins function as pioneer factors that occupy silenced target genes and keep them in a poised state for activation at subsequent stages of differentiation. At appropriate stage of development, SOX members that maintain stemness are down-regulated in cells that are competent to differentiate, while other SOX members take over their functions and govern the process of differentiation. Distinct SOX members determine down-stream processes of neuronal and glial differentiation. Thus, sequentially acting SOX TFs orchestrate neural lineage development defining neuronal and glial phenotypes. In line with their crucial roles in the nervous system development, deregulation of specific SOX proteins activities is associated with neurodevelopmental disorders (NDDs). The overview of the current knowledge about the link between SOX gene variants and NDDs is presented. We outline the roles of SOX TFs in adult neurogenesis and brain homeostasis and discuss whether impaired adult neurogenesis, detected in neurodegenerative diseases, could be associated with deregulation of SOX proteins activities. We present the current data regarding the interaction between SOX proteins and signaling pathways and microRNAs that play roles in nervous system development. Finally, future research directions that will improve the knowledge about distinct and various roles of SOX TFs in health and diseases are presented and discussed.
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Affiliation(s)
- Milena Stevanovic
- Laboratory for Human Molecular Genetics, 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
| | - Danijela Drakulic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Andrijana Lazic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Danijela Stanisavljevic Ninkovic
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marija Schwirtlich
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marija Mojsin
- Laboratory for Human Molecular Genetics, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
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19
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Li B, Tian Y, Wen H, Qi X, Wang L, Zhang J, Li J, Dong X, Zhang K, Li Y. Systematic identification and expression analysis of the Sox gene family in spotted sea bass (Lateolabrax maculatus). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 38:100817. [PMID: 33677158 DOI: 10.1016/j.cbd.2021.100817] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
The Sox gene family encodes a set of transcription factors characterized by a conserved Sry-related high mobility group (HMG)-box domain, which performs a series of essential biological functions in diverse tissues and developmental processes. In this study, the Sox gene family was systematically characterized in spotted sea bass (Lateolabrax maculatus). A total of 26 Sox genes were identified and classified into eight subfamilies, namely, SoxB1, SoxB2, SoxC, SoxD, SoxE, SoxF, SoxH and SoxK. The phylogenetic relationship, exon-intron and domain structure analyses supported their annotation and classification. Comparison of gene copy numbers and chromosome locations among different species indicated that except tandem duplicated paralogs of Sox17/Sox32, duplicated Sox genes in spotted sea bass were generated from teleost-specific whole genome duplication during evolution. In addition, qRT-PCR was performed to detect the expression profiles of Sox genes during development and adulthood. The results showed that the expression of 16 out of 26 Sox genes was induced dramatically at different starting points after the multicellular stage, which is consistent with embryogenesis. At the early stage of sex differentiation, 9 Sox genes exhibited sexually dimorphic expression patterns, among which Sox3, Sox19 and Sox6b showed the most significant ovary-biased expression. Moreover, the distinct expression pattern of Sox genes was observed in different adult tissues. Our results provide a fundamental resource for further investigating the functions of Sox genes in embryonic processes, sex determination and differentiation as well as controlling the homeostasis of adult tissues in spotted sea bass.
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Affiliation(s)
- Bingyu Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Yuan Tian
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Haishen Wen
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Xin Qi
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Lingyu Wang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Jingru Zhang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Jinku Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Ximeng Dong
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Kaiqiang Zhang
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China
| | - Yun Li
- Key Laboratory of Mariculture (Ocean University of China), Ministry of Education, Qingdao 266003, PR China.
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20
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Chen S, Gan M, Lv H, Jiang R. DeepCAPE: A Deep Convolutional Neural Network for the Accurate Prediction of Enhancers. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:565-577. [PMID: 33581335 PMCID: PMC9040020 DOI: 10.1016/j.gpb.2019.04.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 03/15/2019] [Accepted: 04/29/2019] [Indexed: 12/12/2022]
Abstract
The establishment of a landscape of enhancers across human cells is crucial to deciphering the mechanism of gene regulation, cell differentiation, and disease development. High-throughput experimental approaches, which contain successfully reported enhancers in typical cell lines, are still too costly and time-consuming to perform systematic identification of enhancers specific to different cell lines. Existing computational methods, capable of predicting regulatory elements purely relying on DNA sequences, lack the power of cell line-specific screening. Recent studies have suggested that chromatin accessibility of a DNA segment is closely related to its potential function in regulation, and thus may provide useful information in identifying regulatory elements. Motivated by the aforementioned understanding, we integrate DNA sequences and chromatin accessibility data to accurately predict enhancers in a cell line-specific manner. We proposed DeepCAPE, a deep convolutional neural network to predict enhancers via the integration of DNA sequences and DNase-seq data. Benefitting from the well-designed feature extraction mechanism and skip connection strategy, our model not only consistently outperforms existing methods in the imbalanced classification of cell line-specific enhancers against background sequences, but also has the ability to self-adapt to different sizes of datasets. Besides, with the adoption of auto-encoder, our model is capable of making cross-cell line predictions. We further visualize kernels of the first convolutional layer and show the match of identified sequence signatures and known motifs. We finally demonstrate the potential ability of our model to explain functional implications of putative disease-associated genetic variants and discriminate disease-related enhancers. The source code and detailed tutorial of DeepCAPE are freely available at https://github.com/ShengquanChen/DeepCAPE.
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Affiliation(s)
- Shengquan Chen
- MOE Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Mingxin Gan
- Department of Management Science and Engineering, School of Economics and Management, University of Science and Technology Beijing, Beijing 100083, China
| | - Hairong Lv
- MOE Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Rui Jiang
- MOE Key Laboratory of Bioinformatics, Research Department of Bioinformatics at the Beijing National Research Center for Information Science and Technology, Center for Synthetic and Systems Biology, Department of Automation, Tsinghua University, Beijing 100084, China.
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21
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Saito K, Chiba Y, Yamada A, Fukumoto S. Identification and function analysis of ameloblast differentiation-related molecules using mouse incisors. PEDIATRIC DENTAL JOURNAL 2020. [DOI: 10.1016/j.pdj.2020.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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22
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Yoshizaki K, Fukumoto S, Bikle DD, Oda Y. Transcriptional Regulation of Dental Epithelial Cell Fate. Int J Mol Sci 2020; 21:ijms21238952. [PMID: 33255698 PMCID: PMC7728066 DOI: 10.3390/ijms21238952] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
Dental enamel is hardest tissue in the body and is produced by dental epithelial cells residing in the tooth. Their cell fates are tightly controlled by transcriptional programs that are facilitated by fate determining transcription factors and chromatin regulators. Understanding the transcriptional program controlling dental cell fate is critical for our efforts to build and repair teeth. In this review, we describe the current understanding of these regulators essential for regeneration of dental epithelial stem cells and progeny, which are identified through transgenic mouse models. We first describe the development and morphogenesis of mouse dental epithelium in which different subpopulations of epithelia such as ameloblasts contribute to enamel formation. Then, we describe the function of critical factors in stem cells or progeny to drive enamel lineages. We also show that gene mutations of these factors are associated with dental anomalies in craniofacial diseases in humans. We also describe the function of the master regulators to govern dental lineages, in which the genetic removal of each factor switches dental cell fate to that generating hair. The distinct and related mechanisms responsible for the lineage plasticity are discussed. This knowledge will lead us to develop a potential tool for bioengineering new teeth.
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Affiliation(s)
- Keigo Yoshizaki
- Section of Orthodontics and Dentofacial Orthopedics, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka 812-8582, Japan;
| | - Satoshi Fukumoto
- Section of Pediatric Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka 812-8582, Japan;
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Daniel D. Bikle
- Departments of Medicine and Endocrinology, University of California San Francisco and Veterans Affairs Medical Center, San Francisco, CA 94158, USA;
| | - Yuko Oda
- Departments of Medicine and Endocrinology, University of California San Francisco and Veterans Affairs Medical Center, San Francisco, CA 94158, USA;
- Correspondence:
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23
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Metz EP, Wuebben EL, Wilder PJ, Cox JL, Datta K, Coulter D, Rizzino A. Tumor quiescence: elevating SOX2 in diverse tumor cell types downregulates a broad spectrum of the cell cycle machinery and inhibits tumor growth. BMC Cancer 2020; 20:941. [PMID: 32998722 PMCID: PMC7528478 DOI: 10.1186/s12885-020-07370-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/31/2020] [Indexed: 11/17/2022] Open
Abstract
Background Quiescent tumor cells pose a major clinical challenge due to their ability to resist conventional chemotherapies and to drive tumor recurrence. Understanding the molecular mechanisms that promote quiescence of tumor cells could help identify therapies to eliminate these cells. Significantly, recent studies have determined that the function of SOX2 in cancer cells is highly dose dependent. Specifically, SOX2 levels in tumor cells are optimized to promote tumor growth: knocking down or elevating SOX2 inhibits proliferation. Furthermore, recent studies have shown that quiescent tumor cells express higher levels of SOX2 compared to adjacent proliferating cells. Currently, the mechanisms through which elevated levels of SOX2 restrict tumor cell proliferation have not been characterized. Methods To understand how elevated levels of SOX2 restrict the proliferation of tumor cells, we engineered diverse types of tumor cells for inducible overexpression of SOX2. Using these cells, we examined the effects of elevating SOX2 on their proliferation, both in vitro and in vivo. In addition, we examined how elevating SOX2 influences their expression of cyclins, cyclin-dependent kinases (CDKs), and p27Kip1. Results Elevating SOX2 in diverse tumor cell types led to growth inhibition in vitro. Significantly, elevating SOX2 in vivo in pancreatic ductal adenocarcinoma, medulloblastoma, and prostate cancer cells induced a reversible state of tumor growth arrest. In all three tumor types, elevation of SOX2 in vivo quickly halted tumor growth. Remarkably, tumor growth resumed rapidly when SOX2 returned to endogenous levels. We also determined that elevation of SOX2 in six tumor cell lines decreased the levels of cyclins and CDKs that control each phase of the cell cycle, while upregulating p27Kip1. Conclusions Our findings indicate that elevating SOX2 above endogenous levels in a diverse set of tumor cell types leads to growth inhibition both in vitro and in vivo. Moreover, our findings indicate that SOX2 can function as a master regulator by controlling the expression of a broad spectrum of cell cycle machinery. Importantly, our SOX2-inducible tumor studies provide a novel model system for investigating the molecular mechanisms by which elevated levels of SOX2 restrict cell proliferation and tumor growth.
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Affiliation(s)
- Ethan P Metz
- Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Erin L Wuebben
- Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Phillip J Wilder
- Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Jesse L Cox
- Department of Pathology and Microbiology, University of Nebraska Medical Center Fred & Pamela Buffett Cancer Center, Omaha, NE, 68198-6805, USA
| | - Kaustubh Datta
- Department of Biochemistry and Molecular Biology Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Donald Coulter
- Department of Pediatrics, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA. .,Department of Pathology and Microbiology, University of Nebraska Medical Center Fred & Pamela Buffett Cancer Center, Omaha, NE, 68198-6805, USA. .,Department of Biochemistry and Molecular Biology Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, 68198-6805, USA.
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24
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Hou L, Wei Y, Lin Y, Wang X, Lai Y, Yin M, Chen Y, Guo X, Wu S, Zhu Y, Yuan J, Tariq M, Li N, Sun H, Wang H, Zhang X, Chen J, Bao X, Jauch R. Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2. Nucleic Acids Res 2020; 48:3869-3887. [PMID: 32016422 PMCID: PMC7144947 DOI: 10.1093/nar/gkaa067] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 01/16/2020] [Accepted: 01/22/2020] [Indexed: 02/03/2023] Open
Abstract
Some transcription factors that specifically bind double-stranded DNA appear to also function as RNA-binding proteins. Here, we demonstrate that the transcription factor Sox2 is able to directly bind RNA in vitro as well as in mouse and human cells. Sox2 targets RNA via a 60-amino-acid RNA binding motif (RBM) positioned C-terminally of the DNA binding high mobility group (HMG) box. Sox2 can associate with RNA and DNA simultaneously to form ternary RNA/Sox2/DNA complexes. Deletion of the RBM does not affect selection of target genes but mitigates binding to pluripotency related transcripts, switches exon usage and impairs the reprogramming of somatic cells to a pluripotent state. Our findings designate Sox2 as a multi-functional factor that associates with RNA whilst binding to cognate DNA sequences, suggesting that it may co-transcriptionally regulate RNA metabolism during somatic cell reprogramming.
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Affiliation(s)
- Linlin Hou
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangzhou/Shenzhen, China.,CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yuanjie Wei
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yingying Lin
- Department of Biochemistry, Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangzhou/Shenzhen, China.,Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiwei Wang
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yiwei Lai
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Menghui Yin
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China
| | - Yanpu Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Max Planck Institute for Heart and Lung Research, 61231 Bad Nauheim, Germany
| | - Xiangpeng Guo
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Senbin Wu
- Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | | | - Jie Yuan
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Muqddas Tariq
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Na Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Laboratory of RNA, Chromatin, and Human Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hao Sun
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Huating Wang
- Department of Orthopaedics and Traumatology, Li Ka Shing Institute of Health Sciences, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Xiaofei Zhang
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,CAS Key Laboratory of Regenerative Biology, Hefei Institute of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xichen Bao
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,Laboratory of RNA Molecular Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Ralf Jauch
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences and Guangzhou Medical University, Guangzhou 511436, China.,Genome Regulation Laboratory, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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25
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Saito K, Michon F, Yamada A, Inuzuka H, Yamaguchi S, Fukumoto E, Yoshizaki K, Nakamura T, Arakaki M, Chiba Y, Ishikawa M, Okano H, Thesleff I, Fukumoto S. Sox21 Regulates Anapc10 Expression and Determines the Fate of Ectodermal Organ. iScience 2020; 23:101329. [PMID: 32674056 PMCID: PMC7363706 DOI: 10.1016/j.isci.2020.101329] [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: 02/19/2020] [Revised: 05/22/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022] Open
Abstract
The transcription factor Sox21 is expressed in the epithelium of developing teeth. The present study aimed to determine the role of Sox21 in tooth development. We found that disruption of Sox21 caused severe enamel hypoplasia, regional osteoporosis, and ectopic hair formation in the gingiva in Sox21 knockout incisors. Differentiation markers were lost in ameloblasts, which formed hair follicles expressing hair keratins. Molecular analysis and chromatin immunoprecipitation sequencing indicated that Sox21 regulated Anapc10, which recognizes substrates for ubiquitination-mediated degradation, and determined dental-epithelial versus hair follicle cell fate. Disruption of either Sox21 or Anapc10 induced Smad3 expression, accelerated TGF-β1-induced promotion of epithelial-to-mesenchymal transition (EMT), and resulted in E-cadherin degradation via Skp2. We conclude that Sox21 disruption in the dental epithelium leads to the formation of a unique microenvironment promoting hair formation and that Sox21 controls dental epithelial differentiation and enamel formation by inhibiting EMT via Anapc10. Sox21 was induced by Shh in dental epithelial cells Sox21 deficiency in dental epithelium caused differentiation into hair cells Sox21 deficiency did not cause differentiation into mature ameloblasts Anapc10 induced by Sox21 bound to Fzr1 and regulated EMT via Skp2
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Affiliation(s)
- Kan Saito
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan.
| | - Frederic Michon
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; Institute for Neurosciences of Montpellier, Inserm U1051, University of Montpellier, 34295 Montpellier, France
| | - Aya Yamada
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Hiroyuki Inuzuka
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Satoko Yamaguchi
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Emiko Fukumoto
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Keigo Yoshizaki
- Section of Orthodontics, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Takashi Nakamura
- Division of Molecular Pharmacology and Cell Biophysics, Department of Oral Biology, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Makiko Arakaki
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Yuta Chiba
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Masaki Ishikawa
- Division of Operative Dentistry, Department of Restorative Dentistry, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Irma Thesleff
- Developmental Biology Program, Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Satoshi Fukumoto
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Section of Pediatric Dentistry, Division of Oral Health, Growth and Development, Faculty of Dental Science, Kyushu University, Fukuoka 812-8582, Japan
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26
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Bunina D, Abazova N, Diaz N, Noh KM, Krijgsveld J, Zaugg JB. Genomic Rewiring of SOX2 Chromatin Interaction Network during Differentiation of ESCs to Postmitotic Neurons. Cell Syst 2020; 10:480-494.e8. [PMID: 32553182 PMCID: PMC7322528 DOI: 10.1016/j.cels.2020.05.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 03/19/2020] [Accepted: 05/15/2020] [Indexed: 02/08/2023]
Abstract
Cellular differentiation requires dramatic changes in chromatin organization, transcriptional regulation, and protein production. To understand the regulatory connections between these processes, we generated proteomic, transcriptomic, and chromatin accessibility data during differentiation of mouse embryonic stem cells (ESCs) into postmitotic neurons and found extensive associations between different molecular layers within and across differentiation time points. We observed that SOX2, as a regulator of pluripotency and neuronal genes, redistributes from pluripotency enhancers to neuronal promoters during differentiation, likely driven by changes in its protein interaction network. We identified ATRX as a major SOX2 partner in neurons, whose co-localization correlated with an increase in active enhancer marks and increased expression of nearby genes, which we experimentally confirmed for three loci. Collectively, our data provide key insights into the regulatory transformation of SOX2 during neuronal differentiation, and we highlight the significance of multi-omic approaches in understanding gene regulation in complex systems. Complex interplay of RNA, protein, and chromatin during neuronal differentiation Multi-omic profiling reveals divergent roles of SOX2 in stem cells and neurons SOX2 on-chromatin interaction network changes from pluripotent to neuronal factors ATRX interacts with SOX2 in neurons and co-binds highly expressed neuronal genes
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Affiliation(s)
- Daria Bunina
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Nade Abazova
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany; Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Nichole Diaz
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany
| | - Kyung-Min Noh
- Genome Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
| | - Jeroen Krijgsveld
- Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Heidelberg University, Medical Faculty Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.
| | - Judith B Zaugg
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, EMBL, Meyerhofstrasse 1 Heidelberg 69117, Germany.
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27
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Holmes ZE, Hamilton DJ, Hwang T, Parsonnet NV, Rinn JL, Wuttke DS, Batey RT. The Sox2 transcription factor binds RNA. Nat Commun 2020; 11:1805. [PMID: 32286318 PMCID: PMC7156710 DOI: 10.1038/s41467-020-15571-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 03/18/2020] [Indexed: 01/06/2023] Open
Abstract
Certain transcription factors are proposed to form functional interactions with RNA to facilitate proper regulation of gene expression. Sox2, a transcription factor critical for maintenance of pluripotency and neurogenesis, has been found associated with several lncRNAs, although it is unknown whether these interactions are direct or via other proteins. Here we demonstrate that human Sox2 interacts directly with one of these lncRNAs with high affinity through its HMG DNA-binding domain in vitro. These interactions are primarily with double-stranded RNA in a non-sequence specific fashion, mediated by a similar but not identical interaction surface. We further determined that Sox2 directly binds RNA in mouse embryonic stem cells by UV-cross-linked immunoprecipitation of Sox2 and more than a thousand Sox2-RNA interactions in vivo were identified using fRIP-seq. Together, these data reveal that Sox2 employs a high-affinity/low-specificity paradigm for RNA binding in vitro and in vivo. Some transcription factors have been proposed to functionally interact with RNA to facilitate proper regulation of gene expression. Here the authors demonstrate that human Sox2 interact directly and with high affinity to RNAs through its HMG DNA-binding domain.
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Affiliation(s)
- Zachariah E Holmes
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA
| | - Desmond J Hamilton
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA
| | - Taeyoung Hwang
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA
| | - Nicholas V Parsonnet
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA
| | - John L Rinn
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA.,BioFrontiers Institute, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA.
| | - Robert T Batey
- Department of Biochemistry, University of Colorado at Boulder, Campus Box 596, Boulder, CO, 80309, USA.
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28
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Chaudhary S, Islam Z, Mishra V, Rawat S, Ashraf GM, Kolatkar PR. Sox2: A Regulatory Factor in Tumorigenesis and Metastasis. Curr Protein Pept Sci 2019; 20:495-504. [PMID: 30907312 DOI: 10.2174/1389203720666190325102255] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 02/17/2019] [Accepted: 03/12/2019] [Indexed: 01/29/2023]
Abstract
The transcription factor Sox2 plays an important role in various phases of embryonic development, including cell fate and differentiation. These key regulatory functions are facilitated by binding to specific DNA sequences in combination with partner proteins to exert their effects. Recently, overexpression and gene amplification of Sox2 has been associated with tumor aggression and metastasis in various cancer types, including breast, prostate, lung, ovarian and colon cancer. All the different roles for Sox2 involve complicated regulatory networks consisting of protein-protein and protein-nucleic acid interactions. Their involvement in the EMT modulation is possibly enabled by Wnt/ β-catenin and other signaling pathways. There are number of in vivo models which show Sox2 association with increased cancer aggressiveness, resistance to chemo-radiation therapy and decreased survival rate suggesting Sox2 as a therapeutic target. This review will focus on the different roles for Sox2 in metastasis and tumorigenesis. We will also review the mechanism of action underlying the cooperative Sox2- DNA/partner factors binding where Sox2 can be potentially explored for a therapeutic opportunity to treat cancers.
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Affiliation(s)
| | - Zeyaul Islam
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Vijaya Mishra
- RASA Life science Informatics, Pune, Maharashtra, India
| | - Sakshi Rawat
- RASA Life science Informatics, Pune, Maharashtra, India
| | - Ghulam Md Ashraf
- King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Prasanna R Kolatkar
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
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29
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Samudyata, Amaral PP, Engström PG, Robson SC, Nielsen ML, Kouzarides T, Castelo-Branco G. Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells. Exp Cell Res 2019; 381:129-138. [PMID: 31077711 PMCID: PMC6994247 DOI: 10.1016/j.yexcr.2019.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 01/08/2023]
Abstract
Sox2 is a master transcriptional regulator of embryonic development. In this study, we determined the protein interactome of Sox2 in the chromatin and nucleoplasm of mouse embryonic stem (mES) cells. Apart from canonical interactions with pluripotency-regulating transcription factors, we identified interactions with several chromatin modulators, including members of the heterochromatin protein 1 (HP1) family, suggesting a role for Sox2 in chromatin-mediated transcriptional repression. Sox2 was also found to interact with RNA binding proteins (RBPs), including proteins involved in RNA processing. RNA immunoprecipitation followed by sequencing revealed that Sox2 associates with different messenger RNAs, as well as small nucleolar RNA Snord34 and the non-coding RNA 7SK. 7SK has been shown to regulate transcription at gene regulatory regions, which could suggest a functional interaction with Sox2 for chromatin recruitment. Nevertheless, we found no evidence of Sox2 modulating recruitment of 7SK to chromatin when examining 7SK chromatin occupancy by Chromatin Isolation by RNA Purification (ChIRP) in Sox2 depleted mES cells. In addition, knockdown of 7SK in mES cells did not lead to any change in Sox2 occupancy at 7SK-regulated genes. Thus, our results show that Sox2 extensively interacts with RBPs, and suggest that Sox2 and 7SK co-exist in a ribonucleoprotein complex whose function is not to regulate chromatin recruitment, but could rather regulate other processes in the nucleoplasm.
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Affiliation(s)
- Samudyata
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Paulo P Amaral
- The Gurdon Institute, University of Cambridge, United Kingdom
| | - Pär G Engström
- National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Samuel C Robson
- School of Pharmacy and Biomedical Science, University of Portsmouth, United Kingdom
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Tony Kouzarides
- The Gurdon Institute, University of Cambridge, United Kingdom
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Ming Wai Lau Centre for Reparative Medicine, Stockholm Node, Karolinska Institutet, Stockholm, Sweden.
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30
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Zaletel I, Schwirtlich M, Perović M, Jovanović M, Stevanović M, Kanazir S, Puškaš N. Early Impairments of Hippocampal Neurogenesis in 5xFAD Mouse Model of Alzheimer’s Disease Are Associated with Altered Expression of SOXB Transcription Factors. J Alzheimers Dis 2018; 65:963-976. [DOI: 10.3233/jad-180277] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Ivan Zaletel
- Institute of Histology and Embryology “Aleksandar Đ Kostić”, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Marija Schwirtlich
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Milka Perović
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Mirna Jovanović
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Milena Stevanović
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
- University of Belgrade, Faculty of Biology, Belgrade, Serbia
- Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | - Selma Kanazir
- Institute for Biological Research “Siniša Stanković”, University of Belgrade, Belgrade, Serbia
| | - Nela Puškaš
- Institute of Histology and Embryology “Aleksandar Đ Kostić”, School of Medicine, University of Belgrade, Belgrade, Serbia
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31
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Sanosaka T, Imamura T, Hamazaki N, Chai M, Igarashi K, Ideta-Otsuka M, Miura F, Ito T, Fujii N, Ikeo K, Nakashima K. DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells. Cell Rep 2018; 20:2992-3003. [PMID: 28930691 DOI: 10.1016/j.celrep.2017.08.086] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 07/10/2017] [Accepted: 08/25/2017] [Indexed: 12/17/2022] Open
Abstract
Regulation of the epigenome during in vivo specification of brain stem cells is still poorly understood. Here, we report DNA methylome analyses of directly sampled cortical neural stem and progenitor cells (NS/PCs) at different development stages, as well as those of terminally differentiated cortical neurons, astrocytes, and oligodendrocytes. We found that sequential specification of cortical NS/PCs is regulated by two successive waves of demethylation at early and late development stages, which are responsible for the establishment of neuron- and glia-specific low-methylated regions (LMRs), respectively. The regulatory role of demethylation of the gliogenic genes was substantiated by the enrichment of nuclear factor I (NFI)-binding sites. We provide evidence that de novo DNA methylation of neuron-specific LMRs establishes glia-specific epigenotypes, essentially by silencing neuronal genes. Our data highlight the in vivo implications of DNA methylation dynamics in shaping epigenomic features that confer the differentiation potential of NS/PCs sequentially during development.
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Affiliation(s)
- Tsukasa Sanosaka
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Takuya Imamura
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
| | - Nobuhiko Hamazaki
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - MuhChyi Chai
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Katsuhide Igarashi
- Life Science Tokyo Advanced Research Center (L-StaR), Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Maky Ideta-Otsuka
- Life Science Tokyo Advanced Research Center (L-StaR), Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-5801, Japan
| | - Fumihito Miura
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Nobuyuki Fujii
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kazuho Ikeo
- Center for Information Biology, National Institute of Genetics, Research Organization of Information and Systems, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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A role for SOX9 in post-transcriptional processes: insights from the amphibian oocyte. Sci Rep 2018; 8:7191. [PMID: 29740094 PMCID: PMC5940923 DOI: 10.1038/s41598-018-25356-1] [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: 03/27/2017] [Accepted: 03/22/2018] [Indexed: 11/13/2022] Open
Abstract
Sox9 is a member of the gene family of SOX transcription factors, which is highly conserved among vertebrates. It is involved in different developmental processes including gonadogenesis. In all amniote species examined thus far, Sox9 is expressed in the Sertoli cells of the male gonad, suggesting an evolutionarily conserved role in testis development. However, in the anamniotes, fishes and amphibians, it is also expressed in the oocyte but the significance of such an expression remains to be elucidated. Here, we have investigated the nuclear localization of the SOX9 protein in the oocyte of three amphibian species, the urodelan Pleurodeles waltl, and two anurans, Xenopus laevis and Xenopus tropicalis. We demonstrate that SOX9 is associated with ribonucleoprotein (RNP) transcripts of lampbrush chromosomes in an RNA-dependent manner. This association can be visualized by Super-resolution Structured Illumination Microscopy (SIM). Our results suggest that SOX9, known to bind DNA, also carries an additional function in the posttranscriptional processes. We also discuss the significance of the acquisition or loss of Sox9 expression in the oocyte during evolution at the transition between anamniotes and amniotes.
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Makrides N, Panayiotou E, Fanis P, Karaiskos C, Lapathitis G, Malas S. Sequential Role of SOXB2 Factors in GABAergic Neuron Specification of the Dorsal Midbrain. Front Mol Neurosci 2018; 11:152. [PMID: 29867344 PMCID: PMC5952183 DOI: 10.3389/fnmol.2018.00152] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/17/2018] [Indexed: 12/23/2022] Open
Abstract
Studies proposed a model for embryonic neurogenesis where the expression levels of the SOXB2 and SOXB1 factors regulate the differentiation status of the neural stem cells. However, the precise role of the SOXB2 genes remains controversial. Therefore, this study aims to investigate the effects of individual deletions of the SOX21 and SOX14 genes during the development of the dorsal midbrain. We show that SOX21 and SOX14 function distinctly during the commitment of the GABAergic lineage. More explicitly, deletion of SOX21 reduced the expression of the GABAergic precursor marker GATA3 and BHLHB5 while the expression of GAD6, which marks GABAergic terminal differentiation, was not affected. In contrast deletion of SOX14 alone was sufficient to inhibit terminal differentiation of the dorsal midbrain GABAergic neurons. Furthermore, we demonstrate through gain-of-function experiments, that despite the homology of SOX21 and SOX14, they have unique gene targets and cannot compensate for the loss of each other. Taken together, these data do not support a pan-neurogenic function for SOXB2 genes in the dorsal midbrain, but instead they influence, sequentially, the specification of GABAergic neurons.
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Affiliation(s)
- Neoklis Makrides
- Developmental and Functional Genetics Group, The Cyprus Institute of Neurology & Genetics and Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Elena Panayiotou
- Neurologic Clinic A, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Pavlos Fanis
- Department of Molecular Genetics, Function & Therapy, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Christos Karaiskos
- Neuroscience Laboratory, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - George Lapathitis
- Neuroscience Laboratory, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Stavros Malas
- Developmental and Functional Genetics Group, The Cyprus Institute of Neurology & Genetics and Cyprus School of Molecular Medicine, Nicosia, Cyprus
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Wuebben EL, Rizzino A. The dark side of SOX2: cancer - a comprehensive overview. Oncotarget 2018; 8:44917-44943. [PMID: 28388544 PMCID: PMC5546531 DOI: 10.18632/oncotarget.16570] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 03/16/2017] [Indexed: 12/14/2022] Open
Abstract
The pluripotency-associated transcription factor SOX2 is essential during mammalian embryogenesis and later in life, but SOX2 expression can also be highly detrimental. Over the past 10 years, SOX2 has been shown to be expressed in at least 25 different cancers. This review provides a comprehensive overview of the roles of SOX2 in cancer and focuses on two broad topics. The first delves into the expression and function of SOX2 in cancer focusing on the connection between SOX2 levels and tumor grade as well as patient survival. As part of this discussion, we address the developing connection between SOX2 expression and tumor drug resistance. We also call attention to an under-appreciated property of SOX2, its levels in actively proliferating tumor cells appear to be optimized to maximize tumor growth - too little or too much SOX2 dramatically alters tumor growth. The second topic of this review focuses on the exquisite array of molecular mechanisms that control the expression and transcriptional activity of SOX2. In addition to its complex regulation at the transcriptional level, SOX2 expression and activity are controlled carefully by microRNAs, long non-coding RNAs, and post-translational modifications. In the Conclusion and Future Perspectives section, we point out that there are still important unanswered questions. Addressing these questions is expected to lead to new insights into the functions of SOX2 in cancer, which will help design novels strategies for more effectively treating some of the most deadly cancers.
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Affiliation(s)
- Erin L Wuebben
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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Wuebben EL, Wilder PJ, Cox JL, Grunkemeyer JA, Caffrey T, Hollingsworth MA, Rizzino A. SOX2 functions as a molecular rheostat to control the growth, tumorigenicity and drug responses of pancreatic ductal adenocarcinoma cells. Oncotarget 2017; 7:34890-906. [PMID: 27145457 PMCID: PMC5085197 DOI: 10.18632/oncotarget.8994] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/16/2016] [Indexed: 12/16/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly deadly malignancy. Expression of the stem cell transcription factor SOX2 increases during progression of PDAC. Knockdown of SOX2 in PDAC cell lines decreases growth in vitro; whereas, stable overexpression of SOX2 in one PDAC cell line reportedly increases growth in vitro. Here, we reexamined the role of SOX2 in PDAC cells, because inducible SOX2 overexpression in other tumor cell types inhibits growth. In this study, four PDAC cell lines were engineered for inducible overexpression of SOX2 or inducible knockdown of SOX2. Remarkably, inducible overexpression of SOX2 in PDAC cells inhibits growth in vitro and reduces tumorigenicity. Additionally, inducible knockdown of SOX2 in PDAC cells reduces growth in vitro and in vivo. Thus, growth and tumorigenicity of PDAC cells is highly dependent on the expression of optimal levels of SOX2 – a hallmark of molecular rheostats. We also determined that SOX2 alters the responses of PDAC cells to drugs used in PDAC clinical trials. Increasing SOX2 reduces growth inhibition mediated by MEK and AKT inhibitors; whereas knockdown of SOX2 further reduces growth when PDAC cells are treated with these inhibitors. Thus, targeting SOX2, or its mode of action, could improve the treatment of PDAC.
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Affiliation(s)
- Erin L Wuebben
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950, USA
| | - Phillip J Wilder
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950, USA
| | - Jesse L Cox
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska 68198-3135, USA
| | - James A Grunkemeyer
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950, USA
| | - Thomas Caffrey
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950, USA
| | - Michael A Hollingsworth
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, Nebraska 68198-5950, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68198-5870, USA
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36
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Kim BR, Coyaud E, Laurent EMN, St-Germain J, Van de Laar E, Tsao MS, Raught B, Moghal N. Identification of the SOX2 Interactome by BioID Reveals EP300 as a Mediator of SOX2-dependent Squamous Differentiation and Lung Squamous Cell Carcinoma Growth. Mol Cell Proteomics 2017; 16:1864-1888. [PMID: 28794006 PMCID: PMC5629269 DOI: 10.1074/mcp.m116.064451] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 05/05/2017] [Indexed: 11/06/2022] Open
Abstract
Lung cancer is the leading cause of cancer mortality worldwide, with squamous cell carcinoma (SQCC) being the second most common form. SQCCs are thought to originate in bronchial basal cells through an injury response to smoking, which results in this stem cell population committing to hyperplastic squamous rather than mucinous and ciliated fates. Copy number gains in SOX2 in the region of 3q26-28 occur in 94% of SQCCs, and appear to act both early and late in disease progression by stabilizing the initial squamous injury response in stem cells and promoting growth of invasive carcinoma. Thus, anti-SOX2 targeting strategies could help treat early and/or advanced disease. Because SOX2 itself is not readily druggable, we sought to characterize SOX2 binding partners, with the hope of identifying new strategies to indirectly interfere with SOX2 activity. We now report the first use of proximity-dependent biotin labeling (BioID) to characterize the SOX2 interactome in vivo We identified 82 high confidence SOX2-interacting partners. An interaction with the coactivator EP300 was subsequently validated in both basal cells and SQCCs, and we demonstrate that EP300 is necessary for SOX2 activity in basal cells, including for induction of the squamous fate. We also report that EP300 copy number gains are common in SQCCs and that growth of lung cancer cell lines with 3q gains, including SQCC cells, is dependent on EP300. Finally, we show that EP300 inhibitors can be combined with other targeted therapeutics to achieve more effective growth suppression. Our work supports the use of BioID to identify interacting protein partners of nondruggable oncoproteins such as SOX2, as an effective strategy to discover biologically relevant, druggable targets.
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Affiliation(s)
- Bo Ram Kim
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- §Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Etienne Coyaud
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Estelle M N Laurent
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Jonathan St-Germain
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Emily Van de Laar
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Ming-Sound Tsao
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- ¶Department of Laboratory Medicine and Pathobiology, University of Toronto, Ontario, Canada
| | - Brian Raught
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
- §Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Nadeem Moghal
- From the ‡Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada;
- §Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
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Abazova N, Krijgsveld J. Advances in stem cell proteomics. Curr Opin Genet Dev 2017; 46:149-155. [PMID: 28806595 DOI: 10.1016/j.gde.2017.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/14/2017] [Accepted: 07/20/2017] [Indexed: 12/15/2022]
Abstract
Stem cells are at the basis of organismal development, characterized by their potential to differentiate towards specific lineages upon receiving proper signals. To understand the molecular principles underlying gain and loss of pluripotency, proteomics plays an increasingly important role owing to technical developments in mass spectrometry and implementation of innovative biochemical approaches. Here we review how quantitative proteomics has been used to investigate protein expression, localization, interaction and modification in stem cells both in vitro and in vivo, thereby complementing other omics approaches to study fundamental properties of stem cell plasticity.
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Affiliation(s)
- Nade Abazova
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, Heidelberg, Germany.
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38
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Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J. Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins. Mol Cell 2016; 64:624-635. [PMID: 27773674 PMCID: PMC5101186 DOI: 10.1016/j.molcel.2016.09.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/11/2016] [Accepted: 09/14/2016] [Indexed: 12/13/2022]
Abstract
Maintenance of pluripotency is regulated by a network of transcription factors coordinated by Oct4, Sox2, and Nanog (OSN), yet a systematic investigation of the composition and dynamics of the OSN protein network specifically on chromatin is still missing. Here we have developed a method combining ChIP with selective isolation of chromatin-associated proteins (SICAP) followed by mass spectrometry to identify chromatin-bound partners of a protein of interest. ChIP-SICAP in mouse embryonic stem cells (ESCs) identified over 400 proteins associating with OSN, including several whose interaction depends on the pluripotent state. Trim24, a previously unrecognized protein in the network, converges with OSN on multiple enhancers and suppresses the expression of developmental genes while activating cell cycle genes. Consistently, Trim24 significantly improved efficiency of cellular reprogramming, demonstrating its direct functionality in establishing pluripotency. Collectively, ChIP-SICAP provides a powerful tool to decode chromatin protein composition, further enhanced by its integrative capacity to perform ChIP-seq. ChIP-SICAP isolates and identifies proteins that colocalize on chromatin Chromatin composition around Oct4, Sox2, and Nanog depends on the pluripotent state Trim24 is part of the pluripotency network and promotes reprogramming ChIP-SICAP allows recovery of DNA for sequencing with ChIP-seq quality
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Affiliation(s)
- Mahmoud-Reza Rafiee
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Charles Girardot
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gianluca Sigismondo
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120 Heidelberg, Germany; Excellence Cluster CellNetworks, Heidelberg University, 69120 Heidelberg, Germany; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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Liu Z, Lam N, Thiele CJ. Zinc finger transcription factor CASZ1 interacts with histones, DNA repair proteins and recruits NuRD complex to regulate gene transcription. Oncotarget 2016; 6:27628-40. [PMID: 26296975 PMCID: PMC4695013 DOI: 10.18632/oncotarget.4733] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 07/27/2015] [Indexed: 11/25/2022] Open
Abstract
The zinc finger transcription factor CASZ1 has been found to control neural fate-determination in flies, regulate murine and frog cardiac development, control murine retinal cell progenitor expansion and function as a tumor suppressor gene in humans. However, the molecular mechanism by which CASZ1 regulates gene transcription to exert these diverse biological functions has not been described. Here we identify co-factors that are recruited by CASZ1b to regulate gene transcription using co-immunoprecipitation (co-IP) and mass spectrometry assays. We find that CASZ1b binds to the nucleosome remodeling and histone deacetylase (NuRD) complex, histones and DNA repair proteins. Mutagenesis of the CASZ1b protein assay demonstrates that the N-terminus of CASZ1b is required for NuRD binding, and a poly(ADP-ribose) binding motif in the CASZ1b protein is required for histone H3 and DNA repair proteins binding. The N-terminus of CASZ1b fused to an artificial DNA-binding domain (GAL4DBD) causes a significant repression of transcription (5xUAS-luciferase assay), which could be blocked by treatment with an HDAC inhibitor. Realtime PCR results show that the transcriptional activity of CASZ1b mutants that abrogate NuRD or histone H3/DNA binding is significantly decreased. This indicates a model in which CASZ1b binds to chromatin and recruits NuRD complexes to orchestrate epigenetic-mediated transcriptional programs.
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Affiliation(s)
- Zhihui Liu
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Norris Lam
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
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40
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Focareta L, Cole AG. Analyses of Sox-B and Sox-E Family Genes in the Cephalopod Sepia officinalis: Revealing the Conserved and the Unusual. PLoS One 2016; 11:e0157821. [PMID: 27331398 PMCID: PMC4917168 DOI: 10.1371/journal.pone.0157821] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 06/05/2016] [Indexed: 11/18/2022] Open
Abstract
Cephalopods provide an unprecedented opportunity for comparative studies of the developmental genetics of organ systems that are convergent with analogous vertebrate structures. The Sox-family of transcription factors is an important class of DNA-binding proteins that are known to be involved in many aspects of differentiation, but have been largely unstudied in lophotrochozoan systems. Using a degenerate primer strategy we have isolated coding sequence for three members of the Sox family of transcription factors from a cephalopod mollusk, the European cuttlefish Sepia officinalis: Sof-SoxE, Sof-SoxB1, and Sof-SoxB2. Analyses of their expression patterns during organogenesis reveals distinct spatial and temporal expression domains. Sof-SoxB1 shows early ectodermal expression throughout the developing epithelium, which is gradually restricted to presumptive sensory epithelia. Expression within the nervous system appears by mid-embryogenesis. Sof-SoxB2 expression is similar to Sof-SoxB1 within the developing epithelia in early embryogenesis, however appears in largely non-overlapping expression domains within the central nervous system and is not expressed in the maturing sensory epithelium. In contrast, Sof-SoxE is expressed throughout the presumptive mesodermal territories at the onset of organogenesis. As development proceeds, Sof-SoxE expression is elevated throughout the developing peripheral circulatory system. This expression disappears as the circulatory system matures, but expression is maintained within undifferentiated connective tissues throughout the animal, and appears within the nervous system near the end of embryogenesis. SoxB proteins are widely known for their role in neural specification in numerous phylogenetic lineages. Our data suggests that Sof-SoxB genes play similar roles in cephalopods. In contrast, Sof-SoxE appears to be involved in the early stages of vasculogenesis of the cephalopod closed circulatory system, a novel role for a member of this gene family.
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41
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Leung CY, Zhu M, Zernicka-Goetz M. Polarity in Cell-Fate Acquisition in the Early Mouse Embryo. Curr Top Dev Biol 2016; 120:203-34. [PMID: 27475853 DOI: 10.1016/bs.ctdb.2016.04.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Establishing polarity is a fundamental part of embryogenesis and can be traced back to the earliest developmental stages. It can be achieved in one of two ways: through the preexisting polarization of germ cells before fertilization or via symmetry breaking after fertilization. In mammals, it seems to be the latter, and we will discuss the various cytological and molecular events that lead up to this event, its mechanisms and the consequences. In mammals, the first polarization event occurs in the preimplantation period, when the embryo is but a cluster of cells, free-floating in the oviduct. This provides a unique, autonomous system to study the de novo polarization that is essential to life. In this review, we will cover modern and past studies on the polarization of the early embryo, using the mouse as a model system, as well as hypothesizing the potential implications and functions of the biological events involved.
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Affiliation(s)
- C Y Leung
- University of Cambridge, Cambridge, United Kingdom
| | - M Zhu
- University of Cambridge, Cambridge, United Kingdom
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42
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Qi D, Wang Q, Yu M, Lan R, Li S, Lu F. Mitotic phosphorylation of SOX2 mediated by Aurora kinase A is critical for the stem-cell like cell maintenance in PA-1 cells. Cell Cycle 2016; 15:2009-18. [PMID: 27249336 DOI: 10.1080/15384101.2016.1192729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Transcription factor SOX2 is multiple phosphorylated. However, the kinase and the timing regulating SOX2 phosphorylation remains poorly understood. Here we reported mitotic phosphorylation of SOX2 by Aurora kinase A (AURKA). AURKA inhibitors (VX680, Aurora kinase Inhibitor I) but not PLK1 inhibitors (BI2536, CBB2001) eliminate the mitotic phosphorylation of SOX2. Consistently, siRNA inhibition of AURKA can eliminate mitotic SOX2 phosphorylation. Ser220 and Ser251 are two sites that identified for mitotic phosphorylation on SOX2. Moreover, SOX2 mutants (S220A and S251A) can promote SOX2 induced OCT4 re-expression in differentiated cells. These findings reveal a novel regulation mechanism of SOX2 phosphorylation mediated by AURKA in mitosis and its function in stem cell pluripotency maintenance in cancer cells.
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Affiliation(s)
- Dandan Qi
- a Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School , Shenzhen , China
| | - Qianqian Wang
- a Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School , Shenzhen , China
| | - Min Yu
- a Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School , Shenzhen , China
| | - Rongfeng Lan
- b Institute of Research and Continuing Education, Hong Kong Baptist University , Shenzhen , China
| | - Shuiming Li
- c Key Laboratory of Marine Bioresources and Ecology, College of Life Science, Shenzhen University , Shenzhen , China
| | - Fei Lu
- a Laboratory of Chemical Genomics, School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School , Shenzhen , China
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Goolam M, Scialdone A, Graham SJL, Macaulay IC, Jedrusik A, Hupalowska A, Voet T, Marioni JC, Zernicka-Goetz M. Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos. Cell 2016; 165:61-74. [PMID: 27015307 PMCID: PMC4819611 DOI: 10.1016/j.cell.2016.01.047] [Citation(s) in RCA: 284] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/10/2015] [Accepted: 01/22/2016] [Indexed: 01/08/2023]
Abstract
The major and essential objective of pre-implantation development is to establish embryonic and extra-embryonic cell fates. To address when and how this fundamental process is initiated in mammals, we characterize transcriptomes of all individual cells throughout mouse pre-implantation development. This identifies targets of master pluripotency regulators Oct4 and Sox2 as being highly heterogeneously expressed between blastomeres of the 4-cell embryo, with Sox21 showing one of the most heterogeneous expression profiles. Live-cell tracking demonstrates that cells with decreased Sox21 yield more extra-embryonic than pluripotent progeny. Consistently, decreasing Sox21 results in premature upregulation of the differentiation regulator Cdx2, suggesting that Sox21 helps safeguard pluripotency. Furthermore, Sox21 is elevated following increased expression of the histone H3R26-methylase CARM1 and is lowered following CARM1 inhibition, indicating the importance of epigenetic regulation. Therefore, our results indicate that heterogeneous gene expression, as early as the 4-cell stage, initiates cell-fate decisions by modulating the balance of pluripotency and differentiation.
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Affiliation(s)
- Mubeen Goolam
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Antonio Scialdone
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Sarah J L Graham
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Iain C Macaulay
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Agnieszka Jedrusik
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Anna Hupalowska
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK
| | - Thierry Voet
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - John C Marioni
- European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK; Cancer Research UK-Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK.
| | - Magdalena Zernicka-Goetz
- Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.
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The zinc-finger transcription factor SALL4 is frequently expressed in human cancers: association with clinical outcome in squamous cell carcinoma but not in adenocarcinoma of the esophagus. Virchows Arch 2016; 468:483-92. [PMID: 26818834 DOI: 10.1007/s00428-016-1908-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 01/05/2016] [Accepted: 01/14/2016] [Indexed: 12/18/2022]
Abstract
SALL4 is a transcription factor originally identified as a homeotic gene essential for organ development. Early studies suggested that SALL4 is a useful marker to identify testicular and ovarian germ cell tumors. The aim of the study was to evaluate the diagnostic potential of SALL4 immunohistochemistry. Immunohistochemical staining was performed on a tissue microarray (TMA) with 3966 samples from 94 different tumor types and on a further TMA with 492 esophagus carcinomas. SALL4 immunostaining was by far most prevalent and most intensive in testicular tumors with a positivity rate of 93.1% in seminomas, 80% in mixed germ cell tumors (embryonic carcinomas/yolk sac tumors), and 18.5% in teratomas, respectively. However, SALL4 expression is not specific to germ cell tumors. We observed SALL4 positivity in non-germ cell tumors as carcinomas of the kidney (28.9% of chromophobe, 34.4% of clear cell carcinoma), in intestinal type adenocarcinoma of the stomach (10.9%), in adenocarcinoma (10.5%) and squamous cell carcinoma (7.2%) of the esophagus, and in malignant melanoma (8.1%) and invasive urothelial bladder carcinoma (20%). SALL4 expression was not found in lymphomas, in soft tissue tumors or breast tumors. At analysis of esophagus carcinoma TMA, no significant association was seen between SALL4 expression and overall survival in adenocarcinoma. However, SALL4 expression was strongly associated with worse overall survival in squamous cell carcinoma. SALL4 expression can be found at relevant frequencies in various tumors of different primary sites. SALL4 expression in squamous cell carcinoma of the esophagus may constitute a sign of dedifferentiation leading to poor patient prognosis.
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Winiecka-Klimek M, Smolarz M, Walczak MP, Zieba J, Hulas-Bigoszewska K, Kmieciak B, Piaskowski S, Rieske P, Grzela DP, Stoczynska-Fidelus E. SOX2 and SOX2-MYC Reprogramming Process of Fibroblasts to the Neural Stem Cells Compromised by Senescence. PLoS One 2015; 10:e0141688. [PMID: 26535892 PMCID: PMC4633175 DOI: 10.1371/journal.pone.0141688] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 10/11/2015] [Indexed: 11/19/2022] Open
Abstract
Tumorigenic potential of induced pluripotent stem cells (iPSCs) infiltrating population of induced neural stem cells (iNSCs) generated from iPSCs may limit their medical applications. To overcome such a difficulty, direct reprogramming of adult somatic cells into iNSCs was proposed. The aim of this study was the systematic comparison of induced neural cells (iNc) obtained with different methods—direct reprogramming of human adult fibroblasts with either SOX2 (SiNSc-like) or SOX2 and c-MYC (SMiNSc-like) and induced pluripotent stem cells differentiation to ebiNSc—in terms of gene expression profile, differentiation potential as well as proliferation properties. Immunocytochemistry and real-time PCR analyses were used to evaluate gene expression profile and differentiation potential of various iNc types. Bromodeoxyuridine (BrdU) incorporation and senescence-associated beta-galactosidase (SA-β-gal) assays were used to estimate proliferation potential. All three types of iNc were capable of neuronal differentiation; however, astrocytic differentiation was possible only in case of ebiNSc. Contrary to ebiNSc generation, the direct reprogramming was rarely a propitious process, despite 100% transduction efficiency. The potency of direct iNSCs-like cells generation was lower as compared to iNSCs obtained by iPSCs differentiation, and only slightly improved when c-MYC was added. Directly reprogrammed iNSCs-like cells were lacking the ability to differentiate into astrocytic cells and characterized by poor efficiency of neuronal cells formation. Such features indicated that these cells could not be fully reprogrammed, as confirmed mainly with senescence detection. Importantly, SiNSc-like and SMiNSc-like cells were unable to achieve the long-term survival and became senescent, which limits their possible therapeutic applicability. Our results suggest that iNSCs-like cells, generated in the direct reprogramming attempts, were either not fully reprogrammed or reprogrammed only into neuronal progenitors, mainly because of the inaccuracies of currently available protocols.
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Affiliation(s)
- Marta Winiecka-Klimek
- Department of Research and Development, Celther Polska, Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
- * E-mail:
| | - Maciej Smolarz
- Department of Research and Development, Celther Polska, Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Maciej P. Walczak
- Department of Research and Development, Celther Polska, Lodz, Poland
| | - Jolanta Zieba
- Department of Research and Development, Celther Polska, Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | | | - Blazej Kmieciak
- Department of Medical Law, Chair of Human Sciences, Medical University of Lodz, Lodz, Poland
| | - Sylwester Piaskowski
- Department of Research and Development, Celther Polska, Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Piotr Rieske
- Department of Research and Development, Celther Polska, Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
| | - Dawid P. Grzela
- Department of Research and Development, Celther Polska, Lodz, Poland
| | - Ewelina Stoczynska-Fidelus
- Department of Research and Development, Celther Polska, Lodz, Poland
- Department of Tumor Biology, Medical University of Lodz, Lodz, Poland
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Moretto Zita M, Soncin F, Natale D, Pizzo D, Parast M. Gene Expression Profiling Reveals a Novel Regulatory Role for Sox21 Protein in Mouse Trophoblast Stem Cell Differentiation. J Biol Chem 2015; 290:30152-62. [PMID: 26491013 DOI: 10.1074/jbc.m115.659094] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Indexed: 11/06/2022] Open
Abstract
Appropriate self-renewal and differentiation of trophoblast stem cells (TSCs) are key factors for proper placental development and function and, in turn, for appropriate in utero fetal growth. To identify novel TSC-specific genes, we performed genome-wide expression profiling of TSCs, embryonic stem cells, epiblast stem cells, and mouse embryo fibroblasts, derived from mice of the same genetic background. Our analysis revealed a high expression of Sox21 in TSCs compared with other cell types. Sox21 levels were high in undifferentiated TSCs and were dramatically reduced upon differentiation. In addition, modulation of Sox21 expression in TSCs affected lineage-specific differentiation, based on both marker analysis and functional assessment. Our results implicate Sox21 specifically in the promotion of spongiotrophoblast and giant cell differentiation and establish a new mechanism through which trophoblast sublineages are specified.
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Affiliation(s)
| | | | - David Natale
- Reproductive Medicine, University of California San Diego, La Jolla, California 92093
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47
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Jamin A, Wiebe MS. Barrier to Autointegration Factor (BANF1): interwoven roles in nuclear structure, genome integrity, innate immunity, stress responses and progeria. Curr Opin Cell Biol 2015; 34:61-8. [PMID: 26072104 DOI: 10.1016/j.ceb.2015.05.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 05/20/2015] [Accepted: 05/27/2015] [Indexed: 11/24/2022]
Abstract
The Barrier to Autointegration Factor (BAF or BANF1) is an abundant, highly conserved DNA binding protein. BAF is involved in multiple pathways including mitosis, nuclear assembly, viral infection, chromatin and gene regulation and the DNA damage response. BAF is also essential for early development in metazoans and relevant to human physiology; BANF1 mutations cause a progeroid syndrome, placing BAF within the laminopathy disease spectrum. This review summarizes previous knowledge about BAF in the context of recent discoveries about its protein partners, posttranslational regulation, dynamic subcellular localizations and roles in disease, innate immunity, transposable elements and genome integrity.
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Affiliation(s)
- Augusta Jamin
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE 68583-0900, USA; Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA
| | - Matthew S Wiebe
- School of Veterinary Medicine and Biomedical Sciences, University of Nebraska, Lincoln, NE 68583-0900, USA; Nebraska Center for Virology, University of Nebraska, Lincoln, NE 68583-0900, USA.
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48
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Ding J, Huang X, Shao N, Zhou H, Lee DF, Faiola F, Fidalgo M, Guallar D, Saunders A, Shliaha PV, Wang H, Waghray A, Papatsenko D, Sánchez-Priego C, Li D, Yuan Y, Lemischka IR, Shen L, Kelley K, Deng H, Shen X, Wang J. Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming. Cell Stem Cell 2015; 16:653-68. [PMID: 25936917 PMCID: PMC4458159 DOI: 10.1016/j.stem.2015.04.001] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 03/25/2015] [Accepted: 04/03/2015] [Indexed: 12/12/2022]
Abstract
Super-enhancers (SEs) are large clusters of transcriptional enhancers that are co-occupied by multiple lineage-specific transcription factors driving expression of genes that define cell identity. In embryonic stem cells (ESCs), SEs are highly enriched for the core pluripotency factors Oct4, Sox2, and Nanog. In this study, we sought to dissect the molecular control mechanism of SE activity in pluripotency and reprogramming. Starting from a protein interaction network surrounding Sox2, we identified Tex10 as a key pluripotency factor that plays a functionally significant role in ESC self-renewal, early embryo development, and reprogramming. Tex10 is enriched at SEs in a Sox2-dependent manner and coordinates histone acetylation and DNA demethylation at SEs. Tex10 activity is also important for pluripotency and reprogramming in human cells. Our study therefore highlights Tex10 as a core component of the pluripotency network and sheds light on its role in epigenetic control of SE activity for cell fate determination.
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Affiliation(s)
- Junjun Ding
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xin Huang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ningyi Shao
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Hongwei Zhou
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dung-Fang Lee
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Francesco Faiola
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Miguel Fidalgo
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Diana Guallar
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arven Saunders
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Pavel V Shliaha
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB21QR, UK
| | - Hailong Wang
- Organ Transplantation Institute, Xiamen University, Xiamen City, Fujian Province 361102, China
| | - Avinash Waghray
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitri Papatsenko
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carlos Sánchez-Priego
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dan Li
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ye Yuan
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ihor R Lemischka
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Shen
- Fishberg Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Kevin Kelley
- Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Haiteng Deng
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jianlong Wang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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49
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Gayle S, Pan Y, Landrette S, Xu T. piggyBac insertional mutagenesis screen identifies a role for nuclear RHOA in human ES cell differentiation. Stem Cell Reports 2015; 4:926-38. [PMID: 25866159 PMCID: PMC4437468 DOI: 10.1016/j.stemcr.2015.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/02/2015] [Accepted: 03/02/2015] [Indexed: 01/22/2023] Open
Abstract
The mechanisms regulating human embryonic stem (ES) cell self-renewal and differentiation are not well defined in part due to the lack of tools for forward genetic analysis. We present a piggyBac transposon gain of function screen in human ES cells that identifies DENND2C, which genetically cooperates with NANOG to maintain self-renewal in the presence of retinoic acid. We show that DENND2C negatively regulates RHOA activity, which cooperates with NANOG to block differentiation. It has been recently shown that RHOA exists in the nucleus and is activated by DNA damage; however, its nuclear function remains unknown. We discovered that RHOA associates with DNA and that DENND2C affects nuclear RHOA localization, activity, and DNA association. Our study illustrates the power of piggyBac as a cost-effective, efficient, and easy to use tool for forward genetic screens in human ES cells and provides insight into the role of RHOA in the nucleus. NANOG-sensitized piggyBac screen for regulators of stem cell differentiation DENND2C is a negative regulator of RHOA Genetic cooperation exists between RHOA and NANOG Nuclear RHOA associates with DNA
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Affiliation(s)
- Sophia Gayle
- Howard Hughes Medical Institute and Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yukun Pan
- Howard Hughes Medical Institute and Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sean Landrette
- Howard Hughes Medical Institute and Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Tian Xu
- Howard Hughes Medical Institute and Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
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50
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Whittington N, Cunningham D, Le TK, De Maria D, Silva EM. Sox21 regulates the progression of neuronal differentiation in a dose-dependent manner. Dev Biol 2015; 397:237-47. [PMID: 25448693 PMCID: PMC4325979 DOI: 10.1016/j.ydbio.2014.11.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 11/12/2014] [Indexed: 12/27/2022]
Abstract
Members of the SoxB transcription factor family play critical roles in the regulation of neurogenesis. The SoxB1 proteins are required for the induction and maintenance of a proliferating neural progenitor population in numerous vertebrates, however the role of the SoxB2 protein, Sox21, is less clear due to conflicting results. To clarify the role of Sox21 in neurogenesis, we examined its function in the Xenopus neural plate. Here we report that misexpression of Sox21 expands the neural progenitor domain, and represses neuron formation by binding to Neurogenin (Ngn2) and blocking its function. Conversely, we found that Sox21 is also required for neuron formation, as cells lacking Sox21 undergo cell death and thus are unable to differentiate. Together our data indicate that Sox21 plays more than one role in neurogenesis, where a threshold level is required for cell viability and normal differentiation of neurons, but a higher concentration of Sox21 inhibits neuron formation and instead promotes progenitor maintenance.
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Affiliation(s)
- Niteace Whittington
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Doreen Cunningham
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Thien-Kim Le
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - David De Maria
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
| | - Elena M Silva
- Department of Biology, Georgetown University, 37th and O Streets NW, Regents Hall 408, Washington, DC 20057, USA.
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