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Mitra S, Bp K, C R S, Saikumar NV, Philip P, Narayanan M. Alzheimer's disease rewires gene coexpression networks coupling different brain regions. NPJ Syst Biol Appl 2024; 10:50. [PMID: 38724582 PMCID: PMC11082197 DOI: 10.1038/s41540-024-00376-y] [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: 10/21/2023] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Connectome studies have shown how Alzheimer's disease (AD) disrupts functional and structural connectivity among brain regions. But the molecular basis of such disruptions is less studied, with most genomic/transcriptomic studies performing within-brain-region analyses. To inspect how AD rewires the correlation structure among genes in different brain regions, we performed an Inter-brain-region Differential Correlation (Inter-DC) analysis of RNA-seq data from Mount Sinai Brain Bank on four brain regions (frontal pole, superior temporal gyrus, parahippocampal gyrus and inferior frontal gyrus, comprising 264 AD and 372 control human post-mortem samples). An Inter-DC network was assembled from all pairs of genes across two brain regions that gained (or lost) correlation strength in the AD group relative to controls at FDR 1%. The differentially correlated (DC) genes in this network complemented known differentially expressed genes in AD, and likely reflects cell-intrinsic changes since we adjusted for cell compositional effects. Each brain region used a distinctive set of DC genes when coupling with other regions, with parahippocampal gyrus showing the most rewiring, consistent with its known vulnerability to AD. The Inter-DC network revealed master dysregulation hubs in AD (at genes ZKSCAN1, SLC5A3, RCC1, IL17RB, PLK4, etc.), inter-region gene modules enriched for known AD pathways (synaptic signaling, endocytosis, etc.), and candidate signaling molecules that could mediate region-region communication. The Inter-DC network generated in this study is a valuable resource of gene pairs, pathways and signaling molecules whose inter-brain-region functional coupling is disrupted in AD, thereby offering a new perspective of AD etiology.
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Affiliation(s)
- Sanga Mitra
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Kailash Bp
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Srivatsan C R
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Naga Venkata Saikumar
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India
| | - Philge Philip
- Centre for Integrative Biology and Systems Medicine, IIT Madras, Chennai, India
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, Chennai, India
| | - Manikandan Narayanan
- Bioinformatics and Integrative Data Science group, Department of Computer Science and Engineering, Indian Institute of Technology (IIT) Madras, Chennai, India.
- Centre for Integrative Biology and Systems Medicine, IIT Madras, Chennai, India.
- Robert Bosch Centre for Data Science and Artificial Intelligence, IIT Madras, Chennai, India.
- Sudha Gopalakrishnan Brain Centre, IIT Madras, Chennai, India.
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2
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Pang Y, Zhou S, Zumbo P, Betel D, Cisse B. TCF12 Deficiency Impairs the Proliferation of Glioblastoma Tumor Cells and Improves Survival. Cancers (Basel) 2023; 15:cancers15072033. [PMID: 37046694 PMCID: PMC10093168 DOI: 10.3390/cancers15072033] [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: 03/03/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
Isocitrate dehydrogenase (IDH)-wild-type glioblastoma (GBM) is the most common and aggressive primary brain tumor which carries a very poor overall prognosis and is universally fatal. Understanding the transcriptional regulation of the proliferation of GBM tumor cells is critical for developing novel and effective treatments. In this study, we investigate the role of the transcription factor TCF12 in the regulation of GBM proliferation using human and murine GBM cell lines and an in vivo GBM xenograft model. Our study shows that TCF12 deficiency severely impairs proliferation of tumor cells in vitro by disrupting/blocking the G1 to S phase transition. We also discover that TCF12 loss significantly improves animal survival and that TCF12-deficient tumors grow much slower in vivo. Overexpression of TCF12, on the other hand, leads to an increase in the proliferation of tumor cells in vitro and more aggressive tumor progression in vivo. Interestingly, loss of TCF12 leads to upregulation of signature genes of the oligodendrocytic lineage in GBM stem cells, suggesting a role for TCF12 in inhibiting differentiation along the oligodendrocytic lineage. Transcriptomic data also reveals that loss of TCF12 leads to dysregulation of the expression of key genes in the cell cycle. Our work demonstrates critical roles of TCF12 in GBM tumor progression.
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Affiliation(s)
- Yunong Pang
- Department of Neurological Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Sichang Zhou
- Department of Neurological Surgery, Weill Cornell Medicine, New York, NY 10065, USA
| | - Paul Zumbo
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Doron Betel
- Institute of Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Babacar Cisse
- Department of Neurological Surgery, Weill Cornell Medicine, New York, NY 10065, USA
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3
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van Nijnatten J, Brandsma CA, Steiling K, Hiemstra PS, Timens W, van den Berge M, Faiz A. High miR203a-3p and miR-375 expression in the airways of smokers with and without COPD. Sci Rep 2022; 12:5610. [PMID: 35379844 PMCID: PMC8980043 DOI: 10.1038/s41598-022-09093-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
Smoking is a leading cause of chronic obstructive pulmonary disease (COPD). It is known to have a significant impact on gene expression and (inflammatory) cell populations in the airways involved in COPD pathogenesis. In this study, we investigated the impact of smoking on the expression of miRNAs in healthy and COPD individuals. We aimed to elucidate the overall smoking-induced miRNA changes and those specific to COPD. In addition, we investigated the downstream effects on regulatory gene expression and the correlation to cellular composition. We performed a genome-wide miRNA expression analysis on a dataset of 40 current- and 22 ex-smoking COPD patients and a dataset of 35 current- and 38 non-smoking respiratory healthy controls and validated the results in an independent dataset. miRNA expression was then correlated with mRNA expression in the same patients to assess potential regulatory effects of the miRNAs. Finally, cellular deconvolution analysis was used to relate miRNAs changes to specific cell populations. Current smoking was associated with increased expression of three miRNAs in the COPD patients and 18 miRNAs in the asymptomatic smokers compared to respiratory healthy controls. In comparison, four miRNAs were lower expressed with current smoking in asymptomatic controls. Two of the three smoking-related miRNAs in COPD, miR-203a-3p and miR-375, were also higher expressed with current smoking in COPD patients and the asymptomatic controls. The other smoking-related miRNA in COPD patients, i.e. miR-31-3p, was not present in the respiratory healthy control dataset. miRNA-mRNA correlations demonstrated that miR-203a-3p, miR-375 and also miR-31-3p expression were negatively associated with genes involved in pro-inflammatory pathways and positively associated with genes involved in the xenobiotic pathway. Cellular deconvolution showed that higher levels of miR-203a-3p were associated with higher proportions of proliferating-basal cells and secretory (club and goblet) cells and lower levels of fibroblasts, luminal macrophages, endothelial cells, B-cells, amongst other cell types. MiR-375 expression was associated with lower levels of secretory cells, ionocytes and submucosal cells, but higher levels of endothelial cells, smooth muscle cells, and mast cells, amongst other cell types. In conclusion, we identified two smoking-induced miRNAs (miR-375 and miR-203a-3p) that play a role in regulating inflammation and detoxification pathways, regardless of the presence or absence of COPD. Additionally, in patients with COPD, we identified miR-31-3p as a miRNA induced by smoking. Our identified miRNAs should be studied further to unravel which smoking-induced inflammatory mechanisms are reactive and which are involved in COPD pathogenesis.
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4
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Bou Zerdan M, Assi HI. Oligodendroglioma: A Review of Management and Pathways. Front Mol Neurosci 2021; 14:722396. [PMID: 34675774 PMCID: PMC8523914 DOI: 10.3389/fnmol.2021.722396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/15/2021] [Indexed: 12/31/2022] Open
Abstract
Anaplastic oligodendrogliomas are a type of glioma that occurs primarily in adults but are also found in children. These tumors are genetically defined according to the mutations they harbor. Grade II and grade III tumors can be differentiated most of the times by the presence of anaplastic features. The earliest regimen used for the treatment of these tumors was procarbazine, lomustine, and vincristine. The treatment modalities have shifted over time, and recent studies are considering immunotherapy as an option as well. This review assesses the latest management modalities along with the pathways involved in the pathogenesis of this malignancies.
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Affiliation(s)
| | - Hazem I. Assi
- Division of Hematology and Oncology, Department of Internal Medicine, Naef K. Basile Cancer Institute, American University of Beirut Medical Center, Beirut, Lebanon
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5
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Oleari R, Massa V, Cariboni A, Lettieri A. The Differential Roles for Neurodevelopmental and Neuroendocrine Genes in Shaping GnRH Neuron Physiology and Deficiency. Int J Mol Sci 2021; 22:9425. [PMID: 34502334 PMCID: PMC8431607 DOI: 10.3390/ijms22179425] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 01/19/2023] Open
Abstract
Gonadotropin releasing hormone (GnRH) neurons are hypothalamic neuroendocrine cells that control sexual reproduction. During embryonic development, GnRH neurons migrate from the nose to the hypothalamus, where they receive inputs from several afferent neurons, following the axonal scaffold patterned by nasal nerves. Each step of GnRH neuron development depends on the orchestrated action of several molecules exerting specific biological functions. Mutations in genes encoding for these essential molecules may cause Congenital Hypogonadotropic Hypogonadism (CHH), a rare disorder characterized by GnRH deficiency, delayed puberty and infertility. Depending on their action in the GnRH neuronal system, CHH causative genes can be divided into neurodevelopmental and neuroendocrine genes. The CHH genetic complexity, combined with multiple inheritance patterns, results in an extreme phenotypic variability of CHH patients. In this review, we aim at providing a comprehensive and updated description of the genes thus far associated with CHH, by dissecting their biological relevance in the GnRH system and their functional relevance underlying CHH pathogenesis.
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Affiliation(s)
- Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milano, Italy;
| | - Valentina Massa
- Department of Health Sciences, University of Milan, 20142 Milano, Italy;
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan, 20142 Milano, Italy
| | - Anna Cariboni
- Department of Pharmacological and Biomolecular Sciences, University of Milan, 20133 Milano, Italy;
| | - Antonella Lettieri
- Department of Health Sciences, University of Milan, 20142 Milano, Italy;
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Department of Health Sciences, University of Milan, 20142 Milano, Italy
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6
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Davis EE, Balasubramanian R, Kupchinsky ZA, Keefe DL, Plummer L, Khan K, Meczekalski B, Heath KE, Lopez-Gonzalez V, Ballesta-Martinez MJ, Margabanthu G, Price S, Greening J, Brauner R, Valenzuela I, Cusco I, Fernandez-Alvarez P, Wierman ME, Li T, Lage K, Barroso PS, Chan YM, Crowley WF, Katsanis N. TCF12 haploinsufficiency causes autosomal dominant Kallmann syndrome and reveals network-level interactions between causal loci. Hum Mol Genet 2021; 29:2435-2450. [PMID: 32620954 DOI: 10.1093/hmg/ddaa120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Dysfunction of the gonadotropin-releasing hormone (GnRH) axis causes a range of reproductive phenotypes resulting from defects in the specification, migration and/or function of GnRH neurons. To identify additional molecular components of this system, we initiated a systematic genetic interrogation of families with isolated GnRH deficiency (IGD). Here, we report 13 families (12 autosomal dominant and one autosomal recessive) with an anosmic form of IGD (Kallmann syndrome) with loss-of-function mutations in TCF12, a locus also known to cause syndromic and non-syndromic craniosynostosis. We show that loss of tcf12 in zebrafish larvae perturbs GnRH neuronal patterning with concomitant attenuation of the orthologous expression of tcf3a/b, encoding a binding partner of TCF12, and stub1, a gene that is both mutated in other syndromic forms of IGD and maps to a TCF12 affinity network. Finally, we report that restored STUB1 mRNA rescues loss of tcf12 in vivo. Our data extend the mutational landscape of IGD, highlight the genetic links between craniofacial patterning and GnRH dysfunction and begin to assemble the functional network that regulates the development of the GnRH axis.
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Affiliation(s)
- Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.,Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ravikumar Balasubramanian
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital (MGH), Boston, MA 02114, USA.,Harvard Medical School, Boston, MA 02115, USA
| | | | - David L Keefe
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
| | - Lacey Plummer
- Harvard Reproductive Endocrine Science Center, Massachusetts General Hospital (MGH), Boston, MA 02114, USA
| | - Kamal Khan
- Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Blazej Meczekalski
- Department of Gynecological Endocrinology, Poznan University of Medical Sciences, 60-512 Poznan, Poland
| | - Karen E Heath
- Institute of Medical and Molecular Genetics (INGEMM) Hospital Universitario La Paz, Universidad Autonoma de Madrid, IdiPAZ, Madrid, Spain and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, 28046 Madrid, Spain
| | - Vanesa Lopez-Gonzalez
- Medical Genetics Unit, Department of Pediatrics, Hospital Clinico, Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain and CIBERER, ISCIII, 28046 Madrid, Spain
| | - Mary J Ballesta-Martinez
- Medical Genetics Unit, Department of Pediatrics, Hospital Clinico, Universitario Virgen de la Arrixaca, IMIB-Arrixaca, Murcia, Spain and CIBERER, ISCIII, 28046 Madrid, Spain
| | | | - Susan Price
- Northampton General Hospital, Northampton NN1 5BD, UK
| | - James Greening
- University Hospitals of Leicester, Leicester LE3 9QP, UK
| | - Raja Brauner
- Pediatric Endocrinology Unit, Fondation Ophtalmologique Adolphe de Rothschild and Université Paris Descartes, 75019 Paris, France
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Ivon Cusco
- Department of Clinical and Molecular Genetics, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Paula Fernandez-Alvarez
- Department of Clinical and Molecular Genetics, Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Margaret E Wierman
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Taibo Li
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.,Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Kasper Lage
- Harvard Medical School, Boston, MA 02115, USA.,Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Priscila Sales Barroso
- Divisao de Endocrinologia e Metabologia, Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo, Sao Paulo, 05403-900 Brazil
| | - Yee-Ming Chan
- Division of Endocrinology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - William F Crowley
- Harvard Medical School, Boston, MA 02115, USA.,MGH Center for Human Genetics & The Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston MA 02114, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.,Advanced Center for Translational and Genetic Medicine (ACT-GeM), Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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7
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Noorani I, de la Rosa J, Choi YH, Strong A, Ponstingl H, Vijayabaskar MS, Lee J, Lee E, Richard-Londt A, Friedrich M, Furlanetto F, Fuente R, Banerjee R, Yang F, Law F, Watts C, Rad R, Vassiliou G, Kim JK, Santarius T, Brandner S, Bradley A. PiggyBac mutagenesis and exome sequencing identify genetic driver landscapes and potential therapeutic targets of EGFR-mutant gliomas. Genome Biol 2020; 21:181. [PMID: 32727536 PMCID: PMC7392733 DOI: 10.1186/s13059-020-02092-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/06/2020] [Indexed: 12/25/2022] Open
Abstract
Background Glioma is the most common intrinsic brain tumor and also occurs in the spinal cord. Activating EGFR mutations are common in IDH1 wild-type gliomas. However, the cooperative partners of EGFR driving gliomagenesis remain poorly understood. Results We explore EGFR-mutant glioma evolution in conditional mutant mice by whole-exome sequencing, transposon mutagenesis forward genetic screening, and transcriptomics. We show mutant EGFR is sufficient to initiate gliomagenesis in vivo, both in the brain and spinal cord. We identify significantly recurrent somatic alterations in these gliomas including mutant EGFR amplifications and Sub1, Trp53, and Tead2 loss-of-function mutations. Comprehensive functional characterization of 96 gliomas by genome-wide piggyBac insertional mutagenesis in vivo identifies 281 known and novel EGFR-cooperating driver genes, including Cdkn2a, Nf1, Spred1, and Nav3. Transcriptomics confirms transposon-mediated effects on expression of these genes. We validate the clinical relevance of new putative tumor suppressors by showing these are frequently altered in patients’ gliomas, with prognostic implications. We discover shared and distinct driver mutations in brain and spinal gliomas and confirm in vivo differential tumor suppressive effects of Pten between these tumors. Functional validation with CRISPR-Cas9-induced mutations in novel genes Tead2, Spred1, and Nav3 demonstrates heightened EGFRvIII-glioma cell proliferation. Chemogenomic analysis of mutated glioma genes reveals potential drug targets, with several investigational drugs showing efficacy in vitro. Conclusion Our work elucidates functional driver landscapes of EGFR-mutant gliomas, uncovering potential therapeutic strategies, and provides new tools for functional interrogation of gliomagenesis.
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Affiliation(s)
- Imran Noorani
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. .,Department of Neurosurgery, Addenbrookes Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Jorge de la Rosa
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Yoon Ha Choi
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.,Department of New Biology, DGIST, 333, Techno Jungang Daero, Hyeonpung-Myeon, Dalseong-Gun, Daegu, 42988, South Korea
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Hannes Ponstingl
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - M S Vijayabaskar
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jusung Lee
- Department of New Biology, DGIST, 333, Techno Jungang Daero, Hyeonpung-Myeon, Dalseong-Gun, Daegu, 42988, South Korea
| | - Eunmin Lee
- Department of New Biology, DGIST, 333, Techno Jungang Daero, Hyeonpung-Myeon, Dalseong-Gun, Daegu, 42988, South Korea
| | - Angela Richard-Londt
- Division of Neuropathology and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, Mailbox 126, London, WC1N 3BG, UK
| | - Mathias Friedrich
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.,Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, Munich, Germany
| | - Federica Furlanetto
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, Munich, Germany
| | - Rocio Fuente
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Ruby Banerjee
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Frances Law
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Colin Watts
- Department of Neurosurgery, Addenbrookes Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK.,Birmingham Brain Cancer Program, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Roland Rad
- Department of Internal Medicine II, Klinikum rechts der Isar, Technische Universität München, Ismaninger Strasse 22, 81675, Munich, Germany
| | - George Vassiliou
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Jong Kyoung Kim
- Department of New Biology, DGIST, 333, Techno Jungang Daero, Hyeonpung-Myeon, Dalseong-Gun, Daegu, 42988, South Korea
| | - Thomas Santarius
- Department of Neurosurgery, Addenbrookes Hospital, University of Cambridge, Hills Road, Cambridge, CB2 0QQ, UK
| | - Sebastian Brandner
- Division of Neuropathology and Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, Mailbox 126, London, WC1N 3BG, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
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8
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Mesman S, Smidt MP. Acquisition of the Midbrain Dopaminergic Neuronal Identity. Int J Mol Sci 2020; 21:ijms21134638. [PMID: 32629812 PMCID: PMC7369932 DOI: 10.3390/ijms21134638] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023] Open
Abstract
The mesodiencephalic dopaminergic (mdDA) group of neurons comprises molecularly distinct subgroups, of which the substantia nigra (SN) and ventral tegmental area (VTA) are the best known, due to the selective degeneration of the SN during Parkinson’s disease. However, although significant research has been conducted on the molecular build-up of these subsets, much is still unknown about how these subsets develop and which factors are involved in this process. In this review, we aim to describe the life of an mdDA neuron, from specification in the floor plate to differentiation into the different subsets. All mdDA neurons are born in the mesodiencephalic floor plate under the influence of both SHH-signaling, important for floor plate patterning, and WNT-signaling, involved in establishing the progenitor pool and the start of the specification of mdDA neurons. Furthermore, transcription factors, like Ngn2, Ascl1, Lmx1a, and En1, and epigenetic factors, like Ezh2, are important in the correct specification of dopamine (DA) progenitors. Later during development, mdDA neurons are further subdivided into different molecular subsets by, amongst others, Otx2, involved in the specification of subsets in the VTA, and En1, Pitx3, Lmx1a, and WNT-signaling, involved in the specification of subsets in the SN. Interestingly, factors involved in early specification in the floor plate can serve a dual function and can also be involved in subset specification. Besides the mdDA group of neurons, other systems in the embryo contain different subsets, like the immune system. Interestingly, many factors involved in the development of mdDA neurons are similarly involved in immune system development and vice versa. This indicates that similar mechanisms are used in the development of these systems, and that knowledge about the development of the immune system may hold clues for the factors involved in the development of mdDA neurons, which may be used in culture protocols for cell replacement therapies.
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9
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de la Fuente L, Arzalluz-Luque Á, Tardáguila M, Del Risco H, Martí C, Tarazona S, Salguero P, Scott R, Lerma A, Alastrue-Agudo A, Bonilla P, Newman JRB, Kosugi S, McIntyre LM, Moreno-Manzano V, Conesa A. tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing. Genome Biol 2020; 21:119. [PMID: 32423416 PMCID: PMC7236505 DOI: 10.1186/s13059-020-02028-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/23/2020] [Indexed: 12/26/2022] Open
Abstract
Recent advances in long-read sequencing solve inaccuracies in alternative transcript identification of full-length transcripts in short-read RNA-Seq data, which encourages the development of methods for isoform-centered functional analysis. Here, we present tappAS, the first framework to enable a comprehensive Functional Iso-Transcriptomics (FIT) analysis, which is effective at revealing the functional impact of context-specific post-transcriptional regulation. tappAS uses isoform-resolved annotation of coding and non-coding functional domains, motifs, and sites, in combination with novel analysis methods to interrogate different aspects of the functional readout of transcript variants and isoform regulation. tappAS software and documentation are available at https://app.tappas.org.
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Affiliation(s)
- Lorena de la Fuente
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
- Present Address: Bioinformatics Unit, IIS Fundación Jiménez Díaz, Madrid, Spain
| | - Ángeles Arzalluz-Luque
- Department of Statistics and Operational Research, Polytechnical University of Valencia, Valencia, Spain
| | - Manuel Tardáguila
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Héctor Del Risco
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Cristina Martí
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Sonia Tarazona
- Department of Statistics and Operational Research, Polytechnical University of Valencia, Valencia, Spain
| | - Pedro Salguero
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Raymond Scott
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA
| | - Alberto Lerma
- Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Valencia, Spain
| | - Ana Alastrue-Agudo
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Pablo Bonilla
- Present Address: Human Genetics Department, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jeremy R B Newman
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Department of Pathology, University of Florida, Gainesville, FL, USA
| | - Shunichi Kosugi
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Laboratory for Statistical and Translational Genetics, Center for Integrative Medical Sciences, RIKEN, Wako, Japan
| | - Lauren M McIntyre
- Genetics Institute, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | | | - Ana Conesa
- Department of Microbiology and Cell Science, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
- Genetics Institute, University of Florida, Gainesville, FL, USA.
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10
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TWIST1 Homodimers and Heterodimers Orchestrate Lineage-Specific Differentiation. Mol Cell Biol 2020; 40:MCB.00663-19. [PMID: 32179550 DOI: 10.1128/mcb.00663-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 02/27/2020] [Indexed: 01/09/2023] Open
Abstract
The extensive array of basic helix-loop-helix (bHLH) transcription factors and their combinations as dimers underpin the diversity of molecular function required for cell type specification during embryogenesis. The bHLH factor TWIST1 plays pleiotropic roles during development. However, which combinations of TWIST1 dimers are involved and what impact each dimer imposes on the gene regulation network controlled by TWIST1 remain elusive. In this work, proteomic profiling of human TWIST1-expressing cell lines and transcriptome analysis of mouse cranial mesenchyme have revealed that TWIST1 homodimers and heterodimers with TCF3, TCF4, and TCF12 E-proteins are the predominant dimer combinations. Disease-causing mutations in TWIST1 can impact dimer formation or shift the balance of different types of TWIST1 dimers in the cell, which may underpin the defective differentiation of the craniofacial mesenchyme. Functional analyses of the loss and gain of TWIST1-E-protein dimer activity have revealed previously unappreciated roles in guiding lineage differentiation of embryonic stem cells: TWIST1-E-protein heterodimers activate the differentiation of mesoderm and neural crest cells, which is accompanied by the epithelial-to-mesenchymal transition. At the same time, TWIST1 homodimers maintain the stem cells in a progenitor state and block entry to the endoderm lineage.
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11
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Prajapati B, Fatima M, Fatma M, Maddhesiya P, Arora H, Naskar T, Devasenapathy S, Seth P, Sinha S. Temporal transcriptome analysis of neuronal commitment reveals the preeminent role of the divergent lncRNA biotype and a critical candidate gene during differentiation. Cell Death Discov 2020; 6:28. [PMID: 32351715 PMCID: PMC7181654 DOI: 10.1038/s41420-020-0263-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2019] [Revised: 03/19/2020] [Accepted: 04/02/2020] [Indexed: 02/08/2023] Open
Abstract
lncRNA genes can be genic or "intergenic". "Genic" RNAs can be further divided into six biotypes. Through genome-wide analysis of a publicly available data set on corticogenesis, we found that the divergent lncRNA (XH) biotype, comprising the lncRNA and the coding gene being in opposite directions in a head-to-head manner, was most prominent during neural commitment. Within this biotype, a coding gene/divergent RNA pair of the BASP1 gene and the uncharacterized RNA loc285696 (hitherto referred as BASP1-AS1) formed a major HUB gene during neuronal differentiation. Experimental validation during the in vitro differentiation of human neural progenitor cells (hNPCs) showed that BASP1-AS1 regulates the expression of its adjacent coding gene, BASP1. Both transcripts increased sharply on the first day of neuronal differentiation of hNPCs, to fall steadily thereafter, reaching very low levels in differentiated neurons. BASP1-AS1 RNA and the BASP1 gene formed a molecular complex that also included the transcription factor TCF12. TCF12 is coded by the DYX1 locus, associated with inherited dyslexia and neurodevelopmental defects. Knockdown of BASP1-AS1, BASP1, or TCF12 impaired the neuronal differentiation of hNPCs, as seen by reduction in DCX and TUJ1-positive cells and by reduced neurite length. There was also increased cell proliferation. A common set of critical genes was affected by the three molecules in the complex. Our study thus identified the role of the XH biotype and a novel mediator of neuronal differentiation-the complex of BASP1-AS1, BASP1, and TCF12. It also linked a neuronal differentiation pathway to inherited dyslexia.
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Affiliation(s)
| | - Mahar Fatima
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | - Mena Fatma
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | | | - Himali Arora
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | - Teesta Naskar
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | | | - Pankaj Seth
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
| | - Subrata Sinha
- National Brain Research Centre, Manesar, Gurgaon, Haryana India
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029 India
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12
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TCF12 overexpression as a poor prognostic factor in ovarian cancer. Pathol Res Pract 2019; 215:152527. [DOI: 10.1016/j.prp.2019.152527] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 06/10/2019] [Accepted: 07/05/2019] [Indexed: 02/03/2023]
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13
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Ferdousi F, Sasaki K, Uchida Y, Ohkohchi N, Zheng YW, Isoda H. Exploring the Potential Role of Rosmarinic Acid in Neuronal Differentiation of Human Amnion Epithelial Cells by Microarray Gene Expression Profiling. Front Neurosci 2019; 13:779. [PMID: 31396047 PMCID: PMC6667736 DOI: 10.3389/fnins.2019.00779] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/11/2019] [Indexed: 01/01/2023] Open
Abstract
In the present study, we conducted microarray gene expression profiling to explore the direction of differentiation of human amnion epithelial cells (hAECs) treated with rosmarinic acid (RA). hAECs have several clinical advantages over other types of stem cells, including availability, low immunogenicity, low rejection rate, non-tumorigenicity, and less ethical constraint. On the other hand, RA is a phenolic compound having several health benefits, including neuroprotective and antidepressant-like activities. In this study, hAECs were isolated from discarded term placenta and were treated with 20 μM RA for 7 days. Microarray gene expression profiling was conducted for three biological replicates of RA-treated and untreated control cells on day 0 and day 7. Gene set enrichment analysis, and gene annotation and pathway analysis were conducted using online data mining tools GSEA and DAVID. Gene expression profiling showed that RA treatment biased hAECs toward ectodermal lineage progression, regulated transcription factors involved in neuronal differentiation, regulated neural specific epigenetic modifiers and several extracellular signaling pathways of neural induction, and significantly inhibited Notch signaling pathway. Gene expression profiling of RA-treated hAECs reveals for the first time a potential role of RA in neural induction and neuronal differentiation of hAECs. Having a naturally occurring compound as differentiation inducer as well as a readily available source of stem cells would have great advantages for the cell-based therapies. Findings from our genome-wide analysis could provide a foundation for further in-depth investigation.
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Affiliation(s)
- Farhana Ferdousi
- Alliance for Research on the Mediterranean and North Africa, University of Tsukuba, Tsukuba, Japan
| | - Kazunori Sasaki
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Yoshiaki Uchida
- School of Integrative and Global Majors, University of Tsukuba, Tsukuba, Japan
| | - Nobuhiro Ohkohchi
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Yun-Wen Zheng
- Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Hiroko Isoda
- Alliance for Research on the Mediterranean and North Africa, University of Tsukuba, Tsukuba, Japan.,National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
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14
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On the traces of tcf12: Investigation of the gene expression pattern during development and cranial suture patterning in zebrafish (Danio rerio). PLoS One 2019; 14:e0218286. [PMID: 31188878 PMCID: PMC6561585 DOI: 10.1371/journal.pone.0218286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 05/29/2019] [Indexed: 12/11/2022] Open
Abstract
The transcription factor 12 (tcf12) is a basic Helix-Loop-Helix protein (bHLH) of the E-protein family, proven to play an important role in developmental processes like neurogenesis, mesoderm formation, and cranial vault development. In humans, mutations in TCF12 lead to craniosynostosis, a congenital birth disorder characterized by the premature fusion of one or several of the cranial sutures. Current research has been primarily focused on functional studies of TCF12, hence the cellular expression profile of this gene during embryonic development and early stages of ossification remains poorly understood. Here we present the establishment and detailed analysis of two transgenic tcf12:EGFP fluorescent zebrafish (Danio rerio) reporter lines. Using these transgenic lines, we analyzed the general spatiotemporal expression pattern of tcf12 during different developmental stages and put emphasis on skeletal development and cranial suture patterning. We identified robust tcf12 promoter-driven EGFP expression in the central nervous system (CNS), the heart, the pronephros, and the somites of zebrafish embryos. Additionally, expression was observed inside the muscles and bones of the viscerocranium in juvenile and adult fish. During cranial vault development, the transgenic fish show a high amount of tcf12 expressing cells at the growth fronts of the ossifying frontal and parietal bones and inside the emerging cranial sutures. Subsequently, we tested the transcriptional activity of three evolutionary conserved non-coding elements (CNEs) located in the tcf12 locus by transient transgenic assays and compared their in vivo activity to the expression pattern determined in the transgenic tcf12:EGFP lines. We could validate two of them as tcf12 enhancer elements driving specific gene expression in the CNS during embryogenesis. Our newly established transgenic lines enhance the understanding of tcf12 gene regulation and open up the possibilities for further functional investigation of these novel tcf12 enhancer elements in zebrafish.
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15
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Hawi Z, Tong J, Dark C, Yates H, Johnson B, Bellgrove MA. The role of cadherin genes in five major psychiatric disorders: A literature update. Am J Med Genet B Neuropsychiatr Genet 2018; 177:168-180. [PMID: 28921840 DOI: 10.1002/ajmg.b.32592] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 07/31/2017] [Indexed: 12/20/2022]
Abstract
Converging evidence from candidate gene, genome-wide linkage, and association studies support a role of cadherins in the pathophysiology of five major psychiatric disorders including attention deficit hyperactivity disorder, autism spectrum disorder (ASD), schizophrenia (SCZ), bipolar disorder (BD), and major depressive disorder (MDD). These molecules are transmembrane proteins which act as cell adhesives by forming adherens junctions (AJs) to bind cells within tissues. Members of the cadherin superfamily are also involved in biological processes such as signal transduction and plasticity that have been implicated in the etiology of major psychiatric conditions. Although there are over 110 genes mapped to the cadherin superfamily, our literature survey showed that evidence of association with psychiatric disorders is strongest for CDH7, CHD11, and CDH13. Gene enrichment analysis showed that those cadherin genes implicated in psychiatric disorders were overrepresented in biological processes such as in cell-cell adhesion (GO:0007156 & GO:0098742) and adherens junction organization (GO:0034332). Further, cadherin genes were also mapped to processes that have been linked to the development of psychiatric disorders such as nervous system development (GO:0007399). To further understand the role of cadherin SNPs implicated in psychiatric disorders, we utilized an in silico computational pipeline to functionally annotate associated variants. This analysis yielded eight variants mapped to PCDH1-13, CDH7, CDH11, and CDH13 that are predicted to be biologically functional. Functional genomic evaluation is now required to understand the molecular mechanism by which these variants might confer susceptibility to psychiatric disorders.
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Affiliation(s)
- Ziarih Hawi
- Monash Institute for Cognitive and Clinical Neurosciences (MICCN), School of Psychological Sciences, Monash University, Melbourne, Australia
| | - Janette Tong
- Monash Institute for Cognitive and Clinical Neurosciences (MICCN), School of Psychological Sciences, Monash University, Melbourne, Australia
| | - Callum Dark
- Monash Institute for Cognitive and Clinical Neurosciences (MICCN), School of Psychological Sciences, Monash University, Melbourne, Australia
| | - Hannah Yates
- Monash Institute for Cognitive and Clinical Neurosciences (MICCN), School of Psychological Sciences, Monash University, Melbourne, Australia
| | - Beth Johnson
- Monash Institute for Cognitive and Clinical Neurosciences (MICCN), School of Psychological Sciences, Monash University, Melbourne, Australia
| | - Mark A Bellgrove
- Monash Institute for Cognitive and Clinical Neurosciences (MICCN), School of Psychological Sciences, Monash University, Melbourne, Australia
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16
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Mesman S, Smidt MP. Tcf12 Is Involved in Early Cell-Fate Determination and Subset Specification of Midbrain Dopamine Neurons. Front Mol Neurosci 2017; 10:353. [PMID: 29163030 PMCID: PMC5671939 DOI: 10.3389/fnmol.2017.00353] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 10/17/2017] [Indexed: 11/23/2022] Open
Abstract
The basic helix-loop-helix (bHLH) protein family has previously been shown to be involved in the development of mesodiencephalic dopaminergic (mdDA) neurons in the murine midbrain. Specifically, Ngn2 and Mash1 are known to have a role in the specification of neural progenitors in the ventricular zone (VZ) of the midbrain towards an mdDA neuronal cell-fate. Furthermore, other members of the bHLH protein family, the E-box factors, are expressed in the developing midbrain and are thought to have a role in neuronal differentiation. Here we show that the E-box factor Tcf12 is implicated in early and late development of mdDA neurons. Tcf12 is expressed in the midbrain and in young TH-expressing mdDA neurons throughout development. Tcf12lox/lox;En1cre/+ embryos, that lose Tcf12 at ~embryonic day (E)9 throughout the En1 expression domain, have a changed spatial expression of Lmx1a and Nurr1 and a consistent loss of rostral TH expression. Expression of the subset marker Ahd2 is initially delayed, but recovers during development, eventually showing an ~10% increase in AHD2-expressing cells at postnatal day (P)30. Tcf12lox/lox;Pitx3cre/+ embryos, that lose Tcf12 at ~E12 in post-mitotic mdDA neurons, show no effect on the amount of TH-expressing neurons in the developing midbrain. However, similar as to Tcf12lox/lox;En1cre/+ embryos, subset specification is delayed during development. Taken together, we have identified Tcf12 as a novel factor in mdDA neuronal development. It serves a dual function; one in early cell-fate commitment of neural progenitors and one late in subset specification.
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Affiliation(s)
- Simone Mesman
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, Amsterdam, Netherlands
| | - Marten P Smidt
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, Amsterdam, Netherlands
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17
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Hayakawa-Yano Y, Suyama S, Nogami M, Yugami M, Koya I, Furukawa T, Zhou L, Abe M, Sakimura K, Takebayashi H, Nakanishi A, Okano H, Yano M. An RNA-binding protein, Qki5, regulates embryonic neural stem cells through pre-mRNA processing in cell adhesion signaling. Genes Dev 2017; 31:1910-1925. [PMID: 29021239 PMCID: PMC5693031 DOI: 10.1101/gad.300822.117] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 09/14/2017] [Indexed: 01/07/2023]
Abstract
Cell type-specific transcriptomes are enabled by the action of multiple regulators, which are frequently expressed within restricted tissue regions. In the present study, we identify one such regulator, Quaking 5 (Qki5), as an RNA-binding protein (RNABP) that is expressed in early embryonic neural stem cells and subsequently down-regulated during neurogenesis. mRNA sequencing analysis in neural stem cell culture indicates that Qki proteins play supporting roles in the neural stem cell transcriptome and various forms of mRNA processing that may result from regionally restricted expression and subcellular localization. Also, our in utero electroporation gain-of-function study suggests that the nuclear-type Qki isoform Qki5 supports the neural stem cell state. We next performed in vivo transcriptome-wide protein-RNA interaction mapping to search for direct targets of Qki5 and elucidate how Qki5 regulates neural stem cell function. Combined with our transcriptome analysis, this mapping analysis yielded a bona fide map of Qki5-RNA interaction at single-nucleotide resolution, the identification of 892 Qki5 direct target genes, and an accurate Qki5-dependent alternative splicing rule in the developing brain. Last, our target gene list provides the first compelling evidence that Qki5 is associated with specific biological events; namely, cell-cell adhesion. This prediction was confirmed by histological analysis of mice in which Qki proteins were genetically ablated, which revealed disruption of the apical surface of the lateral wall in the developing brain. These data collectively indicate that Qki5 regulates communication between neural stem cells by mediating numerous RNA processing events and suggest new links between splicing regulation and neural stem cell states.
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Affiliation(s)
- Yoshika Hayakawa-Yano
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Satoshi Suyama
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masahiro Nogami
- Shonan Incubation Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan.,Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan
| | - Masato Yugami
- Shonan Incubation Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan.,Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan
| | - Ikuko Koya
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takako Furukawa
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Li Zhou
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8585, Japan
| | - Manabu Abe
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8585, Japan
| | - Kenji Sakimura
- Department of Cellular Neurobiology, Brain Research Institute, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8585, Japan
| | - Hirohide Takebayashi
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan
| | - Atsushi Nakanishi
- Shonan Incubation Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan.,Integrated Technology Research Laboratories, Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa 251-8555, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Masato Yano
- Division of Neurobiology and Anatomy, Graduate School of Medical and Dental Sciences, Niigata University, Asahimachidori, Chuo-ku, Niigata, Niigata 951-8510, Japan.,Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
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18
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Mesman S, Krüse SJ, Smidt MP. Expression analyzes of early factors in midbrain differentiation programs. Gene Expr Patterns 2017; 27:8-15. [PMID: 28958789 DOI: 10.1016/j.gep.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/22/2017] [Accepted: 09/23/2017] [Indexed: 10/18/2022]
Abstract
Mesodiencephalic dopaminergic (mdDA) neurons are born in the ventricular zone (VZ) of the midbrain between E10 and E12. Although these neurons all express specific DA markers like Th and Pitx3, they are subdivided into distinct subsets, each depending on a unique set of transcription factors and signaling cascades for their differentiation. How a neural progenitor commits to an mdDA neuronal cell-fate and how the specification into the different subsets is determined remains unclear. To gain more insight into the development and specification of these neurons we have previously conducted a genome-wide expression analysis, in which dissected midbrain material (E10.5-E13.5) was compared to the adult mdDA region (Chakrabarty et al., 2012). In the present study, we have compared the genome-wide expression analysis including PITX3-GFP sorted (E12.5-E15.5) neurons to available expression data to search for genes specifically expressed in the midbrain during early stages of mdDA differentiation. We have divided these genes into 3 groups: (I) genes upregulated throughout differentiation (Mest, NeuroD1, and Tcf12), (II) genes upregulated during early stages of differentiation (Hes5, and Tcf3), and (III) genes upregulated during late stages of differentiation (Enc1). Here, we show the expression profile of these genes in the embryonic midbrain during development and adult stage and compared that to the appearance of mdDA neurons via co-staining for TH. With this analysis we have identified 6 novel factors that may play a role during cell-fate commitment of neural progenitors or later during differentiation of the mdDA group of neurons.
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Affiliation(s)
- Simone Mesman
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, The Netherlands
| | - Sonja J Krüse
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, The Netherlands
| | - Marten P Smidt
- Swammerdam Institute for Life Sciences, FNWI University of Amsterdam, The Netherlands.
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19
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Lawlor N, Youn A, Kursawe R, Ucar D, Stitzel ML. Alpha TC1 and Beta-TC-6 genomic profiling uncovers both shared and distinct transcriptional regulatory features with their primary islet counterparts. Sci Rep 2017; 7:11959. [PMID: 28931935 PMCID: PMC5607285 DOI: 10.1038/s41598-017-12335-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 09/06/2017] [Indexed: 01/09/2023] Open
Abstract
Alpha TC1 (αTC1) and Beta-TC-6 (βTC6) mouse islet cell lines are cellular models of islet (dys)function and type 2 diabetes (T2D). However, genomic characteristics of these cells, and their similarities to primary islet alpha and beta cells, are undefined. Here, we report the epigenomic (ATAC-seq) and transcriptomic (RNA-seq) landscapes of αTC1 and βTC6 cells. Each cell type exhibits hallmarks of its primary islet cell counterpart including cell-specific expression of beta (e.g., Pdx1) and alpha (e.g., Arx) cell transcription factors (TFs), and enrichment of binding motifs for these TFs in αTC1/βTC6 cis-regulatory elements. αTC1/βTC6 transcriptomes overlap significantly with the transcriptomes of primary mouse/human alpha and beta cells. Our data further indicate that ATAC-seq detects cell-specific regulatory elements for cell types comprising ≥ 20% of a mixed cell population. We identified αTC1/βTC6 cis-regulatory elements orthologous to those containing type 2 diabetes (T2D)-associated SNPs in human islets for 33 loci, suggesting these cells’ utility to dissect T2D molecular genetics in these regions. Together, these maps provide important insights into the conserved regulatory architecture between αTC1/βTC6 and primary islet cells that can be leveraged in functional (epi)genomic approaches to dissect the genetic and molecular factors controlling islet cell identity and function.
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Affiliation(s)
- Nathan Lawlor
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ahrim Youn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Romy Kursawe
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Duygu Ucar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA. .,Institute for Systems Genomics, University of Connecticut, Farmington, CT, 06032, USA. .,Department of Genetics & Genome Sciences, University of Connecticut, Farmington, CT, 06032, USA.
| | - Michael L Stitzel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA. .,Institute for Systems Genomics, University of Connecticut, Farmington, CT, 06032, USA. .,Department of Genetics & Genome Sciences, University of Connecticut, Farmington, CT, 06032, USA.
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20
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Chen QB, Liang YK, Zhang YQ, Jiang MY, Han ZD, Liang YX, Wan YP, Yin J, He HC, Zhong WD. Decreased expression of TCF12 contributes to progression and predicts biochemical recurrence in patients with prostate cancer. Tumour Biol 2017. [PMID: 28651494 DOI: 10.1177/1010428317703924] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Qing-biao Chen
- Affiliated Foshan Hospital of Southern Medical University, Southern Medical University, Foshan, China
- Department of Urology, Huadu District People’s Hospital, Southern Medical University, Guangzhou, China
| | - Ying-ke Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yan-qiong Zhang
- China Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Min-yao Jiang
- Department of Urology, Huadu District People’s Hospital, Southern Medical University, Guangzhou, China
| | - Zhao-dong Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yu-xiang Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yue-ping Wan
- Department of Urology, Huadu District People’s Hospital, Southern Medical University, Guangzhou, China
| | - Jie Yin
- Affiliated Foshan Hospital of Southern Medical University, Southern Medical University, Foshan, China
| | - Hui-Chan He
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
| | - Wei-de Zhong
- Department of Urology, Huadu District People’s Hospital, Southern Medical University, Guangzhou, China
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, Guangzhou Medical University, Guangzhou, China
- Urology Key Laboratory of Guangdong Province, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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21
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Yang J, Zhang X, Chen X, Wang L, Yang G. Exosome Mediated Delivery of miR-124 Promotes Neurogenesis after Ischemia. MOLECULAR THERAPY-NUCLEIC ACIDS 2017. [PMID: 28624203 PMCID: PMC5415550 DOI: 10.1016/j.omtn.2017.04.010] [Citation(s) in RCA: 374] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The intrinsic ability of neurogenesis after stroke has been proven weak, which results in insufficient repair of injury in the nerve system. Recent studies suggest multiple microRNAs (miRNAs) are involved in the neuroremodeling process. Targeted miRNAs delivery for amplification of neurogenesis is promising in promoting the prognosis after ischemia. Here, we showed that modified exosomes, with rabies virus glycoprotein (RVG) fused to exosomal protein lysosome-associated membrane glycoprotein 2b (Lamp2b), could efficiently deliver miR-124 to the infarct site. Systemic administration of RVG-exosomes loaded with miR-124 promoted cortical neural progenitors to obtain neuronal identity and protect against ischemic injury by robust cortical neurogenesis. Our study suggests that RVG-exosomes can be utilized therapeutically for the targeted delivery of gene drugs to the brain, thus having great potential for clinical applications.
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Affiliation(s)
- Jialei Yang
- Department of Neurology, New Era Stroke Care and Research Institute, The General Hospital of the PLA Rocket Force, 16 Xinjiekouwai Avenue, Beijing 100088, China; The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, School of Basic Medicine, The Fourth Military Medical University, 169 Changlexi Road, Xi'an, Shaanxi 710032, China
| | - Xiufen Zhang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, School of Basic Medicine, The Fourth Military Medical University, 169 Changlexi Road, Xi'an, Shaanxi 710032, China
| | - Xiangjie Chen
- Department of Mathematics, Southeast University, Nanjing 211189, China
| | - Lei Wang
- Department of Neurology, New Era Stroke Care and Research Institute, The General Hospital of the PLA Rocket Force, 16 Xinjiekouwai Avenue, Beijing 100088, China.
| | - Guodong Yang
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, School of Basic Medicine, The Fourth Military Medical University, 169 Changlexi Road, Xi'an, Shaanxi 710032, China.
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22
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Furchtgott LA, Melton S, Menon V, Ramanathan S. Discovering sparse transcription factor codes for cell states and state transitions during development. eLife 2017; 6:e20488. [PMID: 28296636 PMCID: PMC5352226 DOI: 10.7554/elife.20488] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 01/31/2017] [Indexed: 12/16/2022] Open
Abstract
Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes that could control this lineage decision. Our work allows us to simultaneously infer both the identity and lineage of cell types as well as a small set of key genes whose expression patterns reflect these relationships.
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Affiliation(s)
- Leon A Furchtgott
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Biophysics Program, Harvard University, Cambridge, United States
| | - Samuel Melton
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, United States
| | - Vilas Menon
- Allen Institute for Brain Science, Seattle, United States
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Sharad Ramanathan
- FAS Center for Systems Biology, Harvard University, Cambridge, United States
- Harvard Stem Cell Institute, Harvard University, Cambridge, United States
- Allen Institute for Brain Science, Seattle, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, United States
- School of Engineering and Applied Sciences, Harvard University, Cambridge, United States
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23
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Yi S, Yu M, Yang S, Miron RJ, Zhang Y. Tcf12, A Member of Basic Helix-Loop-Helix Transcription Factors, Mediates Bone Marrow Mesenchymal Stem Cell Osteogenic Differentiation In Vitro and In Vivo. Stem Cells 2017; 35:386-397. [PMID: 27574032 DOI: 10.1002/stem.2491] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 07/05/2016] [Accepted: 07/29/2016] [Indexed: 01/12/2023]
Abstract
Several basic Helix-Loop-Helix transcription factors have recently been identified to regulate mesenchymal stem cell (MSC) differentiation. In the present study, Tcf12 was investigated for its involvement in the osteoblastic cell commitment of MSCs. Tcf12 was found highly expressed in undifferentiated MSCs whereas its expression decreased following osteogenic culture differentiation. Interestingly, Tcf12 endogenous silencing using shRNA lentivirus significantly promoted the differentiation ability of MSCs evaluated by alkaline phosphatase staining, alizarin red staining and expression of osteoblast-specific markers by real-time PCR. Conversely, overexpression of Tcf12 in MSCs suppressed osteoblast differentiation. It was further found that silencing of Tcf12 activated bone morphogenetic protein (BMP) signaling and extracellular signal-regulated kinase (Erk)1/2 signaling pathway activity and upregulated the expression of phospho-SMAD1 and phospho-Erk1/2. A BMP inhibitor (LDN-193189) and Erk1/2 signaling pathway inhibitor (U0126) reduced these findings in the Tcf12 silencing group. Following these in vitro results, a poly-L-lactic acid/Hydroxyappatite scaffold carrying Tcf12 silencing lentivirus was utilized to investigate the repair of bone defects in vivo. The use of Tcf12 silencing lentivirus significantly promoted new bone formation in 3-mm mouse calvarial defects as assessed by micro-CT and histological examination whereas overexpression of Tcf12 inhibited new bone formation. Collectively, these data indicate that Tcf12 is a transcription factor highly expressed in the nuclei of stem cells and its downregulation plays an essential role in osteoblast differentiation partially via BMP and Erk1/2 signaling pathways. Stem Cells 2017;35:386-397.
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Affiliation(s)
- Siqi Yi
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
- Medical Research Institute, Wuhan University, Wuhan, People's Republic of China
| | - Miao Yu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
| | - Shuang Yang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
| | - Richard J Miron
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
- Department of Periodontology, College of Dental Medicine, Nova Southeastern University, Fort Lauderdale, Florida, USA
- Department of Preventive, Restorative and Pediatric Dentistry, School of Dental Medicine, University of Bern, Switzerland
| | - Yufeng Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, People's Republic of China
- Medical Research Institute, Wuhan University, Wuhan, People's Republic of China
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24
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Godoy PRDV, Montaldi APL, Sakamoto-Hojo ET. HEB silencing induces anti-proliferative effects on U87MG cells cultured as neurospheres and monolayers. Mol Med Rep 2016; 14:5253-5260. [PMID: 27779678 DOI: 10.3892/mmr.2016.5877] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/14/2016] [Indexed: 11/06/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a lethal tumor and novel strategies are required to overcome resistance. Transcription factor 12 (HEB) has been associated with neural and stem cell proliferation, is overexpressed in certain tumor types and is induced in irradiated U87MG cells. The present study aimed to determine whether HEB knockdown, with or without irradiation, may sensitize GBM cells. U87MG GBM and ACBRI‑371 primary human astrocytes were cultured in monolayers or neurospheres. Cell proliferation and death, cell cycle and sub‑G1 detection, and cluster of differentiation (CD) 133 immunofluorescence were analyzed by flow cytometry, whereas HEB protein expression was analyzed by immunocytochemistry and western blotting. Greater HEB protein expression was observed in U87MG neurospheres compared with ACBRI‑371, and the two cell lines exhibited nuclear HEB expression. HEB silencing in cells grown in monolayers induced a significant reduction in proliferation and decreased the proportion of cells in G0/G1 phase. In addition, HEB silencing reduced (two‑fold) the number of neurospheres compared with control scrambled (SCR) cells. HEB silencing combined with irradiation reduced U87MG cell proliferation when cultured in monolayers and reduced neurosphere cell number compared with the SCR irradiated group; however, not significantly. Differentiation of U87MG cells from neurospheres was reduced in HEB‑silenced cells, whereas in irradiated cells the proportion of CD133+ cells was similar in HEB‑silenced cells compared with the SCR control. These results suggest that HEB may contribute to the proliferation and maintenance of GBM cells. However, only limited effects were exerted by irradiation in HEB‑silenced cells. HEB may be a potential target to decrease proliferation in U87MG GBM cells, grown as monolayers or neurospheres, and may provide important information for the development of novel strategies for cancer therapy.
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Affiliation(s)
- Paulo R D V Godoy
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040‑901, Brazil
| | - Ana Paula L Montaldi
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040‑901, Brazil
| | - Elza T Sakamoto-Hojo
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040‑901, Brazil
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25
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Benítez-Burraco A, Lattanzi W, Murphy E. Language Impairments in ASD Resulting from a Failed Domestication of the Human Brain. Front Neurosci 2016; 10:373. [PMID: 27621700 PMCID: PMC5002430 DOI: 10.3389/fnins.2016.00373] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 08/02/2016] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorders (ASD) are pervasive neurodevelopmental disorders entailing social and cognitive deficits, including marked problems with language. Numerous genes have been associated with ASD, but it is unclear how language deficits arise from gene mutation or dysregulation. It is also unclear why ASD shows such high prevalence within human populations. Interestingly, the emergence of a modern faculty of language has been hypothesized to be linked to changes in the human brain/skull, but also to the process of self-domestication of the human species. It is our intention to show that people with ASD exhibit less marked domesticated traits at the morphological, physiological, and behavioral levels. We also discuss many ASD candidates represented among the genes known to be involved in the “domestication syndrome” (the constellation of traits exhibited by domesticated mammals, which seemingly results from the hypofunction of the neural crest) and among the set of genes involved in language function closely connected to them. Moreover, many of these genes show altered expression profiles in the brain of autists. In addition, some candidates for domestication and language-readiness show the same expression profile in people with ASD and chimps in different brain areas involved in language processing. Similarities regarding the brain oscillatory behavior of these areas can be expected too. We conclude that ASD may represent an abnormal ontogenetic itinerary for the human faculty of language resulting in part from changes in genes important for the “domestication syndrome” and, ultimately, from the normal functioning of the neural crest.
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Affiliation(s)
| | - Wanda Lattanzi
- Institute of Anatomy and Cell Biology, Università Cattolica del Sacro Cuore Rome, Italy
| | - Elliot Murphy
- Division of Psychology and Language Sciences, University College London London, UK
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26
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Chen YF, Yang CC, Kao SY, Liu CJ, Lin SC, Chang KW. MicroRNA-211 Enhances the Oncogenicity of Carcinogen-Induced Oral Carcinoma by Repressing TCF12 and Increasing Antioxidant Activity. Cancer Res 2016; 76:4872-86. [PMID: 27221705 DOI: 10.1158/0008-5472.can-15-1664] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 04/09/2016] [Indexed: 11/16/2022]
Abstract
miR-211 expression in human oral squamous cell carcinoma (OSCC) has been implicated in poor patient survival. To investigate the oncogenic roles of miR-211, we generated K14-EGFP-miR-211 transgenic mice tagged with GFP. Induction of oral carcinogenesis in transgenic mice using 4-nitroquinoline 1-oxide (4NQO) resulted in more extensive and severe tongue tumorigenesis compared with control animals. We found that 4NQO and arecoline upregulated miR-211 expression in OSCC cells. In silico and experimental evidence further revealed that miR-211 directly targeted transcription factor 12 (TCF12), which mediated suppressor activities in OSCC cells and was drastically downregulated in tumor tissues. We used GeneChip analysis and bioinformatic algorithms to identify transcriptional targets of TCF12 and confirmed through reporter and ChIP assays that family with sequence similarity 213, member A (FAM213A), a peroxiredoxin-like antioxidative protein, was repressed transcriptionally by TCF12. FAM213A silencing in OSCC cells diminished oncogenic activity, reduced the ALDH1-positive cell population, and increased reactive oxygen species. TCF12 and FAM213A expression was correlated inversely in head and neck carcinoma samples according to The Cancer Genome Atlas. OSCC patients bearing tumors with high FAM213A expression tended to have worse survival. Furthermore, 4NQO treatment downregulated TCF12 and upregulated FAM213A by modulating miR-211 both in vitro and in vivo Overall, our findings develop a mouse model that recapitulates the molecular and histopathologic alterations of human OSCC pathogenesis and highlight a new miRNA-mediated oncogenic mechanism. Cancer Res; 76(16); 4872-86. ©2016 AACR.
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Affiliation(s)
- Yi-Fen Chen
- Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan
| | - Cheng-Chieh Yang
- Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan. Department of Dentistry, National Yang-Ming University, Taipei, Taiwan. Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Shou-Yen Kao
- Department of Dentistry, National Yang-Ming University, Taipei, Taiwan. Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chung-Ji Liu
- Department of Dentistry, National Yang-Ming University, Taipei, Taiwan. Department of Dentistry, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shu-Chun Lin
- Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan. Department of Dentistry, National Yang-Ming University, Taipei, Taiwan. Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan.
| | - Kuo-Wei Chang
- Institute of Oral Biology, National Yang-Ming University, Taipei, Taiwan. Department of Dentistry, National Yang-Ming University, Taipei, Taiwan. Department of Stomatology, Taipei Veterans General Hospital, Taipei, Taiwan.
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27
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Mapping Breakpoints of Complex Chromosome Rearrangements Involving a Partial Trisomy 15q23.1-q26.2 Revealed by Next Generation Sequencing and Conventional Techniques. PLoS One 2016; 11:e0154574. [PMID: 27218255 PMCID: PMC4878739 DOI: 10.1371/journal.pone.0154574] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 04/16/2016] [Indexed: 11/25/2022] Open
Abstract
Complex chromosome rearrangements (CCRs), which are rather rare in the whole population, may be associated with aberrant phenotypes. Next-generation sequencing (NGS) and conventional techniques, could be used to reveal specific CCRs for better genetic counseling. We report the CCRs of a girl and her mother, which were identified using a combination of NGS and conventional techniques including G-banding, fluorescence in situ hybridization (FISH) and PCR. The girl demonstrated CCRs involving chromosomes 3 and 8, while the CCRs of her mother involved chromosomes 3, 5, 8, 11 and 15. HumanCytoSNP-12 Chip analysis identified a 35.4 Mb duplication on chromosome 15q21.3-q26.2 in the proband and a 1.6 Mb microdeletion at chromosome 15q21.3 in her mother. The proband inherited the rearranged chromosomes 3 and 8 from her mother, and the duplicated region on chromosome 15 of the proband was inherited from the mother. Approximately one hundred genes were identified in the 15q21.3-q26.2 duplicated region of the proband. In particular, TPM1, SMAD6, SMAD3, and HCN4 may be associated with her heart defects, and HEXA, KIF7, and IDH2 are responsible for her developmental and mental retardation. In addition, we suggest that a microdeletion on the 15q21.3 region of the mother, which involved TCF2, TCF12, ADMA10 and AQP9, might be associated with mental retardation. We delineate the precise structures of the derivative chromosomes, chromosome duplication origin and possible molecular mechanisms for aberrant phenotypes by combining NGS data with conventional techniques.
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28
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Labreche K, Simeonova I, Kamoun A, Gleize V, Chubb D, Letouzé E, Riazalhosseini Y, Dobbins SE, Elarouci N, Ducray F, de Reyniès A, Zelenika D, Wardell CP, Frampton M, Saulnier O, Pastinen T, Hallout S, Figarella-Branger D, Dehais C, Idbaih A, Mokhtari K, Delattre JY, Huillard E, Mark Lathrop G, Sanson M, Houlston RS. TCF12 is mutated in anaplastic oligodendroglioma. Nat Commun 2015; 6:7207. [PMID: 26068201 PMCID: PMC4490400 DOI: 10.1038/ncomms8207] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 04/17/2015] [Indexed: 11/09/2022] Open
Abstract
Anaplastic oligodendroglioma (AO) are rare primary brain tumours that are generally incurable, with heterogeneous prognosis and few treatment targets identified. Most oligodendrogliomas have chromosomes 1p/19q co-deletion and an IDH mutation. Here we analysed 51 AO by whole-exome sequencing, identifying previously reported frequent somatic mutations in CIC and FUBP1. We also identified recurrent mutations in TCF12 and in an additional series of 83 AO. Overall, 7.5% of AO are mutated for TCF12, which encodes an oligodendrocyte-related transcription factor. Eighty percent of TCF12 mutations identified were in either the bHLH domain, which is important for TCF12 function as a transcription factor, or were frameshift mutations leading to TCF12 truncated for this domain. We show that these mutations compromise TCF12 transcriptional activity and are associated with a more aggressive tumour type. Our analysis provides further insights into the unique and shared pathways driving AO.
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Affiliation(s)
- Karim Labreche
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
| | - Iva Simeonova
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
| | - Aurélie Kamoun
- Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, 75013 Paris, France
| | - Vincent Gleize
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
| | - Daniel Chubb
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Eric Letouzé
- Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, 75013 Paris, France
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada H3A 0G1
| | - Sara E. Dobbins
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Nabila Elarouci
- Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, 75013 Paris, France
| | - Francois Ducray
- INSERM U1028, CNRS UMR5292, Service de Neuro-oncologie, Hopital neurologique, Hospices civils de Lyon, Lyon Neuroscience Research Center, Neuro-Oncology and Neuro-Inflammation Team, 69677 Lyon, France
| | - Aurélien de Reyniès
- Programme Cartes d’Identité des Tumeurs (CIT), Ligue Nationale Contre Le Cancer, 75013 Paris, France
| | - Diana Zelenika
- Centre National de Génotypage, IG/CEA, 2 rue Gaston Crémieux, CP 5721, Evry 91057, France
| | - Christopher P. Wardell
- Division of Molecular Pathology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Mathew Frampton
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
| | - Olivier Saulnier
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada H3A 0G1
| | - Sabrina Hallout
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
| | - Dominique Figarella-Branger
- AP-HM, Hôpital de la Timone, Service d’anatomie pathologique et de neuropathologie, 13385 Marseille, France
- Université de la Méditerranée, Aix-Marseille, Faculté de Médecine La Timone, CRO2, UMR 911 Marseille, France
| | - Caroline Dehais
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, 75013 Paris, France
| | - Ahmed Idbaih
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, 75013 Paris, France
| | - Karima Mokhtari
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Laboratoire de Neuropathologie R. Escourolle, 75013 Paris, France
| | - Jean-Yves Delattre
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, 75013 Paris, France
| | - Emmanuelle Huillard
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
| | - G. Mark Lathrop
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada H3A 0G1
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada H3A 0G1
| | - Marc Sanson
- Inserm, U 1127, ICM, F-75013 Paris, France
- CNRS, UMR 7225, ICM, F-75013 Paris, France
- Institut du Cerveau et de la Moelle épinière ICM, Paris 75013, France
- Sorbonne Universités, UPMC Université Paris 06, UMR S 1127, F-75013 Paris, France
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, Service de neurologie 2-Mazarin, 75013 Paris, France
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, Sutton, Surrey SM2 5NG, UK
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29
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Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature 2014; 518:355-359. [PMID: 25533951 PMCID: PMC4336237 DOI: 10.1038/nature13990] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Accepted: 10/21/2014] [Indexed: 12/16/2022]
Abstract
Models derived from human pluripotent stem cells that accurately recapitulate neural development in vitro and allow for the generation of specific neuronal subtypes are of major interest to the stem cell and biomedical community. Notch signalling, particularly through the Notch effector HES5, is a major pathway critical for the onset and maintenance of neural progenitor cells in the embryonic and adult nervous system. Here we report the transcriptional and epigenomic analysis of six consecutive neural progenitor cell stages derived from a HES5::eGFP reporter human embryonic stem cell line. Using this system, we aimed to model cell-fate decisions including specification, expansion and patterning during the ontogeny of cortical neural stem and progenitor cells. In order to dissect regulatory mechanisms that orchestrate the stage-specific differentiation process, we developed a computational framework to infer key regulators of each cell-state transition based on the progressive remodelling of the epigenetic landscape and then validated these through a pooled short hairpin RNA screen. We were also able to refine our previous observations on epigenetic priming at transcription factor binding sites and suggest here that they are mediated by combinations of core and stage-specific factors. Taken together, we demonstrate the utility of our system and outline a general framework, not limited to the context of the neural lineage, to dissect regulatory circuits of differentiation.
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30
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Tao H, Mei S, Sun X, Peng X, Zhang X, Ma C, Wang L, Hua L, Li F. Associations of TCF12, CTNNAL1 and WNT10B gene polymorphisms with litter size in pigs. Anim Reprod Sci 2013; 140:189-94. [PMID: 23820070 DOI: 10.1016/j.anireprosci.2013.05.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 05/21/2013] [Accepted: 05/23/2013] [Indexed: 11/27/2022]
Abstract
In previous research, several WNT signaling pathway genes including transcription factor 12 (TCF12), catenin alpha-like protein 1 (CTNNAL1) and wingless-type MMTV integration site family, member 10B (WNT10B) were differentially expressed in PMSG-hCG stimulated preovulatory ovarian follicles of Large White and Chinese Taihu sows. In the present research, these three genes were selected as the candidate genes for litter size traits in pigs. Four mutations (TCF12 c.-201+65 G>A, TCF12 c.-200-300 G>A, CTNNAL1 c.1878 G>C and WNT10B c.*12 C>T) were detected in eleven pig populations, and results indicated CTNNAL1 c.1878 G and WNT10B c.*12 C were the major alleles in all tested pig populations, while TCF12 c.-201+65 A and TCF12 c.-200-300 A were the major alleles in several Chinese native pig breeds. Association analysis of four mutations with litter size in Large White and DIV pigs showed that both the signficant differences of total number born (TNB) and number born alive (NBA) among three genotypes and the significance of additive effects appeared at TCF12 c.-200-300 G>A and CTNNAL1 c.1878 G>C loci, suggesting these two mutations might be reliable markers for pig selection and breeding.
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Affiliation(s)
- Hu Tao
- Key Laboratory of Pig Genetics and Breeding of Ministry of Agriculture & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, PR China
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Tandon P, Miteva YV, Kuchenbrod LM, Cristea IM, Conlon FL. Tcf21 regulates the specification and maturation of proepicardial cells. Development 2013; 140:2409-21. [PMID: 23637334 DOI: 10.1242/dev.093385] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The epicardium is a mesothelial cell layer essential for vertebrate heart development and pertinent for cardiac repair post-injury in the adult. The epicardium initially forms from a dynamic precursor structure, the proepicardial organ, from which cells migrate onto the heart surface. During the initial stage of epicardial development crucial epicardial-derived cell lineages are thought to be determined. Here, we define an essential requirement for transcription factor Tcf21 during early stages of epicardial development in Xenopus, and show that depletion of Tcf21 results in a disruption in proepicardial cell specification and failure to form a mature epithelial epicardium. Using a mass spectrometry-based approach we defined Tcf21 interactions and established its association with proteins that function as transcriptional co-repressors. Furthermore, using an in vivo systems-based approach, we identified a panel of previously unreported proepicardial precursor genes that are persistently expressed in the epicardial layer upon Tcf21 depletion, thereby confirming a primary role for Tcf21 in the correct determination of the proepicardial lineage. Collectively, these studies lead us to propose that Tcf21 functions as a transcriptional repressor to regulate proepicardial cell specification and the correct formation of a mature epithelial epicardium.
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Affiliation(s)
- Panna Tandon
- University of North Carolina McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA
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Yamawaki Y, Fuchikami M, Morinobu S, Segawa M, Matsumoto T, Yamawaki S. Antidepressant-like effect of sodium butyrate (HDAC inhibitor) and its molecular mechanism of action in the rat hippocampus. World J Biol Psychiatry 2012; 13:458-67. [PMID: 21812623 DOI: 10.3109/15622975.2011.585663] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES Epigenetic mechanisms, such as changes in gene expression resulting from chromatin remodeling through histone acetylation, have been implicated in the pathophysiology of depression. However, the antidepressant-like effect of the histone deacetylase inhibitor sodium butyrate (SB) has been inconclusive. The aim of this study was to examine the antidepressant-like effect of SB and elucidate its molecular mechanisms. METHODS We examined the antidepressant-like effect of SB in a forced swim test (FST) and a tail suspension test (TST). Hippocampal gene expression analyses using DNA microarray and real-time PCR were undertaken. Western blotting and ChIP assay were undertaken to examine whether histone acetylation was associated with changes in gene expression by SB. RESULTS Repeated administration of SB significantly reduced immobility on the FST and the TST, and significantly altered the levels of mRNA for several genes; e.g., upregulation of transthyretin (Ttr) and downregulation of serotonin 2A receptor (Htr2a). Western blotting and ChIP assay revealed selective increases in histone H4 acetylation at the promoter of the Ttr gene with a significant increase in Ttr immunoreactivity 24 h after the final administration of SB. CONCLUSION These findings suggest the possibility that alterations in gene expression, including upregulation of Ttr and downregulation of several other genes, including Htr2a, may be involved in antidepressant-like effect of SB.
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Affiliation(s)
- Yosuke Yamawaki
- Department of Psychiatry and Neurosciences, Division of Frontier Medical Sciences, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
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Wang R, Xie H, Huang Z, Ma J, Fang X, Ding Y, Sun Z. Transcription factor network regulating CD(+)CD8(+) thymocyte survival. Crit Rev Immunol 2012; 31:447-58. [PMID: 22321106 DOI: 10.1615/critrevimmunol.v31.i6.10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
More than 80% of thymocytes are CD4(+)CD8(+) double positive (DP) cells subject to positive/ negative selection. The lifespan of DP thymocytes is critical in shaping the peripheral T-cell repertoire essential for mounting immune responses against foreign, but not self, antigens. During T-cell maturation, if the first round of T-cell receptor (TCR) α chain rearrangement fails to generate a productive T-cell receptor, DP cells start another round of α chain rearrangement until positive selection or cell death intervenes. Thus, the lifespan of DP cells determines how many rounds of α chain rearrangement can be carried out, and influences the likelihood of completing positive selection. The antiapoptotic protein Bcl-x(L) is the ultimate effector regulating DP cell survival, and several transcription factors critical for T-cell development, such as TCF-1, E proteins, c-Myb, and RORγt, regulate DP survival via a Bcl-x(L)-dependent pathway. However, the relationship between these transcription factors in this process is largely unclear. Recent results are revealing an interactive network among these critical factors during regulation of DP thymocyte survival. This review will discuss how these transcription factors potentially work together to control DP thymocyte survival that is critical for successful completion of T-cell development.
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Affiliation(s)
- Ruiqing Wang
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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Lee CC, Chen WS, Chen CC, Chen LL, Lin YS, Fan CS, Huang TS. TCF12 protein functions as transcriptional repressor of E-cadherin, and its overexpression is correlated with metastasis of colorectal cancer. J Biol Chem 2011; 287:2798-809. [PMID: 22130667 DOI: 10.1074/jbc.m111.258947] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A correlation of TCF12 mRNA overexpression with colorectal cancer (CRC) metastasis was suggested by microarray data and validated by the survey of 120 patients. Thirty-three (27.5%) of the 120 patients showed tumor TCF12 mRNA overexpression and had a higher rate of metastatic occurrence (p = 0.020) and a poorer survival outcome (p = 0.014). Abundant TCF12 levels were also observed in human CRC cell lines such as SW620 and LoVo, but a relatively low level was detected in SW480 cells. Knockdown of TCF12 expression in SW620 and LoVo cells drastically reduced their activities of migration, invasion, and metastasis. Tight cell-cell contact and an increase in E-cadherin but a concomitant decrease in fibronectin were observed in TCF12-knockdown cells. Connexin 26, connexin 43, and gap-junction activity were also increased upon TCF12-knockdown. In contrast, ectopic TCF12 overexpression in SW480 cells facilitated fibronectin expression and cell migration and invasion activities but diminished cellular levels of E-cadherin, connexin 26, connexin 43, and gap junction. A physical association of TCF12 with the E-cadherin promoter was evidenced by chromatin immunoprecipitation assay. TCF12 was tightly correlated with cellular expression of Bmi1 and EZH2 and was co-immunoprecipitable with Bmi1 and EZH2, suggesting that TCF12 transcriptionally suppressed E-cadherin expression via polycomb group-repressive complexes. Clinically, TCF12 mRNA overexpression was also correlated with E-cadherin mRNA down-regulation in the tumor tissues of our 120 patients (p = 0.013). These studies suggested that TCF12 functioned as a transcriptional repressor of E-cadherin and its overexpression was significantly correlated with the occurrence of CRC metastasis.
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Affiliation(s)
- Chun-Chung Lee
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 350, Taiwan
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Wu K, Li S, Bodhinathan K, Meyers C, Chen W, Campbell-Thompson M, McIntyre L, Foster TC, Muzyczka N, Kumar A. Enhanced expression of Pctk1, Tcf12 and Ccnd1 in hippocampus of rats: Impact on cognitive function, synaptic plasticity and pathology. Neurobiol Learn Mem 2011; 97:69-80. [PMID: 21982980 DOI: 10.1016/j.nlm.2011.09.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/24/2011] [Accepted: 09/14/2011] [Indexed: 10/17/2022]
Abstract
We previously identified a set of 50 genes that were differentially transcribed in the hippocampal CA1 region of aged, learning-impaired rats compared to aged, superior learning animals during a Morris water maze paradigm. In the current study, we expressed three of these genes (Pctk1, Tcf12 and Ccnd1), which had shown increased transcription in aged, learning impaired rats, in the hippocampus of young rats using viral gene transfer and tested for learning and memory deficits at age 7-14months. Pctk1 injected animals displayed a modest deficit in acquiring latency in both the Morris water maze and the reverse Morris maze. In the radial arm water maze paradigm, Pctk1, Tcf12 and Ccnd1 expressing animals all showed significant deficits in spatial working memory compared to controls. Rats injected with Ccnd1 and Tcf12, but not Pctk1, also showed a significant deficit in spatial reference memory in the radial arm water maze. Electrophysiological experiments revealed no difference in LTP in Ccnd1 and Pctk1 animals. However, LTD induced by low frequency stimulation was observed in control and Ccnd1 animals, but not in Pctk1 treated animals. In addition, neither Ccnd1 nor Pctk1 expression produced any detectable neuropathology. In contrast Tcf12 expressing animals displayed significant neurodegeneration in both CA1 and dentate gyrus. Several Tcf12 animals also developed tumors that appeared to be glioblastomas, suggesting that aberrant Tcf12 expression in the hippocampus is tumorigenic. Thus, behavioral experiments suggested that overexpression of Pctk1 and Ccnd1 produce a deficit in learning and memory, but electrophysiological experiments do not point to a simple mechanism. In contrast, the learning and memory deficits in Tcf12 animals are likely due to neuropathology associated with Tcf12 gene expression.
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Affiliation(s)
- Ke Wu
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
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Nowick K, Fields C, Gernat T, Caetano-Anolles D, Kholina N, Stubbs L. Gain, loss and divergence in primate zinc-finger genes: a rich resource for evolution of gene regulatory differences between species. PLoS One 2011; 6:e21553. [PMID: 21738707 PMCID: PMC3126818 DOI: 10.1371/journal.pone.0021553] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 06/01/2011] [Indexed: 12/14/2022] Open
Abstract
The molecular changes underlying major phenotypic differences between humans and other primates are not well understood, but alterations in gene regulation are likely to play a major role. Here we performed a thorough evolutionary analysis of the largest family of primate transcription factors, the Krüppel-type zinc finger (KZNF) gene family. We identified and curated gene and pseudogene models for KZNFs in three primate species, chimpanzee, orangutan and rhesus macaque, to allow for a comparison with the curated set of human KZNFs. We show that the recent evolutionary history of primate KZNFs has been complex, including many lineage-specific duplications and deletions. We found 213 species-specific KZNFs, among them 7 human-specific and 23 chimpanzee-specific genes. Two human-specific genes were validated experimentally. Ten genes have been lost in humans and 13 in chimpanzees, either through deletion or pseudogenization. We also identified 30 KZNF orthologs with human-specific and 42 with chimpanzee-specific sequence changes that are predicted to affect DNA binding properties of the proteins. Eleven of these genes show signatures of accelerated evolution, suggesting positive selection between humans and chimpanzees. During primate evolution the most extensive re-shaping of the KZNF repertoire, including most gene additions, pseudogenizations, and structural changes occurred within the subfamily homininae. Using zinc finger (ZNF) binding predictions, we suggest potential impact these changes have had on human gene regulatory networks. The large species differences in this family of TFs stands in stark contrast to the overall high conservation of primate genomes and potentially represents a potent driver of primate evolution.
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Affiliation(s)
- Katja Nowick
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Christopher Fields
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Tim Gernat
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Derek Caetano-Anolles
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Nadezda Kholina
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Lisa Stubbs
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Cell and Developmental Biology, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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Kompass KS, Witte JS. Co-regulatory expression quantitative trait loci mapping: method and application to endometrial cancer. BMC Med Genomics 2011; 4:6. [PMID: 21226949 PMCID: PMC3032645 DOI: 10.1186/1755-8794-4-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 01/12/2011] [Indexed: 01/16/2023] Open
Abstract
Background Expression quantitative trait loci (eQTL) studies have helped identify the genetic determinants of gene expression. Understanding the potential interacting mechanisms underlying such findings, however, is challenging. Methods We describe a method to identify the trans-acting drivers of multiple gene co-expression, which reflects the action of regulatory molecules. This method-termed co-regulatory expression quantitative trait locus (creQTL) mapping-allows for evaluation of a more focused set of phenotypes within a clear biological context than conventional eQTL mapping. Results Applying this method to a study of endometrial cancer revealed regulatory mechanisms supported by the literature: a creQTL between a locus upstream of STARD13/DLC2 and a group of seven IFNβ-induced genes. This suggests that the Rho-GTPase encoded by STARD13 regulates IFNβ-induced genes and the DNA damage response. Conclusions Because of the importance of IFNβ in cancer, our results suggest that creQTL may provide a finer picture of gene regulation and may reveal additional molecular targets for intervention. An open source R implementation of the method is available at http://sites.google.com/site/kenkompass/.
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Affiliation(s)
- Kenneth S Kompass
- Department of Epidemiology and Biostatistics, Institute for Human Genetics, University of California, San Francisco, USA
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A Cohort of Balanced Reciprocal Translocations Associated with Dyslexia: Identification of Two Putative Candidate Genes at DYX1. Behav Genet 2010; 41:125-33. [PMID: 20798984 DOI: 10.1007/s10519-010-9389-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Accepted: 08/11/2010] [Indexed: 01/22/2023]
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Li H, Costantini C, Scrable H, Weindruch R, Puglielli L. Egr-1 and Hipk2 are required for the TrkA to p75(NTR) switch that occurs downstream of IGF1-R. Neurobiol Aging 2008; 30:2010-20. [PMID: 18378044 DOI: 10.1016/j.neurobiolaging.2008.02.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2007] [Revised: 02/14/2008] [Accepted: 02/14/2008] [Indexed: 02/07/2023]
Abstract
The aging program mediated by IGF1-R is responsible for a naturally occurring TrkA to p75(NTR) switch that leads to activation of the second messenger ceramide and increased production of the Alzheimer's disease amyloid beta-peptide. Biochemical and genetic approaches that target IGF1-R signaling, p75(NTR), or ceramide are able to block the above events. Here, we show that the transcription factors Egr-1 and Hipk2 are required elements for the TrkA to p75(NTR) switch downstream of IGF1-R signaling. Specifically, Egr-1 is required for the upregulation of p75(NTR), whereas Hipk2 is required for the downregulation of TrkA. In fact, gene silencing of Egr-1 abolished the ability of IGF1 to upregulate p75(NTR), whereas similar approaches directed against Hipk2 blocked the downregulation of TrkA. In addition, IGF1 treatment favored binding of Egr-1 and Hipk2 to the promoter of p75(NTR) and TrkA, respectively. Finally, the expression levels of both Egr-1 and Hipk2 are upregulated in an age-dependent fashion. Such an event is opposed by caloric restriction, a model of delayed aging, and favored by the p44 transgene in p44(+/+) animals, a model of accelerated aging.
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Affiliation(s)
- Hui Li
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
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40
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Aenlle KK, Kumar A, Cui L, Jackson TC, Foster TC. Estrogen effects on cognition and hippocampal transcription in middle-aged mice. Neurobiol Aging 2007; 30:932-45. [PMID: 17950954 DOI: 10.1016/j.neurobiolaging.2007.09.004] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2007] [Revised: 09/06/2007] [Accepted: 09/12/2007] [Indexed: 10/22/2022]
Abstract
Young and middle-aged female mice were ovariectomized and given cyclic injections of either estradiol or vehicle treatments. During the fifth week after surgery the Morris water maze was used to assess cognitive function. Age and treatment effects emerged over the course of spatial training such that middle-aged vehicle treated mice exhibited deficits in acquiring a spatial search strategy compared to younger vehicle treated mice and middle-age estradiol treated mice. Following behavioral characterization, mice were maintained on their injection schedule until week seven and hippocampi were collected 24h after the last injection. Hippocampal RNA was extracted and genes responsive to age and estrogen were identified using cDNA microarrays. Estradiol treatment in middle-aged mice altered the expression of genes related to transcriptional regulation, biosynthesis, growth, neuroprotection, and elements of cell signaling pathways. Expression profiles for representative genes were confirmed in a separate set of animals using oligonucleotide arrays and RT-PCR. Our results indicate that estrogen treatment in middle-aged animals may promote hippocampal health during the aging process.
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Affiliation(s)
- Kristina K Aenlle
- Department of Neuroscience, McKnight Brain Institute, University of Florida, P.O. Box 100244, Gainesville, FL 32610-0244, USA
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Flora A, Garcia JJ, Thaller C, Zoghbi HY. The E-protein Tcf4 interacts with Math1 to regulate differentiation of a specific subset of neuronal progenitors. Proc Natl Acad Sci U S A 2007; 104:15382-7. [PMID: 17878293 PMCID: PMC1978485 DOI: 10.1073/pnas.0707456104] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Proneural factors represent <10 transcriptional regulators required for specifying all of the different neurons of the mammalian nervous system. The mechanisms by which such a small number of factors creates this diversity are still unknown. We propose that proteins interacting with proneural factors confer such specificity. To test this hypothesis we isolated proteins that interact with Math1, a proneural transcription factor essential for the establishment of a neural progenitor population (rhombic lip) that gives rise to multiple hindbrain structures and identified the E-protein Tcf4. Interestingly, haploinsufficiency of TCF4 causes the Pitt-Hopkins mental retardation syndrome, underscoring the important role for this protein in neural development. To investigate the functional relevance of the Math1/Tcf4 interaction in vivo, we studied Tcf4(-/-) mice and found that they have disrupted pontine nucleus development. Surprisingly, this selective deficit occurs without affecting other rhombic lip-derived nuclei, despite expression of Math1 and Tcf4 throughout the rhombic lip. Importantly, deletion of any of the other E-protein-encoding genes does not have detectable effects on Math1-dependent neurons, suggesting a specialized role for Tcf4 in distinct neural progenitors. Our findings provide the first in vivo evidence for an exclusive function of dimers formed between a proneural basic helix-loop-helix factor and a specific E-protein, offering insight about the mechanisms underlying transcriptional programs that regulate development of the mammalian nervous system.
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Affiliation(s)
- Adriano Flora
- *Howard Hughes Medical Institute
- Departments of Molecular and Human Genetics
- To whom correspondence may be addressed. E-mail: or
| | - Jesus J. Garcia
- *Howard Hughes Medical Institute
- Departments of Molecular and Human Genetics
| | | | - Huda Y. Zoghbi
- *Howard Hughes Medical Institute
- Departments of Molecular and Human Genetics
- Neuroscience, and
- Pediatrics, and
- **Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030
- To whom correspondence may be addressed. E-mail: or
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Fernández-Medarde A, Porteros A, de las Rivas J, Núñez A, Fuster JJ, Santos E. Laser microdissection and microarray analysis of the hippocampus of Ras-GRF1 knockout mice reveals gene expression changes affecting signal transduction pathways related to memory and learning. Neuroscience 2007; 146:272-85. [PMID: 17321057 DOI: 10.1016/j.neuroscience.2007.01.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2006] [Revised: 12/19/2006] [Accepted: 01/03/2007] [Indexed: 11/25/2022]
Abstract
We used manual macrodissection or laser capture microdissection (LCM) to isolate tissue sections of the hippocampus area of Ras-GRF1 wild type and knockout mice brains, and analyzed their transcriptional patterns using commercial oligonucleotide microarrays. Comparison between the transcriptomes of macrodissected and microdissected samples showed that the LCM samples allowed detection of significantly higher numbers of differentially expressed genes, with higher statistical rates of significance. These results validate LCM as a reliable technique for in vivo genomic studies in the brain hippocampus, where contamination by surrounding areas (not expressing Ras-GRF1) increases background noise and impairs identification of differentially expressed genes. Comparison between wild type and knockout LCM hippocampus samples revealed that Ras-GRF1 elimination caused significant gene expression changes, mostly affecting signal transduction and related neural processes. The list of 36 most differentially expressed genes included loci concerned mainly with Ras/G protein signaling and cytoskeletal organization (i.e. 14-3-3gamma/zeta, Kcnj6, Clasp2) or related, cross-talking pathways (i.e. jag2, decorin, strap). Consistent with the phenotypes shown by Ras-GRF1 knockout mice, many of these differentially expressed genes play functional roles in processes such as sensory development and function (i.e. Sptlc1, antiquitin, jag2) and/or neurological development/neurodegeneration processes affecting memory and learning. Indeed, potential links to neurodegenerative diseases such as Alzheimer disease (AD) or Creutzfeldt-Jacobs disease (CJD), have been reported for a number of differentially expressed genes identified in this study (Ptma, Aebp2, Clasp2, Hebp1, 14-3-3gamma/zeta, Csnk1delta, etc.). These data, together with the previously described role of IRS and insulin (known Ras-GRF1 activators) in AD, warrant further investigation of a potential functional link of Ras-GRF1 to neurodegenerative processes.
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Affiliation(s)
- A Fernández-Medarde
- Centro de Investigación del Cáncer, IBMCC (CSIC-USAL), Campus Unamuno, University of Salamanca, 37007 Salamanca, Spain
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Tanigawa Y, Yakura R, Komiya T. The bHLH transcription factor Tcf12 (ME1) mRNA is abundantly expressed in Paneth cells of mouse intestine. Gene Expr Patterns 2007; 7:709-13. [PMID: 17405739 DOI: 10.1016/j.modgep.2007.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2006] [Revised: 02/06/2007] [Accepted: 02/23/2007] [Indexed: 10/23/2022]
Abstract
Using a large-scale in situ hybridization screening system, we found that mRNA coding for ME1, a basic helix-loop-helix (bHLH) transcription factor, was abundantly expressed in Paneth cells of adult small intestinal crypts. Other functionally related E-protein mRNAs, ME2, and E2A, however, could not be detected in the cells. ME1 mRNA was first detected in the jejunum and ileum two weeks after birth when the number of Paneth cells starts to increase. ME1 is the first identified bHLH transcription factor expressed in the Paneth cells and may be used as a molecular marker and a key molecule for analyzing transcriptional regulation in the Paneth cell.
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Affiliation(s)
- Yoko Tanigawa
- Department of Biological Function, Graduate School of Science, Osaka City University, Sumiyoshi, Osaka, Japan
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Bailey PJ, Klos JM, Andersson E, Karlén M, Källström M, Ponjavic J, Muhr J, Lenhard B, Sandelin A, Ericson J. A global genomic transcriptional code associated with CNS-expressed genes. Exp Cell Res 2006; 312:3108-19. [PMID: 16919269 DOI: 10.1016/j.yexcr.2006.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 06/05/2006] [Accepted: 06/12/2006] [Indexed: 01/28/2023]
Abstract
Highly conserved non-coding DNA regions (HCNR) occur frequently in vertebrate genomes, but their functional roles remain unclear. Here, we provide evidence that a large portion of HCNRs are enriched for binding sites for Sox, POU and Homeodomain transcription factors, and such HCNRs can act as cis-regulatory regions active in neural stem cells. Strikingly, these HCNRs are linked to several hundreds of genes expressed in the developing CNS and they may exert locus-wide regulatory effects on multiple genes flanking their genomic location. Moreover, these data imply a unifying transcriptional logic for a large set of CNS-expressed genes in which Sox and POU proteins act as generic promoters of transcription while Homeodomain proteins control the spatial expression of genes through active repression.
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Affiliation(s)
- Peter J Bailey
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institute, S-171, 77 Stockholm, Sweden
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Forsberg EC, Prohaska SS, Katzman S, Heffner GC, Stuart JM, Weissman IL. Differential expression of novel potential regulators in hematopoietic stem cells. PLoS Genet 2006; 1:e28. [PMID: 16151515 PMCID: PMC1200425 DOI: 10.1371/journal.pgen.0010028] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 07/14/2005] [Indexed: 12/12/2022] Open
Abstract
The hematopoietic system is an invaluable model both for understanding basic developmental biology and for developing clinically relevant cell therapies. Using highly purified cells and rigorous microarray analysis we have compared the expression pattern of three of the most primitive hematopoietic subpopulations in adult mouse bone marrow: long-term hematopoietic stem cells (HSC), short-term HSC, and multipotent progenitors. All three populations are capable of differentiating into a spectrum of mature blood cells, but differ in their self-renewal and proliferative capacity. We identified numerous novel potential regulators of HSC self-renewal and proliferation that were differentially expressed between these closely related cell populations. Many of the differentially expressed transcripts fit into pathways and protein complexes not previously identified in HSC, providing evidence for new HSC regulatory units. Extending these observations to the protein level, we demonstrate expression of several of the corresponding proteins, which provide novel surface markers for HSC. We discuss the implications of our findings for HSC biology. In particular, our data suggest that cell–cell and cell–matrix interactions are major regulators of long-term HSC, and that HSC themselves play important roles in regulating their immediate microenvironment. Hematopoietic, or blood-forming, stem cells (HSC) are responsible for the continual replenishment of all blood cells throughout life. This ability to both renew themselves and give rise to expanded populations of differentiating and mature cells is a hallmark of stem cells and is therefore an area of intense research. The rarity of HSC as well as their location in the bone marrow environment has made it difficult to identify the genes that regulate these properties. The earliest stages of blood development begins with the long-term (LT) repopulating HSC that then differentiate into short-term (ST) repopulating HSC and non-self renewing multipotent progenitors (MPP). The authors investigated the gene expression differences in these highly purified populations that differ mainly in their capacity to self renew, and identified a number of genes specific to each of these populations. Intriguingly, many of these genes code for proteins that are involved in cell–cell and cell–matrix interactions that were not previously identified on these populations. These novel discoveries will, together with future experiments, enhance our understanding of the basic biology of stem cells and their clinical uses.
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Affiliation(s)
- E Camilla Forsberg
- Department of Pathology, Institute of Cancer and Stem Cell Biology and Medicine, Stanford University Medical School, Stanford, California, USA.
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Gurok U, Steinhoff C, Lipkowitz B, Ropers HH, Scharff C, Nuber UA. Gene expression changes in the course of neural progenitor cell differentiation. J Neurosci 2004; 24:5982-6002. [PMID: 15229246 PMCID: PMC6729244 DOI: 10.1523/jneurosci.0809-04.2004] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The molecular changes underlying neural progenitor differentiation are essentially unknown. We applied cDNA microarrays with 13,627 clones to measure dynamic gene expression changes during the in vitro differentiation of neural progenitor cells that were isolated from the subventricular zone of postnatal day 7 mice and grown in vitro as neurospheres. In two experimental series in which we withdrew epidermal growth factor and added the neurotrophins Neurotrophin-4 or BDNF, four time points were investigated: undifferentiated cells grown as neurospheres, and cells 24, 48, and 96 hr after differentiation. Expression changes of selected genes were confirmed by semiquantitative RT-PCR. Ten different groups of gene expression dynamics obtained by cluster analysis are described. To correlate selected gene expression changes to the localization of respective proteins, we performed immunostainings of cultured neurospheres and of brain sections from adult mice. Our results provide new insights into the genetic program of neural progenitor differentiation and give strong hints to as yet unknown cellular communications within the adult subventricular zone stem cell niche.
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Affiliation(s)
- Ulf Gurok
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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Uittenbogaard M, Martinka DL, Chiaramello A. The basic helix-loop-helix differentiation factor Nex1/MATH-2 functions as a key activator of the GAP-43 gene. J Neurochem 2003; 84:678-88. [PMID: 12562512 PMCID: PMC1413589 DOI: 10.1046/j.1471-4159.2003.01572.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nex1/MATH-2 is a neurogenic basic Helix-Loop-Helix (bHLH) transcription factor that belongs to the NeuroD subfamily. Its expression parallels that of the GAP-43 gene and peaks during brain development, when neurite outgrowth and synaptogenesis are highly active. We previously observed a direct correlation between the levels of expression of Nex1 and GAP-43 proteins, which resulted in extensive neurite outgrowth and neuronal differentiation of PC12 cells in the absence of nerve growth factor. Since the GAP-43 gene is a target for bHLH regulation, we investigated whether Nex1 could regulate the activity of the GAP-43 promoter. We found that among the members of the NeuroD subfamily, Nex1 promoted maximal activity of the GAP-43 promoter. The Nex1-mediated activity is restricted to the conserved E1-E2 cluster located near the major transcription start sites. By electrophoretic mobility shift assay and site-directed mutagenesis, we showed that Nex1 binds as homodimers and that the E1 E-box is a high affinity binding site. We further found that Nex1 released the ME1 E-protein-mediated repression in a concentration dependent manner. Thus, the E1-E2 cluster has a dual function: it can mediate activation or repression depending on the interacting bHLH proteins. Finally, a series of N-terminal and C-terminal deletions revealed that Nex1 transcriptional activity is linked to two distinct transactivation domains, TAD1 and TAD2, with TAD1 being unique to Nex1. Together, our results suggest that Nex1 may engage in selective interactions with components of the core transcriptional machinery whose assembly is dictated by the architecture of the GAP-43 promoter and cellular environment.
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Affiliation(s)
- Martine Uittenbogaard
- Department of Anatomy and Cell Biology, George Washington University Medical Center, Washington DC, USA
| | - Debra L. Martinka
- Department of Anatomy and Cell Biology, George Washington University Medical Center, Washington DC, USA
- Program of Neuroscience, George Washington University Medical Center, Washington DC, USA
| | - Anne Chiaramello
- Department of Anatomy and Cell Biology, George Washington University Medical Center, Washington DC, USA
- Program of Neuroscience, George Washington University Medical Center, Washington DC, USA
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Iacobas DA, Massimi AB, Urban M, Iacobas S, Spray DC. Hits and misses from gene expression ratio measurements in cDNA microarray studies. J Biomol Tech 2002; 13:143-157. [PMID: 19498978 PMCID: PMC2279857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA microarray users face many challenges to obtain accurate results, including complex technical errors, natural variability of biological systems, imperfect reproducibility of reference standards, and difficulties in acquisition and processing of large amounts of data. Therefore, investigators should be aware of potential sources of variability and account for them in the experimental design and execution. This work reports our experience in identifying factors that alter the reliability of the results and in diminishing effects of these factors. We have studied the hybridization reproducibility in cDNA microarray chips, both as absolute values and expression ratios, and the nature and impact of several technical, acquisition, and processing errors. A new experimental strategy is proposed and mathematical algorithms developed that efficiently correct the errors and thereby increase the information obtainable through microarray studies. These algorithms reduced the variability not associated with biological system to less than a quarter of its initial value and have substantially enhanced reliability in experiments on brain and cultured neuroblastoma cells.
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Affiliation(s)
- Dumitru A Iacobas
- Department of Neuroscience, Molecular Biology Core, Kennedy Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA.
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