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Lambourne L, Mattioli K, Santoso C, Sheynkman G, Inukai S, Kaundal B, Berenson A, Spirohn-Fitzgerald K, Bhattacharjee A, Rothman E, Shrestha S, Laval F, Yang Z, Bisht D, Sewell JA, Li G, Prasad A, Phanor S, Lane R, Campbell DM, Hunt T, Balcha D, Gebbia M, Twizere JC, Hao T, Frankish A, Riback JA, Salomonis N, Calderwood MA, Hill DE, Sahni N, Vidal M, Bulyk ML, Fuxman Bass JI. Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.12.584681. [PMID: 38617209 PMCID: PMC11014633 DOI: 10.1101/2024.03.12.584681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Most human Transcription factors (TFs) genes encode multiple protein isoforms differing in DNA binding domains, effector domains, or other protein regions. The global extent to which this results in functional differences between isoforms remains unknown. Here, we systematically compared 693 isoforms of 246 TF genes, assessing DNA binding, protein binding, transcriptional activation, subcellular localization, and condensate formation. Relative to reference isoforms, two-thirds of alternative TF isoforms exhibit differences in one or more molecular activities, which often could not be predicted from sequence. We observed two primary categories of alternative TF isoforms: "rewirers" and "negative regulators", both of which were associated with differentiation and cancer. Our results support a model wherein the relative expression levels of, and interactions involving, TF isoforms add an understudied layer of complexity to gene regulatory networks, demonstrating the importance of isoform-aware characterization of TF functions and providing a rich resource for further studies.
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Affiliation(s)
- Luke Lambourne
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Kaia Mattioli
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Clarissa Santoso
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Gloria Sheynkman
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Sachi Inukai
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Babita Kaundal
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna Berenson
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
| | - Kerstin Spirohn-Fitzgerald
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Anukana Bhattacharjee
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Florent Laval
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Zhipeng Yang
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Deepa Bisht
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jared A Sewell
- Department of Biology, Boston University, Boston, MA, USA
| | - Guangyuan Li
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Anisa Prasad
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Harvard College, Cambridge MA, USA
| | - Sabrina Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ryan Lane
- Department of Biology, Boston University, Boston, MA, USA
| | | | - Toby Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marinella Gebbia
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute (LTRI), Sinai Health System, Toronto, Ontario, Canada
| | - Jean-Claude Twizere
- TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Adam Frankish
- Laboratory of Viral Interactomes, GIGA Institute, University of Liège, Liège, Belgium
| | - Josh A Riback
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nathan Salomonis
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Marc Vidal
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Juan I Fuxman Bass
- Department of Biology, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Boston University, Boston, MA, USA
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2
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Sacco JC, Starr E, Weaver A, Dietz R, Spocter MA. Resequencing of the TMF-1 (TATA Element Modulatory Factor) regulated protein (TRNP1) gene in domestic and wild canids. Canine Med Genet 2023; 10:10. [PMID: 37968761 PMCID: PMC10647097 DOI: 10.1186/s40575-023-00133-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND Cortical folding is related to the functional organization of the brain. The TMF-1 regulated protein (TRNP1) regulates the expansion and folding of the mammalian cerebral cortex, a process that may have been accelerated by the domestication of dogs. The objectives of this study were to sequence the TRNP1 gene in dogs and related canid species, provide evidence of its expression in dog brain and compare the genetic variation within dogs and across the Canidae. The gene was located in silico to dog chromosome 2. The sequence was experimentally confirmed by amplifying and sequencing the TRNP1 exonic and promoter regions in 72 canids (36 purebred dogs, 20 Gy wolves and wolf-dog hybrids, 10 coyotes, 5 red foxes and 1 Gy fox). RESULTS A partial TRNP1 transcript was isolated from several regions in the dog brain. Thirty genetic polymorphisms were found in the Canis sp. with 17 common to both dogs and wolves, and only one unique to dogs. Seven polymorphisms were observed only in coyotes. An additional 9 variants were seen in red foxes. Dogs were the least genetically diverse. Several polymorphisms in the promoter and 3'untranslated region were predicted to alter TRNP1 function by interfering with the binding of transcriptional repressors and miRNAs expressed in neural precursors. A c.259_264 deletion variant that encodes a polyalanine expansion was polymorphic in all species studied except for dogs. A stretch of 15 nucleotides that is found in other mammalian sequences (corresponding to 5 amino acids located between Pro58 and Ala59 in the putative dog protein) was absent from the TRNP1 sequences of all 5 canid species sequenced. Both of these aforementioned coding sequence variations were predicted to affect the formation of alpha helices in the disordered region of the TRNP1 protein. CONCLUSIONS Potentially functionally important polymorphisms in the TRNP1 gene are found within and across various Canis species as well as the red fox, and unique differences in protein structure have evolved and been conserved in the Canidae compared to all other mammalian species.
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Affiliation(s)
- James C Sacco
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA.
| | - Emma Starr
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Alyssa Weaver
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Rachel Dietz
- Ellis Pharmacogenomics Laboratory, College of Pharmacy and Health Sciences, Drake University, 50311, Des Moines, IA, USA
| | - Muhammad A Spocter
- Department of Anatomy, Des Moines University, 50266, Des Moines, IA, USA
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3
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Kliesmete Z, Wange LE, Vieth B, Esgleas M, Radmer J, Hülsmann M, Geuder J, Richter D, Ohnuki M, Götz M, Hellmann I, Enard W. Regulatory and coding sequences of TRNP1 co-evolve with brain size and cortical folding in mammals. eLife 2023; 12:83593. [PMID: 36947129 PMCID: PMC10032658 DOI: 10.7554/elife.83593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 03/01/2023] [Indexed: 03/23/2023] Open
Abstract
Brain size and cortical folding have increased and decreased recurrently during mammalian evolution. Identifying genetic elements whose sequence or functional properties co-evolve with these traits can provide unique information on evolutionary and developmental mechanisms. A good candidate for such a comparative approach is TRNP1, as it controls proliferation of neural progenitors in mice and ferrets. Here, we investigate the contribution of both regulatory and coding sequences of TRNP1 to brain size and cortical folding in over 30 mammals. We find that the rate of TRNP1 protein evolution (ω) significantly correlates with brain size, slightly less with cortical folding and much less with body size. This brain correlation is stronger than for >95% of random control proteins. This co-evolution is likely affecting TRNP1 activity, as we find that TRNP1 from species with larger brains and more cortical folding induce higher proliferation rates in neural stem cells. Furthermore, we compare the activity of putative cis-regulatory elements (CREs) of TRNP1 in a massively parallel reporter assay and identify one CRE that likely co-evolves with cortical folding in Old World monkeys and apes. Our analyses indicate that coding and regulatory changes that increased TRNP1 activity were positively selected either as a cause or a consequence of increases in brain size and cortical folding. They also provide an example how phylogenetic approaches can inform biological mechanisms, especially when combined with molecular phenotypes across several species.
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Affiliation(s)
- Zane Kliesmete
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Lucas Esteban Wange
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Beate Vieth
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Miriam Esgleas
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-Universität, Munich, Germany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental Health, Munich, Germany
| | - Jessica Radmer
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Matthias Hülsmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
- Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Johanna Geuder
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Daniel Richter
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Mari Ohnuki
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdelena Götz
- Physiological Genomics, BioMedical Center - BMC, Ludwig-Maximilians-Universität, Munich, Germany
- Institute for Stem Cell Research, Helmholtz Zentrum München, Germany Research Center for Environmental Health, Munich, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, BioMedical Center (BMC), Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Wolfgang Enard
- Anthropology and Human Genomics, Faculty of Biology, Ludwig-Maximilians-Universität, Munich, Germany
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4
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Esgleas M, Falk S, Forné I, Thiry M, Najas S, Zhang S, Mas-Sanchez A, Geerlof A, Niessing D, Wang Z, Imhof A, Götz M. Trnp1 organizes diverse nuclear membrane-less compartments in neural stem cells. EMBO J 2020; 39:e103373. [PMID: 32627867 PMCID: PMC7429739 DOI: 10.15252/embj.2019103373] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 11/09/2022] Open
Abstract
TMF1‐regulated nuclear protein 1 (Trnp1) has been shown to exert potent roles in neural development affecting neural stem cell self‐renewal and brain folding, but its molecular function in the nucleus is still unknown. Here, we show that Trnp1 is a low complexity protein with the capacity to phase separate. Trnp1 interacts with factors located in several nuclear membrane‐less organelles, the nucleolus, nuclear speckles, and condensed chromatin. Importantly, Trnp1 co‐regulates the architecture and function of these nuclear compartments in vitro and in the developing brain in vivo. Deletion of a highly conserved region in the N‐terminal intrinsic disordered region abolishes the capacity of Trnp1 to regulate nucleoli and heterochromatin size, proliferation, and M‐phase length; decreases the capacity to phase separate; and abrogates most of Trnp1 protein interactions. Thus, we identified Trnp1 as a novel regulator of several nuclear membrane‐less compartments, a function important to maintain cells in a self‐renewing proliferative state.
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Affiliation(s)
- Miriam Esgleas
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians Universitaet Muenchen, Planegg/Munich, Germany.,Institute for Stem Cell Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sven Falk
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians Universitaet Muenchen, Planegg/Munich, Germany.,Institute for Stem Cell Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universitaet Muenchen, Planegg/Munich, Germany
| | - Marc Thiry
- Cell and Tissue Biology Unit, GIGA-Neurosciences, University of Liege, C.H.U. Sart Tilman, Liege, Belgium
| | - Sonia Najas
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians Universitaet Muenchen, Planegg/Munich, Germany.,Institute for Stem Cell Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Aina Mas-Sanchez
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians Universitaet Muenchen, Planegg/Munich, Germany.,Institute for Stem Cell Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany
| | - Arie Geerlof
- Institute of Structural Biology, Helmholtz Zentrum Muenchen, Neuherberg, Germany
| | - Dierk Niessing
- Group Intracellular Transport and RNA Biology at the Institute of Structural Biology, Helmholtz Zentrum Muenchen, Neuherberg, Germany.,Department of Cell Biology, BioMedical Center (BMC), Ludwig-Maximilians-Universitaet Muenchen, Planegg/Munich, Germany
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center (BMC), Ludwig-Maximilians-Universitaet Muenchen, Planegg/Munich, Germany.,SYNERGY, Excellence Cluster of Systems Neurology, BioMedical Center (BMC), Ludwig-Maximilians-Universitaet Muenchen, Planegg/Munich, Germany
| | - Magdalena Götz
- Physiological Genomics, Biomedical Center (BMC), Ludwig-Maximilians Universitaet Muenchen, Planegg/Munich, Germany.,Institute for Stem Cell Research, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg, Germany.,SYNERGY, Excellence Cluster of Systems Neurology, BioMedical Center (BMC), Ludwig-Maximilians-Universitaet Muenchen, Planegg/Munich, Germany
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5
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Osipovich AB, Stancill JS, Cartailler JP, Dudek KD, Magnuson MA. Excitotoxicity and Overnutrition Additively Impair Metabolic Function and Identity of Pancreatic β-Cells. Diabetes 2020; 69:1476-1491. [PMID: 32332159 PMCID: PMC7809715 DOI: 10.2337/db19-1145] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 04/20/2020] [Indexed: 12/14/2022]
Abstract
A sustained increase in intracellular Ca2+ concentration (referred to hereafter as excitotoxicity), brought on by chronic metabolic stress, may contribute to pancreatic β-cell failure. To determine the additive effects of excitotoxicity and overnutrition on β-cell function and gene expression, we analyzed the impact of a high-fat diet (HFD) on Abcc8 knockout mice. Excitotoxicity caused β-cells to be more susceptible to HFD-induced impairment of glucose homeostasis, and these effects were mitigated by verapamil, a Ca2+ channel blocker. Excitotoxicity, overnutrition, and the combination of both stresses caused similar but distinct alterations in the β-cell transcriptome, including additive increases in genes associated with mitochondrial energy metabolism, fatty acid β-oxidation, and mitochondrial biogenesis and their key regulator Ppargc1a Overnutrition worsened excitotoxicity-induced mitochondrial dysfunction, increasing metabolic inflexibility and mitochondrial damage. In addition, excitotoxicity and overnutrition, individually and together, impaired both β-cell function and identity by reducing expression of genes important for insulin secretion, cell polarity, cell junction, cilia, cytoskeleton, vesicular trafficking, and regulation of β-cell epigenetic and transcriptional program. Sex had an impact on all β-cell responses, with male animals exhibiting greater metabolic stress-induced impairments than females. Together, these findings indicate that a sustained increase in intracellular Ca2+, by altering mitochondrial function and impairing β-cell identity, augments overnutrition-induced β-cell failure.
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Affiliation(s)
- Anna B Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN
| | - Jennifer S Stancill
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | | | - Karrie D Dudek
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
| | - Mark A Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
- Vanderbilt Center for Stem Cell Biology, Vanderbilt University, Nashville, TN
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN
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6
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Vaid S, Huttner WB. Transcriptional Regulators and Human-Specific/Primate-Specific Genes in Neocortical Neurogenesis. Int J Mol Sci 2020; 21:ijms21134614. [PMID: 32610533 PMCID: PMC7369782 DOI: 10.3390/ijms21134614] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/09/2020] [Accepted: 06/26/2020] [Indexed: 12/15/2022] Open
Abstract
During development, starting from a pool of pluripotent stem cells, tissue-specific genetic programs help to shape and develop functional organs. To understand the development of an organ and its disorders, it is important to understand the spatio-temporal dynamics of the gene expression profiles that occur during its development. Modifications in existing genes, the de-novo appearance of new genes, or, occasionally, even the loss of genes, can greatly affect the gene expression profile of any given tissue and contribute to the evolution of organs or of parts of organs. The neocortex is evolutionarily the most recent part of the brain, it is unique to mammals, and is the seat of our higher cognitive abilities. Progenitors that give rise to this tissue undergo sequential waves of differentiation to produce the complete sets of neurons and glial cells that make up a functional neocortex. We will review herein our understanding of the transcriptional regulators that control the neural precursor cells (NPCs) during the generation of the most abundant class of neocortical neurons, the glutametergic neurons. In addition, we will discuss the roles of recently-identified human- and primate-specific genes in promoting neurogenesis, leading to neocortical expansion.
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7
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Oldani M, Fabbri M, Melchioretto P, Callegaro G, Fusi P, Gribaldo L, Forcella M, Urani C. In vitro and bioinformatics mechanistic-based approach for cadmium carcinogenicity understanding. Toxicol In Vitro 2020; 65:104757. [PMID: 31904401 PMCID: PMC7166080 DOI: 10.1016/j.tiv.2020.104757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/28/2019] [Accepted: 01/01/2020] [Indexed: 02/07/2023]
Abstract
Cadmium is a toxic metal able to enter the cells through channels and transport pathways dedicated to essential ions, leading, among others, to the dysregulation of divalent ions homeostasis. Despite its recognized human carcinogenicity, the mechanisms are still under investigation. A powerful tool for mechanistic studies of carcinogenesis is the Cell Transformation Assay (CTA). We have isolated and characterized by whole genome microarray and bioinformatics analysis of differentially expressed genes (DEGs) cadmium-transformed cells from different foci (F1, F2, and F3) at the end of CTA (6 weeks). The systematic analysis of up- and down-regulated transcripts and the comparison of DEGs in transformed cells evidence different functional targets and the complex picture of cadmium-induced transformation. Only 34 in common DEGs are found in cells from all foci, and among these, only 4 genes are jointly up-regulated (Ccl2, Ccl5, IL6 and Spp1), all responsible for cytokines/chemokines coding. Most in common DEGs are down-regulated, suggesting that the switching-off of specific functions plays a major role in this process. In addition, the comparison of dysregulated pathways immediately after cadmium treatment with those in transformed cells provides a valuable means to the comprehension of the overall process. Cell transformation Assay and toxicogenomics are integrated to study cadmium carcinogenesis mechanisms Inflammatory response is the only common feature in Cd-transformed cells from all different foci Switching-off of specific functions plays a major role in Cd-induced carcinogenesis Comparison of triggering signals and deregulated pathways in transformed cells provides hints on cadmium mechanisms
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Affiliation(s)
- Monica Oldani
- Department of Biotechnology and Biosciences, University of Milan - Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Marco Fabbri
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA
| | - Pasquale Melchioretto
- Department of Earth and Environmental Sciences, University of Milan - Bicocca, Piazza della Scienza 1, 20126 Milan, Italy
| | - Giulia Callegaro
- Department of Earth and Environmental Sciences, University of Milan - Bicocca, Piazza della Scienza 1, 20126 Milan, Italy; Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), Leiden University, The Netherlands
| | - Paola Fusi
- Department of Biotechnology and Biosciences, University of Milan - Bicocca, Piazza della Scienza 3, 20126 Milan, Italy; Integrated Models for Prevention and Protection in Environmental and Occupational Health, (MISTRAL) Interuniversity Research Center, Italy
| | - Laura Gribaldo
- European Commission, DG Joint Research Centre, Via Fermi 2749, 21027 Ispra, VA, Italy.
| | - Matilde Forcella
- Department of Biotechnology and Biosciences, University of Milan - Bicocca, Piazza della Scienza 3, 20126 Milan, Italy
| | - Chiara Urani
- Department of Earth and Environmental Sciences, University of Milan - Bicocca, Piazza della Scienza 1, 20126 Milan, Italy; Integrated Models for Prevention and Protection in Environmental and Occupational Health, (MISTRAL) Interuniversity Research Center, Italy
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8
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Papadopoulos N, Lennartsson J, Heldin CH. PDGFRβ translocates to the nucleus and regulates chromatin remodeling via TATA element-modifying factor 1. J Cell Biol 2018; 217:1701-1717. [PMID: 29545370 PMCID: PMC5940298 DOI: 10.1083/jcb.201706118] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 01/05/2018] [Accepted: 02/01/2018] [Indexed: 12/24/2022] Open
Abstract
PDGFRβ translocates to the nucleus in a ligand-dependent manner tethered by TATA element–modifying factor 1 (TMF-1). Papadopoulos et al. show that PDGFRβ interacts with TMF-1 and Fer kinase in the nucleus, regulating chromatin remodeling by the SWI–SNF complex and controlling proliferation via a p21-dependent mechanism. Translocation of full-length or fragments of receptors to the nucleus has been reported for several tyrosine kinase receptors. In this paper, we show that a fraction of full-length cell surface platelet-derived growth factor (PDGF) receptor β (PDGFRβ) accumulates in the nucleus at the chromatin and the nuclear matrix after ligand stimulation. Nuclear translocation of PDGFRβ was dependent on PDGF-BB–induced receptor dimerization, clathrin-mediated endocytosis, β-importin, and intact Golgi, occurring in both normal and cancer cells. In the nucleus, PDGFRβ formed ligand-inducible complexes with the tyrosine kinase Fer and its substrate, TATA element–modifying factor 1 (TMF-1). PDGF-BB stimulation decreased TMF-1 binding to the transcriptional regulator Brahma-related gene 1 (Brg-1) and released Brg-1 from the SWI–SNF chromatin remodeling complex. Moreover, knockdown of TMF-1 by small interfering RNA decreased nuclear translocation of PDGFRβ and caused significant up-regulation of the Brg-1/p53-regulated cell cycle inhibitor CDKN1A (encoding p21) without affecting PDGFRβ-inducible immediate-early genes. In conclusion, nuclear interactions of PDGFRβ control proliferation by chromatin remodeling and regulation of p21 levels.
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Affiliation(s)
- Natalia Papadopoulos
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Ludwig Institute for Cancer Research, Uppsala University, Uppsala, Sweden
| | - Johan Lennartsson
- Science for Life Laboratory, Ludwig Institute for Cancer Research, Uppsala University, Uppsala, Sweden.,Department of Pharmaceutical Biomedicine, Uppsala University, Uppsala, Sweden
| | - Carl-Henrik Heldin
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden .,Science for Life Laboratory, Ludwig Institute for Cancer Research, Uppsala University, Uppsala, Sweden
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9
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Chen YM, Li H, Fan Y, Zhang QJ, Li X, Wu LJ, Chen ZJ, Zhu C, Qian LM. Identification of differentially expressed lncRNAs involved in transient regeneration of the neonatal C57BL/6J mouse heart by next-generation high-throughput RNA sequencing. Oncotarget 2018; 8:28052-28062. [PMID: 28427208 PMCID: PMC5438630 DOI: 10.18632/oncotarget.15887] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/20/2017] [Indexed: 02/01/2023] Open
Abstract
Previous studies have shown that mammalian cardiac tissue has a regenerative capacity. Remarkably, neonatal mice can regenerate their cardiac tissue for up to 6 days after birth, but this capacity is lost by day 7. In this study, we aimed to explore the expression pattern of long noncoding RNA (lncRNA) during this period and examine the mechanisms underlying this process. We found that 685 lncRNAs and 1833 mRNAs were differentially expressed at P1 and P7 by the next-generation high-throughput RNA sequencing. The coding genes associated with differentially expressed lncRNAs were mainly involved in metabolic processes and cell proliferation, and also were potentially associated with several key regeneration signalling pathways, including PI3K-Akt, MAPK, Hippo and Wnt. In addition, we identified some correlated targets of highly-dysregulated lncRNAs such as Igfbp3, Trnp1, Itgb6, and Pim3 by the coding-noncoding gene co-expression network. These data may offer a reference resource for further investigation about the mechanisms by which lncRNAs regulate cardiac regeneration.
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Affiliation(s)
- Yu-Mei Chen
- Department of Emergency, Zhongshan Hospital, Fudan University, Shanghai 200032, P.R. China
| | - Hua Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Yi Fan
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Qi-Jun Zhang
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Xing Li
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Li-Jie Wu
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Zi-Jie Chen
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Chun Zhu
- Department of Pediatrics, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing, Jiangsu 210004, P. R. China
| | - Ling-Mei Qian
- Department of Cardiology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
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10
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Park KU, Randazzo G, Jones KL, Brzezinski JA. Gsg1, Trnp1, and Tmem215 Mark Subpopulations of Bipolar Interneurons in the Mouse Retina. Invest Ophthalmol Vis Sci 2017; 58:1137-1150. [PMID: 28199486 PMCID: PMC5317276 DOI: 10.1167/iovs.16-19767] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Purpose How retinal bipolar cell interneurons are specified and assigned to specialized subtypes is only partially understood. In part, this is due to a lack of early pan- and subtype-specific bipolar cell markers. To discover these factors, we identified genes that were upregulated in Blimp1 (Prdm1) mutant retinas, which exhibit precocious bipolar cell development. Methods Postnatal day (P)2 retinas from Blimp1 conditional knock-out (CKO) mice and controls were processed for RNA sequencing. Genes that increased at least 45% and were statistically different between conditions were considered candidate bipolar-specific factors. Candidates were further evaluated by RT-PCR, in situ hybridization, and immunohistochemistry. Knock-in Tmem215-LacZ mice were used to better trace retinal expression. Results A comparison between Blimp1 CKO and control RNA-seq datasets revealed approximately 40 significantly upregulated genes. We characterized the expression of three genes that have no known function in the retina, Gsg1 (germ cell associated gene), Trnp1 (TMF-regulated nuclear protein), and Tmem215 (a predicted transmembrane protein). Germ cell associated gene appeared restricted to a small subset of cone bipolars while Trnp1 was seen in all ON type bipolar cells. Using Tmem215-LacZ heterozygous knock-in mice, we observed that β-galactosidase expression started early in bipolar cell development. In adults, Tmem215 was expressed by a subset of ON and OFF cone bipolar cells. Conclusions We have identified Gsg1, Tmem215, and Trnp1 as novel bipolar subtype-specific genes. The spatial and temporal pattern of their expression is consistent with a role in controlling bipolar subtype fate choice, differentiation, or physiology.
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Affiliation(s)
- Ko Uoon Park
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Grace Randazzo
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
| | - Kenneth L Jones
- Department of Pediatrics, Section Hematology/Oncology, University of Colorado Denver, Aurora, Colorado, United States
| | - Joseph A Brzezinski
- Department of Ophthalmology, University of Colorado Denver, Aurora, Colorado, United States
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11
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Dehay C, Kennedy H, Kosik KS. The outer subventricular zone and primate-specific cortical complexification. Neuron 2015; 85:683-94. [PMID: 25695268 DOI: 10.1016/j.neuron.2014.12.060] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Evolutionary expansion and complexification of the primate cerebral cortex are largely linked to the emergence of the outer subventricular zone (OSVZ), a uniquely structured germinal zone that generates the expanded primate supragranular layers. The primate OSVZ departs from rodent germinal zones in that it includes a higher diversity of precursor types, inter-related in bidirectional non-hierarchical lineages. In addition, primate-specific regulatory mechanisms are operating in primate cortical precursors via the occurrence of novel miRNAs. Here, we propose that the origin and evolutionary importance of the OSVZ is related to genetic changes in multiple regulatory loops and that cell-cycle regulation is a favored target for evolutionary adaptation of the cortex.
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Affiliation(s)
- Colette Dehay
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003, Lyon, France.
| | - Henry Kennedy
- Stem Cell and Brain Research Institute, INSERM U846, 18 Avenue Doyen Lepine, 69500 Bron, France; Université de Lyon, Université Lyon I, 69003, Lyon, France.
| | - Kenneth S Kosik
- Neuroscience Research Institute and Dept Cellular Molecular and Developmental Biology, University of California, Santa Barbara, CA 93106, USA.
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12
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Tuoc TC, Pavlakis E, Tylkowski MA, Stoykova A. Control of cerebral size and thickness. Cell Mol Life Sci 2014; 71:3199-218. [PMID: 24614969 PMCID: PMC11113230 DOI: 10.1007/s00018-014-1590-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 02/10/2014] [Accepted: 02/13/2014] [Indexed: 11/24/2022]
Abstract
The mammalian neocortex is a sheet of cells covering the cerebrum that provides the structural basis for the perception of sensory inputs, motor output responses, cognitive function, and mental capacity of primates. Recent discoveries promote the concept that increased cortical surface size and thickness in phylogenetically advanced species is a result of an increased generation of neurons, a process that underlies higher cognitive and intellectual performance in higher primates and humans. Here, we review some of the advances in the field, focusing on the diversity of neocortical progenitors in different species and the cellular mechanisms of neurogenesis. We discuss recent views on intrinsic and extrinsic molecular determinants, including the role of epigenetic chromatin modifiers and microRNA, in the control of neuronal output in developing cortex and in the establishment of normal cortical architecture.
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Affiliation(s)
- Tran Cong Tuoc
- Institute of Neuroanatomy, Universitätsmedizin Göttingen, Kreuzbergring 40, 37075, Göttingen, Germany,
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13
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Stahl R, Walcher T, De Juan Romero C, Pilz GA, Cappello S, Irmler M, Sanz-Aquela JM, Beckers J, Blum R, Borrell V, Götz M. Trnp1 regulates expansion and folding of the mammalian cerebral cortex by control of radial glial fate. Cell 2013; 153:535-49. [PMID: 23622239 DOI: 10.1016/j.cell.2013.03.027] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Revised: 01/31/2013] [Accepted: 03/13/2013] [Indexed: 11/19/2022]
Abstract
Evolution of the mammalian brain encompassed a remarkable increase in size of the cerebral cortex, which includes tangential and radial expansion. However, the mechanisms underlying these key features are still largely unknown. Here, we identified the DNA-associated protein Trnp1 as a regulator of cerebral cortex expansion in both of these dimensions. Gain- and loss-of-function experiments in the mouse cerebral cortex in vivo demonstrate that high Trnp1 levels promote neural stem cell self-renewal and tangential expansion. In contrast, lower levels promote radial expansion, with a potent increase of the number of intermediate progenitors and basal radial glial cells leading to folding of the otherwise smooth murine cerebral cortex. Remarkably, TRNP1 expression levels exhibit regional differences in the cerebral cortex of human fetuses, anticipating radial or tangential expansion. Thus, the dynamic regulation of Trnp1 is critical to control tangential and radial expansion of the cerebral cortex in mammals.
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Affiliation(s)
- Ronny Stahl
- Physiological Genomics, Institute of Physiology, Ludwig-Maximilian University Munich, Munich, Germany
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14
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Elkis Y, Bel S, Lerer-Goldstein T, Nyska A, Creasy DM, Shpungin S, Nir U. Testosterone deficiency accompanied by testicular and epididymal abnormalities in TMF(-/-) mice. Mol Cell Endocrinol 2013; 365:52-63. [PMID: 23000399 DOI: 10.1016/j.mce.2012.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Revised: 08/01/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Abstract
TMF/ARA160 is a Golgi-associated protein, which is essential for spermiogenesis. In this study, we show that lack of TMF/ARA160 leads to defects in both the testis and the epididymis. In the testis, spermatid retention and extensive proliferation of Leydig cells were observed. Concomitantly, the serum levels of luteinizing hormone (LH), a stimulator of Leydig cell proliferation, were significantly increased in TMF(-/-) mice. Structural and functional defects were also seen in the epididymis. These included apoptosis of epithelial epididymal cells and sperm stasis in the cauda. Notably, the serum testosterone levels of TMF(-/-) mice were significantly lower than those of wt mice, and external testosterone administration decreased the number of apoptotic epithelial epididymal cells in TMF(-/-) animals. In summary, we show here for the first time that TMF/ARA160 participates in the control of serum testosterone levels in males, and its absence results in major testicular and epididymal defects.
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Affiliation(s)
- Yoav Elkis
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel
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15
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Lerer-Goldshtein T, Bel S, Shpungin S, Pery E, Motro B, Goldstein RS, Bar-Sheshet SI, Breitbart H, Nir U. TMF/ARA160: A key regulator of sperm development. Dev Biol 2010; 348:12-21. [DOI: 10.1016/j.ydbio.2010.07.033] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2010] [Revised: 07/21/2010] [Accepted: 07/27/2010] [Indexed: 11/28/2022]
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16
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Abrham G, Volpe M, Shpungin S, Nir U. TMF/ARA160 downregulates proangiogenic genes and attenuates the progression of PC3 xenografts. Int J Cancer 2009; 125:43-53. [PMID: 19330832 DOI: 10.1002/ijc.24277] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
TMF/ARA160 is a Golgi-associated protein whose level is downregulated in solid tumors. TMF changes its subcellular localization on exposure of cells to stress cues, thereby, directing proteins, such as the key transcription factor, Stat3, to proteasomal degradation. Here, we show that enforced ectopic expression of HA-TMF in PC3 prostate carcinoma cells, which do not express Stat3, significantly attenuated the development and growth of xenograft tumors elicited by these cells in athymic mice. Immunohistochemical analysis revealed impaired angiogenesis and accelerated onset of apoptosis in the HA-TMF-expressing tumors. RNA expression profiling revealed the downregulation of several proangiogenic genes in HA-TMF-expressing xenografts. Among these were the interleukin-8 and interleukin-1beta genes, whose expression is controlled by nuclear factor-kB. The level of the nuclear factor-kB component, p65/RelA, was decreased in HA-TMF-expressing xenografts, and TMF was found to direct the ubiquitination and proteasomal degradation of p65/RelA in metabolically stressed PC3 clones. Taken together, our findings indicate that TMF/ARA160 is a regulator of key transcription factors under metabolic constraints, thereby affecting angiogenesis and progression of solid tumors, which are subjected to metabolic stress.
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Affiliation(s)
- Galya Abrham
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
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