Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability
Identifieur interne : 002049 ( Pmc/Curation ); précédent : 002048; suivant : 002050Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability
Auteurs : Ls Nguyen [Australie] ; L. Jolly [Australie] ; C. Shoubridge [Australie] ; Wk Chan [États-Unis] ; L. Huang [États-Unis] ; F. Laumonnier [France] ; M. Raynaud [France] ; A. Hackett [Australie] ; M. Field [Australie] ; J. Rodriguez [États-Unis] ; Ak Srivastava [États-Unis] ; Y. Lee [États-Unis] ; R. Long [États-Unis] ; Am Addington [États-Unis] ; Jl Rapoport [États-Unis] ; S. Suren [Royaume-Uni] ; Cn Hahn [Australie] ; J. Gamble [Australie] ; Mf Wilkinson [États-Unis] ; Ma Corbett [Australie] ; J. Gecz [Australie]Source :
- Molecular psychiatry [ 1359-4184 ] ; 2011.
Abstract
The nonsense-mediated mRNA decay (NMD) pathway was originally discovered by virtue of its ability to rapidly degrade aberrant mRNAs with premature termination codons. More recently, it was shown that NMD also directly regulates subsets of normal transcripts, suggesting that NMD has roles in normal biological processes. Indeed, several NMD factors have been shown to regulate neurological events (for example, neurogenesis and synaptic plasticity) in numerous vertebrate species. In man, mutations in the NMD factor gene
Url:
DOI: 10.1038/mp.2011.163
PubMed: 22182939
PubMed Central: 4281019
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<author><name sortKey="Gecz, J" sort="Gecz, J" uniqKey="Gecz J" first="J" last="Gecz">J. Gecz</name>
<affiliation wicri:level="1"><nlm:aff id="A1">Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Paediatrics, University of Adelaide, Adelaide, SA</wicri:regionArea>
</affiliation>
<affiliation wicri:level="1"><nlm:aff id="A2">Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia</nlm:aff>
<country xml:lang="fr">Australie</country>
<wicri:regionArea>Department of Genetic Medicine, SA Pathology, Adelaide, SA</wicri:regionArea>
</affiliation>
</author>
</analytic>
<series><title level="j">Molecular psychiatry</title>
<idno type="ISSN">1359-4184</idno>
<idno type="eISSN">1476-5578</idno>
<imprint><date when="2011">2011</date>
</imprint>
</series>
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<front><div type="abstract" xml:lang="en"><p id="P1">The nonsense-mediated mRNA decay (NMD) pathway was originally discovered by virtue of its ability to rapidly degrade aberrant mRNAs with premature termination codons. More recently, it was shown that NMD also directly regulates subsets of normal transcripts, suggesting that NMD has roles in normal biological processes. Indeed, several NMD factors have been shown to regulate neurological events (for example, neurogenesis and synaptic plasticity) in numerous vertebrate species. In man, mutations in the NMD factor gene <italic>UPF3B</italic>
, which disrupts a branch of the NMD pathway, cause various forms of intellectual disability (ID). Using Epstein Barr virus—immortalized B cells, also known as lymphoblastoid cell lines (LCLs), from ID patients that have loss-of-function mutations in <italic>UPF3B</italic>
, we investigated the genome-wide consequences of compromised NMD and the role of NMD in neuronal development and function. We found that ~5% of the human transcriptome is impacted in <italic>UPF3B</italic>
patients. The UPF3B paralog, UPF3A, is stabilized in all <italic>UPF3B</italic>
patients, and partially compensates for the loss of UPF3B function. Interestingly, UPF3A protein, but not mRNA, was stabilised in a quantitative manner that inversely correlated with the severity of patients’ phenotype. This suggested that the ability to stabilize the UPF3A protein is a crucial modifier of the neurological symptoms due to loss of UPF3B. We also identified <italic>ARHGAP24</italic>
, which encodes a GTPase-activating protein, as a canonical target of NMD, and we provide evidence that deregulation of this gene inhibits axon and dendrite outgrowth and branching. Our results demonstrate that the UPF3B-dependent NMD pathway is a major regulator of the transcriptome and that its targets have important roles in neuronal cells.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9607835</journal-id>
<journal-id journal-id-type="pubmed-jr-id">20545</journal-id>
<journal-id journal-id-type="nlm-ta">Mol Psychiatry</journal-id>
<journal-id journal-id-type="iso-abbrev">Mol. Psychiatry</journal-id>
<journal-title-group><journal-title>Molecular psychiatry</journal-title>
</journal-title-group>
<issn pub-type="ppub">1359-4184</issn>
<issn pub-type="epub">1476-5578</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22182939</article-id>
<article-id pub-id-type="pmc">4281019</article-id>
<article-id pub-id-type="doi">10.1038/mp.2011.163</article-id>
<article-id pub-id-type="manuscript">NIHMS377183</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Transcriptome profiling of UPF3B/NMD-deficient lymphoblastoid cells from patients with various forms of intellectual disability</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Nguyen</surname>
<given-names>LS</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Jolly</surname>
<given-names>L</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Shoubridge</surname>
<given-names>C</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chan</surname>
<given-names>WK</given-names>
</name>
<xref ref-type="aff" rid="A3">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Huang</surname>
<given-names>L</given-names>
</name>
<xref ref-type="aff" rid="A4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Laumonnier</surname>
<given-names>F</given-names>
</name>
<xref ref-type="aff" rid="A5">5</xref>
<xref ref-type="aff" rid="A6">6</xref>
<xref ref-type="aff" rid="A7">7</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Raynaud</surname>
<given-names>M</given-names>
</name>
<xref ref-type="aff" rid="A5">5</xref>
<xref ref-type="aff" rid="A7">7</xref>
<xref ref-type="aff" rid="A8">8</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hackett</surname>
<given-names>A</given-names>
</name>
<xref ref-type="aff" rid="A9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Field</surname>
<given-names>M</given-names>
</name>
<xref ref-type="aff" rid="A9">9</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rodriguez</surname>
<given-names>J</given-names>
</name>
<xref ref-type="aff" rid="A10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Srivastava</surname>
<given-names>AK</given-names>
</name>
<xref ref-type="aff" rid="A10">10</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lee</surname>
<given-names>Y</given-names>
</name>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Long</surname>
<given-names>R</given-names>
</name>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Addington</surname>
<given-names>AM</given-names>
</name>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Rapoport</surname>
<given-names>JL</given-names>
</name>
<xref ref-type="aff" rid="A11">11</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Suren</surname>
<given-names>S</given-names>
</name>
<xref ref-type="aff" rid="A12">12</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Hahn</surname>
<given-names>CN</given-names>
</name>
<xref ref-type="aff" rid="A13">13</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gamble</surname>
<given-names>J</given-names>
</name>
<xref ref-type="aff" rid="A14">14</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wilkinson</surname>
<given-names>MF</given-names>
</name>
<xref ref-type="aff" rid="A4">4</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Corbett</surname>
<given-names>MA</given-names>
</name>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gecz</surname>
<given-names>J</given-names>
</name>
<xref ref-type="aff" rid="A1">1</xref>
<xref ref-type="aff" rid="A2">2</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>1</label>
Department of Paediatrics, University of Adelaide, Adelaide, SA, Australia</aff>
<aff id="A2"><label>2</label>
Department of Genetic Medicine, SA Pathology, Adelaide, SA, Australia</aff>
<aff id="A3"><label>3</label>
Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA</aff>
<aff id="A4"><label>4</label>
Department of Reproductive Medicine, University of California, San Diego, CA, USA</aff>
<aff id="A5"><label>5</label>
INSERM, U930, Tours, France</aff>
<aff id="A6"><label>6</label>
CNRS, ERL3106, Tours, France</aff>
<aff id="A7"><label>7</label>
University Francois-Rabelais, UMR ‘Imaging and Brain’, Tours, France</aff>
<aff id="A8"><label>8</label>
CHRU de Tours, Service de Genetique, Tours, France</aff>
<aff id="A9"><label>9</label>
GOLD Service, Hunter Genetics, Newcastle, Australia</aff>
<aff id="A10"><label>10</label>
J.C. Self Research Institute, Greenwood Genetic Centre, Greenwood, SC, USA</aff>
<aff id="A11"><label>11</label>
Child Psychiatry Branch, National Institute of Mental Health, Bethesda, MD, USA</aff>
<aff id="A12"><label>12</label>
Human Developmental Biology Resource, Neural Development Unit, UCL Institute of Child Health, London, UK</aff>
<aff id="A13"><label>13</label>
Department of Molecular Pathology, Centre for Cancer Biology, SA Pathology, Adelaide, SA, Australia</aff>
<aff id="A14"><label>14</label>
Centenary Institute of Cancer Medicine & Cell Biology, University of Sydney, NSW, Australia</aff>
<author-notes><corresp id="cor1">Correspondence: Professor J Gecz, Department of Genetic Medicine, SA Pathology, 72 King William Road, Womens and Childrens Hospital, North Adelaide, South Australia 5006, Australia. <email>jozef.gecz@adelaide.edu.au</email>
</corresp>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>16</day>
<month>12</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>20</day>
<month>12</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="ppub"><month>11</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>31</day>
<month>12</month>
<year>2014</year>
</pub-date>
<volume>17</volume>
<issue>11</issue>
<fpage>1103</fpage>
<lpage>1115</lpage>
<pmc-comment>elocation-id from pubmed: 10.1038/mp.2011.163</pmc-comment>
<permissions><copyright-statement>© 2012 Macmillan Publishers Limited All rights reserved</copyright-statement>
<copyright-year>2012</copyright-year>
</permissions>
<abstract><p id="P1">The nonsense-mediated mRNA decay (NMD) pathway was originally discovered by virtue of its ability to rapidly degrade aberrant mRNAs with premature termination codons. More recently, it was shown that NMD also directly regulates subsets of normal transcripts, suggesting that NMD has roles in normal biological processes. Indeed, several NMD factors have been shown to regulate neurological events (for example, neurogenesis and synaptic plasticity) in numerous vertebrate species. In man, mutations in the NMD factor gene <italic>UPF3B</italic>
, which disrupts a branch of the NMD pathway, cause various forms of intellectual disability (ID). Using Epstein Barr virus—immortalized B cells, also known as lymphoblastoid cell lines (LCLs), from ID patients that have loss-of-function mutations in <italic>UPF3B</italic>
, we investigated the genome-wide consequences of compromised NMD and the role of NMD in neuronal development and function. We found that ~5% of the human transcriptome is impacted in <italic>UPF3B</italic>
patients. The UPF3B paralog, UPF3A, is stabilized in all <italic>UPF3B</italic>
patients, and partially compensates for the loss of UPF3B function. Interestingly, UPF3A protein, but not mRNA, was stabilised in a quantitative manner that inversely correlated with the severity of patients’ phenotype. This suggested that the ability to stabilize the UPF3A protein is a crucial modifier of the neurological symptoms due to loss of UPF3B. We also identified <italic>ARHGAP24</italic>
, which encodes a GTPase-activating protein, as a canonical target of NMD, and we provide evidence that deregulation of this gene inhibits axon and dendrite outgrowth and branching. Our results demonstrate that the UPF3B-dependent NMD pathway is a major regulator of the transcriptome and that its targets have important roles in neuronal cells.</p>
</abstract>
<kwd-group><kwd>intellectual disability</kwd>
<kwd>Nonsense-mediated mRNA decay</kwd>
<kwd>RNA-SEQ</kwd>
<kwd>UPF3A</kwd>
<kwd>UPF3B</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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