Identification of Novel Components of Target-of-Rapamycin Signaling Pathway by Network-Based Multi-Omics Integrative Analysis.
Identifieur interne : 000327 ( Main/Exploration ); précédent : 000326; suivant : 000328Identification of Novel Components of Target-of-Rapamycin Signaling Pathway by Network-Based Multi-Omics Integrative Analysis.
Auteurs : Elif Dereli Eke [Italie, Turquie] ; Kazim Yalcin Arga [Turquie] ; Duygu Dikicioglu [Turquie, Royaume-Uni] ; Serpil Eraslan [Turquie] ; Emir Erkol [Turquie] ; Arzu Celik [Turquie] ; Betul Kirdar [Turquie] ; Barbara Di Camillo [Italie]Source :
- Omics : a journal of integrative biology [ 1557-8100 ] ; 2019.
Descripteurs français
- KwdFr :
- Complexe-1 cible mécanistique de la rapamycine (métabolisme), Complexe-2 cible mécanistique de la rapamycine (métabolisme), Protéines de Saccharomyces cerevisiae (métabolisme), Protéomique (MeSH), Saccharomyces cerevisiae (pathogénicité), Sérine-thréonine kinases TOR (métabolisme), Transduction du signal (MeSH).
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Mechanistic Target of Rapamycin Complex 1, Mechanistic Target of Rapamycin Complex 2, Saccharomyces cerevisiae Proteins, TOR Serine-Threonine Kinases.
- pathogenicity : Saccharomyces cerevisiae.
- Proteomics, Signal Transduction.
Abstract
Target of rapamycin (TOR) is a major signaling pathway and regulator of cell growth. TOR serves as a hub of many signaling routes, and is implicated in the pathophysiology of numerous human diseases, including cancer, diabetes, and neurodegeneration. Therefore, elucidation of unknown components of TOR signaling that could serve as potential biomarkers and drug targets has a great clinical importance. In this study, our aim is to integrate transcriptomics, interactomics, and regulomics data in Saccharomyces cerevisiae using a network-based multiomics approach to enlighten previously unidentified, potential components of TOR signaling. We constructed the TOR-signaling protein interaction network, which was used as a template to search for TOR-mediated rapamycin and caffeine signaling paths. We scored the paths passing from at least one component of TOR Complex 1 or 2 (TORC1/TORC2) using the co-expression levels of the genes in the transcriptome data of the cells grown in the presence of rapamycin or caffeine. The resultant network revealed seven hitherto unannotated proteins, namely, Atg14p, Rim20p, Ret2p, Spt21p, Ylr257wp, Ymr295cp, and Ygr017wp, as potential components of TOR-mediated rapamycin and caffeine signaling in yeast. Among these proteins, we suggest further deciphering of the role of Ylr257wp will be particularly informative in the future because it was the only protein whose removal from the constructed network hindered the signal transduction to the TORC1 effector kinase Npr1p. In conclusion, this study underlines the value of network-based multiomics integrative data analysis in discovering previously unidentified components of the signaling networks by revealing potential components of TOR signaling for future experimental validation.
DOI: 10.1089/omi.2019.0021
PubMed: 30985253
Affiliations:
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Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>2 Department of Chemical Engineering, Bogazici University, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>5 Diagnostic Centre for Genetic Diseases, Koc University Hospital, Istanbul, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>5 Diagnostic Centre for Genetic Diseases, Koc University Hospital, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation></author><author><name sortKey="Erkol, Emir" sort="Erkol, Emir" uniqKey="Erkol E" first="Emir" last="Erkol">Emir Erkol</name><affiliation wicri:level="1"><nlm:affiliation>6 Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey.</nlm:affiliation><country xml:lang="fr">Turquie</country><wicri:regionArea>6 Department of 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University, Istanbul</wicri:regionArea><wicri:noRegion>Istanbul</wicri:noRegion></affiliation></author><author><name sortKey="Di Camillo, Barbara" sort="Di Camillo, Barbara" uniqKey="Di Camillo B" first="Barbara" last="Di Camillo">Barbara Di Camillo</name><affiliation wicri:level="1"><nlm:affiliation>1 Department of Information Engineering, University of Padua, Padua, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>1 Department of Information Engineering, University of Padua, Padua</wicri:regionArea><wicri:noRegion>Padua</wicri:noRegion></affiliation></author></analytic><series><title level="j">Omics : a journal of integrative biology</title><idno type="eISSN">1557-8100</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Mechanistic Target of Rapamycin Complex 1 (metabolism)</term><term>Mechanistic Target of Rapamycin Complex 2 (metabolism)</term><term>Proteomics (MeSH)</term><term>Saccharomyces cerevisiae (pathogenicity)</term><term>Saccharomyces cerevisiae Proteins (metabolism)</term><term>Signal Transduction (MeSH)</term><term>TOR Serine-Threonine Kinases (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Complexe-1 cible mécanistique de la rapamycine (métabolisme)</term><term>Complexe-2 cible mécanistique de la rapamycine (métabolisme)</term><term>Protéines de Saccharomyces cerevisiae (métabolisme)</term><term>Protéomique (MeSH)</term><term>Saccharomyces cerevisiae (pathogénicité)</term><term>Sérine-thréonine kinases TOR (métabolisme)</term><term>Transduction du signal (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Mechanistic Target of Rapamycin Complex 1</term><term>Mechanistic Target of Rapamycin Complex 2</term><term>Saccharomyces cerevisiae Proteins</term><term>TOR Serine-Threonine Kinases</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Complexe-1 cible mécanistique de la rapamycine</term><term>Complexe-2 cible mécanistique de la rapamycine</term><term>Protéines de Saccharomyces cerevisiae</term><term>Sérine-thréonine kinases TOR</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Proteomics</term><term>Signal Transduction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Protéomique</term><term>Transduction du signal</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Target of rapamycin (TOR) is a major signaling pathway and regulator of cell growth. TOR serves as a hub of many signaling routes, and is implicated in the pathophysiology of numerous human diseases, including cancer, diabetes, and neurodegeneration. Therefore, elucidation of unknown components of TOR signaling that could serve as potential biomarkers and drug targets has a great clinical importance. In this study, our aim is to integrate transcriptomics, interactomics, and regulomics data in <i>Saccharomyces cerevisiae</i> using a network-based multiomics approach to enlighten previously unidentified, potential components of TOR signaling. We constructed the TOR-signaling protein interaction network, which was used as a template to search for TOR-mediated rapamycin and caffeine signaling paths. We scored the paths passing from at least one component of TOR Complex 1 or 2 (TORC1/TORC2) using the co-expression levels of the genes in the transcriptome data of the cells grown in the presence of rapamycin or caffeine. The resultant network revealed seven hitherto unannotated proteins, namely, Atg14p, Rim20p, Ret2p, Spt21p, Ylr257wp, Ymr295cp, and Ygr017wp, as potential components of TOR-mediated rapamycin and caffeine signaling in yeast. Among these proteins, we suggest further deciphering of the role of Ylr257wp will be particularly informative in the future because it was the only protein whose removal from the constructed network hindered the signal transduction to the TORC1 effector kinase Npr1p. In conclusion, this study underlines the value of network-based multiomics integrative data analysis in discovering previously unidentified components of the signaling networks by revealing potential components of TOR signaling for future experimental validation.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30985253</PMID><DateCompleted><Year>2020</Year><Month>04</Month><Day>13</Day></DateCompleted><DateRevised><Year>2020</Year><Month>04</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1557-8100</ISSN><JournalIssue CitedMedium="Internet"><Volume>23</Volume><Issue>5</Issue><PubDate><Year>2019</Year><Month>05</Month></PubDate></JournalIssue><Title>Omics : a journal of integrative biology</Title><ISOAbbreviation>OMICS</ISOAbbreviation></Journal><ArticleTitle>Identification of Novel Components of Target-of-Rapamycin Signaling Pathway by Network-Based Multi-Omics Integrative Analysis.</ArticleTitle><Pagination><MedlinePgn>274-284</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1089/omi.2019.0021</ELocationID><Abstract><AbstractText>Target of rapamycin (TOR) is a major signaling pathway and regulator of cell growth. TOR serves as a hub of many signaling routes, and is implicated in the pathophysiology of numerous human diseases, including cancer, diabetes, and neurodegeneration. Therefore, elucidation of unknown components of TOR signaling that could serve as potential biomarkers and drug targets has a great clinical importance. In this study, our aim is to integrate transcriptomics, interactomics, and regulomics data in <i>Saccharomyces cerevisiae</i> using a network-based multiomics approach to enlighten previously unidentified, potential components of TOR signaling. We constructed the TOR-signaling protein interaction network, which was used as a template to search for TOR-mediated rapamycin and caffeine signaling paths. We scored the paths passing from at least one component of TOR Complex 1 or 2 (TORC1/TORC2) using the co-expression levels of the genes in the transcriptome data of the cells grown in the presence of rapamycin or caffeine. The resultant network revealed seven hitherto unannotated proteins, namely, Atg14p, Rim20p, Ret2p, Spt21p, Ylr257wp, Ymr295cp, and Ygr017wp, as potential components of TOR-mediated rapamycin and caffeine signaling in yeast. Among these proteins, we suggest further deciphering of the role of Ylr257wp will be particularly informative in the future because it was the only protein whose removal from the constructed network hindered the signal transduction to the TORC1 effector kinase Npr1p. In conclusion, this study underlines the value of network-based multiomics integrative data analysis in discovering previously unidentified components of the signaling networks by revealing potential components of TOR signaling for future experimental validation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dereli Eke</LastName><ForeName>Elif</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>1 Department of Information Engineering, University of Padua, Padua, Italy.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>2 Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Arga</LastName><ForeName>Kazim Yalcin</ForeName><Initials>KY</Initials><AffiliationInfo><Affiliation>3 Department of Bioengineering, Marmara University, Istanbul, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Dikicioglu</LastName><ForeName>Duygu</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>2 Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>4 Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Eraslan</LastName><ForeName>Serpil</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>2 Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>5 Diagnostic Centre for Genetic Diseases, Koc University Hospital, Istanbul, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Erkol</LastName><ForeName>Emir</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>6 Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Celik</LastName><ForeName>Arzu</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>6 Department of Molecular Biology and Genetics, Bogazici University, Istanbul, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kirdar</LastName><ForeName>Betul</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>2 Department of Chemical Engineering, Bogazici University, Istanbul, Turkey.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Di Camillo</LastName><ForeName>Barbara</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>1 Department of Information Engineering, University of Padua, Padua, Italy.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>04</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>OMICS</MedlineTA><NlmUniqueID>101131135</NlmUniqueID><ISSNLinking>1536-2310</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D029701">Saccharomyces cerevisiae Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.1.1</RegistryNumber><NameOfSubstance UI="D058570">TOR Serine-Threonine Kinases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.11.1</RegistryNumber><NameOfSubstance UI="D000076222">Mechanistic Target of Rapamycin Complex 1</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 2.7.11.1</RegistryNumber><NameOfSubstance UI="D000076225">Mechanistic Target of Rapamycin Complex 2</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000076222" MajorTopicYN="N">Mechanistic Target of Rapamycin Complex 1</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000076225" MajorTopicYN="N">Mechanistic Target of Rapamycin Complex 2</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D040901" MajorTopicYN="N">Proteomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012441" MajorTopicYN="N">Saccharomyces cerevisiae</DescriptorName><QualifierName UI="Q000472" MajorTopicYN="N">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029701" MajorTopicYN="N">Saccharomyces cerevisiae Proteins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015398" MajorTopicYN="N">Signal Transduction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058570" MajorTopicYN="N">TOR Serine-Threonine Kinases</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">biomarkers</Keyword><Keyword MajorTopicYN="Y">caffeine</Keyword><Keyword MajorTopicYN="Y">drug targets</Keyword><Keyword MajorTopicYN="Y">multiomics</Keyword><Keyword MajorTopicYN="Y">network-based analysis</Keyword><Keyword MajorTopicYN="Y">target of rapamycin (TOR) signaling</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>4</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>4</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>4</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30985253</ArticleId><ArticleId IdType="doi">10.1089/omi.2019.0021</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Italie</li><li>Royaume-Uni</li><li>Turquie</li></country><region><li>Angleterre</li><li>Angleterre de l'Est</li></region><settlement><li>Cambridge</li></settlement><orgName><li>Université de Cambridge</li></orgName></list><tree><country name="Italie"><noRegion><name sortKey="Dereli Eke, Elif" sort="Dereli Eke, Elif" uniqKey="Dereli Eke E" first="Elif" last="Dereli Eke">Elif Dereli Eke</name></noRegion><name sortKey="Di Camillo, Barbara" sort="Di Camillo, Barbara" uniqKey="Di Camillo B" first="Barbara" last="Di Camillo">Barbara Di Camillo</name></country><country name="Turquie"><noRegion><name sortKey="Dereli Eke, Elif" sort="Dereli Eke, Elif" uniqKey="Dereli Eke E" first="Elif" last="Dereli Eke">Elif Dereli Eke</name></noRegion><name sortKey="Arga, Kazim Yalcin" sort="Arga, Kazim Yalcin" uniqKey="Arga K" first="Kazim Yalcin" last="Arga">Kazim Yalcin Arga</name><name sortKey="Celik, Arzu" sort="Celik, Arzu" uniqKey="Celik A" first="Arzu" last="Celik">Arzu Celik</name><name sortKey="Dikicioglu, Duygu" sort="Dikicioglu, Duygu" uniqKey="Dikicioglu D" first="Duygu" last="Dikicioglu">Duygu Dikicioglu</name><name sortKey="Eraslan, Serpil" sort="Eraslan, Serpil" uniqKey="Eraslan S" first="Serpil" last="Eraslan">Serpil Eraslan</name><name sortKey="Eraslan, Serpil" sort="Eraslan, Serpil" uniqKey="Eraslan S" first="Serpil" last="Eraslan">Serpil Eraslan</name><name sortKey="Erkol, Emir" sort="Erkol, Emir" uniqKey="Erkol E" first="Emir" last="Erkol">Emir Erkol</name><name sortKey="Kirdar, Betul" sort="Kirdar, Betul" uniqKey="Kirdar B" first="Betul" last="Kirdar">Betul Kirdar</name></country><country name="Royaume-Uni"><region name="Angleterre"><name sortKey="Dikicioglu, Duygu" sort="Dikicioglu, Duygu" uniqKey="Dikicioglu D" first="Duygu" last="Dikicioglu">Duygu Dikicioglu</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|wiki= Bois
|area= RapamycinFungusV1
|flux= Main
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|texte= Identification of Novel Components of Target-of-Rapamycin Signaling Pathway by Network-Based Multi-Omics Integrative Analysis.
}}
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