Suberoylanilide Hydroxamic Acid Treatment Reveals Crosstalks among Proteome, Ubiquitylome and Acetylome in Non-Small Cell Lung Cancer A549 Cell Line
Suberoylanilide hydroxamic acid (SAHA) is a well-known histone deacetylase (HDAC) inhibitor and has been used as practical therapy for breast cancer and non-small cell lung cancer (NSCLC). It is previously demonstrated that SAHA treatment could extensively change the profile of acetylome and proteom...
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| Veröffentlicht in: | Scientific reports 2015-03, Vol.5 (1), p.9520-9520, Article 9520 |
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| creator | Wu, Quan Cheng, Zhongyi Zhu, Jun Xu, Weiqing Peng, Xiaojun Chen, Chuangbin Li, Wenting Wang, Fengsong Cao, Lejie Yi, Xingling Wu, Zhiwei Li, Jing Fan, Pingsheng |
| description | Suberoylanilide hydroxamic acid (SAHA) is a well-known histone deacetylase (HDAC) inhibitor and has been used as practical therapy for breast cancer and non-small cell lung cancer (NSCLC). It is previously demonstrated that SAHA treatment could extensively change the profile of acetylome and proteome in cancer cells. However, little is known about the impact of SAHA on other protein modifications and the crosstalks among different modifications and proteome, hindering the deep understanding of SAHA-mediated cancer therapy. In this work, by using SILAC technique, antibody-based affinity enrichment and high-resolution LC-MS/MS analysis, we investigated quantitative proteome, acetylome and ubiquitylome as well as crosstalks among the three datasets in A549 cells toward SAHA treatment. In total, 2968 proteins, 1099 acetylation sites and 1012 ubiquitination sites were quantified in response to SAHA treatment, respectively. With the aid of intensive bioinformatics, we revealed that the proteome and ubiquitylome were negatively related upon SAHA treatment. Moreover, the impact of SAHA on acetylome resulted in 258 up-regulated and 99 down-regulated acetylation sites at the threshold of 1.5 folds. Finally, we identified 55 common sites with both acetylation and ubiquitination, among which ubiquitination level in 43 sites (78.2%) was positive related to acetylation level. |
| doi_str_mv | 10.1038/srep09520 |
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It is previously demonstrated that SAHA treatment could extensively change the profile of acetylome and proteome in cancer cells. However, little is known about the impact of SAHA on other protein modifications and the crosstalks among different modifications and proteome, hindering the deep understanding of SAHA-mediated cancer therapy. In this work, by using SILAC technique, antibody-based affinity enrichment and high-resolution LC-MS/MS analysis, we investigated quantitative proteome, acetylome and ubiquitylome as well as crosstalks among the three datasets in A549 cells toward SAHA treatment. In total, 2968 proteins, 1099 acetylation sites and 1012 ubiquitination sites were quantified in response to SAHA treatment, respectively. With the aid of intensive bioinformatics, we revealed that the proteome and ubiquitylome were negatively related upon SAHA treatment. Moreover, the impact of SAHA on acetylome resulted in 258 up-regulated and 99 down-regulated acetylation sites at the threshold of 1.5 folds. Finally, we identified 55 common sites with both acetylation and ubiquitination, among which ubiquitination level in 43 sites (78.2%) was positive related to acetylation level.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/srep09520</identifier><identifier>PMID: 25825284</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/45/475 ; 692/699/67 ; 82/1 ; 82/16 ; 82/58 ; 82/81 ; 82/83 ; Acetylation ; Acetylation - drug effects ; Antineoplastic Agents - pharmacology ; Bioinformatics ; Breast cancer ; Carcinoma, Non-Small-Cell Lung - metabolism ; Cell Line, Tumor ; Chromatin ; Cluster Analysis ; Histone deacetylase ; Histone Deacetylase Inhibitors - pharmacology ; Histones ; Humanities and Social Sciences ; Humans ; Hydroxamic acid ; Hydroxamic Acids - pharmacology ; Lung cancer ; Lung Neoplasms - metabolism ; multidisciplinary ; Non-small cell lung carcinoma ; Protein Binding ; Protein Interaction Mapping ; Protein Interaction Maps ; Proteome ; Proteomes ; Proteomics ; Science ; Tandem Mass Spectrometry ; Ubiquitination ; Ubiquitination - drug effects</subject><ispartof>Scientific reports, 2015-03, Vol.5 (1), p.9520-9520, Article 9520</ispartof><rights>The Author(s) 2015</rights><rights>Copyright Nature Publishing Group Mar 2015</rights><rights>Copyright © 2015, Macmillan Publishers Limited. All rights reserved 2015 Macmillan Publishers Limited. All rights reserved</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c504t-6567084075a1b2981a0e310aec8b85e139c829c4a43596bd93dbe164bd89351a3</citedby><cites>FETCH-LOGICAL-c504t-6567084075a1b2981a0e310aec8b85e139c829c4a43596bd93dbe164bd89351a3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379480/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4379480/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,27901,27902,41096,42165,51551,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25825284$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wu, Quan</creatorcontrib><creatorcontrib>Cheng, Zhongyi</creatorcontrib><creatorcontrib>Zhu, Jun</creatorcontrib><creatorcontrib>Xu, Weiqing</creatorcontrib><creatorcontrib>Peng, Xiaojun</creatorcontrib><creatorcontrib>Chen, Chuangbin</creatorcontrib><creatorcontrib>Li, Wenting</creatorcontrib><creatorcontrib>Wang, Fengsong</creatorcontrib><creatorcontrib>Cao, Lejie</creatorcontrib><creatorcontrib>Yi, Xingling</creatorcontrib><creatorcontrib>Wu, Zhiwei</creatorcontrib><creatorcontrib>Li, Jing</creatorcontrib><creatorcontrib>Fan, Pingsheng</creatorcontrib><title>Suberoylanilide Hydroxamic Acid Treatment Reveals Crosstalks among Proteome, Ubiquitylome and Acetylome in Non-Small Cell Lung Cancer A549 Cell Line</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Suberoylanilide hydroxamic acid (SAHA) is a well-known histone deacetylase (HDAC) inhibitor and has been used as practical therapy for breast cancer and non-small cell lung cancer (NSCLC). It is previously demonstrated that SAHA treatment could extensively change the profile of acetylome and proteome in cancer cells. However, little is known about the impact of SAHA on other protein modifications and the crosstalks among different modifications and proteome, hindering the deep understanding of SAHA-mediated cancer therapy. In this work, by using SILAC technique, antibody-based affinity enrichment and high-resolution LC-MS/MS analysis, we investigated quantitative proteome, acetylome and ubiquitylome as well as crosstalks among the three datasets in A549 cells toward SAHA treatment. In total, 2968 proteins, 1099 acetylation sites and 1012 ubiquitination sites were quantified in response to SAHA treatment, respectively. With the aid of intensive bioinformatics, we revealed that the proteome and ubiquitylome were negatively related upon SAHA treatment. Moreover, the impact of SAHA on acetylome resulted in 258 up-regulated and 99 down-regulated acetylation sites at the threshold of 1.5 folds. Finally, we identified 55 common sites with both acetylation and ubiquitination, among which ubiquitination level in 43 sites (78.2%) was positive related to acetylation level.</description><subject>631/45/475</subject><subject>692/699/67</subject><subject>82/1</subject><subject>82/16</subject><subject>82/58</subject><subject>82/81</subject><subject>82/83</subject><subject>Acetylation</subject><subject>Acetylation - drug effects</subject><subject>Antineoplastic Agents - pharmacology</subject><subject>Bioinformatics</subject><subject>Breast cancer</subject><subject>Carcinoma, Non-Small-Cell Lung - metabolism</subject><subject>Cell Line, Tumor</subject><subject>Chromatin</subject><subject>Cluster Analysis</subject><subject>Histone deacetylase</subject><subject>Histone Deacetylase Inhibitors - pharmacology</subject><subject>Histones</subject><subject>Humanities and Social Sciences</subject><subject>Humans</subject><subject>Hydroxamic acid</subject><subject>Hydroxamic Acids - pharmacology</subject><subject>Lung cancer</subject><subject>Lung Neoplasms - metabolism</subject><subject>multidisciplinary</subject><subject>Non-small cell lung carcinoma</subject><subject>Protein Binding</subject><subject>Protein Interaction Mapping</subject><subject>Protein Interaction Maps</subject><subject>Proteome</subject><subject>Proteomes</subject><subject>Proteomics</subject><subject>Science</subject><subject>Tandem Mass Spectrometry</subject><subject>Ubiquitination</subject><subject>Ubiquitination - drug effects</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2015</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><recordid>eNplkc1uEzEQx1eIilZtD7wAssQFqi74O_YFKVpBixQBou3Z8nqnwWXXTu3dirxHHxhXCVEAH2yP5zf_mfFU1UuC3xHM1PucYIW1oPhZdUQxFzVllD7fux9Wpznf4bIE1ZzoF9UhFYoKqvhR9Xg1tZDiurfB974DdLnuUvxlB-_Q3PkOXSew4wBhRN_hAWyfUZNizqPtf2ZkhxiW6FuKI8QBztFN6-8nP677YiEbuiIBW8sH9CWG-mqwfY8aKNtiKrGNDQ4Smguut68-wEl1cFsywen2PK5uPn28bi7rxdeLz818UTuB-VhLIWdYcTwTlrRUK2IxMIItONUqAYRpp6h23HImtGw7zboWiORtpzQTxLLj6sNGdzW1A3SudJlsb1bJDzatTbTe_O0J_odZxgfD2UxzhYvAm61AivcT5NEMPrvShg0Qp2yIlIoyKTkr6Ot_0Ls4pVDaM0RpJRknmBbq7YZyT5-c4HZXDMHmadxmN-7Cvtqvfkf-GW4BzjZALq6whLSX8j-13wR9tLE</recordid><startdate>20150331</startdate><enddate>20150331</enddate><creator>Wu, Quan</creator><creator>Cheng, Zhongyi</creator><creator>Zhu, Jun</creator><creator>Xu, Weiqing</creator><creator>Peng, Xiaojun</creator><creator>Chen, Chuangbin</creator><creator>Li, Wenting</creator><creator>Wang, Fengsong</creator><creator>Cao, Lejie</creator><creator>Yi, Xingling</creator><creator>Wu, Zhiwei</creator><creator>Li, Jing</creator><creator>Fan, Pingsheng</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20150331</creationdate><title>Suberoylanilide Hydroxamic Acid Treatment Reveals Crosstalks among Proteome, Ubiquitylome and Acetylome in Non-Small Cell Lung Cancer A549 Cell Line</title><author>Wu, Quan ; Cheng, Zhongyi ; Zhu, Jun ; Xu, Weiqing ; Peng, Xiaojun ; Chen, Chuangbin ; Li, Wenting ; Wang, Fengsong ; Cao, Lejie ; Yi, Xingling ; Wu, Zhiwei ; Li, Jing ; Fan, Pingsheng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c504t-6567084075a1b2981a0e310aec8b85e139c829c4a43596bd93dbe164bd89351a3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>631/45/475</topic><topic>692/699/67</topic><topic>82/1</topic><topic>82/16</topic><topic>82/58</topic><topic>82/81</topic><topic>82/83</topic><topic>Acetylation</topic><topic>Acetylation - drug effects</topic><topic>Antineoplastic Agents - pharmacology</topic><topic>Bioinformatics</topic><topic>Breast cancer</topic><topic>Carcinoma, Non-Small-Cell Lung - metabolism</topic><topic>Cell Line, Tumor</topic><topic>Chromatin</topic><topic>Cluster Analysis</topic><topic>Histone deacetylase</topic><topic>Histone Deacetylase Inhibitors - pharmacology</topic><topic>Histones</topic><topic>Humanities and Social Sciences</topic><topic>Humans</topic><topic>Hydroxamic acid</topic><topic>Hydroxamic Acids - pharmacology</topic><topic>Lung cancer</topic><topic>Lung Neoplasms - metabolism</topic><topic>multidisciplinary</topic><topic>Non-small cell lung carcinoma</topic><topic>Protein Binding</topic><topic>Protein Interaction Mapping</topic><topic>Protein Interaction Maps</topic><topic>Proteome</topic><topic>Proteomes</topic><topic>Proteomics</topic><topic>Science</topic><topic>Tandem Mass Spectrometry</topic><topic>Ubiquitination</topic><topic>Ubiquitination - drug effects</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wu, Quan</creatorcontrib><creatorcontrib>Cheng, Zhongyi</creatorcontrib><creatorcontrib>Zhu, Jun</creatorcontrib><creatorcontrib>Xu, Weiqing</creatorcontrib><creatorcontrib>Peng, Xiaojun</creatorcontrib><creatorcontrib>Chen, Chuangbin</creatorcontrib><creatorcontrib>Li, Wenting</creatorcontrib><creatorcontrib>Wang, Fengsong</creatorcontrib><creatorcontrib>Cao, Lejie</creatorcontrib><creatorcontrib>Yi, Xingling</creatorcontrib><creatorcontrib>Wu, Zhiwei</creatorcontrib><creatorcontrib>Li, Jing</creatorcontrib><creatorcontrib>Fan, Pingsheng</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wu, Quan</au><au>Cheng, Zhongyi</au><au>Zhu, Jun</au><au>Xu, Weiqing</au><au>Peng, Xiaojun</au><au>Chen, Chuangbin</au><au>Li, Wenting</au><au>Wang, Fengsong</au><au>Cao, Lejie</au><au>Yi, Xingling</au><au>Wu, Zhiwei</au><au>Li, Jing</au><au>Fan, Pingsheng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Suberoylanilide Hydroxamic Acid Treatment Reveals Crosstalks among Proteome, Ubiquitylome and Acetylome in Non-Small Cell Lung Cancer A549 Cell Line</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2015-03-31</date><risdate>2015</risdate><volume>5</volume><issue>1</issue><spage>9520</spage><epage>9520</epage><pages>9520-9520</pages><artnum>9520</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Suberoylanilide hydroxamic acid (SAHA) is a well-known histone deacetylase (HDAC) inhibitor and has been used as practical therapy for breast cancer and non-small cell lung cancer (NSCLC). It is previously demonstrated that SAHA treatment could extensively change the profile of acetylome and proteome in cancer cells. However, little is known about the impact of SAHA on other protein modifications and the crosstalks among different modifications and proteome, hindering the deep understanding of SAHA-mediated cancer therapy. In this work, by using SILAC technique, antibody-based affinity enrichment and high-resolution LC-MS/MS analysis, we investigated quantitative proteome, acetylome and ubiquitylome as well as crosstalks among the three datasets in A549 cells toward SAHA treatment. In total, 2968 proteins, 1099 acetylation sites and 1012 ubiquitination sites were quantified in response to SAHA treatment, respectively. With the aid of intensive bioinformatics, we revealed that the proteome and ubiquitylome were negatively related upon SAHA treatment. Moreover, the impact of SAHA on acetylome resulted in 258 up-regulated and 99 down-regulated acetylation sites at the threshold of 1.5 folds. Finally, we identified 55 common sites with both acetylation and ubiquitination, among which ubiquitination level in 43 sites (78.2%) was positive related to acetylation level.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>25825284</pmid><doi>10.1038/srep09520</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | 631/45/475 692/699/67 82/1 82/16 82/58 82/81 82/83 Acetylation Acetylation - drug effects Antineoplastic Agents - pharmacology Bioinformatics Breast cancer Carcinoma, Non-Small-Cell Lung - metabolism Cell Line, Tumor Chromatin Cluster Analysis Histone deacetylase Histone Deacetylase Inhibitors - pharmacology Histones Humanities and Social Sciences Humans Hydroxamic acid Hydroxamic Acids - pharmacology Lung cancer Lung Neoplasms - metabolism multidisciplinary Non-small cell lung carcinoma Protein Binding Protein Interaction Mapping Protein Interaction Maps Proteome Proteomes Proteomics Science Tandem Mass Spectrometry Ubiquitination Ubiquitination - drug effects |
| title | Suberoylanilide Hydroxamic Acid Treatment Reveals Crosstalks among Proteome, Ubiquitylome and Acetylome in Non-Small Cell Lung Cancer A549 Cell Line |
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