Integrated Analysis of Long Noncoding RNA and mRNA Expression Profile in Advanced Laryngeal Squamous Cell Carcinoma
Long non-coding RNA (lncRNA) plays an important role in tumorigenesis. However, the expression pattern and function of lncRNAs in laryngeal squamous cell carcinoma (LSCC) are still unclear. To investigate the aberrantly expressed lncRNAs and mRNAs in advanced LSCC, we screened lncRNA and mRNA expres...
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| description | Long non-coding RNA (lncRNA) plays an important role in tumorigenesis. However, the expression pattern and function of lncRNAs in laryngeal squamous cell carcinoma (LSCC) are still unclear. To investigate the aberrantly expressed lncRNAs and mRNAs in advanced LSCC, we screened lncRNA and mRNA expression profiles in 9 pairs of primary Stage IVA LSCC tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays. Gene Ontology and pathway analysis were performed to find out the significant function and pathway of the differentially expressed mRNAs, gene-gene functional interaction network and ceRNA network were constructed to select core mRNAs, and lncRNA-mRNA expression correlation network was built to identify the interactions between lncRNA and mRNA. qRT-PCR was performed to further validate the expressions of selected lncRNAs and mRNAs in advanced LSCC. We found 1459 differentially expressed lncRNAs and 2381 differentially expressed mRNAs, including 846 up-regulated lncRNAs and 613 down-regulated lncRNAs, 1542 up-regulated mRNAs and 839 down-regulated mRNAs. The mRNAs ITGB1, HIF1A, and DDIT4 were selected as core mRNAs, which are mainly involved in biological processes, such as matrix organization, cell cycle, adhesion, and metabolic pathway. LncRNA-mRNA expression correlation network showed LncRNA NR_027340, MIR31HG were positively correlated with ITGB1, HIF1A respectively. LncRNA SOX2-OT was negatively correlated with DDIT4. qRT-PCR further validated the expression of these lncRNAs and mRNAs. The work provides convincing evidence that the identified lncRNAs and mRNAs are potential biomarkers in advanced LSCC for further future studies. |
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However, the expression pattern and function of lncRNAs in laryngeal squamous cell carcinoma (LSCC) are still unclear. To investigate the aberrantly expressed lncRNAs and mRNAs in advanced LSCC, we screened lncRNA and mRNA expression profiles in 9 pairs of primary Stage IVA LSCC tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays. Gene Ontology and pathway analysis were performed to find out the significant function and pathway of the differentially expressed mRNAs, gene-gene functional interaction network and ceRNA network were constructed to select core mRNAs, and lncRNA-mRNA expression correlation network was built to identify the interactions between lncRNA and mRNA. qRT-PCR was performed to further validate the expressions of selected lncRNAs and mRNAs in advanced LSCC. We found 1459 differentially expressed lncRNAs and 2381 differentially expressed mRNAs, including 846 up-regulated lncRNAs and 613 down-regulated lncRNAs, 1542 up-regulated mRNAs and 839 down-regulated mRNAs. The mRNAs ITGB1, HIF1A, and DDIT4 were selected as core mRNAs, which are mainly involved in biological processes, such as matrix organization, cell cycle, adhesion, and metabolic pathway. LncRNA-mRNA expression correlation network showed LncRNA NR_027340, MIR31HG were positively correlated with ITGB1, HIF1A respectively. LncRNA SOX2-OT was negatively correlated with DDIT4. qRT-PCR further validated the expression of these lncRNAs and mRNAs. The work provides convincing evidence that the identified lncRNAs and mRNAs are potential biomarkers in advanced LSCC for further future studies.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0169232</identifier><identifier>PMID: 28033431</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Bioindicators ; Biological activity ; Biology and life sciences ; Biomarkers ; Breast cancer ; Cancer therapies ; Carcinoma, Squamous Cell - genetics ; Carcinoma, Squamous Cell - pathology ; Cell cycle ; Cell growth ; Computational Biology - methods ; Computer and Information Sciences ; Correlation ; Development and progression ; DNA microarrays ; Education ; Female ; Gastric cancer ; Gene expression ; Gene Expression Profiling ; Gene Ontology ; Gene Regulatory Networks ; Genetic aspects ; Humans ; Hypoxia ; Laboratories ; Laryngeal cancer ; Laryngeal Neoplasms - genetics ; Laryngeal Neoplasms - pathology ; Male ; Medical prognosis ; Metastasis ; MicroRNA ; Middle Aged ; Non-coding RNA ; Ostomy ; Otolaryngology ; Pathology ; Patients ; Physiological aspects ; Radiation therapy ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; RNA, Long Noncoding - genetics ; RNA, Messenger - genetics ; Squamous cell carcinoma ; Stomach cancer ; Surgery ; Tissues ; Tumorigenesis</subject><ispartof>PloS one, 2016-12, Vol.11 (12), p.e0169232-e0169232</ispartof><rights>COPYRIGHT 2016 Public Library of Science</rights><rights>2016 Feng et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2016 Feng et al 2016 Feng et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c725t-23455a8c17b385fa4f51b5eeb2c80279108639ce9e2b3941d1c33cfcac7ccdb23</citedby><cites>FETCH-LOGICAL-c725t-23455a8c17b385fa4f51b5eeb2c80279108639ce9e2b3941d1c33cfcac7ccdb23</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/PMC5199101/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5199101/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28033431$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Ahmad, Aamir</contributor><creatorcontrib>Feng, Ling</creatorcontrib><creatorcontrib>Wang, Ru</creatorcontrib><creatorcontrib>Lian, Meng</creatorcontrib><creatorcontrib>Ma, Hongzhi</creatorcontrib><creatorcontrib>He, Ning</creatorcontrib><creatorcontrib>Liu, Honggang</creatorcontrib><creatorcontrib>Wang, Haizhou</creatorcontrib><creatorcontrib>Fang, Jugao</creatorcontrib><title>Integrated Analysis of Long Noncoding RNA and mRNA Expression Profile in Advanced Laryngeal Squamous Cell Carcinoma</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Long non-coding RNA (lncRNA) plays an important role in tumorigenesis. However, the expression pattern and function of lncRNAs in laryngeal squamous cell carcinoma (LSCC) are still unclear. To investigate the aberrantly expressed lncRNAs and mRNAs in advanced LSCC, we screened lncRNA and mRNA expression profiles in 9 pairs of primary Stage IVA LSCC tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays. Gene Ontology and pathway analysis were performed to find out the significant function and pathway of the differentially expressed mRNAs, gene-gene functional interaction network and ceRNA network were constructed to select core mRNAs, and lncRNA-mRNA expression correlation network was built to identify the interactions between lncRNA and mRNA. qRT-PCR was performed to further validate the expressions of selected lncRNAs and mRNAs in advanced LSCC. We found 1459 differentially expressed lncRNAs and 2381 differentially expressed mRNAs, including 846 up-regulated lncRNAs and 613 down-regulated lncRNAs, 1542 up-regulated mRNAs and 839 down-regulated mRNAs. The mRNAs ITGB1, HIF1A, and DDIT4 were selected as core mRNAs, which are mainly involved in biological processes, such as matrix organization, cell cycle, adhesion, and metabolic pathway. LncRNA-mRNA expression correlation network showed LncRNA NR_027340, MIR31HG were positively correlated with ITGB1, HIF1A respectively. LncRNA SOX2-OT was negatively correlated with DDIT4. qRT-PCR further validated the expression of these lncRNAs and mRNAs. The work provides convincing evidence that the identified lncRNAs and mRNAs are potential biomarkers in advanced LSCC for further future studies.</description><subject>Bioindicators</subject><subject>Biological activity</subject><subject>Biology and life sciences</subject><subject>Biomarkers</subject><subject>Breast cancer</subject><subject>Cancer therapies</subject><subject>Carcinoma, Squamous Cell - genetics</subject><subject>Carcinoma, Squamous Cell - pathology</subject><subject>Cell cycle</subject><subject>Cell growth</subject><subject>Computational Biology - methods</subject><subject>Computer and Information Sciences</subject><subject>Correlation</subject><subject>Development and progression</subject><subject>DNA microarrays</subject><subject>Education</subject><subject>Female</subject><subject>Gastric cancer</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Ontology</subject><subject>Gene Regulatory Networks</subject><subject>Genetic aspects</subject><subject>Humans</subject><subject>Hypoxia</subject><subject>Laboratories</subject><subject>Laryngeal cancer</subject><subject>Laryngeal Neoplasms - genetics</subject><subject>Laryngeal Neoplasms - pathology</subject><subject>Male</subject><subject>Medical prognosis</subject><subject>Metastasis</subject><subject>MicroRNA</subject><subject>Middle Aged</subject><subject>Non-coding RNA</subject><subject>Ostomy</subject><subject>Otolaryngology</subject><subject>Pathology</subject><subject>Patients</subject><subject>Physiological aspects</subject><subject>Radiation therapy</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA, Long Noncoding - genetics</subject><subject>RNA, Messenger - genetics</subject><subject>Squamous cell carcinoma</subject><subject>Stomach cancer</subject><subject>Surgery</subject><subject>Tissues</subject><subject>Tumorigenesis</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNk01r3DAQhk1padK0_6C0gkJpD7u1PvyhS2FZknZhSUrS9irGsuzVYksbyQ7Jv4_cdcK65BB88GA_82r0zkwUvcfxHNMMf9va3hlo5jtr1DzGKSeUvIiOMadklpKYvjyIj6I33m_jOKF5mr6OjkgeU8ooPo78ynSqdtCpEi2C3J3XHtkKra2p0bk10pY6RJfnCwSmRO0QnN7unPJeW4N-OVvpRiFt0KK8ASODzBrcnakVNOjquofW9h4tVdOgJTipjW3hbfSqgsard-P7JPpzdvp7-XO2vvixWi7WM5mRpJsRypIEcomzguZJBaxKcJEoVRCZxyTjOM5TyqXiihSUM1xiSamsJMhMyrIg9CT6uNfdNdaL0S8vcJ4wjBmlWSBWe6K0sBU7p9tQu7Cgxb8P1tUCXKdlowRADBkuK8bylHEejicgecV4ISGTqgha38fT-qJVpVSmc9BMRKd_jN6I2t6IBPNwFxwEvowCzl73ynei1V4G58CoYOJQN2c542n6HJSFvocmB_TTf-jTRoxUDeGu2lQ2lCgHUbFgWcJiwngSqPkTVHhK1WoZ5nCYhWnC10lCYDp129XQey9WV5fPZy_-TtnPB-wmzFq38bbpuzCTfgqyPSid9d6p6rEfOBbDGj24IYY1EuMahbQPh718THrYG3oPAkkXCg</recordid><startdate>20161229</startdate><enddate>20161229</enddate><creator>Feng, Ling</creator><creator>Wang, Ru</creator><creator>Lian, Meng</creator><creator>Ma, Hongzhi</creator><creator>He, Ning</creator><creator>Liu, Honggang</creator><creator>Wang, Haizhou</creator><creator>Fang, Jugao</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><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>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20161229</creationdate><title>Integrated Analysis of Long Noncoding RNA and mRNA Expression Profile in Advanced Laryngeal Squamous Cell Carcinoma</title><author>Feng, Ling ; Wang, Ru ; Lian, Meng ; Ma, Hongzhi ; He, Ning ; Liu, Honggang ; Wang, Haizhou ; Fang, Jugao</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c725t-23455a8c17b385fa4f51b5eeb2c80279108639ce9e2b3941d1c33cfcac7ccdb23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2016</creationdate><topic>Bioindicators</topic><topic>Biological activity</topic><topic>Biology and life sciences</topic><topic>Biomarkers</topic><topic>Breast cancer</topic><topic>Cancer therapies</topic><topic>Carcinoma, Squamous Cell - genetics</topic><topic>Carcinoma, Squamous Cell - pathology</topic><topic>Cell cycle</topic><topic>Cell growth</topic><topic>Computational Biology - methods</topic><topic>Computer and Information Sciences</topic><topic>Correlation</topic><topic>Development and progression</topic><topic>DNA microarrays</topic><topic>Education</topic><topic>Female</topic><topic>Gastric cancer</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Ontology</topic><topic>Gene Regulatory Networks</topic><topic>Genetic aspects</topic><topic>Humans</topic><topic>Hypoxia</topic><topic>Laboratories</topic><topic>Laryngeal cancer</topic><topic>Laryngeal Neoplasms - genetics</topic><topic>Laryngeal Neoplasms - pathology</topic><topic>Male</topic><topic>Medical prognosis</topic><topic>Metastasis</topic><topic>MicroRNA</topic><topic>Middle Aged</topic><topic>Non-coding RNA</topic><topic>Ostomy</topic><topic>Otolaryngology</topic><topic>Pathology</topic><topic>Patients</topic><topic>Physiological aspects</topic><topic>Radiation therapy</topic><topic>Research and Analysis Methods</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA, Long Noncoding - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Feng, Ling</au><au>Wang, Ru</au><au>Lian, Meng</au><au>Ma, Hongzhi</au><au>He, Ning</au><au>Liu, Honggang</au><au>Wang, Haizhou</au><au>Fang, Jugao</au><au>Ahmad, Aamir</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Integrated Analysis of Long Noncoding RNA and mRNA Expression Profile in Advanced Laryngeal Squamous Cell Carcinoma</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2016-12-29</date><risdate>2016</risdate><volume>11</volume><issue>12</issue><spage>e0169232</spage><epage>e0169232</epage><pages>e0169232-e0169232</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Long non-coding RNA (lncRNA) plays an important role in tumorigenesis. However, the expression pattern and function of lncRNAs in laryngeal squamous cell carcinoma (LSCC) are still unclear. To investigate the aberrantly expressed lncRNAs and mRNAs in advanced LSCC, we screened lncRNA and mRNA expression profiles in 9 pairs of primary Stage IVA LSCC tissues and adjacent non-neoplastic tissues by lncRNA and mRNA integrated microarrays. Gene Ontology and pathway analysis were performed to find out the significant function and pathway of the differentially expressed mRNAs, gene-gene functional interaction network and ceRNA network were constructed to select core mRNAs, and lncRNA-mRNA expression correlation network was built to identify the interactions between lncRNA and mRNA. qRT-PCR was performed to further validate the expressions of selected lncRNAs and mRNAs in advanced LSCC. We found 1459 differentially expressed lncRNAs and 2381 differentially expressed mRNAs, including 846 up-regulated lncRNAs and 613 down-regulated lncRNAs, 1542 up-regulated mRNAs and 839 down-regulated mRNAs. The mRNAs ITGB1, HIF1A, and DDIT4 were selected as core mRNAs, which are mainly involved in biological processes, such as matrix organization, cell cycle, adhesion, and metabolic pathway. LncRNA-mRNA expression correlation network showed LncRNA NR_027340, MIR31HG were positively correlated with ITGB1, HIF1A respectively. LncRNA SOX2-OT was negatively correlated with DDIT4. qRT-PCR further validated the expression of these lncRNAs and mRNAs. The work provides convincing evidence that the identified lncRNAs and mRNAs are potential biomarkers in advanced LSCC for further future studies.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28033431</pmid><doi>10.1371/journal.pone.0169232</doi><tpages>e0169232</tpages><oa>free_for_read</oa></addata></record> |
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| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Bioindicators Biological activity Biology and life sciences Biomarkers Breast cancer Cancer therapies Carcinoma, Squamous Cell - genetics Carcinoma, Squamous Cell - pathology Cell cycle Cell growth Computational Biology - methods Computer and Information Sciences Correlation Development and progression DNA microarrays Education Female Gastric cancer Gene expression Gene Expression Profiling Gene Ontology Gene Regulatory Networks Genetic aspects Humans Hypoxia Laboratories Laryngeal cancer Laryngeal Neoplasms - genetics Laryngeal Neoplasms - pathology Male Medical prognosis Metastasis MicroRNA Middle Aged Non-coding RNA Ostomy Otolaryngology Pathology Patients Physiological aspects Radiation therapy Research and Analysis Methods Ribonucleic acid RNA RNA, Long Noncoding - genetics RNA, Messenger - genetics Squamous cell carcinoma Stomach cancer Surgery Tissues Tumorigenesis |
| title | Integrated Analysis of Long Noncoding RNA and mRNA Expression Profile in Advanced Laryngeal Squamous Cell Carcinoma |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-29T01%3A04%3A26IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Integrated%20Analysis%20of%20Long%20Noncoding%20RNA%20and%20mRNA%20Expression%20Profile%20in%20Advanced%20Laryngeal%20Squamous%20Cell%20Carcinoma&rft.jtitle=PloS%20one&rft.au=Feng,%20Ling&rft.date=2016-12-29&rft.volume=11&rft.issue=12&rft.spage=e0169232&rft.epage=e0169232&rft.pages=e0169232-e0169232&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0169232&rft_dat=%3Cgale_plos_%3EA475402495%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1854114337&rft_id=info:pmid/28033431&rft_galeid=A475402495&rft_doaj_id=oai_doaj_org_article_aa0a71df44864997912ac9f49bca7ceb&rfr_iscdi=true |