Identification of microRNAs as potential prognostic markers in ependymoma
We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers. We...
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| creator | Costa, Fabricio F Bischof, Jared M Vanin, Elio F Lulla, Rishi R Wang, Min Sredni, Simone T Rajaram, Veena Bonaldo, Maria de Fátima Wang, Deli Goldman, Stewart Tomita, Tadanori Soares, Marcelo B |
| description | We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers.
We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features.
We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival.
We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas. |
| doi_str_mv | 10.1371/journal.pone.0025114 |
| format | Article |
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We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features.
We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival.
We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0025114</identifier><identifier>PMID: 22053178</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adolescent ; Biology ; Biomarkers, Tumor - genetics ; Biomarkers, Tumor - metabolism ; Brain ; Brain cancer ; Brain research ; Brain tumors ; Cancer therapies ; Case-Control Studies ; Cell cycle ; Child ; Child, Preschool ; Children & youth ; Chromosome 14 ; Chromosomes ; Coding ; Computational Biology ; Correlation ; Development and progression ; Ependymal cells ; Ependymoma - genetics ; Ependymoma - pathology ; Epigenetics ; Female ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Histology ; Hospitals ; Humans ; Identification ; Infant ; Male ; Markers ; Medical prognosis ; Medicine ; Metastasis ; MicroRNA ; MicroRNAs ; MicroRNAs - genetics ; MicroRNAs - metabolism ; miRNA ; mRNA stability ; Multivariate Analysis ; Mutation ; Non-coding RNA ; Paraffin ; Parameter identification ; Pediatrics ; Prognosis ; Proportional Hazards Models ; Regression Analysis ; Stem cells ; Survival Analysis ; Translation (Genetics) ; Tumors</subject><ispartof>PloS one, 2011-10, Vol.6 (10), p.e25114-e25114</ispartof><rights>COPYRIGHT 2011 Public Library of Science</rights><rights>2011 Costa et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: https://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>Costa et al. 2011</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c757t-265721032463a8ad4c7ec4680600f90b0debcf5799810ff334a1c60b80893d403</citedby><cites>FETCH-LOGICAL-c757t-265721032463a8ad4c7ec4680600f90b0debcf5799810ff334a1c60b80893d403</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/PMC3203863/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203863/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/22053178$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Costa, Fabricio F</creatorcontrib><creatorcontrib>Bischof, Jared M</creatorcontrib><creatorcontrib>Vanin, Elio F</creatorcontrib><creatorcontrib>Lulla, Rishi R</creatorcontrib><creatorcontrib>Wang, Min</creatorcontrib><creatorcontrib>Sredni, Simone T</creatorcontrib><creatorcontrib>Rajaram, Veena</creatorcontrib><creatorcontrib>Bonaldo, Maria de Fátima</creatorcontrib><creatorcontrib>Wang, Deli</creatorcontrib><creatorcontrib>Goldman, Stewart</creatorcontrib><creatorcontrib>Tomita, Tadanori</creatorcontrib><creatorcontrib>Soares, Marcelo B</creatorcontrib><title>Identification of microRNAs as potential prognostic markers in ependymoma</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers.
We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features.
We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival.
We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas.</description><subject>Adolescent</subject><subject>Biology</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Biomarkers, Tumor - metabolism</subject><subject>Brain</subject><subject>Brain cancer</subject><subject>Brain research</subject><subject>Brain tumors</subject><subject>Cancer therapies</subject><subject>Case-Control Studies</subject><subject>Cell cycle</subject><subject>Child</subject><subject>Child, Preschool</subject><subject>Children & youth</subject><subject>Chromosome 14</subject><subject>Chromosomes</subject><subject>Coding</subject><subject>Computational Biology</subject><subject>Correlation</subject><subject>Development and progression</subject><subject>Ependymal cells</subject><subject>Ependymoma - genetics</subject><subject>Ependymoma - pathology</subject><subject>Epigenetics</subject><subject>Female</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Histology</subject><subject>Hospitals</subject><subject>Humans</subject><subject>Identification</subject><subject>Infant</subject><subject>Male</subject><subject>Markers</subject><subject>Medical prognosis</subject><subject>Medicine</subject><subject>Metastasis</subject><subject>MicroRNA</subject><subject>MicroRNAs</subject><subject>MicroRNAs - genetics</subject><subject>MicroRNAs - metabolism</subject><subject>miRNA</subject><subject>mRNA stability</subject><subject>Multivariate Analysis</subject><subject>Mutation</subject><subject>Non-coding RNA</subject><subject>Paraffin</subject><subject>Parameter identification</subject><subject>Pediatrics</subject><subject>Prognosis</subject><subject>Proportional Hazards Models</subject><subject>Regression Analysis</subject><subject>Stem cells</subject><subject>Survival Analysis</subject><subject>Translation (Genetics)</subject><subject>Tumors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2011</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl2L1DAUhoso7jr6D0QLguLFjPlq2twIw7LqwOLC-nEb0jTpZGybmrSy--89s9NdprIX0ouG5Dlvct7zJslLjFaY5vjDzo-hU82q951ZIUQyjNmj5BQLSpacIPr4aH2SPItxh1BGC86fJieEwBLnxWmy2VSmG5x1Wg3Od6m3aet08Fdf1zFVMe39sD9XTdoHX3c-Dk6nrQq_TIip61LTm666aX2rnidPrGqieTH9F8mPT-ffz74sLy4_b87WF0udZ_mwJDzLCUaUME5VoSqmc6MZLxBHyApUosqU2ma5EAVG1lLKFNYclQUqBK0Yoovk9UG3b3yUkwtRYoqEABp6XiSbA1F5tZN9cPDeG-mVk7cbPtRSBeijMZJkXGiCqcU2Y8iS0mZCKcG44YoJmoPWx-m2sWxNpcGMoJqZ6Pykc1tZ-z-Sgu0FpyDwbhII_vdo4iBbF7VpGtUZP0YpEKHAYg7km3_Ih5ubqFrB-11nPVyr95pyzXIO881uqdUDFHyVgfFCYqyD_VnB-1kBMIO5Hmo1xig3367-n738OWffHrFbo5phG30z7sMW5yA7gBC-GIOx9x5jJPeBv3ND7gMvp8BD2avj-dwX3SWc_gWY8vlC</recordid><startdate>20111028</startdate><enddate>20111028</enddate><creator>Costa, Fabricio F</creator><creator>Bischof, Jared M</creator><creator>Vanin, Elio F</creator><creator>Lulla, Rishi R</creator><creator>Wang, Min</creator><creator>Sredni, Simone T</creator><creator>Rajaram, Veena</creator><creator>Bonaldo, Maria de Fátima</creator><creator>Wang, Deli</creator><creator>Goldman, Stewart</creator><creator>Tomita, Tadanori</creator><creator>Soares, Marcelo B</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>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20111028</creationdate><title>Identification of microRNAs as potential prognostic markers in ependymoma</title><author>Costa, Fabricio F ; Bischof, Jared M ; Vanin, Elio F ; Lulla, Rishi R ; Wang, Min ; Sredni, Simone T ; Rajaram, Veena ; Bonaldo, Maria de Fátima ; Wang, Deli ; Goldman, Stewart ; Tomita, Tadanori ; Soares, Marcelo B</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c757t-265721032463a8ad4c7ec4680600f90b0debcf5799810ff334a1c60b80893d403</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2011</creationdate><topic>Adolescent</topic><topic>Biology</topic><topic>Biomarkers, Tumor - 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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>Costa, Fabricio F</au><au>Bischof, Jared M</au><au>Vanin, Elio F</au><au>Lulla, Rishi R</au><au>Wang, Min</au><au>Sredni, Simone T</au><au>Rajaram, Veena</au><au>Bonaldo, Maria de Fátima</au><au>Wang, Deli</au><au>Goldman, Stewart</au><au>Tomita, Tadanori</au><au>Soares, Marcelo B</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of microRNAs as potential prognostic markers in ependymoma</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2011-10-28</date><risdate>2011</risdate><volume>6</volume><issue>10</issue><spage>e25114</spage><epage>e25114</epage><pages>e25114-e25114</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers.
We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features.
We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival.
We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>22053178</pmid><doi>10.1371/journal.pone.0025114</doi><tpages>e25114</tpages><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2011-10, Vol.6 (10), p.e25114-e25114 |
| issn | 1932-6203 1932-6203 |
| language | eng |
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| source | MEDLINE; DOAJ Directory of Open Access Journals; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Adolescent Biology Biomarkers, Tumor - genetics Biomarkers, Tumor - metabolism Brain Brain cancer Brain research Brain tumors Cancer therapies Case-Control Studies Cell cycle Child Child, Preschool Children & youth Chromosome 14 Chromosomes Coding Computational Biology Correlation Development and progression Ependymal cells Ependymoma - genetics Ependymoma - pathology Epigenetics Female Gene expression Gene Expression Profiling Gene Expression Regulation, Neoplastic Histology Hospitals Humans Identification Infant Male Markers Medical prognosis Medicine Metastasis MicroRNA MicroRNAs MicroRNAs - genetics MicroRNAs - metabolism miRNA mRNA stability Multivariate Analysis Mutation Non-coding RNA Paraffin Parameter identification Pediatrics Prognosis Proportional Hazards Models Regression Analysis Stem cells Survival Analysis Translation (Genetics) Tumors |
| title | Identification of microRNAs as potential prognostic markers in ependymoma |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-04T21%3A11%3A09IST&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=Identification%20of%20microRNAs%20as%20potential%20prognostic%20markers%20in%20ependymoma&rft.jtitle=PloS%20one&rft.au=Costa,%20Fabricio%20F&rft.date=2011-10-28&rft.volume=6&rft.issue=10&rft.spage=e25114&rft.epage=e25114&rft.pages=e25114-e25114&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0025114&rft_dat=%3Cgale_plos_%3EA476866519%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=1309933419&rft_id=info:pmid/22053178&rft_galeid=A476866519&rft_doaj_id=oai_doaj_org_article_2569c213f1f540f2bf59aa946e6a4937&rfr_iscdi=true |