Identification of MicroRNAs as Potential Prognostic Markers in Ependymoma
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{"title"=>"Identification of micrornas as potential prognostic markers in ependymoma", "type"=>"journal", "authors"=>[{"first_name"=>"Fabricio F.", "last_name"=>"Costa", "scopus_author_id"=>"15519007800"}, {"first_name"=>"Jared M.", "last_name"=>"Bischof", "scopus_author_id"=>"8272356300"}, {"first_name"=>"Elio F.", "last_name"=>"Vanin", "scopus_author_id"=>"35480951500"}, {"first_name"=>"Rishi R.", "last_name"=>"Lulla", "scopus_author_id"=>"35269243700"}, {"first_name"=>"Min", "last_name"=>"Wang", "scopus_author_id"=>"55553728775"}, {"first_name"=>"Simone T.", "last_name"=>"Sredni", "scopus_author_id"=>"35600612800"}, {"first_name"=>"Veena", "last_name"=>"Rajaram", "scopus_author_id"=>"7004355193"}, {"first_name"=>"Maria", "last_name"=>"de Fátima Bonaldo", "scopus_author_id"=>"7004358379"}, {"first_name"=>"Deli", "last_name"=>"Wang", "scopus_author_id"=>"56875869600"}, {"first_name"=>"Stewart", "last_name"=>"Goldman", "scopus_author_id"=>"35268606400"}, {"first_name"=>"Tadanori", "last_name"=>"Tomita", "scopus_author_id"=>"35479560300"}, {"first_name"=>"Marcelo B.", "last_name"=>"Soares", "scopus_author_id"=>"7203087051"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "isbn"=>"1932-6203", "pmid"=>"22053178", "scopus"=>"2-s2.0-80055029189", "doi"=>"10.1371/journal.pone.0025114", "sgr"=>"80055029189", "pui"=>"362826173"}, "id"=>"3cd36eca-8233-385e-b0f5-ef53ea4a5291", "abstract"=>"INTRODUCTION: 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.\\n\\nMATERIALS AND METHODS: 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.\\n\\nRESULTS: 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.\\n\\nCONCLUSION: 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.", "link"=>"http://www.mendeley.com/research/identification-micrornas-potential-prognostic-markers-ependymoma-2", "reader_count"=>48, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Researcher"=>11, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Researcher"=>11, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>9, "Other"=>1, "Student > Bachelor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>8, "Medicine and Dentistry"=>12, "Agricultural and Biological Sciences"=>22, "Neuroscience"=>1, "Psychology"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Neuroscience"=>{"Neuroscience"=>1}, "Psychology"=>{"Psychology"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Turkey"=>1, "Brazil"=>1, "France"=>1, "India"=>1}, "group_count"=>4}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/718205"], "description"=>"<p><b>Abbreviations:</b> IT, Infratentorial; ST, Supratentorial; C, Chemotherapy treatment; RT, Radiotherapy treatment; NR, No Relapse to date; AWD, Alive With Disease; NED, No Evidence of Disease; DOD, Dead as a result Of the Disease;</p><p>*Based on standard WHO (World Health Organization) classification for ependymomas.</p><p><b>Note</b>: The letters represent different samples from the same patient.</p>", "links"=>[], "tags"=>["characteristics", "ependymoma", "samples"], "article_id"=>388557, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Fabricio F. Costa", "Jared M. Bischof", "Elio F. Vanin", "Rishi R. Lulla", "Min Wang", "Simone T. Sredni", "Veena Rajaram", "Maria de Fatima Bonaldo", "Deli Wang", "Stewart Goldman", "Tadanori Tomita", "Marcelo B. Soares"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025114.t001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clinicopathologic_characteristics_of_the_ependymoma_samples_used_in_this_study_/388557", "title"=>"Clinicopathologic characteristics of the ependymoma samples used in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-28 02:22:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/718260"], "description"=>"<p>Selected miRNAs after adjusting the clinical variables using Cox regression analyses for both Overall Survival and Time-to-Relapse.</p>", "links"=>[], "tags"=>["mirnas", "adjusting", "variables", "cox", "regression", "analyses"], "article_id"=>388605, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Fabricio F. Costa", "Jared M. Bischof", "Elio F. Vanin", "Rishi R. Lulla", "Min Wang", "Simone T. Sredni", "Veena Rajaram", "Maria de Fatima Bonaldo", "Deli Wang", "Stewart Goldman", "Tadanori Tomita", "Marcelo B. Soares"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025114.t003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selected_miRNAs_after_adjusting_the_clinical_variables_using_Cox_regression_analyses_for_both_Overall_Survival_and_Time_to_Relapse_/388605", "title"=>"Selected miRNAs after adjusting the clinical variables using Cox regression analyses for both Overall Survival and Time-to-Relapse.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-28 02:23:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/363823", "https://ndownloader.figshare.com/files/363850", "https://ndownloader.figshare.com/files/363863", "https://ndownloader.figshare.com/files/363881", "https://ndownloader.figshare.com/files/363979"], "description"=>"<div><h3>Introduction</h3><p>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.</p> <h3>Materials and Methods</h3><p>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.</p> <h3>Results</h3><p>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.</p> <h3>Conclusion</h3><p>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.</p> </div>", "links"=>[], "tags"=>["micrornas", "prognostic", "markers", "ependymoma"], "article_id"=>131906, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Fabricio F. Costa", "Jared M. Bischof", "Elio F. Vanin", "Rishi R. Lulla", "Min Wang", "Simone T. Sredni", "Veena Rajaram", "Maria de Fatima Bonaldo", "Deli Wang", "Stewart Goldman", "Tadanori Tomita", "Marcelo B. Soares"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0025114.s001", "https://dx.doi.org/10.1371/journal.pone.0025114.s002", "https://dx.doi.org/10.1371/journal.pone.0025114.s003", "https://dx.doi.org/10.1371/journal.pone.0025114.s004", "https://dx.doi.org/10.1371/journal.pone.0025114.s005"], "stats"=>{"downloads"=>33, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Identification_of_MicroRNAs_as_Potential_Prognostic_Markers_in_Ependymoma/131906", "title"=>"Identification of MicroRNAs as Potential Prognostic Markers in Ependymoma", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-10-28 00:31:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/718302"], "description"=>"<p><b>Abbreviations:</b> E, Ependymomas; C, All Normal Controls; I, Infratentorial Tumors; IC, Infratentorial Normal Controls; S, Supratentorial Tumors; SC, Supratentorial Normal Controls.</p>§<p>miRs that were confirmed by individual assays.</p><p><b>Note:</b> The cut off used in these analyses was 10 fold up and/or down with a p≤0.01 according to individual confirmation assays.</p>", "links"=>[], "tags"=>["differentially", "ependymomas"], "article_id"=>388655, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Fabricio F. Costa", "Jared M. Bischof", "Elio F. Vanin", "Rishi R. Lulla", "Min Wang", "Simone T. Sredni", "Veena Rajaram", "Maria de Fatima Bonaldo", "Deli Wang", "Stewart Goldman", "Tadanori Tomita", "Marcelo B. Soares"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025114.t002", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_miRNAs_differentially_expressed_in_ependymomas_p_8804_0_01_FDR_lt_0_05_/388655", "title"=>"miRNAs differentially expressed in ependymomas (p≤0.01, FDR<0.05).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-28 02:24:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/717995"], "description"=>"<p>(<b>A</b>) Unsupervised Hierarchical Clustering of all normal brain control samples against the ependymomas used in this study. The clustering and tree are based on Pearson's correlation and were generated by the MeV 4.1 software according to Delta Ct values. The miRNAs that are not represented in this Figure were not detected in any of the groups. (<b>B</b>) Higher magnification of the Unsupervised Hierarchical Clustering from panel A with the supporting tree showing the separation between normal samples and ependymomas from different locations. Black, Normal controls; Yellow, Infratentorial samples; Orange, Supratentorial samples. NB-I, Normal ependymal cells from infratentorial location; NB-S, Normal ependymal cells from Supratentorial location. (<b>C</b>) Histogram graphical representation of the statistically differentially expressed miRNAs when comparing all normal samples against the ependymoma samples used in this study. The values in the Y axis are of fold changes based on the StatMiner software. Twenty-eight miRNAs are differentially expressed - twenty-three miRNAs are over-expressed and five miRNAs are downregulated (p≤0.01; FDR<0.05).</p>", "links"=>[], "tags"=>["representations", "mirna", "ependymomas"], "article_id"=>388349, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Fabricio F. Costa", "Jared M. Bischof", "Elio F. Vanin", "Rishi R. Lulla", "Min Wang", "Simone T. Sredni", "Veena Rajaram", "Maria de Fatima Bonaldo", "Deli Wang", "Stewart Goldman", "Tadanori Tomita", "Marcelo B. Soares"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025114.g001", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heat_Map_representations_for_miRNA_expression_in_ependymomas_and_normal_controls_/388349", "title"=>"Heat Map representations for miRNA expression in ependymomas and normal controls.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-28 02:19:09"}
  • {"files"=>["https://ndownloader.figshare.com/files/718122"], "description"=>"<p>(<b>A</b>) Correlation matrix among miRNAs that were identified by Cox regression analyses for Time to Relapse. The lower triangle of the matrix shows the scatter plots of pair-wised relationship between miRNAs. The diagonal panel shows histograms of expression. The upper triangle represents Spearman correlation coefficients for each pair of miRNA (<b>B</b>) Kaplan-Meier curves of a cluster of miRNAs on human chromosome 14q32 and associations to Time to Relapse. The thresholds of cut-off points were determined using a survival tree analysis approach. Delta CT values were used for miRNA expression in this analysis. The Y axis represents relapse free probability and the X axis represents time of follow-up in years.</p>", "links"=>[], "tags"=>["correlations", "clinicopathological"], "article_id"=>388473, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Fabricio F. Costa", "Jared M. Bischof", "Elio F. Vanin", "Rishi R. Lulla", "Min Wang", "Simone T. Sredni", "Veena Rajaram", "Maria de Fatima Bonaldo", "Deli Wang", "Stewart Goldman", "Tadanori Tomita", "Marcelo B. Soares"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025114.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_miRNAs_and_correlations_to_clinicopathological_features_/388473", "title"=>"miRNAs and correlations to clinicopathological features.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-28 02:21:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/718360"], "description"=>"<p>Multivariate Cox Regression Analyses for Time to Relapse and Overall Survival.</p>", "links"=>[], "tags"=>["cox", "regression", "analyses", "relapse"], "article_id"=>388708, "categories"=>["Cancer", "Biological Sciences", "Genetics"], "users"=>["Fabricio F. Costa", "Jared M. Bischof", "Elio F. Vanin", "Rishi R. Lulla", "Min Wang", "Simone T. Sredni", "Veena Rajaram", "Maria de Fatima Bonaldo", "Deli Wang", "Stewart Goldman", "Tadanori Tomita", "Marcelo B. Soares"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0025114.t004", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multivariate_Cox_Regression_Analyses_for_Time_to_Relapse_and_Overall_Survival_/388708", "title"=>"Multivariate Cox Regression Analyses for Time to Relapse and Overall Survival.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-28 02:25:08"}

PMC Usage Stats | Further Information

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Relative Metric

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