Epigenetic Regulation of MicroRNA Genes and the Role of miR-34b in Cell Invasion and Motility in Human Melanoma
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{"title"=>"Epigenetic regulation of microRNA genes and the role of miR-34b in cell invasion and motility in human melanoma", "type"=>"journal", "authors"=>[{"first_name"=>"Joseph", "last_name"=>"Mazar", "scopus_author_id"=>"15019592400"}, {"first_name"=>"Divya", "last_name"=>"Khaitan", "scopus_author_id"=>"8855753300"}, {"first_name"=>"Dan", "last_name"=>"DeBlasio", "scopus_author_id"=>"35104548000"}, {"first_name"=>"Cuncong", "last_name"=>"Zhong", "scopus_author_id"=>"36631186600"}, {"first_name"=>"Subramaniam S.", "last_name"=>"Govindarajan", "scopus_author_id"=>"54888389100"}, {"first_name"=>"Sharmila", "last_name"=>"Kopanathi", "scopus_author_id"=>"50561452600"}, {"first_name"=>"Shaojie", "last_name"=>"Zhang", "scopus_author_id"=>"36641041500"}, {"first_name"=>"Animesh", "last_name"=>"Ray", "scopus_author_id"=>"55435183700"}, {"first_name"=>"Ranjan J.", "last_name"=>"Perera", "scopus_author_id"=>"8638324300"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-80052889937", "sgr"=>"80052889937", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0024922", "pmid"=>"21949788", "isbn"=>"1932-6203", "pui"=>"362577540"}, "id"=>"760f9682-7033-3ad2-b1e6-5b30917ed3c6", "abstract"=>"Invasive melanoma is the most lethal form of skin cancer. The treatment of melanoma-derived cell lines with 5-aza-2'-deoxycytidine (5-Aza-dC) markedly increases the expression of several miRNAs, suggesting that the miRNA-encoding genes might be epigenetically regulated, either directly or indirectly, by DNA methylation. We have identified a group of epigenetically regulated miRNA genes in melanoma cells, and have confirmed that the upstream CpG island sequences of several such miRNA genes are hypermethylated in cell lines derived from different stages of melanoma, but not in melanocytes and keratinocytes. We used direct DNA bisulfite and immunoprecipitated DNA (Methyl-DIP) to identify changes in CpG island methylation in distinct melanoma patient samples classified as primary in situ, regional metastatic, and distant metastatic. Two melanoma cell lines (WM1552C and A375 derived from stage 3 and stage 4 human melanoma, respectively) were engineered to ectopically express one of the epigenetically modified miRNA: miR-34b. Expression of miR-34b reduced cell invasion and motility rates of both WM1552C and A375, suggesting that the enhanced cell invasiveness and motility observed in metastatic melanoma cells may be related to their reduced expression of miR-34b. Total RNA isolated from control or miR-34b-expressing WM1552C cells was subjected to deep sequencing to identify gene networks around miR-34b. We identified network modules that are potentially regulated by miR-34b, and which suggest a mechanism for the role of miR-34b in regulating normal cell motility and cytokinesis.", "link"=>"http://www.mendeley.com/research/epigenetic-regulation-microrna-genes-role-mir34b-cell-invasion-motility-human-melanoma-1", "reader_count"=>48, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>21, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>21, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>11, "Student > Postgraduate"=>1, "Student > Master"=>5, "Other"=>2, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>8, "Agricultural and Biological Sciences"=>34, "Medicine and Dentistry"=>4, "Social Sciences"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Social Sciences"=>{"Social Sciences"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>34}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}}, "reader_count_by_country"=>{"United States"=>4, "Uruguay"=>1, "Denmark"=>1, "Portugal"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/733520"], "description"=>"<p>Hierarchical clustering of differentially expressed miRNAs in melanoma cells after 5-Aza-dC treatment. 5-Aza-dC-induced expression changes ranged from highly upregulated (bright red) to marginally upregulated (dark red); black represents no change.</p>", "links"=>[], "tags"=>["mirna"], "article_id"=>403866, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Joseph Mazar", "Divya Khaitan", "Dan DeBlasio", "Cuncong Zhong", "Subramaniam S. Govindarajan", "Sharmila Kopanathi", "Shaojie Zhang", "Animesh Ray", "Ranjan J. Perera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024922.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Activation_of_miRNA_expression_in_response_to_5_Aza_dC_/403866", "title"=>"Activation of miRNA expression in response to 5-Aza-dC.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:04:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/370458", "https://ndownloader.figshare.com/files/370492", "https://ndownloader.figshare.com/files/370518", "https://ndownloader.figshare.com/files/370551", "https://ndownloader.figshare.com/files/370571", "https://ndownloader.figshare.com/files/370609"], "description"=>"<div><p>Invasive melanoma is the most lethal form of skin cancer. The treatment of melanoma-derived cell lines with 5-aza-2′-deoxycytidine (5-Aza-dC) markedly increases the expression of several miRNAs, suggesting that the miRNA-encoding genes might be epigenetically regulated, either directly or indirectly, by DNA methylation. We have identified a group of epigenetically regulated miRNA genes in melanoma cells, and have confirmed that the upstream CpG island sequences of several such miRNA genes are hypermethylated in cell lines derived from different stages of melanoma, but not in melanocytes and keratinocytes. We used direct DNA bisulfite and immunoprecipitated DNA (Methyl-DIP) to identify changes in CpG island methylation in distinct melanoma patient samples classified as primary <em>in situ</em>, regional metastatic, and distant metastatic. Two melanoma cell lines (WM1552C and A375 derived from stage 3 and stage 4 human melanoma, respectively) were engineered to ectopically express one of the epigenetically modified miRNA: miR-34b. Expression of miR-34b reduced cell invasion and motility rates of both WM1552C and A375, suggesting that the enhanced cell invasiveness and motility observed in metastatic melanoma cells may be related to their reduced expression of miR-34b. Total RNA isolated from control or miR-34b-expressing WM1552C cells was subjected to deep sequencing to identify gene networks around miR-34b. We identified network modules that are potentially regulated by miR-34b, and which suggest a mechanism for the role of miR-34b in regulating normal cell motility and cytokinesis.</p> </div>", "links"=>[], "tags"=>["epigenetic", "microrna", "genes", "mir-34b", "motility", "melanoma"], "article_id"=>133191, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Joseph Mazar", "Divya Khaitan", "Dan DeBlasio", "Cuncong Zhong", "Subramaniam S. Govindarajan", "Sharmila Kopanathi", "Shaojie Zhang", "Animesh Ray", "Ranjan J. Perera"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0024922.s001", "https://dx.doi.org/10.1371/journal.pone.0024922.s002", "https://dx.doi.org/10.1371/journal.pone.0024922.s003", "https://dx.doi.org/10.1371/journal.pone.0024922.s004", "https://dx.doi.org/10.1371/journal.pone.0024922.s005", "https://dx.doi.org/10.1371/journal.pone.0024922.s006"], "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Epigenetic_Regulation_of_MicroRNA_Genes_and_the_Role_of_miR_34b_in_Cell_Invasion_and_Motility_in_Human_Melanoma/133191", "title"=>"Epigenetic Regulation of MicroRNA Genes and the Role of miR-34b in Cell Invasion and Motility in Human Melanoma", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-09-19 00:53:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/734053"], "description"=>"<p>A) and B) Cell adhesion assays comparing WM1552C/VO and WM1552C/34b cells (A), or A375/VO and A375/34b cells (B). Data are percent of input cells bound, mean ± (SEM) of triplicates. C) and D) Cell invasion assays comparing untransfected WM1552C cells to stable WM1552C/VO and WM1552C/34b cells. E) and F) Cell invasion assays comparing untransfected A375 cells to stable A375/VO and A375/34b cells. All assays were performed in triplicate. Asterisks indicate statistical significance by Kruskal Wallis nonparametric test, <i>P</i><0.005.</p>", "links"=>[], "tags"=>["mir-34b", "melanoma", "attachment"], "article_id"=>404400, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Joseph Mazar", "Divya Khaitan", "Dan DeBlasio", "Cuncong Zhong", "Subramaniam S. Govindarajan", "Sharmila Kopanathi", "Shaojie Zhang", "Animesh Ray", "Ranjan J. Perera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024922.g005", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_miR_34b_on_melanoma_cell_attachment_and_invasion_/404400", "title"=>"Effect of miR-34b on melanoma cell attachment and invasion.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:13:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/734177"], "description"=>"<p>Wound healing assay for melanoma cells. A) and B) Representative images of WM1552C/VO and WM1552C/34b cells or A375/VO and A375/34b cells. Images were taken between 0 and 20 hrs after scratch formation. C) and D) Quantitation of experiments shown in (A) and (B), performed in triplicate. The percent surface area between the wounds was calculated using NIS elements software. Each time point was compared with the 0 hr time point of the respective cell line. Asterisks indicate statistical significance by Kruskal Wallis nonparametric test, <i>P</i><0.005.</p>", "links"=>[], "tags"=>["mir-34b"], "article_id"=>404526, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Joseph Mazar", "Divya Khaitan", "Dan DeBlasio", "Cuncong Zhong", "Subramaniam S. Govindarajan", "Sharmila Kopanathi", "Shaojie Zhang", "Animesh Ray", "Ranjan J. Perera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024922.g006", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effect_of_miR_34b_on_cell_migration_/404526", "title"=>"Effect of miR-34b on cell migration.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:15:26"}
  • {"files"=>["https://ndownloader.figshare.com/files/733686"], "description"=>"<p>CpG island methylation in the putative <i>mir-34b</i> promoter was measured by bisulfite genomic sequencing (conventions are as appeared in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0024922#pone-0024922-g002\" target=\"_blank\">Figure 2</a>). Six clones from each sample were tested. Patient samples are annotated as follows: (P) = primary melanoma, (R) = regional metastasis, (D) = distant metastasis, (N) = nodal metastasis.</p>", "links"=>[], "tags"=>["islands", "hypermethylated", "melanoma"], "article_id"=>404028, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Joseph Mazar", "Divya Khaitan", "Dan DeBlasio", "Cuncong Zhong", "Subramaniam S. Govindarajan", "Sharmila Kopanathi", "Shaojie Zhang", "Animesh Ray", "Ranjan J. Perera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024922.g003", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CpG_islands_5_UPS_of_mir_34b_are_hypermethylated_in_clinical_melanoma_samples_/404028", "title"=>"CpG islands 5′UPS of <i>mir-34b</i> are hypermethylated in clinical melanoma samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:07:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/733896"], "description"=>"<p>A) A heat-map of the top potential miR-34b targets suggested by TargetScan 5.1, based on fold change and transcript differences between WM1552C/34b cells vs. WM1552C/VO cells. Green boxes indicate gene targets associated with the network of cytoskeletal rearrangement shown in (B). B) Pathway mapping of the top potential miR-34b targets reveals 15 targets all associated with the network of cytoskeletal rearrangement. Targets are indicated in green. C) qRT-PCR validation of the differential expression of putative miR-34b targets CDC42 and FN1 in vector-transfected or miR-34b-transfected WM1552C cells. Values are listed as relative quantities (RQ).</p>", "links"=>[], "tags"=>["putative", "mir-34b", "genes", "melanoma"], "article_id"=>404243, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Joseph Mazar", "Divya Khaitan", "Dan DeBlasio", "Cuncong Zhong", "Subramaniam S. Govindarajan", "Sharmila Kopanathi", "Shaojie Zhang", "Animesh Ray", "Ranjan J. Perera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024922.g004", "stats"=>{"downloads"=>2, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Differential_expression_of_putative_miR_34b_target_genes_in_miR_34b_8211_expressing_melanoma_cells_/404243", "title"=>"Differential expression of putative miR-34b target genes in miR-34b–expressing melanoma cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:10:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/733592"], "description"=>"<p>A) Frequency of CpG island methylation in the <i>mir-34b</i> 5′-UPS measured by bisulfite genomic sequencing (horizontal line at top; numbers represent nucleotides relative to the transcription start site, and vertical lines represent the positions of CpG islands). Nine clones from each cell line were tested. Black boxes represent methylated sites, white boxes represent no methylation. WM793B = Stage 1, WM278 = Stage 2, WM1552C = Stage 3, A375 = Stage 4. B) WM1552C cells were treated with 5-Aza-dC and the putative <i>mir-34b</i> promoter in nine clones was then examined for CpG island methylation (conventions as described in A). C) Northern blot analysis of miR-34b expression in WM1552C cells after treatment with various concentrations of 5-Aza-dC. U6 RNA was used as a loading control. D) Methyl-DIP deep sequencing of the upstream CpG island sequences of <i>mir-34b</i> in melanocytes, WM1552C, and 5-Aza-dC treated WM1552C cells. Y-axes depict RPKM values and the horizontal green bar indicates the CpG island. The histograms represent the extent of CpG methylation.</p>", "links"=>[], "tags"=>["cpg", "methylation", "melanoma", "5-aza-dc", "demethylation"], "article_id"=>403937, "categories"=>["Biological Sciences", "Genetics"], "users"=>["Joseph Mazar", "Divya Khaitan", "Dan DeBlasio", "Cuncong Zhong", "Subramaniam S. Govindarajan", "Sharmila Kopanathi", "Shaojie Zhang", "Animesh Ray", "Ranjan J. Perera"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0024922.g002", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_mir_34b_5_UPS_CpG_island_methylation_in_melanocytes_keratinocytes_and_melanoma_cells_and_the_effect_of_5_Aza_dC_demethylation_on_its_expression_in_melanoma_cells_/403937", "title"=>"<i>mir-34b</i> 5′-UPS CpG island methylation in melanocytes, keratinocytes, and melanoma cells, and the effect of 5-Aza-dC demethylation on its expression in melanoma cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-19 01:05:37"}

PMC Usage Stats | Further Information

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