Global Gene Expression Analysis Reveals a Link between NDRG1 and Vesicle Transport
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{"title"=>"Global gene expression analysis reveals a link between NDRG1 and vesicle transport", "type"=>"journal", "authors"=>[{"first_name"=>"Hanne A.", "last_name"=>"Askautrud", "scopus_author_id"=>"18435950900"}, {"first_name"=>"Elisabet", "last_name"=>"Gjernes", "scopus_author_id"=>"6602968157"}, {"first_name"=>"Gjermund", "last_name"=>"Gunnes", "scopus_author_id"=>"6602451961"}, {"first_name"=>"Marit", "last_name"=>"Sletten", "scopus_author_id"=>"7003478521"}, {"first_name"=>"Douglas T.", "last_name"=>"Ross", "scopus_author_id"=>"7404449443"}, {"first_name"=>"Anne Lise", "last_name"=>"Brøresen-Dale", "scopus_author_id"=>"55175599200"}, {"first_name"=>"Nina", "last_name"=>"Iversen", "scopus_author_id"=>"55886505400"}, {"first_name"=>"Michael A.", "last_name"=>"Tranulis", "scopus_author_id"=>"6602148628"}, {"first_name"=>"Eirik", "last_name"=>"Frengen", "scopus_author_id"=>"56033179300"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84900343561", "doi"=>"10.1371/journal.pone.0087268", "issn"=>"19326203", "pui"=>"373059503", "sgr"=>"84900343561", "pmid"=>"24498060"}, "id"=>"b0e381e9-7794-3cca-afd2-1387b78cb708", "abstract"=>"N-myc downstream-regulated gene 1 (NDRG1) is induced by cellular stress such as hypoxia and DNA damage, and in humans, germ line mutations cause Charcot-Marie-Tooth disease. However, the cellular roles of NDRG1 are not fully understood. Previously, NDRG1 was shown to mediate doxorubicin resistance under hypoxia, suggesting a role for NDRG1 in cell survival under these conditions. We found decreased apoptosis in doxorubicin-treated cells expressing NDRG1 shRNAs under normoxia, demonstrating a requirement for NDRG1 in apoptosis in breast epithelial cells under normal oxygen pressure. Also, different cellular stress regimens, such as hypoxia and doxorubicin treatment, induced NDRG1 through different stress signalling pathways. We further compared expression profiles in human breast epithelial cells ectopically over-expressing NDRG1 with cells expressing NDRG1 shRNAs in order to identify biological pathways where NDRG1 is involved. The results suggest that NDRG1 may have roles connected to vesicle transport.", "link"=>"http://www.mendeley.com/research/global-gene-expression-analysis-reveals-link-between-ndrg1-vesicle-transport-1", "reader_count"=>15, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Student > Bachelor"=>1, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>6, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>3, "Student > Master"=>2, "Student > Bachelor"=>1, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Medicine and Dentistry"=>3, "Agricultural and Biological Sciences"=>5, "Neuroscience"=>2, "Chemistry"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}}, "reader_count_by_country"=>{"Poland"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1372499"], "description"=>"<p>(<b>A</b>) Increased NDRG1 expression detected by Western blotting in the breast cell lines MCF-7 and ZR-75-1 grown at 1% O<sub>2</sub> for 24, 48 and 72 hours as indicated, compared to control cells grown at 20% O<sub>2</sub>. (<b>B</b>) Western blots document increased NDRG1 expression in cells grown at 20% O<sub>2</sub>. The ZR-75-1 cell populations transduced with the NDRG1-cDNA (six biological parallels indicated A–F), are compared to ZR-75-1 transduced with the vector pSiRPG <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087268#pone.0087268-Storvold1\" target=\"_blank\">[27]</a> without insert (C2 and C3). α-tubulin was used as loading control (<b>A</b> and <b>B</b>). Note that a reduced level of total protein is loaded in the lane containing extract from MCF-7 grown at 1% O<sub>2</sub> for 24 hours. (<b>C</b>) Treeview presentation of the expression of 18 genes in a hypoxia signature gene list <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087268#pone.0087268-Chi1\" target=\"_blank\">[24]</a> in MCF-7 and ZR-75-1 cells grown at 1% O<sub>2</sub> for 24 or 48 hours as indicated. (<b>D</b>) Treeview presentation of the hypoxia signature genes in six ZR-75-1 cell populations ectopically over-expressing NDRG1 (indicated A–F). The red and green colours show increased and reduced expression levels, respectively (<b>C</b> and <b>D</b>). The colour intensity is from −3 to 3 indicating the magnitude of the fold change in gene expression between the cell population and its control.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene identification and analysis", "Gene regulation", "gene expression", "genetics", "Gene function", "genomics", "Genome expression analysis", "Molecular cell biology", "Cell death", "ndrg1", "hypoxia", "ectopic"], "article_id"=>923073, "categories"=>["Biological Sciences"], "users"=>["Hanne A. Askautrud", "Elisabet Gjernes", "Gjermund Gunnes", "Marit Sletten", "Douglas T. Ross", "Anne Lise Børresen-Dale", "Nina Iversen", "Michael A. Tranulis", "Eirik Frengen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087268.g001", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Increased_NDRG1_expression_due_to_hypoxia_or_ectopic_expression_/923073", "title"=>"Increased NDRG1 expression due to hypoxia or ectopic expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:26:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372503"], "description"=>"<p>(<b>A</b>) Western blots detect increased TP53 and NDRG1 expression in HCT116, MCF-7, ZR-75-1 and SUM102 cells after treatment with doxorubicin (1 µM) for 24 hours (+) compared to control cells (−). α-tubulin was used as loading control. (<b>B</b>) The percentage of apoptotic cells detected by TUNEL assay in the SUM102/pSiRPG, SUM102/NDRG1si4A and SUM102/NDRG1si7A cell lines after treatment with doxorubicin (1 µM) for 24 hours as indicated. Bars are shown with 95% confidence intervals (p<0,02, unpaired two-tailed t-test).</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene identification and analysis", "Gene regulation", "gene expression", "genetics", "Gene function", "genomics", "Genome expression analysis", "Molecular cell biology", "Cell death", "ndrg1", "inhibits", "apoptosis", "sum102"], "article_id"=>923078, "categories"=>["Biological Sciences"], "users"=>["Hanne A. Askautrud", "Elisabet Gjernes", "Gjermund Gunnes", "Marit Sletten", "Douglas T. Ross", "Anne Lise Børresen-Dale", "Nina Iversen", "Michael A. Tranulis", "Eirik Frengen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087268.g002", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Silencing_of_NDRG1_inhibits_apoptosis_in_the_SUM102_cell_line_/923078", "title"=>"Silencing of NDRG1 inhibits apoptosis in the SUM102 cell line.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:26:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372509"], "description"=>"<p>Colors were applied artificially for graphical purposes. (<b>A</b>) NDRG1 (green) and calnexin (red) in untreated, hypoxia and doxorubicin treated cells. Bar: 5 µm. (<b>B</b>) NDRG1 (green) and EEA1 (red) in hypoxia treated cells. Bar: 10 µm.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene identification and analysis", "Gene regulation", "gene expression", "genetics", "Gene function", "genomics", "Genome expression analysis", "Molecular cell biology", "Cell death", "staining", "sum102"], "article_id"=>923083, "categories"=>["Biological Sciences"], "users"=>["Hanne A. Askautrud", "Elisabet Gjernes", "Gjermund Gunnes", "Marit Sletten", "Douglas T. Ross", "Anne Lise Børresen-Dale", "Nina Iversen", "Michael A. Tranulis", "Eirik Frengen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087268.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Immunofluorescence_staining_of_SUM102_cell_cultures_/923083", "title"=>"Immunofluorescence staining of SUM102 cell cultures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:26:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372510"], "description"=>"<p>Western blots detect reduced NDRG1 expression in the breast cell lines ME16C2 and SUM102 expressing the shRNAs NDRG1si4 (si4) and NDRG1si7 (si7), transduced in parallel experiments (A and B) compared to control cells (C) transduced with the empty vector pSiRPG <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0087268#pone.0087268-Storvold1\" target=\"_blank\">[27]</a>. α-tubulin was used as loading control.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene identification and analysis", "Gene regulation", "gene expression", "genetics", "Gene function", "genomics", "Genome expression analysis", "Molecular cell biology", "Cell death", "ndrg1"], "article_id"=>923084, "categories"=>["Biological Sciences"], "users"=>["Hanne A. Askautrud", "Elisabet Gjernes", "Gjermund Gunnes", "Marit Sletten", "Douglas T. Ross", "Anne Lise Børresen-Dale", "Nina Iversen", "Michael A. Tranulis", "Eirik Frengen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087268.g004", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Knock_down_of_NDRG1_expression_by_shRNAs_/923084", "title"=>"Knock down of NDRG1 expression by shRNAs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:26:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372511"], "description"=>"<p>Treeview presentation of the 83 probes representing genes found to be significantly differently expressed in SUM102 and ME16C2 cells expressing NDRG1 shRNAs when compared to ZR-75-1 with ectopic NDRG1 over-expression. The results show a hierarchical clustering of the gene expression pattern, while the arrays are sorted according to cell populations. Genes with no available functional information (14 genes) are indicated with (*). Genes annotated in orange encode proteins that are linked to ER, Golgi, endosomes, as well as genes connected to vesicle transport. The expression of NDRG1 (black) confirms the ectopic over-expression in ZR-75-1 and shRNA-based down-regulation in SUM102 and ME16C2 cells. The red and green colours show over-expression and down-regulation respectively. The colour intensity varies between −2 and 2 indicating the magnitude of the fold change in gene expression between the cell population and its control.</p>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene identification and analysis", "Gene regulation", "gene expression", "genetics", "Gene function", "genomics", "Genome expression analysis", "Molecular cell biology", "Cell death", "cells", "manipulated", "ndrg1"], "article_id"=>923085, "categories"=>["Biological Sciences"], "users"=>["Hanne A. Askautrud", "Elisabet Gjernes", "Gjermund Gunnes", "Marit Sletten", "Douglas T. Ross", "Anne Lise Børresen-Dale", "Nina Iversen", "Michael A. Tranulis", "Eirik Frengen"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0087268.g005", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_profile_of_cells_with_manipulated_NDRG1_expression_/923085", "title"=>"Gene expression profile of cells with manipulated NDRG1 expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-01-31 04:26:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/1372512", "https://ndownloader.figshare.com/files/1372513", "https://ndownloader.figshare.com/files/1372515"], "description"=>"<div><p>N-myc downstream-regulated gene 1 (<i>NDRG1</i>) is induced by cellular stress such as hypoxia and DNA damage, and in humans, germ line mutations cause Charcot-Marie-Tooth disease. However, the cellular roles of NDRG1 are not fully understood. Previously, NDRG1 was shown to mediate doxorubicin resistance under hypoxia, suggesting a role for NDRG1 in cell survival under these conditions. We found decreased apoptosis in doxorubicin-treated cells expressing NDRG1 shRNAs under normoxia, demonstrating a requirement for NDRG1 in apoptosis in breast epithelial cells under normal oxygen pressure. Also, different cellular stress regimens, such as hypoxia and doxorubicin treatment, induced NDRG1 through different stress signalling pathways. We further compared expression profiles in human breast epithelial cells ectopically over-expressing NDRG1 with cells expressing NDRG1 shRNAs in order to identify biological pathways where NDRG1 is involved. The results suggest that NDRG1 may have roles connected to vesicle transport.</p></div>", "links"=>[], "tags"=>["Computational biology", "Molecular genetics", "Gene identification and analysis", "Gene regulation", "gene expression", "genetics", "Gene function", "genomics", "Genome expression analysis", "Molecular cell biology", "Cell death", "reveals", "ndrg1", "vesicle"], "article_id"=>923086, "categories"=>["Biological Sciences"], "users"=>["Hanne A. Askautrud", "Elisabet Gjernes", "Gjermund Gunnes", "Marit Sletten", "Douglas T. Ross", "Anne Lise Børresen-Dale", "Nina Iversen", "Michael A. Tranulis", "Eirik Frengen"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0087268.s001", "https://dx.doi.org/10.1371/journal.pone.0087268.s002", "https://dx.doi.org/10.1371/journal.pone.0087268.s003"], "stats"=>{"downloads"=>16, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Global_Gene_Expression_Analysis_Reveals_a_Link_between_NDRG1_and_Vesicle_Transport_/923086", "title"=>"Global Gene Expression Analysis Reveals a Link between NDRG1 and Vesicle Transport", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-01-31 04:26:14"}

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Genetics", "average_usage"=>[306, 482]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[285]}, {"subject_area"=>"/Medicine and health sciences/Anatomy", "average_usage"=>[266]}, {"subject_area"=>"/Medicine and health sciences/Pulmonology", "average_usage"=>[261, 417]}]}
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