Genomic Profiling Identifies GATA6 as a Candidate Oncogene Amplified in Pancreatobiliary Cancer
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{"title"=>"Genomic profiling identifies GATA6 as a candidate oncogene amplified in pancreatobiliary cancer", "type"=>"journal", "authors"=>[{"first_name"=>"Kevin A.", "last_name"=>"Kwei", "scopus_author_id"=>"6507373968"}, {"first_name"=>"Murali D.", "last_name"=>"Bashyam", "scopus_author_id"=>"6602984496"}, {"first_name"=>"Jessica", "last_name"=>"Kao", "scopus_author_id"=>"14031879400"}, {"first_name"=>"Raman", "last_name"=>"Ratheesh", "scopus_author_id"=>"14527430200"}, {"first_name"=>"Edumakanti C.", "last_name"=>"Reddy", "scopus_author_id"=>"23036862700"}, {"first_name"=>"Young H.", "last_name"=>"Kim", "scopus_author_id"=>"37039805700"}, {"first_name"=>"Kelli", "last_name"=>"Montgomery", "scopus_author_id"=>"7102499348"}, {"first_name"=>"Craig P.", "last_name"=>"Giacomini", "scopus_author_id"=>"8978111400"}, {"first_name"=>"Yoon La", "last_name"=>"Choi", "scopus_author_id"=>"7404777529"}, {"first_name"=>"Sreejata", "last_name"=>"Chatterjee", "scopus_author_id"=>"24342690700"}, {"first_name"=>"Collins A.", "last_name"=>"Karikari", "scopus_author_id"=>"8587349800"}, {"first_name"=>"Keyan", "last_name"=>"Salari", "scopus_author_id"=>"14322379500"}, {"first_name"=>"Pei", "last_name"=>"Wang", "scopus_author_id"=>"55865567254"}, {"first_name"=>"Tina", "last_name"=>"Hernandez-Boussard", "scopus_author_id"=>"57119442800"}, {"first_name"=>"Gowrishankar", "last_name"=>"Swarnalata", "scopus_author_id"=>"14527936800"}, {"first_name"=>"Matt", "last_name"=>"Van De Rijn", "scopus_author_id"=>"7005571510"}, {"first_name"=>"Anirban", "last_name"=>"Maitra", "scopus_author_id"=>"35390791500"}, {"first_name"=>"Jonathan R.", "last_name"=>"Pollack", "scopus_author_id"=>"7101673347"}], "year"=>2008, "source"=>"PLoS Genetics", "identifiers"=>{"sgr"=>"44949129758", "doi"=>"10.1371/journal.pgen.1000081", "issn"=>"15537390", "pui"=>"351811500", "isbn"=>"1553-7404 (Electronic)", "pmid"=>"18535672", "scopus"=>"2-s2.0-44949129758"}, "id"=>"04253c00-e718-3083-8942-000690bf2749", "abstract"=>"Pancreatobiliary cancers have among the highest mortality rates of any cancer type. Discovering the full spectrum of molecular genetic alterations may suggest new avenues for therapy. To catalogue genomic alterations, we carried out array-based genomic profiling of 31 exocrine pancreatic cancers and 6 distal bile duct cancers, expanded as xenografts to enrich the tumor cell fraction. We identified numerous focal DNA amplifications and deletions, including in 19% of pancreatobiliary cases gain at cytoband 18q11.2, a locus uncommonly amplified in other tumor types. The smallest shared amplification at 18q11.2 included GATA6, a transcriptional regulator previously linked to normal pancreas development. When amplified, GATA6 was overexpressed at both the mRNA and protein levels, and strong immunostaining was observed in 25 of 54 (46%) primary pancreatic cancers compared to 0 of 33 normal pancreas specimens surveyed. GATA6 expression in xenografts was associated with specific microarray gene-expression patterns, enriched for GATA binding sites and mitochondrial oxidative phosphorylation activity. siRNA mediated knockdown of GATA6 in pancreatic cancer cell lines with amplification led to reduced cell proliferation, cell cycle progression, and colony formation. Our findings indicate that GATA6 amplification and overexpression contribute to the oncogenic phenotypes of pancreatic cancer cells, and identify GATA6 as a candidate lineage-specific oncogene in pancreatobiliary cancer, with implications for novel treatment strategies.", "link"=>"http://www.mendeley.com/research/genomic-profiling-identifies-gata6-candidate-oncogene-amplified-pancreatobiliary-cancer", "reader_count"=>38, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>7, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Master"=>4, "Other"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>7, "Researcher"=>10, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>12, "Student > Master"=>4, "Other"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>22, "Medicine and Dentistry"=>7, "Neuroscience"=>2}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>7}, "Neuroscience"=>{"Neuroscience"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}}, "reader_count_by_country"=>{"United States"=>1, "Italy"=>1, "India"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/930708"], "description"=>"<p>(A) Confirmation of siRNA-mediated knockdown of GATA6 in AsPC1 and Panc3.27 cells. Two different siRNAs (<i>GATA6</i>-1 and <i>GATA6</i>-2) were used to target GATA6, along with a non-targeting siRNA pool (control). GATA6 levels assayed by Western blot; GAPDH levels provide a loading control. (B) GATA6 knockdown results in decreased cell proliferation in reduced serum, measured by WST-1 assay, in cells with (AsPC1, Panc3.27) but not without (PL45) <i>GATA6</i> gain/overexpression. *, <i>P</i><0.05; **, <i>P</i><0.01 (Student's t-test; <i>GATA6</i> compared to control). (C) GATA6 knockdown reduces cell-cycle progression in AsPC1 cells, evidenced by decreased S-phase fraction following BrdU labeling, quantified by flow cytometry. *, <i>P</i><0.05; (Student's t-test; <i>GATA6</i> compared to control). (D) GATA6 knockdown does not significantly alter levels of apoptosis, quantified by annexin V staining. (E) GATA6 knockdown reduces colony growth of AsPC1 cells in liquid culture. Box plot illustrates 25<sup>th</sup>, mean and 75<sup>th</sup> percentile; <i>P</i> values (Student's t-test) indicated. Representative fields of Giemsa-stained colonies are shown (<i>right</i>).</p>", "links"=>[], "tags"=>["contributes"], "article_id"=>601137, "categories"=>["Medicine", "Genetics", "Cancer"], "users"=>["Kevin A. Kwei", "Murali D. Bashyam", "Jessica Kao", "Raman Ratheesh", "Edumakanti C. Reddy", "Young H. Kim", "Kelli Montgomery", "Craig P. Giacomini", "Yoon-La Choi", "Sreejata Chatterjee", "Collins A. Karikari", "Keyan Salari", "Pei Wang", "Tina Hernandez-Boussard", "Gowrishankar Swarnalata", "Matt van de Rijn", "Anirban Maitra", "Jonathan R. Pollack"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000081.g005", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GATA6_amplification_overexpression_contributes_to_cell_proliferation_/601137", "title"=>"<i>GATA6</i> amplification/overexpression contributes to cell proliferation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-23 00:18:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/930228"], "description"=>"<p>(A) Genomic profiles by CGH on cDNA microarrays of pancreatic (P) and bile duct (B) cancer xenografts across cytoband 18q11.2. Genes are ordered by genome position. Red indicates positive tumor/normal aCGH ratios (scale shown), and samples called gained at 18q11.2 are marked below by closed circle (gains highlighted in yellow). Genes and ESTs (IMAGE clone ID shown) on the microarray residing within the amplicon core are indicated. <i>CTAGE1</i> (asterisked) was not present on the array but resides where shown. (B) Genomic profile of B291 by CGH on an Agilent ultra high-definition custom microarray tiling 18q11.2, mapped onto the UCSC genome browser (<a href=\"http://genome.ucsc.edu\" target=\"_blank\">http://genome.ucsc.edu</a>) <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000081#pgen.1000081-Kent1\" target=\"_blank\">[55]</a>. The amplicon peak spans two genes, <i>GATA6</i> and <i>CTAGE1</i>. (C) Q-PCR validation of <i>GATA6</i> amplification in B291. Note, hybridization measurements by CGH tend to underestimate true CNA ratios <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000081#pgen.1000081-Pollack1\" target=\"_blank\">[8]</a>. (D) FISH validation of <i>GATA6</i> amplification in the parent tumor (paraffin section) from which xenograft B291 was derived (<i>left</i>), and <i>GATA6</i> gain in pancreatic cancer cell lines AsPC1 (<i>center</i>) and Panc3.27 (<i>right</i>). Gain is evident by the increased ratio of <i>GATA6</i>(red)/centromere-18(green) signals. DAPI (nuclear) counterstaining is shown in grayscale.</p>", "links"=>[], "tags"=>["focally", "amplified", "pancreatobiliary"], "article_id"=>600660, "categories"=>["Medicine", "Genetics", "Cancer"], "users"=>["Kevin A. Kwei", "Murali D. Bashyam", "Jessica Kao", "Raman Ratheesh", "Edumakanti C. Reddy", "Young H. Kim", "Kelli Montgomery", "Craig P. Giacomini", "Yoon-La Choi", "Sreejata Chatterjee", "Collins A. Karikari", "Keyan Salari", "Pei Wang", "Tina Hernandez-Boussard", "Gowrishankar Swarnalata", "Matt van de Rijn", "Anirban Maitra", "Jonathan R. Pollack"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000081.g001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GATA6_is_focally_amplified_in_pancreatobiliary_cancer_/600660", "title"=>"<i>GATA6</i> is focally amplified in pancreatobiliary cancer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-23 00:11:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/930459"], "description"=>"<p>Shown are representative IHC stains for GATA6 protein expression in (A) normal pancreas, and in pancreatic ductal adenocarcinoma with (B) absent, (C) moderate, and (D) strong nuclear staining. Filled arrowheads indicate pancreatic ductal epithelial cells (<i>A</i>), or pancreatic adenocarcinoma cells (<i>B</i>–<i>D</i>). Open arrowhead (<i>A</i>) shows non-specific cytoplasmic staining observed in pancreatic acinar cells. (E) Distribution of GATA6 expression among different diagnoses represented on the tissue microarray. The IHC staining score considers both staining intensity and fraction of cells with nuclear staining (see <a href=\"http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1000081#s4\" target=\"_blank\">Materials and Methods</a>). GATA6 expression is significantly elevated in pancreatic cancer compared to normal pancreas (<i>P</i><0.001, χ<sup>2</sup> test).</p>", "links"=>[], "tags"=>["overexpressed", "pancreatic"], "article_id"=>600886, "categories"=>["Medicine", "Genetics", "Cancer"], "users"=>["Kevin A. Kwei", "Murali D. Bashyam", "Jessica Kao", "Raman Ratheesh", "Edumakanti C. Reddy", "Young H. Kim", "Kelli Montgomery", "Craig P. Giacomini", "Yoon-La Choi", "Sreejata Chatterjee", "Collins A. Karikari", "Keyan Salari", "Pei Wang", "Tina Hernandez-Boussard", "Gowrishankar Swarnalata", "Matt van de Rijn", "Anirban Maitra", "Jonathan R. Pollack"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000081.g003", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GATA6_is_overexpressed_in_primary_pancreatic_tumors_/600886", "title"=>"<i>GATA6</i> is overexpressed in primary pancreatic tumors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-23 00:14:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/930352"], "description"=>"<p>(A) Plot of DNA (by array CGH) vs. mRNA (by expression profiling) ratios for genes on chromosome 18 for specimen B291 shows <i>GATA6</i> (indicated) to be the most highly expressed gene within the 18q11.2 amplicon. (B) <i>GATA6</i> mRNA levels, measured by microarray, are elevated in pancreatobiliary xenografts with compared to without DNA gain at 18q11.2 (<i>GATA6</i>). Box plots show 25<sup>th</sup>, 50<sup>th</sup> and 75<sup>th</sup> percentiles; <i>P</i>-values (Mann-Whitney U-Test) for pairwise comparisons are indicated. (C) Q-RT-PCR validation of microarray-measured GATA6 transcript levels in eight specimens, four each with and without 18q11.2 gain. (D) Western blot analysis of representative pancreatic cancer cell lines indicates <i>GATA6</i> (56 kD) is overexpressed at the protein level when amplified; GAPDH serves as a loading control. (E) IHC analysis of GATA6 protein expression (nuclear brown staining) indicates elevated expression in the parent tumor from which xenograft B291 was derived (<i>left</i>), in comparison to normal pancreatic duct from the same paraffin section (<i>right</i>).</p>", "links"=>[], "tags"=>["overexpressed"], "article_id"=>600778, "categories"=>["Medicine", "Genetics", "Cancer"], "users"=>["Kevin A. Kwei", "Murali D. Bashyam", "Jessica Kao", "Raman Ratheesh", "Edumakanti C. Reddy", "Young H. Kim", "Kelli Montgomery", "Craig P. Giacomini", "Yoon-La Choi", "Sreejata Chatterjee", "Collins A. Karikari", "Keyan Salari", "Pei Wang", "Tina Hernandez-Boussard", "Gowrishankar Swarnalata", "Matt van de Rijn", "Anirban Maitra", "Jonathan R. Pollack"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000081.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GATA6_is_overexpressed_when_amplified_/600778", "title"=>"<i>GATA6</i> is overexpressed when amplified.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-23 00:12:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/458777", "https://ndownloader.figshare.com/files/458921"], "description"=>"<div><p>Pancreatobiliary cancers have among the highest mortality rates of any cancer type. Discovering the full spectrum of molecular genetic alterations may suggest new avenues for therapy. To catalogue genomic alterations, we carried out array-based genomic profiling of 31 exocrine pancreatic cancers and 6 distal bile duct cancers, expanded as xenografts to enrich the tumor cell fraction. We identified numerous focal DNA amplifications and deletions, including in 19% of pancreatobiliary cases gain at cytoband 18q11.2, a locus uncommonly amplified in other tumor types. The smallest shared amplification at 18q11.2 included <em>GATA6</em>, a transcriptional regulator previously linked to normal pancreas development. When amplified, <em>GATA6</em> was overexpressed at both the mRNA and protein levels, and strong immunostaining was observed in 25 of 54 (46%) primary pancreatic cancers compared to 0 of 33 normal pancreas specimens surveyed. <em>GATA6</em> expression in xenografts was associated with specific microarray gene-expression patterns, enriched for GATA binding sites and mitochondrial oxidative phosphorylation activity. siRNA mediated knockdown of <em>GATA6</em> in pancreatic cancer cell lines with amplification led to reduced cell proliferation, cell cycle progression, and colony formation. Our findings indicate that <em>GATA6</em> amplification and overexpression contribute to the oncogenic phenotypes of pancreatic cancer cells, and identify <em>GATA6</em> as a candidate lineage-specific oncogene in pancreatobiliary cancer, with implications for novel treatment strategies.</p></div>", "links"=>[], "tags"=>["genomic", "profiling", "identifies", "oncogene", "amplified", "pancreatobiliary", "cancer"], "article_id"=>150379, "categories"=>["Medicine", "Genetics", "Cancer"], "users"=>["Kevin A. Kwei", "Murali D. Bashyam", "Jessica Kao", "Raman Ratheesh", "Edumakanti C. Reddy", "Young H. Kim", "Kelli Montgomery", "Craig P. Giacomini", "Yoon-La Choi", "Sreejata Chatterjee", "Collins A. Karikari", "Keyan Salari", "Pei Wang", "Tina Hernandez-Boussard", "Gowrishankar Swarnalata", "Matt van de Rijn", "Anirban Maitra", "Jonathan R. Pollack"], "doi"=>["https://dx.doi.org/10.1371/journal.pgen.1000081.s001", "https://dx.doi.org/10.1371/journal.pgen.1000081.s002"], "stats"=>{"downloads"=>2, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genomic_Profiling_Identifies_GATA6_as_a_Candidate_Oncogene_Amplified_in_Pancreatobiliary_Cancer/150379", "title"=>"Genomic Profiling Identifies <em>GATA6</em> as a Candidate Oncogene Amplified in Pancreatobiliary Cancer", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2008-05-23 00:06:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/930588"], "description"=>"<p>(A) Heatmap representation of genes identified by SAM analysis with significantly (FDR<1%) increased (73 genes) or decreased (13 genes) expression in xenografts with GATA6 mRNA levels above the mean. Specimens are ordered by GATA6 expression level; genes are ordered in descending rank of their SAM score. Expression levels are indicated by colorimetric ratio-scale (shown). (B) GSEA identifies enrichment of genes with putative GATA binding sites in xenografts with GATA6 expression levels above the mean. Enrichment is evidenced by the early positive deflection of the Kolmogorov-Smirnov running sum. The significance of the maximum running sum (<i>S</i>) was evaluated by comparison to 500 trials with randomly permuted class labels; the <i>P</i>-value is the frequency that <i>S</i> in the actual data is equaled or exceeded in the permuted data. (C) Top ranking (FDR shown) functional gene sets identified by GSEA to be enriched in xenografts with above-average GATA6 expression levels. TCA: tricarboxylic acid (Krebs) cycle.</p>", "links"=>[], "tags"=>["gastroenterology and hepatology/biliary tract", "gastroenterology and hepatology/pancreas", "genetics and genomics/cancer genetics", "genetics and genomics/gene discovery", "genetics and genomics/gene function", "genetics and genomics/genomics", "oncology/gastrointestinal cancers", "pathology/molecular pathology"], "article_id"=>601004, "categories"=>["Medicine", "Genetics", "Cancer"], "users"=>["Kevin A. Kwei", "Murali D. Bashyam", "Jessica Kao", "Raman Ratheesh", "Edumakanti C. Reddy", "Young H. Kim", "Kelli Montgomery", "Craig P. Giacomini", "Yoon-La Choi", "Sreejata Chatterjee", "Collins A. Karikari", "Keyan Salari", "Pei Wang", "Tina Hernandez-Boussard", "Gowrishankar Swarnalata", "Matt van de Rijn", "Anirban Maitra", "Jonathan R. Pollack"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000081.g004", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_GATA6_expression_signature_/601004", "title"=>"<i>GATA6</i> expression signature.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2008-05-23 00:16:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/930805"], "description"=>"a<p>Specimen(s) with high-level amplification or presumptive homozygous deletion.</p>b<p>Includes low-level respective gain/loss at the same locus.</p>c<p>Boldface indicates gene expression well-measured by microarray and elevated when amplified.</p>d<p>Underlined genes are those confirmed homozygously deleted by PCR.</p>e<p>Boundaries vary among specimens; minimum shared region indicated.</p>f<p>43% of specimens exhibited homozygous deletion by PCR.</p>", "links"=>[], "tags"=>["amplifications", "homozygous"], "article_id"=>601226, "categories"=>["Medicine", "Genetics", "Cancer"], "users"=>["Kevin A. Kwei", "Murali D. Bashyam", "Jessica Kao", "Raman Ratheesh", "Edumakanti C. Reddy", "Young H. Kim", "Kelli Montgomery", "Craig P. Giacomini", "Yoon-La Choi", "Sreejata Chatterjee", "Collins A. Karikari", "Keyan Salari", "Pei Wang", "Tina Hernandez-Boussard", "Gowrishankar Swarnalata", "Matt van de Rijn", "Anirban Maitra", "Jonathan R. Pollack"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1000081.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_High_level_amplifications_and_homozygous_deletions_/601226", "title"=>"High-level amplifications and homozygous deletions.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2008-05-23 00:20:26"}

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Relative Metric

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