The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines
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{"title"=>"The human pancreatic islet transcriptome: Expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines", "type"=>"journal", "authors"=>[{"first_name"=>"Décio L.", "last_name"=>"Eizirik", "scopus_author_id"=>"7101723318"}, {"first_name"=>"Michael", "last_name"=>"Sammeth", "scopus_author_id"=>"57193078807"}, {"first_name"=>"Thomas", "last_name"=>"Bouckenooghe", "scopus_author_id"=>"6506746479"}, {"first_name"=>"Guy", "last_name"=>"Bottu", "scopus_author_id"=>"15076821800"}, {"first_name"=>"Giorgia", "last_name"=>"Sisino", "scopus_author_id"=>"6504347866"}, {"first_name"=>"Mariana", "last_name"=>"Igoillo-Esteve", "scopus_author_id"=>"14123213200"}, {"first_name"=>"Fernanda", "last_name"=>"Ortis", "scopus_author_id"=>"7801418543"}, {"first_name"=>"Izortze", "last_name"=>"Santin", "scopus_author_id"=>"16680284800"}, {"first_name"=>"Maikel L.", "last_name"=>"Colli", "scopus_author_id"=>"26642292800"}, {"first_name"=>"Jenny", "last_name"=>"Barthson", "scopus_author_id"=>"46661713100"}, {"first_name"=>"Luc", "last_name"=>"Bouwens", "scopus_author_id"=>"7004422829"}, {"first_name"=>"Linda", "last_name"=>"Hughes", "scopus_author_id"=>"19334770400"}, {"first_name"=>"Lorna", "last_name"=>"Gregory", "scopus_author_id"=>"36016517800"}, {"first_name"=>"Gerton", "last_name"=>"Lunter", "scopus_author_id"=>"8882130500"}, {"first_name"=>"Lorella", "last_name"=>"Marselli", "scopus_author_id"=>"55922091300"}, {"first_name"=>"Piero", "last_name"=>"Marchetti", "scopus_author_id"=>"7103204997"}, {"first_name"=>"Mark I.", "last_name"=>"McCarthy", "scopus_author_id"=>"7402061249"}, {"first_name"=>"Miriam", "last_name"=>"Cnop", "scopus_author_id"=>"6602565343"}], "year"=>2012, "source"=>"PLoS Genetics", "identifiers"=>{"pui"=>"364556478", "doi"=>"10.1371/journal.pgen.1002552", "pmid"=>"22412385", "issn"=>"15537390", "sgr"=>"84859254586", "scopus"=>"2-s2.0-84859254586", "isbn"=>"1553-7404 (Electronic)\\r1553-7390 (Linking)"}, "id"=>"ec6876f2-aa63-3c79-8473-1c672793352d", "abstract"=>"Type 1 diabetes (T1D) is an autoimmune disease in which pancreatic beta cells are killed by infiltrating immune cells and by cytokines released by these cells. Signaling events occurring in the pancreatic beta cells are decisive for their survival or death in diabetes. We have used RNA sequencing (RNA-seq) to identify transcripts, including splice variants, expressed in human islets of Langerhans under control conditions or following exposure to the pro-inflammatory cytokines interleukin-1β (IL-1β) and interferon-γ (IFN-γ). Based on this unique dataset, we examined whether putative candidate genes for T1D, previously identified by GWAS, are expressed in human islets. A total of 29,776 transcripts were identified as expressed in human islets. Expression of around 20% of these transcripts was modified by pro-inflammatory cytokines, including apoptosis- and inflammation-related genes. Chemokines were among the transcripts most modified by cytokines, a finding confirmed at the protein level by ELISA. 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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/670428"], "description"=>"<p>Human islets from 5 organ donors were cultured for 48 h in the presence (CYT) or absence (CTL) of cytokines. Chemokines and cytokines secreted to the culture medium were measured by ELISA. Data were normalized to the geometric mean of <i>β-actin</i> and <i>GAPDH</i> expression and expressed as arbitrary units (AU). *p<0.05, **p<0.01 for CYT vs CTL by Mann Whitney test.</p>", "links"=>[], "tags"=>["induce", "chemokine", "cytokine"], "article_id"=>340890, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_IL_1_946_IFN_947_induce_chemokine_and_cytokine_protein_expression_in_human_islets_/340890", "title"=>"IL-1β+IFN-γ induce chemokine and cytokine protein expression in human islets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-08 00:14:50"}
  • {"files"=>["https://ndownloader.figshare.com/files/670804"], "description"=>"<p>IPA of genes with AS modified by IL-1β+IFN-γ. 425 transcripts were significantly up-regulated in at least 4 out of 5 islet samples and significantly downregulated in none, and 433 transcripts were significantly downregulated using similar criteria. These transcripts could be mapped by RefSeq ID to 546 genes. IPA of these genes for (A) “Molecular and Cellular Function” and (B) “Canonical Pathways”. The length of the blue bars indicates the significance of the association between the set of transcripts and the keyword, and is expressed as minus the logarithm of the probability that a random set of transcripts from the human genome would be associated with the same keyword. The straight red line indicates a threshold of 0.05 (corresponding to a −log(B–H p-value) of 1.3). The curved red line indicates for each pathway the ratio between the number of transcripts observed in the data set and the total number of transcripts in the pathway (as annotated in IPA).</p>", "links"=>[], "tags"=>["changes", "splicing", "induced"], "article_id"=>341268, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.g007", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_IPA_of_changes_in_alternative_splicing_induced_by_cytokines_/341268", "title"=>"IPA of changes in alternative splicing induced by cytokines.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-08 00:21:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/670663"], "description"=>"<p>(A) <i>Nova1</i> mRNA expression was examined by qRT-PCR in 7 human islet preparations and human brain, liver, spleen, colon and lung tissue. Data were normalized to expression levels of the housekeeping gene <i>β-actin</i>. (B, C) Nova1 expression (green) was evaluated by immunofluorescence in human pancreatic sections stained for insulin (B) or glucagon (C, either hormone labeled red). The picture is representative of 3 independent experiments. (D–G) Splicing by Nova1 was examined in INS-1E cells transfected with control (siC) or Nova1 siRNA (siNova1). Efficient Nova1 knockdown was shown by qRT-PCR (D) and Western blot (E) (n = 3). (F) To evaluate the splicing function of Nova1, RT-PCR was performed in siC and siNova1 transfected INS-1E cells, using primers flanking exon 9 of <i>Gabrg2</i>. (G) Nova1 knockdown, expected to lead to less exon 9 inclusion, increased the abundance of the short Gabrg2 transcript variant. The picture is representative of 3 independent experiments. *p<0.05, **p<0.01.</p>", "links"=>[], "tags"=>["pancreatic"], "article_id"=>341135, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.g006", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Nova1_expression_and_function_in_human_pancreatic_islets_/341135", "title"=>"Nova1 expression and function in human pancreatic islets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-08 00:18:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/670309"], "description"=>"<p>(A, B) 1,416 genes were significantly up-regulated by the cytokines IL-1β+IFN-γ in at least 4 out of 5 islet samples, and significantly downregulated in none. These genes were mapped to 1,398 unique entries in the IPA database, which were submitted to gene set enrichment analysis based on Benjamini-Hochberg corrected Fisher tests. IPA of these cytokine-up-regulated genes is shown for (A) “Molecular and Cellular Function” and (B) “Canonical Pathways”. (C, D) 1,652 genes were significantly downregulated by cytokines in at least 4 out of 5 islet samples, and significantly up-regulated in none. They were mapped to 1613 unique entries in the IPA database. IPA of these cytokine-downregulated genes is shown for (C) “Molecular and Cellular Function” and (D) “Canonical Pathways”. The length of the blue bars indicates the significance of the association between the set of genes and the keyword, and is expressed as minus the logarithm of the probability that a random set of genes from the human genome would be associated with the same keyword. The straight red line indicates a threshold of 0.05 (corresponding to a −log(B–H p-value) of 1.3). The curved red line indicates for each pathway the ratio between the number of genes observed in the data set and the total number of genes in the pathway (as annotated in IPA).</p>", "links"=>[], "tags"=>["cytokine-modified"], "article_id"=>340778, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.g003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_IPA_of_cytokine_modified_genes_/340778", "title"=>"IPA of cytokine-modified genes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-08 00:12:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/670557"], "description"=>"<p>(A, B) RNA-seq data were validated for <i>BCL2A1</i> and <i>BMF</i> by qRT-PCR in 5 independent human islet preparations exposed or not (CTL) to the cytokines IL-1β+IFN-γ (CYT). Data were normalized to expression levels of the housekeeping gene <i>β-actin</i>. (C) INS-1E cells were left untreated or treated with IL-1β+IFN-γ for different times. <i>BCL2A1</i> expression was assayed by qRT-PCR and normalized for <i>β-actin</i> expression. The results are means ± SEM of 4 independent experiments. (D, E) INS-1E cells were transfected with control siRNA (siC, black bars) or either a single or a combination of 4 siRNAs (smart pool, sp) targeting <i>BCL2A1</i> (siBCL2A1, grey bars). After 48 h, cells were exposed to IL-1β+IFN-γ (CYT) for 16 h. (D) <i>BCL2A1</i> expression was measured by qRT-PCR and normalized for <i>β-actin</i> expression. Results are mean ± SEM of 4 independent experiments. (E) Apoptosis was examined by fluorescence microscopy after staining with the DNA-binding dyes propidium iodide and Hoechst 33342. Results are mean ± SEM of 4 independent experiments. *p<0.05, **p<0.01 versus untreated control (CTL); p<0.05 for the comparison siC versus siBCL2A1 as indicated.</p>", "links"=>[], "tags"=>["modifies", "bcl2a1", "bmf"], "article_id"=>341016, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.g005", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_IL_1_946_IFN_947_modifies_BCL2A1_and_BMF_expression_/341016", "title"=>"IL-1β+IFN-γ modifies BCL2A1 and BMF expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-08 00:16:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/670187"], "description"=>"<p>(A) T1D candidate genes ranked by the odds ratio for their risk allele (<a href=\"http://t1dbase.org\" target=\"_blank\">http://t1dbase.org</a>). Based on our present data, 25 candidate genes out of 41 (61%) were expressed in human beta cells (marked with *). (B) INS-1E cells were left untreated or treated with IL-1β+IFN-γ for the indicated times. The expression of the T1D candidate gene <i>SH2B3</i> was assayed by qRT-PCR and normalized to the housekeeping gene <i>GAPDH</i>. The results are means ± SEM of 3–6 independent experiments. *p<0.05 versus untreated cells.</p>", "links"=>[], "tags"=>["thirds", "genes", "t1d", "pancreatic", "beta"], "article_id"=>340645, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_thirds_of_candidate_genes_for_T1D_are_expressed_in_pancreatic_beta_cells_/340645", "title"=>"Two thirds of candidate genes for T1D are expressed in pancreatic beta cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-08 00:10:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/670927"], "description"=>"<p>ID: Donor identification number; F: Female; M: Male; BMI: Body mass index; CVD: Cardiovascular disease; CH: Cerebral hemorrhage. Purity indicates the percentage of beta cells in the human islet preparations as determined by staining for insulin.</p>", "links"=>[], "tags"=>["donors", "islet", "preparations", "rna-seq"], "article_id"=>341391, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.t001", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Characteristics_of_the_organ_donors_and_human_islet_preparations_used_for_RNA_seq_and_independent_confirmation_/341391", "title"=>"Characteristics of the organ donors and human islet preparations used for RNA-seq and independent confirmation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-08 00:23:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/670076"], "description"=>"<p>Gene expression levels were compared among the 5 islet preparations (cultured under control condition) and between islets and 5 selected background tissues from the Illumina Human Body Map. Only genes with an RPKM>1 in all samples were considered for analysis. For each pair of samples a Pearson correlation coefficient (PCC) was computed from the power-law normalized expression levels (i.e. the RPKM values). (A) Boxplot for each islet sample (called ID1 to ID5) with the PCC values between the individual islet sample and 4 other islet preparations. (B) Heatmap with clustering dendrograms inferred by employing (1 – PCC) as distance function and complete linkage as clustering function, showing a tight cluster of islet preparations.</p>", "links"=>[], "tags"=>["rna-seq"], "article_id"=>340543, "categories"=>["Chemistry", "Genetics"], "users"=>["Decio L. Eizirik", "Michael Sammeth", "Thomas Bouckenooghe", "Guy Bottu", "Giorgia Sisino", "Mariana Igoillo-Esteve", "Fernanda Ortis", "Izortze Santin", "Maikel L. Colli", "Jenny Barthson", "Luc Bouwens", "Linda Hughes", "Lorna Gregory", "Gerton Lunter", "Lorella Marselli", "Piero Marchetti", "Mark I. McCarthy", "Miriam Cnop"], "doi"=>"https://dx.doi.org/10.1371/journal.pgen.1002552.g001", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_between_RNA_seq_gene_expression_levels_/340543", "title"=>"Correlation between RNA-seq gene expression levels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-08 00:09:03"}

PMC Usage Stats | Further Information

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