Transcriptional Profiling of Human Dendritic Cell Populations and Models - Unique Profiles of In Vitro Dendritic Cells and Implications on Functionality and Applicability
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{"title"=>"Transcriptional Profiling of Human Dendritic Cell Populations and Models - Unique Profiles of In Vitro Dendritic Cells and Implications on Functionality and Applicability", "type"=>"journal", "authors"=>[{"first_name"=>"Kristina", "last_name"=>"Lundberg", "scopus_author_id"=>"8853700500"}, {"first_name"=>"Ann Sofie", "last_name"=>"Albrekt", "scopus_author_id"=>"6507885508"}, {"first_name"=>"Inge", "last_name"=>"Nelissen", "scopus_author_id"=>"6603187504"}, {"first_name"=>"Saskia", "last_name"=>"Santegoets", "scopus_author_id"=>"8590552100"}, {"first_name"=>"Tanja D.", "last_name"=>"de Gruijl", "scopus_author_id"=>"6701507405"}, {"first_name"=>"Sue", "last_name"=>"Gibbs", "scopus_author_id"=>"7103264126"}, {"first_name"=>"Malin", "last_name"=>"Lindstedt", "scopus_author_id"=>"6603560345"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84872282547", "pmid"=>"23341914", "sgr"=>"84872282547", "isbn"=>"1932-6203 (Electronic)\\n1932-6203 (Linking)", "doi"=>"10.1371/journal.pone.0052875", "issn"=>"19326203", "pui"=>"368116060"}, "id"=>"de2c22c5-929a-384d-9eef-d130ccc6aac4", "abstract"=>"Dendritic cells (DCs) comprise heterogeneous populations of cells, which act as central orchestrators of the immune response. Applicability of primary DCs is restricted due to their scarcity and therefore DC models are commonly employed in DC-based immunotherapy strategies and in vitro tests assessing DC function. However, the interrelationship between the individual in vitro DC models and their relative resemblance to specific primary DC populations remain elusive.", "link"=>"http://www.mendeley.com/research/transcriptional-profiling-human-dendritic-cell-populations-models-unique-profiles-vitro-dendritic-ce", "reader_count"=>19, "reader_count_by_academic_status"=>{"Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Other"=>1, "Student > Master"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Researcher"=>4, "Student > Doctoral Student"=>2, "Student > Ph. D. Student"=>7, "Other"=>1, "Student > Master"=>1, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>3, "Immunology and Microbiology"=>6}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>6}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Italy"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/508155"], "description"=>"<p>Human cell types included in the transcriptional study and abbreviations used.</p>", "links"=>[], "tags"=>["types", "included", "transcriptional", "abbreviations"], "article_id"=>178643, "categories"=>["Genetics", "Immunology"], "users"=>["Kristina Lundberg", "Ann-Sofie Albrekt", "Inge Nelissen", "Saskia Santegoets", "Tanja D. de Gruijl", "Sue Gibbs", "Malin Lindstedt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052875.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Human_cell_types_included_in_the_transcriptional_study_and_abbreviations_used_/178643", "title"=>"Human cell types included in the transcriptional study and abbreviations used.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-14 02:24:03"}
  • {"files"=>["https://ndownloader.figshare.com/files/508043"], "description"=>"<p>Signatures identified by expression level >200 and differential expression in one model as compared to all other <i>in vitro</i> DC models (based on fold difference >2 and statistical significance p<0,05; student's T-test). Comparisons performed on MAS5-normalized data and expression ratio calculated on average of replicates as described in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052875#s2\" target=\"_blank\">Methods</a>. Selected immununologically associated transcripts are highlighted in red. Transcripts lacking official gene symbols are identified with respective Affymetrix Probe Set ID.</p>", "links"=>[], "tags"=>["signatures", "dc"], "article_id"=>178534, "categories"=>["Genetics", "Immunology"], "users"=>["Kristina Lundberg", "Ann-Sofie Albrekt", "Inge Nelissen", "Saskia Santegoets", "Tanja D. de Gruijl", "Sue Gibbs", "Malin Lindstedt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052875.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcriptional_signatures_of_individual_in_vitro_DC_subsets_/178534", "title"=>"Transcriptional signatures of individual <i>in vitro</i> DC subsets.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-14 02:22:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/507944"], "description"=>"<p>Clustering using complete linkage algorithm on differentially expressed transcripts (892), identified by ANOVA (p<10<sup>−6</sup>, corresponding to p<0,05 upon Bonferroni correction), demonstrates relationships among <i>in vitro</i> DC models.</p>", "links"=>[], "tags"=>["clustering"], "article_id"=>178438, "categories"=>["Genetics", "Immunology"], "users"=>["Kristina Lundberg", "Ann-Sofie Albrekt", "Inge Nelissen", "Saskia Santegoets", "Tanja D. de Gruijl", "Sue Gibbs", "Malin Lindstedt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052875.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Hierarchical_clustering_of_in_vitro_DCs_/178438", "title"=>"Hierarchical clustering of <i>in vitro</i> DCs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-14 02:20:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/507850"], "description"=>"<p>Hierarchical clustering on differentially expressed transcripts (ANOVA p<10<sup>−6</sup>, corresponding to p<0,05 upon Bonferroni correction) among <i>in vitro</i> DCs (A. 892 transcripts) and <i>ex vivo</i> DCs (B. 9,055 transcripts), using complete linkage and Euclidean measure. Colors represent high (red) and low (green) normalized intensity, respectively.</p>", "links"=>[], "tags"=>["visualizing", "profiles", "dc", "models"], "article_id"=>178345, "categories"=>["Genetics", "Immunology"], "users"=>["Kristina Lundberg", "Ann-Sofie Albrekt", "Inge Nelissen", "Saskia Santegoets", "Tanja D. de Gruijl", "Sue Gibbs", "Malin Lindstedt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052875.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Heatmaps_visualizing_gene_expression_profiles_of_in_vitro_DC_models_and_ex_vivo_DC_populations_/178345", "title"=>"Heatmaps visualizing gene expression profiles of <i>in vitro</i> DC models and <i>ex vivo</i> DC populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-14 02:19:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/507709"], "description"=>"<p>Resemblance demonstrated by principal component analysis (PCA) of expressed transcripts (A. 51,191) and differentially expressed transcripts (B, 18,590) identified by ANOVA p<10<sup>−6</sup> (corresponding to p<0,05 after Bonferroni correction). Replicate similarities visualized using <i>k</i>-Nearest Neighbors (<i>k</i>-NN) algorithm (<i>k</i> = 2 in this case) and relationships between cell types demonstrated by minimal spanning tree analysis (lines connecting the different populations). Axes (marked 1, 2 and 3) correspond to the three main components in the PCA analysis and numbers in brackets correspond to percentage of total variation contained within each component. C) Heatmap visualizing gene expression profiles of differentially expressed genes (18,590) upon hierarchical clustering with complete linkage and Euclidean measure. Colors represent high (red) and low (green) normalized intensity.</p>", "links"=>[], "tags"=>["dc", "models", "tonsillar", "peripheral"], "article_id"=>178198, "categories"=>["Genetics", "Immunology"], "users"=>["Kristina Lundberg", "Ann-Sofie Albrekt", "Inge Nelissen", "Saskia Santegoets", "Tanja D. de Gruijl", "Sue Gibbs", "Malin Lindstedt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052875.g001", "stats"=>{"downloads"=>2, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Resemblance_of_in_vitro_DC_models_with_skin_tonsillar_and_peripheral_blood_DC_populations_/178198", "title"=>"Resemblance of <i>in vitro</i> DC models with skin, tonsillar and peripheral blood DC populations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-01-14 02:16:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/276906", "https://ndownloader.figshare.com/files/276940", "https://ndownloader.figshare.com/files/276974"], "description"=>"<div><h3>Background</h3><p>Dendritic cells (DCs) comprise heterogeneous populations of cells, which act as central orchestrators of the immune response. Applicability of primary DCs is restricted due to their scarcity and therefore DC models are commonly employed in DC-based immunotherapy strategies and <em>in vitro</em> tests assessing DC function. However, the interrelationship between the individual <em>in vitro</em> DC models and their relative resemblance to specific primary DC populations remain elusive.</p> <h3>Objective</h3><p>To describe and assess functionality and applicability of the available <em>in vitro</em> DC models by using a genome-wide transcriptional approach.</p> <h3>Methods</h3><p>Transcriptional profiling was performed with four commonly used <em>in vitro</em> DC models (MUTZ-3-DCs, monocyte-derived DCs, CD34-derived DCs and Langerhans cells (LCs)) and nine primary DC populations (dermal DCs, LCs, blood and tonsillar CD123<sup>+</sup>, CD1c<sup>+</sup> and CD141<sup>+</sup> DCs, and blood CD16<sup>+</sup> DCs).</p> <h3>Results</h3><p>Principal Component Analysis showed that transcriptional profiles of each <em>in vitro</em> DC model most closely resembled CD1c<sup>+</sup> and CD141<sup>+</sup> tonsillar myeloid DCs (mDCs) among primary DC populations. Thus, additional differentiation factors may be required to generate model DCs that more closely resemble other primary DC populations. Also, no model DC stood out in terms of primary DC resemblance. Nevertheless, hierarchical clustering showed clusters of differentially expressed genes among individual DC models as well as primary DC populations. Furthermore, model DCs were shown to differentially express immunologically relevant transcripts and transcriptional signatures identified for each model DC included several immune-associated transcripts.</p> <h3>Conclusion</h3><p>The unique transcriptional profiles of <em>in vitro</em> DC models suggest distinct functionality in immune applications. The presented results will aid in the selection of an appropriate DC model for <em>in vitro</em> assays and assist development of DC-based immunotherapy.</p> </div>", "links"=>[], "tags"=>["transcriptional", "profiling", "dendritic", "populations", "models", "profiles", "vitro", "cells", "implications", "functionality", "applicability"], "article_id"=>114579, "categories"=>["Genetics", "Immunology"], "users"=>["Kristina Lundberg", "Ann-Sofie Albrekt", "Inge Nelissen", "Saskia Santegoets", "Tanja D. de Gruijl", "Sue Gibbs", "Malin Lindstedt"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0052875.s001", "https://dx.doi.org/10.1371/journal.pone.0052875.s002", "https://dx.doi.org/10.1371/journal.pone.0052875.s003"], "stats"=>{"downloads"=>2, "page_views"=>38, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Transcriptional_Profiling_of_Human_Dendritic_Cell_Populations_and_Models_Unique_Profiles_of_In_Vitro_Dendritic_Cells_and_Implications_on_Functionality_and_Applicability__/114579", "title"=>"Transcriptional Profiling of Human Dendritic Cell Populations and Models - Unique Profiles of In Vitro Dendritic Cells and Implications on Functionality and Applicability", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-01-14 01:16:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/508192"], "description"=>"<p>Expression levels of 155 transcripts encoding TLRs, CD antigens, lectins, TNF molecules, chemokines, interleukins and receptors, selected based on positive expression in any of the <i>in vitro</i> DC models.</p><p>\n <i>Signal intensity levels: −: <200; + : 200–500; ++: 500–1000; +++: >1000.</i></p><p>MoDC – monocyte-derived dendritic cell; DDC - Dermal DC; LC - Langerhans Cell; pDC – plasmacytoid dendritic cell; CD34-DC – <i>In vitro</i> derived dendritic cell (from CD34<sup>+</sup> precursor); CD34-LC - <i>In vitro</i> derived Langerhans Cell (from CD34<sup>+</sup> precursor).</p>", "links"=>[], "tags"=>["levels", "immunologically", "transcripts", "dcs"], "article_id"=>178685, "categories"=>["Genetics", "Immunology"], "users"=>["Kristina Lundberg", "Ann-Sofie Albrekt", "Inge Nelissen", "Saskia Santegoets", "Tanja D. de Gruijl", "Sue Gibbs", "Malin Lindstedt"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052875.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Expression_levels_of_immunologically_important_transcripts_in_model_DCs_and_primary_DCs_/178685", "title"=>"Expression levels of immunologically important transcripts in model DCs and primary DCs.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-01-14 02:24:45"}

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Relative Metric

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