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{"title"=>"Effects of different tissue microenvironments on gene expression in breast cancer cells", "type"=>"journal", "authors"=>[{"first_name"=>"Gaelle", "last_name"=>"Rondeau", "scopus_author_id"=>"56961938300"}, {"first_name"=>"Parisa", "last_name"=>"Abedinpour", "scopus_author_id"=>"6506546445"}, {"first_name"=>"Prerak", "last_name"=>"Desai", "scopus_author_id"=>"55203232500"}, {"first_name"=>"Veronique T.", "last_name"=>"Baron", "scopus_author_id"=>"7006827019"}, {"first_name"=>"Per", "last_name"=>"Borgstrom", "scopus_author_id"=>"7003669419"}, {"first_name"=>"John", "last_name"=>"Welsh", "scopus_author_id"=>"7202711374"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84903897691", "doi"=>"10.1371/journal.pone.0101160", "pmid"=>"25004123", "issn"=>"19326203", "scopus"=>"2-s2.0-84903897691", "pui"=>"373472028"}, "id"=>"5102a331-2003-38e3-a417-7ba7909d905f", "abstract"=>"In metastasis, circulating tumor cells penetrate the walls of blood vessels and enter the metastatic target tissue, thereby becoming exposed to novel and relatively unsupportive microenvironments. In the new microenvironments, the tumor cells often remain in a dormant state indefinitely and must adapt before they are able to successfully colonize the tissue. Very little is known about this adaptive process. We studied temporal changes in gene expression when breast cancer cells adapt to survive and grow on brain, bone marrow, and lung tissue maintained in an in vivo culture system, as models of the metastatic colonization of these tissues. We observed the transient activation of genes typically associated with homeostasis and stress during the initial stages of adaptation, followed by the activation of genes that mediate more advanced functions, such as elaboration of cell morphology and cell division, as the cells adapted to thrive in the host tissue microenvironment. We also observed the temporary induction of genes characteristic of the host tissue, which was particularly evident when tumor cells were grown on brain tissue. These early transient gene expression events suggest potential points of therapeutic intervention that are not evident in data from well-established tumors.", "link"=>"http://www.mendeley.com/research/effects-different-tissue-microenvironments-gene-expression-breast-cancer-cells-2", "reader_count"=>25, "reader_count_by_academic_status"=>{"Student > Doctoral Student"=>2, "Researcher"=>8, "Student > Ph. D. Student"=>9, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_user_role"=>{"Student > Doctoral Student"=>2, "Researcher"=>8, "Student > Ph. D. Student"=>9, "Student > Master"=>3, "Student > Bachelor"=>2, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>13, "Medicine and Dentistry"=>4, "Chemical Engineering"=>1, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Hungary"=>1, "United States"=>1, "France"=>1}, "group_count"=>0}

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• http://doi.org/10.1371/journal.pone.0128796
• http://doi.org/10.18632/oncotarget.7056
• http://doi.org/10.1038/nprot.2016.050
• http://doi.org/10.1038/bcj.2015.17
• http://doi.org/10.1177/0271678X17732025
• http://doi.org/10.1007/s13277-015-3088-9
• http://doi.org/10.1158/1535-7163.MCT-14-0474
• http://doi.org/10.1016/j.actbio.2019.11.033
• http://doi.org/10.18632/oncotarget.4194

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• 4394032
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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/1584976"], "description"=>"<p>Several functions important in tumor development are prominently represented in genes grouped by their expression behavior over time. The group designation (KMG) references the groups in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101160#pone-0101160-g002\" target=\"_blank\">Fig. 2</a>, such that the relative timing of the induction or repression of these functions can be seen.</p>", "links"=>[], "tags"=>["Computational biology", "Gene regulatory networks", "genetics", "Genetics of disease", "Genetic disorders", "Cancer genetics", "gene expression", "Gene function", "Molecular genetics", "molecular biology", "neurology", "Neurological tumors", "Brain metastasis", "oncology", "Basic cancer research", "metastasis", "Cancers and neoplasms", "illustrating", "sequential", "adaptation", "n202", "cells"], "article_id"=>1097255, "categories"=>["Biological Sciences"], "users"=>["Gaëlle Rondeau", "Parisa Abedinpour", "Prerak Desai", "Veronique T. Baron", "Per Borgstrom", "John Welsh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101160.t001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Significant_GO_Biological_Process_Terms_Illustrating_Sequential_Adaptation_of_N202_Cells_to_Brain_Tissue_/1097255", "title"=>"Significant GO Biological Process Terms Illustrating Sequential Adaptation of N202 Cells to Brain Tissue.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-08 03:15:28"}
• {"files"=>["https://ndownloader.figshare.com/files/1584977"], "description"=>"<p>*Neurobiological GO processes were defined as those GO Biological Process Terms containing one of the following strings: ‘axon’, ‘neuro’, ‘neural’, ‘brain’, ‘neocortex’, ‘nerv’, ‘glial’, ‘hippocampal’, ‘hippocampus’, ‘cerebellar’, ‘cerebral’, ‘dopa’, ‘synaptic’, ‘sensory’, ‘astrocyte’, ‘olfactory’, and ‘memory’. The genes listed comprise the union of sets of genes associated with significant (i.e. qval≤0.05) neurobiological GO processes assuming 9, 16, 25, and 36 k-means groups. The column labeled UP lists those genes that were up-regulated with P1/P0 expression ratio≥1.5-fold. The column labeled DN lists those genes that were down-regulated with P1/P0 expression ratio≤1.5-fold. UP.cnt and DN.cnt contain the number of genes in UP and DN, respectively.</p>", "links"=>[], "tags"=>["Computational biology", "Gene regulatory networks", "genetics", "Genetics of disease", "Genetic disorders", "Cancer genetics", "gene expression", "Gene function", "Molecular genetics", "molecular biology", "neurology", "Neurological tumors", "Brain metastasis", "oncology", "Basic cancer research", "metastasis", "Cancers and neoplasms", "neurobiological"], "article_id"=>1097256, "categories"=>["Biological Sciences"], "users"=>["Gaëlle Rondeau", "Parisa Abedinpour", "Prerak Desai", "Veronique T. Baron", "Per Borgstrom", "John Welsh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101160.t003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genes_associated_with_neurobiological_GO_processes_in_the_first_passage_P1_/1097256", "title"=>"Genes associated with neurobiological GO processes^* in the first passage (P1).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-08 03:15:28"}
• {"files"=>["https://ndownloader.figshare.com/files/1584975"], "description"=>"<p>Genes were grouped according to expression profiles over time using k-means and assuming 25 groups (i.e. N = 25). The central black line in each frame represents no change, i.e. 1-fold changes, and the gray lines represent 4-fold increases or decreases, relative to the parental cell line. Horizontally, the five positions along the x-axis represent sequential <i>in vivo</i> passages, P0 (i.e. parental cells), P1, P2, P3, P4, and gene expression analysis was performed on cells expanded <i>in vitro</i> from each of these passages. We then explored how GO Biological Process Terms distributed among these 25 groups.</p>", "links"=>[], "tags"=>["Computational biology", "Gene regulatory networks", "genetics", "Genetics of disease", "Genetic disorders", "Cancer genetics", "gene expression", "Gene function", "Molecular genetics", "molecular biology", "neurology", "Neurological tumors", "Brain metastasis", "oncology", "Basic cancer research", "metastasis", "Cancers and neoplasms", "grouping", "adaptation", "n202", "cells"], "article_id"=>1097254, "categories"=>["Biological Sciences"], "users"=>["Gaëlle Rondeau", "Parisa Abedinpour", "Prerak Desai", "Veronique T. Baron", "Per Borgstrom", "John Welsh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101160.g002", "stats"=>{"downloads"=>0, "page_views"=>31, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_K_means_grouping_of_gene_expression_fold_changes_during_adaptation_of_N202_cells_to_brain_tissue_/1097254", "title"=>"K-means grouping of gene expression fold changes during adaptation of N202 cells to brain tissue.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-08 03:15:28"}
• {"files"=>["https://ndownloader.figshare.com/files/1585062", "https://ndownloader.figshare.com/files/1585063", "https://ndownloader.figshare.com/files/1585064", "https://ndownloader.figshare.com/files/1585065", "https://ndownloader.figshare.com/files/1585066", "https://ndownloader.figshare.com/files/1585067", "https://ndownloader.figshare.com/files/1585068", "https://ndownloader.figshare.com/files/1585069", "https://ndownloader.figshare.com/files/1585070", "https://ndownloader.figshare.com/files/1585071", "https://ndownloader.figshare.com/files/1585072", "https://ndownloader.figshare.com/files/1585073", "https://ndownloader.figshare.com/files/1585074"], "description"=>"<div><p>In metastasis, circulating tumor cells penetrate the walls of blood vessels and enter the metastatic target tissue, thereby becoming exposed to novel and relatively unsupportive microenvironments. In the new microenvironments, the tumor cells often remain in a dormant state indefinitely and must adapt before they are able to successfully colonize the tissue. Very little is known about this adaptive process. We studied temporal changes in gene expression when breast cancer cells adapt to survive and grow on brain, bone marrow, and lung tissue maintained in an <i>in vivo</i> culture system, as models of the metastatic colonization of these tissues. We observed the transient activation of genes typically associated with homeostasis and stress during the initial stages of adaptation, followed by the activation of genes that mediate more advanced functions, such as elaboration of cell morphology and cell division, as the cells adapted to thrive in the host tissue microenvironment. We also observed the temporary induction of genes characteristic of the host tissue, which was particularly evident when tumor cells were grown on brain tissue. These early transient gene expression events suggest potential points of therapeutic intervention that are not evident in data from well-established tumors.</p></div>", "links"=>[], "tags"=>["Computational biology", "Gene regulatory networks", "genetics", "Genetics of disease", "Genetic disorders", "Cancer genetics", "gene expression", "Gene function", "Molecular genetics", "molecular biology", "neurology", "Neurological tumors", "Brain metastasis", "oncology", "Basic cancer research", "metastasis", "Cancers and neoplasms", "microenvironments", "cancer"], "article_id"=>1097326, "categories"=>["Biological Sciences"], "users"=>["Gaëlle Rondeau", "Parisa Abedinpour", "Prerak Desai", "Veronique T. Baron", "Per Borgstrom", "John Welsh"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0101160.s001", "https://dx.doi.org/10.1371/journal.pone.0101160.s002", "https://dx.doi.org/10.1371/journal.pone.0101160.s003", "https://dx.doi.org/10.1371/journal.pone.0101160.s004", "https://dx.doi.org/10.1371/journal.pone.0101160.s005", "https://dx.doi.org/10.1371/journal.pone.0101160.s006", "https://dx.doi.org/10.1371/journal.pone.0101160.s007", "https://dx.doi.org/10.1371/journal.pone.0101160.s008", "https://dx.doi.org/10.1371/journal.pone.0101160.s009", "https://dx.doi.org/10.1371/journal.pone.0101160.s010", "https://dx.doi.org/10.1371/journal.pone.0101160.s011", "https://dx.doi.org/10.1371/journal.pone.0101160.s012", "https://dx.doi.org/10.1371/journal.pone.0101160.s013"], "stats"=>{"downloads"=>18, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Effects_of_Different_Tissue_Microenvironments_on_Gene_Expression_in_Breast_Cancer_Cells_/1097326", "title"=>"Effects of Different Tissue Microenvironments on Gene Expression in Breast Cancer Cells", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-07-08 03:15:28"}
• {"files"=>["https://ndownloader.figshare.com/files/1584980"], "description"=>"<p>qval≤0.05, N = 25, P1 Ratio≥1.5-fold.</p><p>Genes typically associated with neurobiological functions tend to be induced more frequently than expected in groups defined by early increases in gene expression (qval≤0.05, N = 25, P1 Ratio≥1.5-fold). Genes with neurobiological functions were defined as those having GO Biological Process Terms containing partial matches with “axon”, “neuro”, “neural”, “brain”, “neocortex”, “nerve”, “glial”, “hippocampal”, “hippocampus”, “cerebellar”, “cerebral”, “dopa”, “synaptic”, “sensory”, “astrocyte”, “olfactory”, and “memory”.</p>", "links"=>[], "tags"=>["Computational biology", "Gene regulatory networks", "genetics", "Genetics of disease", "Genetic disorders", "Cancer genetics", "gene expression", "Gene function", "Molecular genetics", "molecular biology", "neurology", "Neurological tumors", "Brain metastasis", "oncology", "Basic cancer research", "metastasis", "Cancers and neoplasms", "neurobiological", "functions", "n202", "cells", "grafted"], "article_id"=>1097259, "categories"=>["Biological Sciences"], "users"=>["Gaëlle Rondeau", "Parisa Abedinpour", "Prerak Desai", "Veronique T. Baron", "Per Borgstrom", "John Welsh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101160.t002", "stats"=>{"downloads"=>8, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Induction_of_neurobiological_functions_in_N202_cells_grafted_onto_brain_tissue_/1097259", "title"=>"Induction of neurobiological functions in N202 cells grafted onto brain tissue.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-07-08 03:15:28"}
• {"files"=>["https://ndownloader.figshare.com/files/1584958"], "description"=>"<p>Tissue (brain, bone marrow, or lung) is taken from a donor mouse, minced with a razor, and placed in a dorsal skinfold chamber. After ∼7 days, when the tissue has developed vasculature, tumor spheroids prepared initially from the parental (N202) cell line were grafted on top of the vasculaturized tissue bed. After 21 days, the tumor and tissue were placed in cell culture, allowing tumor cells and cells from the tissue to grow. These were selected using G418 and placed back in tissue culture to increase their numbers. These cells were converted into spheroids and reintroduced onto vascularized tissue in a new dorsal skinfold chamber or sorted on the basis fo GFP fluorescence and analyzed for differential gene expression. This was repeated for up to 4 cycles (P0-P4). Genes were grouped by k-means according to differential gene expression in P1-P4 relative to the parental cell line (P0). These k-means groups were then examined for enrichment of Gene Ontology Biological Process Terms.</p>", "links"=>[], "tags"=>["Computational biology", "Gene regulatory networks", "genetics", "Genetics of disease", "Genetic disorders", "Cancer genetics", "gene expression", "Gene function", "Molecular genetics", "molecular biology", "neurology", "Neurological tumors", "Brain metastasis", "oncology", "Basic cancer research", "metastasis", "Cancers and neoplasms"], "article_id"=>1097240, "categories"=>["Biological Sciences"], "users"=>["Gaëlle Rondeau", "Parisa Abedinpour", "Prerak Desai", "Veronique T. Baron", "Per Borgstrom", "John Welsh"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0101160.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Outline_of_the_experiment_/1097240", "title"=>"Outline of the experiment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-07-08 03:15:28"}

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Relative Metric

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F1000Prime