Quantitative-Proteomic Comparison of Alpha and Beta Cells to Uncover Novel Targets for Lineage Reprogramming
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{"title"=>"Quantitative-proteomic comparison of alpha and beta cells to uncover novel targets for lineage reprogramming", "type"=>"journal", "authors"=>[{"first_name"=>"Amit", "last_name"=>"Choudhary", "scopus_author_id"=>"29367575000"}, {"first_name"=>"Kaihui Hu", "last_name"=>"He", "scopus_author_id"=>"54883391900"}, {"first_name"=>"Philipp", "last_name"=>"Mertins", "scopus_author_id"=>"13410570200"}, {"first_name"=>"Namrata D.", "last_name"=>"Udeshi", "scopus_author_id"=>"23029149600"}, {"first_name"=>"Vlado", "last_name"=>"Dančík", "scopus_author_id"=>"6603591172"}, {"first_name"=>"Dina", "last_name"=>"Fomina-Yadlin", "scopus_author_id"=>"36499496900"}, {"first_name"=>"Stefan", "last_name"=>"Kubicek", "scopus_author_id"=>"8068043100"}, {"first_name"=>"Paul A.", "last_name"=>"Clemons", "scopus_author_id"=>"6701589271"}, {"first_name"=>"Stuart L.", "last_name"=>"Schreiber", "scopus_author_id"=>"55089588600"}, {"first_name"=>"Steven A.", "last_name"=>"Carr", "scopus_author_id"=>"7202363695"}, {"first_name"=>"Bridget K.", "last_name"=>"Wagner", "scopus_author_id"=>"35563350300"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-84899769809", "sgr"=>"84899769809", "pui"=>"373007597", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"24759943", "doi"=>"10.1371/journal.pone.0095194"}, "id"=>"98503684-ca69-32ee-b0d1-3b680589d8f0", "abstract"=>"Type-1 diabetes (T1D) is an autoimmune disease in which insulin-secreting pancreatic beta cells are destroyed by the immune system. An emerging strategy to regenerate beta-cell mass is through transdifferentiation of pancreatic alpha cells to beta cells. We previously reported two small molecules, BRD7389 and GW8510, that induce insulin expression in a mouse alpha cell line and provide a glimpse into potential intermediate cell states in beta-cell reprogramming from alpha cells. These small-molecule studies suggested that inhibition of kinases in particular may induce the expression of several beta-cell markers in alpha cells. To identify potential lineage reprogramming protein targets, we compared the transcriptome, proteome, and phosphoproteome of alpha cells, beta cells, and compound-treated alpha cells. Our phosphoproteomic analysis indicated that two kinases, BRSK1 and CAMKK2, exhibit decreased phosphorylation in beta cells compared to alpha cells, and in compound-treated alpha cells compared to DMSO-treated alpha cells. Knock-down of these kinases in alpha cells resulted in expression of key beta-cell markers. These results provide evidence that perturbation of the kinome may be important for lineage reprogramming of alpha cells to beta cells.", "link"=>"http://www.mendeley.com/research/quantitativeproteomic-comparison-alpha-beta-cells-uncover-novel-targets-lineage-reprogramming", "reader_count"=>26, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Other"=>4, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Other"=>4, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>11, "Agricultural and Biological Sciences"=>9, "Medicine and Dentistry"=>2, "Chemistry"=>2, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>9}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>11}}, "reader_count_by_country"=>{"Luxembourg"=>1, "Mexico"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1472191"], "description"=>"<p>(A) Computational prediction and experimental validation of phenotypic differences between mouse alpha cells (αTC1) and beta cells (βTC3) using comparative gene-expression analysis. (B) Workflow for quantitative proteomic and phosphoproteomic analysis of alpha and beta cells, and alpha cells treated with BRD7389 and GW8510. (C) Outline of SILAC conditions upon which quantification was performed. These analyses generated a candidate list of kinases differentially expressed in alpha and beta cells from which target kinases were identified using knockdown, chemical genetics, and immunocytochemistry.</p>", "links"=>[], "tags"=>["Biochemistry", "proteomics", "Protein abundance", "developmental biology", "Cell differentiation", "Endocrinology", "Diabetic endocrinology", "Metabolic disorders", "Diabetes mellitus", "Type 1 diabetes", "comparative", "pancreatic", "alpha", "beta", "cells", "gene-expression", "spectrometry-based", "quantitative"], "article_id"=>1005487, "categories"=>["Biological Sciences"], "users"=>["Amit Choudhary", "Kaihui Hu He", "Philipp Mertins", "Namrata D. Udeshi", "Vlado Dancik", "Dina Fomina-Yadlin", "Stefan Kubicek", "Paul A. Clemons", "Stuart L. Schreiber", "Steven A. Carr", "Bridget K. Wagner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095194.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Experimental_design_for_comparative_analyses_of_pancreatic_alpha_and_beta_cells_using_chemical_probes_gene_expression_analysis_and_mass_spectrometry_based_quantitative_phosphoproteomics_/1005487", "title"=>"Experimental design for comparative analyses of pancreatic alpha and beta cells using chemical probes, gene-expression analysis, and mass spectrometry-based quantitative phosphoproteomics.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-23 15:02:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1472193"], "description"=>"<p>Gene sets with increased expression in (A) alpha or (B) beta cell lines were identified by performing gene-set enrichment analysis (GSEA) on gene-expression profiling data, resulting in an enrichment score profile for each gene set (green line). Individual members of each gene set (vertical black bars) are enriched in either alpha cells (blue) or beta cells (red). To validate the predicted differences in cellular respiration between alpha and beta cells, we determined (C) extracellular acidification rate (ECAR) and (D) oxygen consumption rate (OCR) of alpha cells (red), BRD7389-treated alpha cells (black), βTC3 cells (blue), and INS-1E cells (brown). Glucose (Glu), oligomycin (Oligo), 2-deoxyglucose (DOG), CCCP, and rotenone/antimycin A (Rot/Ant) were added at the indicated times. Data represent the average and standard deviation of 18 biological replicates.</p>", "links"=>[], "tags"=>["Biochemistry", "proteomics", "Protein abundance", "developmental biology", "Cell differentiation", "Endocrinology", "Diabetic endocrinology", "Metabolic disorders", "Diabetes mellitus", "Type 1 diabetes", "alpha", "beta", "lines", "reveals", "higher", "metabolic"], "article_id"=>1005489, "categories"=>["Biological Sciences"], "users"=>["Amit Choudhary", "Kaihui Hu He", "Philipp Mertins", "Namrata D. Udeshi", "Vlado Dancik", "Dina Fomina-Yadlin", "Stefan Kubicek", "Paul A. Clemons", "Stuart L. Schreiber", "Steven A. Carr", "Bridget K. Wagner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095194.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_expression_analysis_of_alpha_and_beta_cell_lines_reveals_higher_metabolic_activity_in_the_alpha_cell_line_/1005489", "title"=>"Gene-expression analysis of alpha and beta cell lines reveals higher metabolic activity in the alpha cell line.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-23 15:02:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1472194"], "description"=>"<p>mRNA expression of beta and alpha cell-specific genes was measured using qPCR after knock-down of (A) <i>Brsk1</i> or (B) <i>Camkk2</i>. Fold changes were calculated compared to untransfected control αTC1 cells, and normalized to <i>Gapdh</i> expression. Significance was determined by t-test. *<i>p</i><0.05, ***<i>p</i><0.005. (C) αTC1 cells transfected with the indicated siRNA, or treated with the indicated compounds, were analyzed for Pdx1 protein expression by immunofluorescence. The percentage of Pdx1<sup>+</sup> cells was calculated for each treatment. The significance was determined by t-test. *<i>p</i><0.05, **<i>p</i><0.01, and ***<i>p</i><0.001.</p>", "links"=>[], "tags"=>["Biochemistry", "proteomics", "Protein abundance", "developmental biology", "Cell differentiation", "Endocrinology", "Diabetic endocrinology", "Metabolic disorders", "Diabetes mellitus", "Type 1 diabetes", "elicit", "beta", "cell-specific", "genes"], "article_id"=>1005490, "categories"=>["Biological Sciences"], "users"=>["Amit Choudhary", "Kaihui Hu He", "Philipp Mertins", "Namrata D. Udeshi", "Vlado Dancik", "Dina Fomina-Yadlin", "Stefan Kubicek", "Paul A. Clemons", "Stuart L. Schreiber", "Steven A. Carr", "Bridget K. Wagner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095194.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Knock_down_of_Brsk1_and_Camkk2_elicit_the_expression_of_key_beta_cell_specific_genes_in_TC1_cells_/1005490", "title"=>"Knock-down of <i>Brsk1</i> and <i>Camkk2</i> elicit the expression of key beta cell-specific genes in αTC1 cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-23 15:02:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1472198"], "description"=>"<p>Cells were infected with lentivirus carrying expression cassettes that encode shRNAs against (A) <i>Brsk1</i>, (B) <i>Camkk2</i>, (C) <i>Stk11</i>, and were selected with puromycin for 10 days. <i>Pdx1</i> mRNA expression (white bars) was measured jointly with the expression of each of the shRNA-targeted genes (black bars). Data represent fold change (in log<sub>2</sub> scale), compared to the average of control empty vectors. Data represent mean and standard deviation of four independent experiments. The significance was determined by t-test. *<i>p</i><0.05 and **<i>p</i><0.01. (D–S) Nuclei (blue), insulin (green), and Pdx1 (red) immunofluorescence, and merged images in 10-day shRNA-expressing αTC1 cells: (D–G) control virus, (H–K) sh1_Camkk2, (L–O) sh1_Brsk1, (P–S) sh1_Stk11. Scale bar = 100 µm.</p>", "links"=>[], "tags"=>["Biochemistry", "proteomics", "Protein abundance", "developmental biology", "Cell differentiation", "Endocrinology", "Diabetic endocrinology", "Metabolic disorders", "Diabetes mellitus", "Type 1 diabetes", "lentiviral", "knockdown", "stimulates", "pdx1", "insulin"], "article_id"=>1005494, "categories"=>["Biological Sciences"], "users"=>["Amit Choudhary", "Kaihui Hu He", "Philipp Mertins", "Namrata D. Udeshi", "Vlado Dancik", "Dina Fomina-Yadlin", "Stefan Kubicek", "Paul A. Clemons", "Stuart L. Schreiber", "Steven A. Carr", "Bridget K. Wagner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095194.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Longer_term_lentiviral_knockdown_of_Brsk1_and_Camkk2_stimulates_PDX1_and_insulin_protein_expression_in_TC1_cells_/1005494", "title"=>"Longer-term lentiviral knockdown of <i>Brsk1</i> and <i>Camkk2</i> stimulates PDX1 and insulin protein expression in αTC1 cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-04-23 15:02:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1472200"], "description"=>"<p>*including 467 phosphorylated kinase peptides.</p><p>Total proteome results based on 24 SCX fractions over two SILAC experiments. pSTY peptide results are based on 12 SCX fractions over two SILAC experiments.</p>", "links"=>[], "tags"=>["Biochemistry", "proteomics", "Protein abundance", "developmental biology", "Cell differentiation", "Endocrinology", "Diabetic endocrinology", "Metabolic disorders", "Diabetes mellitus", "Type 1 diabetes", "proteomic"], "article_id"=>1005496, "categories"=>["Biological Sciences"], "users"=>["Amit Choudhary", "Kaihui Hu He", "Philipp Mertins", "Namrata D. Udeshi", "Vlado Dancik", "Dina Fomina-Yadlin", "Stefan Kubicek", "Paul A. Clemons", "Stuart L. Schreiber", "Steven A. Carr", "Bridget K. Wagner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095194.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_proteomic_studies_/1005496", "title"=>"Summary of proteomic studies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-23 15:02:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1472201"], "description"=>"<p>Proteins with different expression levels in alpha and beta cells.</p>", "links"=>[], "tags"=>["Biochemistry", "proteomics", "Protein abundance", "developmental biology", "Cell differentiation", "Endocrinology", "Diabetic endocrinology", "Metabolic disorders", "Diabetes mellitus", "Type 1 diabetes", "alpha", "beta"], "article_id"=>1005497, "categories"=>["Biological Sciences"], "users"=>["Amit Choudhary", "Kaihui Hu He", "Philipp Mertins", "Namrata D. Udeshi", "Vlado Dancik", "Dina Fomina-Yadlin", "Stefan Kubicek", "Paul A. Clemons", "Stuart L. Schreiber", "Steven A. Carr", "Bridget K. Wagner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095194.t002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteins_with_different_expression_levels_in_alpha_and_beta_cells_/1005497", "title"=>"Proteins with different expression levels in alpha and beta cells.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-04-23 15:02:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/1472220", "https://ndownloader.figshare.com/files/1472222", "https://ndownloader.figshare.com/files/1472223", "https://ndownloader.figshare.com/files/1472224"], "description"=>"<div><p>Type-1 diabetes (T1D) is an autoimmune disease in which insulin-secreting pancreatic beta cells are destroyed by the immune system. An emerging strategy to regenerate beta-cell mass is through transdifferentiation of pancreatic alpha cells to beta cells. We previously reported two small molecules, BRD7389 and GW8510, that induce insulin expression in a mouse alpha cell line and provide a glimpse into potential intermediate cell states in beta-cell reprogramming from alpha cells. These small-molecule studies suggested that inhibition of kinases in particular may induce the expression of several beta-cell markers in alpha cells. To identify potential lineage reprogramming protein targets, we compared the transcriptome, proteome, and phosphoproteome of alpha cells, beta cells, and compound-treated alpha cells. Our phosphoproteomic analysis indicated that two kinases, BRSK1 and CAMKK2, exhibit decreased phosphorylation in beta cells compared to alpha cells, and in compound-treated alpha cells compared to DMSO-treated alpha cells. Knock-down of these kinases in alpha cells resulted in expression of key beta-cell markers. These results provide evidence that perturbation of the kinome may be important for lineage reprogramming of alpha cells to beta cells.</p></div>", "links"=>[], "tags"=>["Biochemistry", "proteomics", "Protein abundance", "developmental biology", "Cell differentiation", "Endocrinology", "Diabetic endocrinology", "Metabolic disorders", "Diabetes mellitus", "Type 1 diabetes", "alpha", "beta", "cells", "targets", "lineage"], "article_id"=>1005512, "categories"=>["Biological Sciences"], "users"=>["Amit Choudhary", "Kaihui Hu He", "Philipp Mertins", "Namrata D. Udeshi", "Vlado Dancik", "Dina Fomina-Yadlin", "Stefan Kubicek", "Paul A. Clemons", "Stuart L. Schreiber", "Steven A. Carr", "Bridget K. Wagner"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0095194.s001", "https://dx.doi.org/10.1371/journal.pone.0095194.s002", "https://dx.doi.org/10.1371/journal.pone.0095194.s003", "https://dx.doi.org/10.1371/journal.pone.0095194.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Quantitative_Proteomic_Comparison_of_Alpha_and_Beta_Cells_to_Uncover_Novel_Targets_for_Lineage_Reprogramming_/1005512", "title"=>"Quantitative-Proteomic Comparison of Alpha and Beta Cells to Uncover Novel Targets for Lineage Reprogramming", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-04-23 15:02:37"}

PMC Usage Stats | Further Information

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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", "average_usage"=>[291]}, {"subject_area"=>"/Biology and life sciences/Biochemistry", "average_usage"=>[282]}, {"subject_area"=>"/Medicine and health sciences/Endocrinology", "average_usage"=>[282, 453]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[262]}]}
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