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{"title"=>"A Natural-Like Synthetic Small Molecule Impairs Bcr-Abl Signaling Cascades and Induces Megakaryocyte Differentiation in Erythroleukemia Cells", "type"=>"journal", "authors"=>[{"first_name"=>"Silvia", "last_name"=>"Turroni", "scopus_author_id"=>"16319673700"}, {"first_name"=>"Manlio", "last_name"=>"Tolomeo", "scopus_author_id"=>"7003836000"}, {"first_name"=>"Gianfranco", "last_name"=>"Mamone", "scopus_author_id"=>"6603196776"}, {"first_name"=>"Gianluca", "last_name"=>"Picariello", "scopus_author_id"=>"6603657999"}, {"first_name"=>"Elisa", "last_name"=>"Giacomini", "scopus_author_id"=>"55769747778"}, {"first_name"=>"Patrizia", "last_name"=>"Brigidi", "scopus_author_id"=>"7003712308"}, {"first_name"=>"Marinella", "last_name"=>"Roberti", "scopus_author_id"=>"7006859305"}, {"first_name"=>"Stefania", "last_name"=>"Grimaudo", "scopus_author_id"=>"6701585979"}, {"first_name"=>"Rosaria Maria", "last_name"=>"Pipitone", "scopus_author_id"=>"23983473600"}, {"first_name"=>"Antonietta", "last_name"=>"Di Cristina", "scopus_author_id"=>"6506091787"}, {"first_name"=>"Maurizio", "last_name"=>"Recanatini", "scopus_author_id"=>"7003506371"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"368445652", "doi"=>"10.1371/journal.pone.0057650", "sgr"=>"84874550086", "scopus"=>"2-s2.0-84874550086", "pmid"=>"23460890"}, "id"=>"e0438bda-4d53-3aa6-8a18-f6359a1f9a22", "abstract"=>"Over the past years, we synthesized a series of new molecules that are hybrids of spirocyclic ketones as complexity-bearing cores with bi- and ter-phenyls as privileged fragments. Some of these newly-shaped small molecules showed antiproliferative, pro-apoptotic and differentiating activity in leukemia cell lines. In the present study, to investigate more in depth the mechanisms of action of these molecules, the protein expression profiles of K562 cells treated with or without the compounds IND_S1, MEL_T1, IND_S7 and MEL_S3 were analyzed using two-dimensional gel electrophoresis coupled with mass spectrometry. Proteome comparisons revealed several differentially expressed proteins, mainly related to cellular metabolism, chaperone activity, cytoskeletal organization and RNA biogenesis. The major results were validated by Western blot and qPCR. To attempt integrating findings into a cellular signaling context, proteomic data were explored using MetaCore. Network analysis highlighted relevant relationships between the identified proteins and additional potential effectors. Notably, qPCR validation of central hubs showed that the compound MEL_S3 induced high mRNA levels of the transcriptional factors EGR1 and HNF4-alpha; the latter to our knowledge is reported here for the first time to be present in K562 cells. Consistently with the known EGR1 involvement in the regulation of differentiation along megakaryocyte lineage, MEL_S3-treated leukemia cells showed a marked expression of glycoprotein IIb/IIIa (CD41) and glycoprotein Ib (CD42), two important cell markers in megakaryocytic differentiation, together with morphological aspects of megakaryoblasts and megakaryocytes.", "link"=>"http://www.mendeley.com/research/naturallike-synthetic-small-molecule-impairs-bcrabl-signaling-cascades-induces-megakaryocyte-differe", "reader_count"=>10, "reader_count_by_academic_status"=>{"Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Other"=>1, "Professor > Associate Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>4, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Master"=>1, "Other"=>1, "Professor > Associate Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>3, "Medicine and Dentistry"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Chemistry"=>3}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>3}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"United Kingdom"=>1, "Germany"=>1}, "group_count"=>1}

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• http://doi.org/10.1021/acs.orglett.0c00637
• http://doi.org/10.1002/ejoc.202000762
• http://doi.org/10.3390/cells9040877
• http://doi.org/10.1039/D0BM01547D
• http://doi.org/10.1111/febs.12673
• http://doi.org/10.1002/adsc.201500091
• http://doi.org/10.5582/irdr.2015.01049
• http://doi.org/10.1002/ajoc.201600145
• http://doi.org/10.1111/jcmm.12319
• http://doi.org/10.1002/pmic.201600141

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Figshare

• {"files"=>["https://ndownloader.figshare.com/files/972577"], "description"=>"<p>Proteins were categorized using information from the Swiss-Prot, GO and COG databases. When proteins were associated with more than one function, one category was chosen arbitrarily. ER, endoplasmic reticulum.</p>", "links"=>[], "tags"=>["proteins", "cellular"], "article_id"=>641217, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Pie_chart_distribution_of_the_identified_proteins_according_to_cellular_location_A_and_biological_function_B_/641217", "title"=>"Pie chart distribution of the identified proteins according to cellular location (A) and biological function (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-28 11:15:33"}
• {"files"=>["https://ndownloader.figshare.com/files/972582"], "description"=>"<p>Top, Representative immunoblots of each protein and GAPDH, as a loading control. Bottom, Bar graphs showing the densitometric analysis of Western blots. For each treatment series, protein values were normalized to GAPDH and expressed as a ratio relative to control K562 cells. Data are presented as mean ± SD from at least 3 separate experiments. *, <i>P</i><0.05 vs control. Dash-dotted line represents transcription levels of genes encoding HSP70, Sti1 and hnRNP L, as determined by qPCR. The transcript amounts were normalized against 3 housekeeping genes (TBP, GAPDH and BCR) following the normalization strategy proposed by Vandesompele <i>et al. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057650#pone.0057650-Vandesompele1\" target=\"_blank\">[17]</a>. Data are presented as mean ± SD of the fold ratio between treated and control K562 cells, derived from at least 2 separate experiments. ^#, <i>P</i><0.05 vs control.</p>", "links"=>[], "tags"=>["blot", "validation", "qpcr", "mrna", "hsp70", "sti1", "hnrnp"], "article_id"=>641219, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.g005", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Western_blot_validation_and_qPCR_determination_of_mRNA_levels_of_HSP70_A_Sti1_B_and_hnRNP_L_C_/641219", "title"=>"Western blot validation and qPCR determination of mRNA levels of HSP70 (A), Sti1 (B) and hnRNP L (C).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-28 11:16:03"}
• {"files"=>["https://ndownloader.figshare.com/files/972585"], "description"=>"<p>The transcription regulation networks initiated through activation of SP1 (A), c-Myc (B), HNF4-alpha (C) and EGR1 (D) are shown together with the mRNA abundances of these transcription factors in K562 cells treated with the four synthetic small molecules. Network proteins are visualized by proper symbols, which specify the functional nature of the protein (network caption). Red, green and gray arrows indicate negative, positive and unspecified effects, respectively. Red and blue circles indicate up- and down-regulated proteins in the treatment series, respectively. Relative transcription levels were quantified by qPCR according to Vandesompele <i>et al. </i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057650#pone.0057650-Vandesompele1\" target=\"_blank\">[17]</a> (see text for details). The bar graph plots mean ± SD of the fold ratio between treated and control K562 cells, derived from at least 2 separate experiments. *, <i>P</i><0.05.</p>", "links"=>[], "tags"=>["differentially", "proteins", "validation", "hubs", "mrna"], "article_id"=>641221, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Network_analysis_of_differentially_expressed_proteins_and_validation_of_central_hubs_at_the_mRNA_level_/641221", "title"=>"Network analysis of differentially expressed proteins and validation of central hubs at the mRNA level.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-28 11:16:35"}
• {"files"=>["https://ndownloader.figshare.com/files/972591"], "description"=>"<p>(A) Control; (B, C and D) <b>MEL_S3-</b>treated K562 cells with the presence of large cells with megakaryocytic morphological aspects.</p>", "links"=>[], "tags"=>["observed", "k562", "cells", "72-h", "15"], "article_id"=>641224, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.g007", "stats"=>{"downloads"=>3, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Morphological_changes_observed_in_K562_cells_after_72_h_exposure_to_15_181_M_of_MEL_S3_/641224", "title"=>"Morphological changes observed in K562 cells after 72-h exposure to 15 µM of MEL_S3.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-28 11:17:28"}
• {"files"=>["https://ndownloader.figshare.com/files/1005629"], "description"=>"<p>NS, not statistically significant. ER, endoplasmic reticulum. A, RNA processing and modification; C, Energy production and conversion; D, Cell cycle control, cell division, chromosome partitioning; E, Amino acid transport and metabolism; G, Carbohydrate transport and metabolism; K, Transcription; O, Post-translational modification, protein turnover, chaperones; P, Inorganic ion transport and metabolism; T, Signal transduction mechanisms; U, Intracellular trafficking, secretion, and vesicular transport; V, Defense mechanisms; Z, Cytoskeleton.</p>", "links"=>[], "tags"=>["differentially", "spots", "maldi-tof"], "article_id"=>666249, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_differentially_expressed_protein_spots_identified_by_MALDI_TOF_MS_/666249", "title"=>"List of differentially expressed protein spots identified by MALDI-TOF MS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-02-27 01:44:09"}
• {"files"=>["https://ndownloader.figshare.com/files/972600", "https://ndownloader.figshare.com/files/972603", "https://ndownloader.figshare.com/files/972606", "https://ndownloader.figshare.com/files/972609", "https://ndownloader.figshare.com/files/972612", "https://ndownloader.figshare.com/files/972613", "https://ndownloader.figshare.com/files/972615", "https://ndownloader.figshare.com/files/972620", "https://ndownloader.figshare.com/files/972624", "https://ndownloader.figshare.com/files/972630"], "description"=>"<div><p>Over the past years, we synthesized a series of new molecules that are hybrids of spirocyclic ketones as complexity-bearing cores with bi- and ter-phenyls as privileged fragments. Some of these newly-shaped small molecules showed antiproliferative, pro-apoptotic and differentiating activity in leukemia cell lines. In the present study, to investigate more in depth the mechanisms of action of these molecules, the protein expression profiles of K562 cells treated with or without the compounds <b>IND_S1, MEL_T1, IND_S7</b> and <b>MEL_S3</b> were analyzed using two-dimensional gel electrophoresis coupled with mass spectrometry. Proteome comparisons revealed several differentially expressed proteins, mainly related to cellular metabolism, chaperone activity, cytoskeletal organization and RNA biogenesis. The major results were validated by Western blot and qPCR. To attempt integrating findings into a cellular signaling context, proteomic data were explored using MetaCore. Network analysis highlighted relevant relationships between the identified proteins and additional potential effectors. Notably, qPCR validation of central hubs showed that the compound <b>MEL_S3</b> induced high mRNA levels of the transcriptional factors EGR1 and HNF4-alpha; the latter to our knowledge is reported here for the first time to be present in K562 cells. Consistently with the known EGR1 involvement in the regulation of differentiation along megakaryocyte lineage, <b>MEL_S3</b>-treated leukemia cells showed a marked expression of glycoprotein IIb/IIIa (CD41) and glycoprotein Ib (CD42), two important cell markers in megakaryocytic differentiation, together with morphological aspects of megakaryoblasts and megakaryocytes.</p> </div>", "links"=>[], "tags"=>["natural-like", "synthetic", "impairs", "bcr-abl", "cascades", "megakaryocyte", "differentiation", "erythroleukemia", "cells"], "article_id"=>641233, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0057650.s001", "https://dx.doi.org/10.1371/journal.pone.0057650.s002", "https://dx.doi.org/10.1371/journal.pone.0057650.s003", "https://dx.doi.org/10.1371/journal.pone.0057650.s004", "https://dx.doi.org/10.1371/journal.pone.0057650.s005", "https://dx.doi.org/10.1371/journal.pone.0057650.s006", "https://dx.doi.org/10.1371/journal.pone.0057650.s007", "https://dx.doi.org/10.1371/journal.pone.0057650.s008", "https://dx.doi.org/10.1371/journal.pone.0057650.s009", "https://dx.doi.org/10.1371/journal.pone.0057650.s010"], "stats"=>{"downloads"=>22, "page_views"=>34, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Natural_Like_Synthetic_Small_Molecule_Impairs_Bcr_Abl_Signaling_Cascades_and_Induces_Megakaryocyte_Differentiation_in_Erythroleukemia_Cells__/641233", "title"=>"A Natural-Like Synthetic Small Molecule Impairs Bcr-Abl Signaling Cascades and Induces Megakaryocyte Differentiation in Erythroleukemia Cells", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-02-28 11:18:52"}
• {"files"=>["https://ndownloader.figshare.com/files/972570"], "description"=>"<p>Synthetic natural-like biphenyl and terphenyl compounds.</p>", "links"=>[], "tags"=>["natural-like", "biphenyl", "terphenyl"], "article_id"=>641210, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.g001", "stats"=>{"downloads"=>1, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Synthetic_natural_like_biphenyl_and_terphenyl_compounds_/641210", "title"=>"Synthetic natural-like biphenyl and terphenyl compounds.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-28 11:14:21"}
• {"files"=>["https://ndownloader.figshare.com/files/972573"], "description"=>"<p>(A) PCA plot of the expression profiles from K562 cells untreated (circles) and after 24-h exposure to <b>IND_S1</b> (triangles), <b>MEL_T1</b> (squares), <b>IND_S7</b> (diamonds), <b>MEL_S3</b> (crosses). Log-transformed data were used. Each symbol represents a 2-DE gel from each treatment group. First and fourth ordination axes are plotted explaining 80 and 5% of the overall variance in the dataset, respectively. (B) Visualization of the SOM component planes of proteome data for all treatment series. Ratios between expression levels in K562 cells treated with the four synthetic small molecules and control cells were calculated and log₂-transformed. Each presentation illustrates the weights that connect each input to each of the artificial neurons, resulting in a sample-specific proteome-wide map (darker colors represent larger weights). All figures are linked by position: in each display, the hexagon in a certain position corresponds to the same map unit.</p>", "links"=>[], "tags"=>["proteomic"], "article_id"=>641213, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.g002", "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multivariate_analysis_of_proteomic_data_/641213", "title"=>"Multivariate analysis of proteomic data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-28 11:14:45"}
• {"files"=>["https://ndownloader.figshare.com/files/972574"], "description"=>"<p>Pearson’s dissimilarity as distance measure and Ward’s method for linkage analysis were used. Log₂ ratios are color coded as indicated. Names of the identified protein spots are shown on the right (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057650#pone-0057650-t001\" target=\"_blank\">Table 1</a>).</p>", "links"=>[], "tags"=>["hierarchical", "clustering", "74", "differentially", "spots", "k562", "cells", "treated", "synthetic", "molecules"], "article_id"=>641214, "categories"=>["Biochemistry", "Chemistry", "Genetics", "Hematology"], "users"=>["Silvia Turroni", "Manlio Tolomeo", "Gianfranco Mamone", "Gianluca Picariello", "Elisa Giacomini", "Patrizia Brigidi", "Marinella Roberti", "Stefania Grimaudo", "Rosaria Maria Pipitone", "Antonietta Di Cristina", "Maurizio Recanatini"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0057650.g003", "stats"=>{"downloads"=>0, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Two_way_hierarchical_clustering_of_the_74_differentially_expressed_protein_spots_between_K562_cells_treated_with_the_four_synthetic_small_molecules_and_control_cells_/641214", "title"=>"Two-way hierarchical clustering of the 74 differentially expressed protein spots between K562 cells treated with the four synthetic small molecules and control cells.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-02-28 11:15:12"}

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Relative Metric

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F1000Prime