Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer
Publication Date
December 31, 2013
Journal
PLOS ONE
Authors
Diederick Duijvesz, Kristin E. Burnum Johnson, Marina A. Gritsenko, A. Marije Hoogland, et al
Volume
8
Issue
12
Pages
e82589
DOI
https://dx.plos.org/10.1371/journal.pone.0082589
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0082589
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24391718
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3876995
Europe PMC
http://europepmc.org/abstract/MED/24391718
Web of Science
000329325200015
Scopus
84894235330
Mendeley
http://www.mendeley.com/research/proteomic-profiling-exosomes-leads-identification-novel-biomarkers-prostate-cancer
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Mendeley | Further Information

{"title"=>"Proteomic profiling of exosomes leads to the identification of novel biomarkers for prostate cancer", "type"=>"journal", "authors"=>[{"first_name"=>"Diederick", "last_name"=>"Duijvesz", "scopus_author_id"=>"35101802900"}, {"first_name"=>"Kristin E.", "last_name"=>"Burnum-Johnson", "scopus_author_id"=>"55341427000"}, {"first_name"=>"Marina A.", "last_name"=>"Gritsenko", "scopus_author_id"=>"6602715160"}, {"first_name"=>"A. Marije", "last_name"=>"Hoogland", "scopus_author_id"=>"45461174300"}, {"first_name"=>"Mirella S.", "last_name"=>"Vredenbregt-van Den Berg", "scopus_author_id"=>"56042051300"}, {"first_name"=>"Rob", "last_name"=>"Willemsen", "scopus_author_id"=>"7005061178"}, {"first_name"=>"Theo", "last_name"=>"Luider", "scopus_author_id"=>"6603826198"}, {"first_name"=>"Ljiljana", "last_name"=>"Paša-Tolić", "scopus_author_id"=>"35462222400"}, {"first_name"=>"Guido", "last_name"=>"Jenster", "scopus_author_id"=>"7004365261"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-84894235330", "pui"=>"372425332", "doi"=>"10.1371/journal.pone.0082589", "issn"=>"19326203", "pmid"=>"24391718", "sgr"=>"84894235330"}, "id"=>"af27d27f-96b2-3624-a856-0dfca632eb6b", "abstract"=>"BACKGROUND: Current markers for prostate cancer, such as PSA lack specificity. Therefore, novel biomarkers are needed. Unfortunately, the complexity of body fluids often hampers biomarker discovery. An attractive alternative approach is the isolation of small vesicles, i.e. exosomes, ∼100 nm, which contain proteins that are specific to the tissue from which they are derived and therefore can be considered as treasure chests for disease-specific biomarker discovery.\\n\\nMATERIALS AND METHODS: Exosomes were isolated from 2 immortalized primary prostate epithelial cells (PNT2C2 and RWPE-1) and 2 PCa cell lines (PC346C and VCaP) by ultracentrifugation. After tryptic digestion, proteomic analyses utilized a nanoLC coupled with an LTQ-Orbitrap operated in tandem MS (MS/MS) mode. Accurate Mass and Time (AMT) tag approach was employed for peptide identification and quantitation. Candidate biomarkers were validated by Western blotting and Immunohistochemistry.\\n\\nRESULTS: Proteomic characterization resulted in the identification of 248, 233, 169, and 216 proteins by at least 2 peptides in exosomes from PNT2C2, RWPE-1, PC346C, and VCaP, respectively. Statistical analyses revealed 52 proteins differently abundant between PCa and control cells, 9 of which were more abundant in PCa. Validation by Western blotting confirmed a higher abundance of FASN, XPO1 and PDCD6IP (ALIX) in PCa exosomes.\\n\\nCONCLUSIONS: Identification of exosomal proteins using high performance LC-FTMS resulted in the discovery of PDCD6IP, FASN, XPO1 and ENO1 as new candidate biomarkers for prostate cancer.", "link"=>"http://www.mendeley.com/research/proteomic-profiling-exosomes-leads-identification-novel-biomarkers-prostate-cancer", "reader_count"=>48, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>10, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Other"=>2, "Student > Master"=>6, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>5, "Researcher"=>10, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Other"=>2, "Student > Master"=>6, "Student > Bachelor"=>2, "Lecturer"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>12, "Nursing and Health Professions"=>1, "Medicine and Dentistry"=>13, "Agricultural and Biological Sciences"=>10, "Neuroscience"=>2, "Physics and Astronomy"=>1, "Chemistry"=>5}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>13}, "Neuroscience"=>{"Neuroscience"=>2}, "Chemistry"=>{"Chemistry"=>5}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>10}, "Nursing and Health Professions"=>{"Nursing and Health Professions"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>12}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Colombia"=>1, "Belgium"=>1, "Hungary"=>1, "India"=>1}, "group_count"=>0}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1333033"], "description"=>"<p>Exosomes from all four cell lines (PNT2C2, RWPE-1, PC346C, VCaP) contained 60% of cytoplasmic proteins and 25% of transmembrane proteins. B. The top seven functions of exosomal proteins according to Ingenuity Pathway Analysis. Fisher's exact test was applied to calculate significance (p-value<0.05).</p>", "links"=>[], "tags"=>["Molecular cell biology", "Cellular structures", "Subcellular organelles", "proteomics", "Protein abundance", "Proteomic databases", "Sequence analysis", "Spectrometric identification of proteins", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "oncology", "Cancers and neoplasms", "Genitourinary tract tumors", "Prostate cancer", "urology", "Prostate diseases", "proteins", "samples"], "article_id"=>889792, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Diederick Duijvesz", "Kristin E. Burnum-Johnson", "Marina A. Gritsenko", "A. Marije Hoogland", "Mirella S. Vredenbregt-van den Berg", "Rob Willemsen", "Theo Luider", "Ljiljana Pasa-Tolic", "Guido Jenster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082589.g003", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Subcellular_assignment_of_the_proteins_identified_within_the_different_samples_in_panel_A_/889792", "title"=>"Subcellular assignment of the proteins identified within the different samples in panel A.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-31 02:46:28"}
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  • {"files"=>["https://ndownloader.figshare.com/files/1333036"], "description"=>"<p>The number of proteins identified in each study are a compilation of the cancer-derived exosomal proteins identified by MS-MS.</p>", "links"=>[], "tags"=>["Molecular cell biology", "Cellular structures", "Subcellular organelles", "proteomics", "Protein abundance", "Proteomic databases", "Sequence analysis", "Spectrometric identification of proteins", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "oncology", "Cancers and neoplasms", "Genitourinary tract tumors", "Prostate cancer", "urology", "Prostate diseases", "proteins", "hosseini-beheshti", "sandvig", "visualized", "venn"], "article_id"=>889795, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Diederick Duijvesz", "Kristin E. Burnum-Johnson", "Marina A. Gritsenko", "A. Marije Hoogland", "Mirella S. Vredenbregt-van den Berg", "Rob Willemsen", "Theo Luider", "Ljiljana Pasa-Tolic", "Guido Jenster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082589.g006", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_proteins_identified_by_Hosseini_Beheshti_et_al_Sandvig_et_al_and_this_study_visualized_by_a_Venn_diagram_/889795", "title"=>"Comparison of proteins identified by Hosseini-Beheshti <i>et al.</i>, Sandvig <i>et al.</i> and this study visualized by a Venn diagram.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-31 02:46:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1333035"], "description"=>"<p>Representative pictures of the staining from 2 independent samples per group.</p>", "links"=>[], "tags"=>["Molecular cell biology", "Cellular structures", "Subcellular organelles", "proteomics", "Protein abundance", "Proteomic databases", "Sequence analysis", "Spectrometric identification of proteins", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "oncology", "Cancers and neoplasms", "Genitourinary tract tumors", "Prostate cancer", "urology", "Prostate diseases", "fasn", "pdcd6ip", "abundance", "immunohistochemistry", "adjacent", "prostate", "low-grade", "cancer"], "article_id"=>889794, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Diederick Duijvesz", "Kristin E. Burnum-Johnson", "Marina A. Gritsenko", "A. Marije Hoogland", "Mirella S. Vredenbregt-van den Berg", "Rob Willemsen", "Theo Luider", "Ljiljana Pasa-Tolic", "Guido Jenster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082589.g005", "stats"=>{"downloads"=>36, "page_views"=>360, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_XPO1_FASN_and_PDCD6IP_abundance_by_immunohistochemistry_on_normal_adjacent_prostate_NAP_low_grade_prostate_cancer_Gleason_score_3_3_8202_8202_6_and_high_grade_prostate_cancer_Gleason_score_4_5_8202_8202_9_/889794", "title"=>"XPO1, FASN and PDCD6IP abundance by immunohistochemistry on normal adjacent prostate (NAP), low-grade prostate cancer (Gleason score 3+3 = 6) and high grade prostate cancer (Gleason score 4+5 = 9).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-31 02:46:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1333038"], "description"=>"<div><p>Background</p><p>Current markers for prostate cancer, such as PSA lack specificity. Therefore, novel biomarkers are needed. Unfortunately, the complexity of body fluids often hampers biomarker discovery. An attractive alternative approach is the isolation of small vesicles, i.e. exosomes, ∼100 nm, which contain proteins that are specific to the tissue from which they are derived and therefore can be considered as treasure chests for disease-specific biomarker discovery.</p><p>Materials and Methods</p><p>Exosomes were isolated from 2 immortalized primary prostate epithelial cells (PNT2C2 and RWPE-1) and 2 PCa cell lines (PC346C and VCaP) by ultracentrifugation. After tryptic digestion, proteomic analyses utilized a nanoLC coupled with an LTQ-Orbitrap operated in tandem MS (MS/MS) mode. Accurate Mass and Time (AMT) tag approach was employed for peptide identification and quantitation. Candidate biomarkers were validated by Western blotting and Immunohistochemistry.</p><p>Results</p><p>Proteomic characterization resulted in the identification of 248, 233, 169, and 216 proteins by at least 2 peptides in exosomes from PNT2C2, RWPE-1, PC346C, and VCaP, respectively. Statistical analyses revealed 52 proteins differently abundant between PCa and control cells, 9 of which were more abundant in PCa. Validation by Western blotting confirmed a higher abundance of FASN, XPO1 and PDCD6IP (ALIX) in PCa exosomes.</p><p>Conclusions</p><p>Identification of exosomal proteins using high performance LC-FTMS resulted in the discovery of PDCD6IP, FASN, XPO1 and ENO1 as new candidate biomarkers for prostate cancer.</p></div>", "links"=>[], "tags"=>["Molecular cell biology", "Cellular structures", "Subcellular organelles", "proteomics", "Protein abundance", "Proteomic databases", "Sequence analysis", "Spectrometric identification of proteins", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "oncology", "Cancers and neoplasms", "Genitourinary tract tumors", "Prostate cancer", "urology", "Prostate diseases", "profiling", "exosomes", "leads", "prostate"], "article_id"=>889797, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Diederick Duijvesz", "Kristin E. Burnum-Johnson", "Marina A. Gritsenko", "A. Marije Hoogland", "Mirella S. Vredenbregt-van den Berg", "Rob Willemsen", "Theo Luider", "Ljiljana Pasa-Tolic", "Guido Jenster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082589", "stats"=>{"downloads"=>10, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteomic_Profiling_of_Exosomes_Leads_to_the_Identification_of_Novel_Biomarkers_for_Prostate_Cancer_/889797", "title"=>"Proteomic Profiling of Exosomes Leads to the Identification of Novel Biomarkers for Prostate Cancer", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-31 02:46:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1333037"], "description"=>"<p>Proteins with significant abundance changes (>1.50 log2 fold) between prostate cancer and immortalized primary prostate epithelial cell lines.</p>", "links"=>[], "tags"=>["Molecular cell biology", "Cellular structures", "Subcellular organelles", "proteomics", "Protein abundance", "Proteomic databases", "Sequence analysis", "Spectrometric identification of proteins", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "oncology", "Cancers and neoplasms", "Genitourinary tract tumors", "Prostate cancer", "urology", "Prostate diseases"], "article_id"=>889796, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Diederick Duijvesz", "Kristin E. Burnum-Johnson", "Marina A. Gritsenko", "A. Marije Hoogland", "Mirella S. Vredenbregt-van den Berg", "Rob Willemsen", "Theo Luider", "Ljiljana Pasa-Tolic", "Guido Jenster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082589.t001", "stats"=>{"downloads"=>5, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Proteins_expression_differences_/889796", "title"=>"Proteins expression differences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-12-31 02:46:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1333034"], "description"=>"<p>All four exosome samples and their corresponding cell lines were used for validation. Furthermore, supernatant from the pelleted exosomes was used as a control. The selected proteins FASN, XPO1, CD9 and PDCD6IP, were tested with ENO1 and GAPDH as controls. PSA was tested to confirm it is secreted through alternative secretion pathway and therefore not present within exosomes. The nearest protein marker (kDa) is indicated for each blot.</p>", "links"=>[], "tags"=>["Molecular cell biology", "Cellular structures", "Subcellular organelles", "proteomics", "Protein abundance", "Proteomic databases", "Sequence analysis", "Spectrometric identification of proteins", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "oncology", "Cancers and neoplasms", "Genitourinary tract tumors", "Prostate cancer", "urology", "Prostate diseases"], "article_id"=>889793, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Diederick Duijvesz", "Kristin E. Burnum-Johnson", "Marina A. Gritsenko", "A. Marije Hoogland", "Mirella S. Vredenbregt-van den Berg", "Rob Willemsen", "Theo Luider", "Ljiljana Pasa-Tolic", "Guido Jenster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082589.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Validation_of_protein_expression_by_Western_blotting_/889793", "title"=>"Validation of protein expression by Western blotting.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-31 02:46:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/1333032"], "description"=>"<p>Each exosome sample was analyzed in triplicate. Results were mean centered and log-transformed. Relative protein abundance is colored-coded with red corresponding to a relatively high abundance, green r corresponding to a relatively low abundance, and grey indicating missing abundance values.</p>", "links"=>[], "tags"=>["Molecular cell biology", "Cellular structures", "Subcellular organelles", "proteomics", "Protein abundance", "Proteomic databases", "Sequence analysis", "Spectrometric identification of proteins", "Diagnostic medicine", "pathology", "General pathology", "biomarkers", "oncology", "Cancers and neoplasms", "Genitourinary tract tumors", "Prostate cancer", "urology", "Prostate diseases", "hierarchical", "clustering", "differentially", "abundant", "proteins", "ms-peak"], "article_id"=>889791, "categories"=>["Biological Sciences", "Medicine"], "users"=>["Diederick Duijvesz", "Kristin E. Burnum-Johnson", "Marina A. Gritsenko", "A. Marije Hoogland", "Mirella S. Vredenbregt-van den Berg", "Rob Willemsen", "Theo Luider", "Ljiljana Pasa-Tolic", "Guido Jenster"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0082589.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unsupervised_hierarchical_clustering_of_differentially_abundant_proteins_n_8202_8202_263_proteins_with_gt_2_peptides_based_on_their_MS_peak_intensity_values_/889791", "title"=>"Unsupervised hierarchical clustering of differentially abundant proteins (n = 263 proteins with >2 peptides) based on their MS-peak intensity values.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-31 02:46:28"}

PMC Usage Stats | Further Information

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Relative Metric

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