title: High-throughput sequencing of two populations of extracellular vesicles provides an mRNA signature that can be detected in the circulation of breast cancer patients.
abstract: Extracellular vesicles (EVs) contain a wide range of RNA types with a reported prevalence of non-coding RNA. To date a comprehensive characterization of the protein coding transcripts in EVs is still lacking. We performed RNA-Sequencing (RNA-Seq) of 2 EV populations and identified a small fraction of transcripts that were expressed at significantly different levels in large oncosomes and exosomes, suggesting they may mediate specialized functions. However, these 2 EV populations exhibited a common mRNA signature that, in comparison to their donor cells, was significantly enriched in mRNAs encoding E2F transcriptional targets and histone proteins. These mRNAs are primarily expressed in the S-phase of the cell cycle, suggesting that they may be packaged into EVs during S-phase. In silico analysis using subcellular compartment transcriptome data from the ENCODE cell line compendium revealed that EV mRNAs originate from a cytoplasmic RNA pool. The EV signature was independently identified in plasma of patients with breast cancer by RNA-Seq. Furthermore, several transcripts differentially expressed in EVs from patients versus controls mirrored differential expression between normal and breast cancer tissues. Altogether, this largest high-throughput profiling of EV mRNA demonstrates that EVs carry tumor-specific alterations and can be interrogated as a source of cancer-derived cargo.
authors.affiliation: a Department of Biomedical Sciences , Cedars-Sinai Medical Center , Los Angeles , CA , USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Conley
authors.affiliation: a Department of Biomedical Sciences , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|b Department of Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|c Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|d Department of Surgery , Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center , Los Angeles , CA , USA.
authors.forename: Valentina R
authors.initials: VR
authors.lastname: Minciacchi
authors.affiliation: a Department of Biomedical Sciences , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|b Department of Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|c Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|d Department of Surgery , Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center , Los Angeles , CA , USA.
authors.forename: Dhong Hyun
authors.initials: DH
authors.lastname: Lee
authors.affiliation: a Department of Biomedical Sciences , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|b Department of Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , CA , USA.
authors.forename: Beatrice S
authors.initials: BS
authors.lastname: Knudsen
authors.affiliation: c Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|e Women's Cancer Program and Division of Gynecologic Oncology Obstetrics and Gynecology, Cedars-Sinai Medical Center , Los Angeles , CA , USA.
authors.forename: Beth Y
authors.initials: BY
authors.lastname: Karlan
authors.affiliation: d Department of Surgery , Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|f Department of Experimental and Clinical Medicine , University Magna Graecia , Catanzaro , Italy.
authors.forename: Luigi
authors.initials: L
authors.lastname: Citrigno
authors.affiliation: f Department of Experimental and Clinical Medicine , University Magna Graecia , Catanzaro , Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Viglietto
authors.affiliation: g Department of Internal Medicine , University of Michigan , Ann Arbor , MI , USA.|h Department of Biomedical Engineering , University of Michigan , Ann Arbor , MI , USA.|i Biointerfaces Institute, University of Michigan , Ann Arbor , MI , USA.|j Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor , MI , USA.|k Comprehensive Cancer Center, University of Michigan , Ann Arbor , MI , USA.
authors.forename: Muneesh
authors.initials: M
authors.lastname: Tewari
authors.affiliation: a Department of Biomedical Sciences , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|c Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|d Department of Surgery , Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|l The Urological Diseases Research Center, Boston Children's Hospital, Harvard Medical School , Boston , MA , USA.|m Department of Medicine , University of California , Los Angeles , USA.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Freeman
authors.affiliation: n Centre for Integrative Biology, University of Trento , Trento , Italy.|o Institute for Precision Medicine, Weill Cornell Medicine , New York NY , USA.
authors.forename: Francesca
authors.initials: F
authors.lastname: Demichelis
authors.affiliation: a Department of Biomedical Sciences , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|b Department of Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , CA , USA.|c Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|d Department of Surgery , Division of Cancer Biology and Therapeutics, Cedars-Sinai Medical Center , Los Angeles , CA , USA.|l The Urological Diseases Research Center, Boston Children's Hospital, Harvard Medical School , Boston , MA , USA.|m Department of Medicine , University of California , Los Angeles , USA.
authors.forename: Dolores
authors.initials: D
authors.lastname: Di Vizio
mesh_terms: D014408:Biomarkers, Tumor; D001943:Breast Neoplasms / Q000097:blood / Q000235:genetics* / Q000378:metabolism*; D002453:Cell Cycle / Q000235:genetics; D045744:Cell Line, Tumor; D019295:Computational Biology / Q000379:methods; D003600:Cytosol / Q000378:metabolism; D050704:E2F4 Transcription Factor / Q000378:metabolism; D000067128:Extracellular Vesicles / Q000378:metabolism*; D005260:Female; D020869:Gene Expression Profiling; D063990:Gene Ontology; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D021382:Protein Sorting Signals / Q000235:genetics; D012333:RNA, Messenger / Q000097:blood / Q000235:genetics*; D059467:Transcriptome; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics / Q000378:metabolism
chemical_list: D014408:Biomarkers, Tumor; D050704:E2F4 Transcription Factor; D021382:Protein Sorting Signals; D012333:RNA, Messenger; D042461:Vascular Endothelial Growth Factor A