title: Transcriptome and long noncoding RNA sequencing of three extracellular vesicle subtypes released from the human colon cancer LIM1863 cell line.
abstract: Previously we reported that LIM1863 colorectal cancer (CRC) cells secrete three distinct extracellular vesicle subtypes - two subpopulations of exosomes (apical EpCAM-Exos and basolateral A33-Exos) and shed microvesicles (sMVs) - with distinct protein and miRNA signatures. Here, we extend our omics approach to understand the fundamental role of LIM1863-derived EVs by performing a comprehensive analysis of their mRNAs and long non-coding RNAs (lncRNAs) using RNA-Seq. We show that 2,389 mRNAs, 317 pseudogene transcripts, 1,028 lncRNAs and 206 short non-coding RNAs selectively distributed to (i.e., are enriched in) LIM1863 EVs, relative to the parent cell. An Ensembl/UniProtKB analysis revealed 1,937 mRNAs encode canonical proteins, 348 isoforms (including splice-variant proteins), and 119 'missing proteins' (i.e., annotated in Ensembl but not UniProtKB). Further dissection of our protein/RNA data revealed that 6/151 observed RNA binding proteins have the potential to interact with ~75% of EV-enriched RNAs. Intriguingly, the co-existence of U1 and U2 ribonucleoproteins and their cognate snRNAs in LIM1863 EVs suggests a possible association of CRC EVs with recipient cell splicing events. Our data reveal several potential lncRNA CRC biomarkers and novel splicing/fusion genes that, collectively, will advance our understanding of EV biology in CRC and accelerate the development of EV-based diagnostics and therapeutics.
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
authors.forename: Maoshan
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
authors.forename: Rong
authors.initials: R
authors.lastname: Xu
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
authors.forename: Hong
authors.initials: H
authors.lastname: Ji
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
authors.forename: David W
authors.initials: DW
authors.lastname: Greening
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.
authors.forename: Alin
authors.initials: A
authors.lastname: Rai
authors.affiliation: Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan.|Global Innovation Research Organisation, Tokyo University of Agriculture and Technology, Tokyo, Japan.
authors.forename: Keiichi
authors.initials: K
authors.lastname: Izumikawa
authors.affiliation: Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan.|Global Innovation Research Organisation, Tokyo University of Agriculture and Technology, Tokyo, Japan.
authors.forename: Hideaki
authors.initials: H
authors.lastname: Ishikawa
authors.affiliation: Department of Applied Biological Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Tokyo, Japan.|Global Innovation Research Organisation, Tokyo University of Agriculture and Technology, Tokyo, Japan.
authors.forename: Nobuhiro
authors.initials: N
authors.lastname: Takahashi
authors.affiliation: Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria, Australia.|Global Innovation Research Organisation, Tokyo University of Agriculture and Technology, Tokyo, Japan.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Simpson
mesh_terms: D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D045744:Cell Line, Tumor; D055252:Cell-Derived Microparticles / Q000737:chemistry / Q000378:metabolism; D003110:Colonic Neoplasms / Q000175:diagnosis* / Q000235:genetics* / Q000473:pathology; D016208:Databases, Factual; D055354:Exosomes / Q000737:chemistry / Q000378:metabolism; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism; D058977:Molecular Sequence Annotation; D062085:RNA, Long Noncoding / Q000235:genetics* / Q000378:metabolism; D012334:RNA, Neoplasm / Q000235:genetics* / Q000378:metabolism; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000235:genetics / Q000378:metabolism; D017413:Ribonucleoprotein, U2 Small Nuclear / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D014408:Biomarkers, Tumor; D035683:MicroRNAs; D062085:RNA, Long Noncoding; D012334:RNA, Neoplasm; D017412:Ribonucleoprotein, U1 Small Nuclear; D017413:Ribonucleoprotein, U2 Small Nuclear