title: Circular RNAs are down-regulated in KRAS mutant colon cancer cells and can be transferred to exosomes.
abstract: Recent studies have shown that circular RNAs (circRNAs) are abundant, widely expressed in mammals, and can display cell-type specific expression. However, how production of circRNAs is regulated and their precise biological function remains largely unknown. To study how circRNAs might be regulated during colorectal cancer progression, we used three isogenic colon cancer cell lines that differ only in KRAS mutation status. Cellular RNAs from the parental DLD-1 cells that contain both wild-type and G13D mutant KRAS alleles and isogenically-matched derivative cell lines, DKO-1 (mutant KRAS allele only) and DKs-8 (wild-type KRAS allele only) were analyzed using RNA-Seq. We developed a bioinformatics pipeline to identify and evaluate circRNA candidates from RNA-Seq data. Hundreds of high-quality circRNA candidates were identified in each cell line. Remarkably, circRNAs were significantly down-regulated at a global level in DLD-1 and DKO-1 cells compared to DKs-8 cells, indicating a widespread effect of mutant KRAS on circRNA abundance. This finding was confirmed in two independent colon cancer cell lines HCT116 (KRAS mutant) and HKe3 (KRAS WT). In all three cell lines, circRNAs were also found in secreted extracellular-vesicles, and circRNAs were more abundant in exosomes than cells. Our results suggest that circRNAs may serve as promising cancer biomarkers.
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Yongchao
authors.initials: Y
authors.lastname: Dou
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Diana J
authors.initials: DJ
authors.lastname: Cha
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.|Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Franklin
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.|Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: James N
authors.initials: JN
authors.lastname: Higginbotham
authors.affiliation: Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Dennis K
authors.initials: DK
authors.lastname: Jeppesen
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.|Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.|Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA.
authors.forename: Alissa M
authors.initials: AM
authors.lastname: Weaver
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.
authors.forename: Nripesh
authors.initials: N
authors.lastname: Prasad
authors.affiliation: HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA.
authors.forename: Shawn
authors.initials: S
authors.lastname: Levy
authors.affiliation: Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee 37232, USA.|Department of Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Coffey
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: James G
authors.initials: JG
authors.lastname: Patton
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
mesh_terms: D045744:Cell Line, Tumor; D003110:Colonic Neoplasms / Q000235:genetics* / Q000473:pathology; D015536:Down-Regulation / Q000235:genetics; D055354:Exosomes / Q000235:genetics*; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016283:Proto-Oncogene Proteins p21(ras) / Q000235:genetics*; D012313:RNA / Q000235:genetics / Q000378:metabolism*; D000079962:RNA, Circular
chemical_list: C117307:KRAS protein, human; D000079962:RNA, Circular; D012313:RNA; D016283:Proto-Oncogene Proteins p21(ras)