title: Sequencing and bioinformatics-based analyses of the microRNA transcriptome in hepatitis B-related hepatocellular carcinoma.
abstract: MicroRNAs (miRNAs) participate in crucial biological processes, and it is now evident that miRNA alterations are involved in the progression of human cancers. Recent studies on miRNA profiling performed with cloning suggest that sequencing is useful for the detection of novel miRNAs, modifications, and precise compositions and that miRNA expression levels calculated by clone count are reproducible. Here we focus on sequencing of miRNA to obtain a comprehensive profile and characterization of these transcriptomes as they relate to human liver. Sequencing using 454 sequencing and conventional cloning from 22 pair of HCC and adjacent normal liver (ANL) and 3 HCC cell lines identified reliable reads of more than 314000 miRNAs from HCC and more than 268000 from ANL for registered human miRNAs. Computational bioinformatics identified 7 novel miRNAs with high conservation, 15 novel opposite miRNAs, and 3 novel antisense miRNAs. Moreover sequencing can detect miRNA modifications including adenosine-to-inosine editing in miR-376 families. Expression profiling using clone count analysis was used to identify miRNAs that are expressed aberrantly in liver cancer including miR-122, miR-21, and miR-34a. Furthermore, sequencing-based miRNA clustering, but not individual miRNA, detects high risk patients who have high potentials for early tumor recurrence after liver surgery (P = 0.006), and which is the only significant variable among pathological and clinical and variables (P = 0,022). We believe that the combination of sequencing and bioinformatics will accelerate the discovery of novel miRNAs and biomarkers involved in human liver cancer.
authors.affiliation: Department of Surgery for Organ Function and Biological Regulation, Nippon Medical School, Tokyo, Japan. yoshi1224@gmail.com
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Mizuguchi
authors.forename: Takuya
authors.initials: T
authors.lastname: Mishima
authors.forename: Shigeki
authors.initials: S
authors.lastname: Yokomuro
authors.forename: Yasuo
authors.initials: Y
authors.lastname: Arima
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Kawahigashi
authors.forename: Kengo
authors.initials: K
authors.lastname: Shigehara
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Kanda
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Yoshida
authors.forename: Eiji
authors.initials: E
authors.lastname: Uchida
authors.forename: Takashi
authors.initials: T
authors.lastname: Tajiri
authors.forename: Toshihiro
authors.initials: T
authors.lastname: Takizawa
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000821:virology; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006509:Hepatitis B / Q000150:complications*; D006801:Humans; D008099:Liver / Q000378:metabolism; D008113:Liver Neoplasms / Q000235:genetics* / Q000821:virology; D035683:MicroRNAs / Q000235:genetics*; D012008:Recurrence; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D035683:MicroRNAs