title: Next generation sequencing reveals microRNA isoforms in liver cirrhosis and hepatocellular carcinoma.
abstract: Hepatocellular carcinoma (HCC) represents the major histological subtype of liver cancer. Tumorigenic changes in hepatic cells potentially result from aberrant expression of microRNAs (miRNAs). Individual microRNA gene may give rise to miRNAs of different length, named isomiRNAs that proved to be functionally relevant. Since microRNA length heterogeneity in hepatic tissue has not been described before, we employed next-generation sequencing to comprehensively analyze microRNA transcriptome in HCC tumors (n=24) and unaffected tissue adjacent to tumors (n=24), including samples with (n=15) and without cirrhosis (n=9). We detected 374 microRNAs expressed in liver, including miR-122-5p that constituted over 39% of the hepatic miRnome. Among the liver expressed miRs, the levels of 64 significantly differed between tumor and control samples (FDR<0.05, fold change>2). Top deregulated miRNAs included miR-1269a (T/N=22.95), miR-3144-3p (T/N=5.24), miR-183-5p (T/N=4.63), miR-10b-5p (T/N=3.87), miR-490-3p (T/N=0.13), miR-199a-5p (T/N=0.17), miR-199a-3p/miR-199b-3p (T/N=0.19), miR-214-5p (T/N=0.20) and miR-214-3p (T/N=0.21). Almost all miRNA genes produced several mature molecules differing in length (isomiRNAs). The reference sequence was not the most prevalent in 38.6% and completely absent in 10.5% of isomiRNAs. Over 26.1% of miRNAs produced isoforms carrying≥2 alternative seed regions, of which 35.5% constituted novel, previously unknown seeds. This fact sheds new light on the percentage of the human genome regulated by microRNAs and their variants. Among the most deregulated miRNAs, miR-199a-3p/miR-199b-3p (T/N fold change=0.18, FDR=0.005) was expressed in 9 isoforms with 3 different seeds, concertedly leading to upregulation of TGF-beta signaling pathway (OR=1.99; p=0.004). In conclusion, the study reveals the comprehensive miRNome of hepatic tissue and provides new tools for investigation of microRNA-dependent pathways in cirrhotic liver and hepatocellular carcinoma. This article is part of a Directed Issue entitled: Rare Cancers.
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland; Laboratory of Human Cancer Genetics, Centre of New Technologies, CENT, University of Warsaw, 02-089 Warsaw, Poland.
authors.forename: Anna
authors.initials: A
authors.lastname: Wojcicka
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland; Department of Nuclear Medicine and Endocrine Oncology, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, 44-101 Gliwice, Poland.
authors.forename: Michal
authors.initials: M
authors.lastname: Swierniak
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Oskar
authors.initials: O
authors.lastname: Kornasiewicz
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Wojciech
authors.initials: W
authors.lastname: Gierlikowski
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Monika
authors.initials: M
authors.lastname: Maciag
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Monika
authors.initials: M
authors.lastname: Kolanowska
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Marta
authors.initials: M
authors.lastname: Kotlarek
authors.affiliation: Department of Pathology, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Barbara
authors.initials: B
authors.lastname: Gornicka
authors.affiliation: Department of Pathology, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Koperski
authors.affiliation: Second Department of Anaesthesiology and Intensive Therapy, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Grzegorz
authors.initials: G
authors.lastname: Niewinski
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Krawczyk
authors.affiliation: Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, 02-091 Warsaw, Poland; Laboratory of Human Cancer Genetics, Centre of New Technologies, CENT, University of Warsaw, 02-089 Warsaw, Poland. Electronic address: krystian.jazdzewski@wum.edu.pl.
authors.forename: Krystian
authors.initials: K
authors.lastname: Jazdzewski
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000473:pathology; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008103:Liver Cirrhosis / Q000235:genetics* / Q000473:pathology; D008113:Liver Neoplasms / Q000235:genetics* / Q000473:pathology; D035683:MicroRNAs / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics; D059467:Transcriptome / Q000235:genetics
chemical_list: D035683:MicroRNAs; D020033:Protein Isoforms
keywords: Deep sequencing; HCC; Isoforms; Liver cancer; miRs