Distinct microRNAs expression profile in primary biliary cirrhosis and evaluation of miR 505-3p and miR197-3p as novel biomarkers

• Published in: PloS one 2013-06, Vol.8 (6), p.e66086-e66086
• Main Authors: Ninomiya, Masashi, Kondo, Yasuteru, Funayama, Ryo, Nagashima, Takeshi, Kogure, Takayuki, Kakazu, Eiji, Kimura, Osamu, Ueno, Yoshiyuki, Nakayama, Keiko, Shimosegawa, Tooru
• Format: Article
• Language: English
• Subjects: Aged; Analysis; Apoptosis; Autoimmune diseases; Biological effects; Biological markers; Biology; Biomarkers; Biomarkers - metabolism; Cell growth; Cirrhosis; Cluster Analysis; Clustering; Computer applications; Female; Gastroenterology; Gene expression; Gene Expression Profiling; Genetic research; Genomes; Hepatitis; High-Throughput Nucleotide Sequencing; Hospitals; Humans; Infections; Liver cirrhosis; Liver Cirrhosis, Biliary - genetics; Liver Cirrhosis, Biliary - metabolism; Liver diseases; Male; Medical prognosis; Medicine; MicroRNA; MicroRNAs; MicroRNAs - metabolism; Middle Aged; miRNA; Ontology; Patients; Primary biliary cirrhosis; Reverse Transcriptase Polymerase Chain Reaction; Reverse transcription; Ribonucleic acid; RNA; Rodents; Statistical analysis; Statistical methods; Statistical significance; Statistics; Variance analysis
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0066086

MicroRNAs are small endogenous RNA molecules with specific expression patterns that can serve as biomarkers for numerous diseases. However, little is known about the expression profile of serum miRNAs in PBC. First, we employed Illumina deep sequencing for the initial screening to indicate the read numbers of miRNA expression in 10 PBC, 5 CH-C, 5 CH-B patients and 5 healthy controls. Comparing the differentially expressed miRNAs in the 4 groups, analysis of variance was performed on the number of sequence reads to evaluate the statistical significance. Hierarchical clustering was performed using an R platform and we have found candidates for specific miRNAs in the PBC patients. Second, a quantitative reverse transcription PCR validation study was conducted in 10 samples in each group. The expression levels of the selected miRNAs were presented as fold-changes (2(-ΔΔCt)). Finally, computer analysis was conducted to predict target genes and biological functions with MiRror 2.0 and DAVID v6.7. We obtained about 12 million 32-mer short RNA reads on average per sample and the mapping rates to miRBase were 16.60% and 81.66% to hg19. In the statistical significance testing, the expression levels of 81 miRNAs were found to be differentially expressed in the 4 groups. The heat map and hierarchical clustering demonstrated that the miRNA profiles from PBC clustered with those of CH-B, CH-C and healthy controls. Additionally, the circulating levels of hsa-miR-505-3p, 197-3p, and 500a-3p were significantly decreased in PBC compared with healthy controls and the expression levels of hsa-miR-505-3p, 139-5p and 197-3p were significantly reduced compared with the viral hepatitis group. Our results indicate that sera from patients with PBC have a unique miRNA expression profile and that the down-regulated expression of hsa-miR-505-3p and miR-197-3p can serve as clinical biomarkers of PBC.