title: Deep sequencing of small RNA transcriptome reveals novel non-coding RNAs in hepatocellular carcinoma.
abstract: OBJECTIVE
  Small non-coding RNAs (ncRNA) are increasingly recognized to play important roles in tumorigenesis. With the advent of deep sequencing, efforts have been put forth to profile the miRNome in a number of human malignancies. However, information on ncRNA in hepatocellular carcinoma (HCC), especially the non-microRNA transcripts, is still lacking.
  
  
  METHODS
  Small RNA transcriptomes of two HCC cell lines (HKCI-4 and HKCI-8) and an immortalized hepatocyte line (MIHA) were examined using Illumina massively parallel sequencing. Dysregulated ncRNAs were verified in paired HCC tumors and non-tumoral livers (n=73) by quantitative reverse transcription-polymerase chain reaction. Clinicopathologic correlations and in vitro functional investigations were further carried out.
  
  
  RESULTS
  The combined bioinformatic and biological analyses showed the presence of ncRNAs and the involvement of a new PIWI-interacting RNA (piRNA), piR-Hep1, in liver tumorigenesis. piR-Hep1 was found to be upregulated in 46.6% of HCC tumors compared to the corresponding adjacent non-tumoral liver. Silencing of piR-Hep1 inhibited cell viability, motility, and invasiveness, with a concomitant reduction in the level of active AKT phosphorylation. In the analysis of miRNA, we showed for the first time, the abundant expression of miR-1323 in HCC and its distinct association in tumors arising from a cirrhotic background. Furthermore, miR-1323 overexpression in cirrhotic HCC correlated with poorer disease-free and overall survivals of patients (p<0.009).
  
  
  CONCLUSIONS
  Our study demonstrated the value of next-generation sequencing in dissecting the ncRNome in cancer. The comprehensive definition of transcriptome unveils virtually all types of ncRNAs and provides new insight into liver carcinogenetic events.
authors: Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong.
authors: Priscilla T-Y
authors: PT
authors: Law
authors: Hao
authors: H
authors: Qin
authors: Arthur K-K
authors: AK
authors: Ching
authors: Keng Po
authors: KP
authors: Lai
authors: Ngai Na
authors: NN
authors: Co
authors: Mian
authors: M
authors: He
authors: Raymond W-M
authors: RW
authors: Lung
authors: Anthony W-H
authors: AW
authors: Chan
authors: Ting-Fung
authors: TF
authors: Chan
authors: Nathalie
authors: N
authors: Wong
mesh_terms: D000328:Adult; D000368:Aged; D006528:Carcinoma, Hepatocellular / Q000235:genetics* / Q000401:mortality; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics* / Q000401:mortality; D008297:Male; D035683:MicroRNAs / Q000502:physiology; D008875:Middle Aged; D034741:RNA, Small Interfering / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D059467:Transcriptome
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering; D022661:RNA, Untranslated