TOH SOO TING

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bchtst@nus.edu.sg


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    Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma
    (BioMed Central Ltd., 2019) Jin, Y.; Lee, W.Y.; Toh, S.T.; Tennakoon, C.; Toh, H.C.; Chow, P.K.-H.; Chung, A.Y.-F.; Chong, S.S.; Ooi, L.L.-P.-J.; Sung, W.-K.; Lee, C.G.-L.; DEPARTMENT OF COMPUTER SCIENCE; DEAN'S OFFICE (DUKE-NUS MEDICAL SCHOOL); DUKE-NUS MEDICAL SCHOOL; PAEDIATRICS; BIOCHEMISTRY
    Background: Hepatocellular carcinoma is the second most deadly cancer with late presentation and limited treatment options, highlighting an urgent need to better understand HCC to facilitate the identification of early-stage biomarkers and uncover therapeutic targets for the development of novel therapies for HCC. Methods: Deep transcriptome sequencing of tumor and paired non-tumor liver tissues was performed to comprehensively evaluate the profiles of both the host and HBV transcripts in HCC patients. Differential gene expression patterns and the dys-regulated genes associated with clinical outcomes were analyzed. Somatic mutations were identified from the sequencing data and the deleterious mutations were predicted. Lastly, human-HBV chimeric transcripts were identified, and their distribution, potential function and expression association were analyzed. Results: Expression profiling identified the significantly upregulated TP73 as a nodal molecule modulating expression of apoptotic genes. Approximately 2.5% of dysregulated genes significantly correlated with HCC clinical characteristics. Of the 110 identified genes, those involved in post-translational modification, cell division and/or transcriptional regulation were upregulated, while those involved in redox reactions were downregulated in tumors of patients with poor prognosis. Mutation signature analysis identified that somatic mutations in HCC tumors were mainly non-synonymous, frequently affecting genes in the micro-environment and cancer pathways. Recurrent mutations occur mainly in ribosomal genes. The most frequently mutated genes were generally associated with a poorer clinical prognosis. Lastly, transcriptome sequencing suggest that HBV replication in the tumors of HCC patients is rare. HBV-human fusion transcripts are a common observation, with favored HBV and host insertion sites being the HBx C-terminus and gene introns (in tumors) and introns/intergenic-regions (in non-tumors), respectively. HBV-fused genes in tumors were mainly involved in RNA binding while those in non-tumors tissues varied widely. These observations suggest that while HBV may integrate randomly during chronic infection, selective expression of functional chimeric transcripts may occur during tumorigenesis. Conclusions: Transcriptome sequencing of HCC patients reveals key cancer molecules and clinically relevant pathways deregulated/mutated in HCC patients and suggests that while HBV may integrate randomly during chronic infection, selective expression of functional chimeric transcripts likely occur during the process of tumorigenesis. © 2019 The Author(s).
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    Publication
    Lethal-7 is down-regulated by the hepatitis B virus x protein and targets signal transducer and activator of transcription 3
    (2010) Wang, Y.; Toh, S.T.; Lee, C.G.L.; Lu, Y.; Sung, W.-K.; Tan, P.; Chow, P.; Chung, A.Y.F.; Jooi, L.L.P.; BIOCHEMISTRY; COMPUTER SCIENCE
    Background & Aims: The pleiotropic hepatitis B virus (HBV) x protein (HBx), associated with hepatocellular carcinoma (HCC), has been implicated in the deregulation of cellular gene expression at the transcriptional level. To date, it remains unknown if HBx regulates the expression of miRNAs which play important roles in gene-regulation at the post-transcriptional and/or translational level. Methods: miRNA microarrays were employed to compare the expression of cellular miRNAs in HBx-versus control-HepG2 cells. Reverse-transcription Taqman realtime-PCR was used to examine let-7a expression in normal liver as well as paired HCC-tumor and adjacent non-tumorous liver. Let-7a miRNA was functionally characterized in cells with transiently altered let-7a expression. The direct target of let-7a was identified in silico and validated using 3′UTR-reporter assay. Results: HBx up-regulates 7 and down-regulates 11 miRNAs, including the let-7 family. HBx expression was found to have a significant inverse correlation with the expression of the highly-expressed members of the let-7 family in HCC patients, highlighting the clinical relevance of our observations. Further characterization of let-7a, the most highly expressed let-7 family member, revealed that it negatively regulates cellular proliferation partly through targeting signal transducer and activator of transcription 3 (STAT3). HBx-mediated down-regulation of let-7a and up-regulation of STAT3 supports cell proliferation in HBx cells. Conclusion: This study thus represents the first demonstration of HBx's ability to deregulate cellular miRNA expression. The deregulation of the expression of the let-7 family of miRNAs by HBx may represent a potential novel pathway through which HBx acts to deregulate cell proliferation leading to hepatocarcinogenesis. © 2010 European Association for the Study of the Liver.