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1.
J Magn Reson Imaging ; 57(2): 485-492, 2023 02.
Article in English | MEDLINE | ID: mdl-35753084

ABSTRACT

BACKGROUND: Liver fibrosis is characterized by macromolecule depositions. Recently, a novel technology termed macromolecular proton fraction quantification based on spin-lock magnetic resonance imaging (MPF-SL) is reported to measure macromolecule levels. HYPOTHESIS: MPF-SL can detect early-stage liver fibrosis by measuring macromolecule levels in the liver. STUDY TYPE: Retrospective. SUBJECTS: Fifty-five participants, including 22 with no fibrosis (F0) and 33 with early-stage fibrosis (F1-2), were recruited. FIELD STRENGTH/SEQUENCE: 3 T; two-dimensional (2D) MPF-SL turbo spin-echo sequence, 2D spin-lock T1rho turbo spin-echo sequence, and multi-slice 2D gradient echo sequence. ASSESSMENT: Macromolecular proton fraction (MPF), T1rho, liver iron concentration (LIC), and fat fraction (FF) biomarkers were quantified within regions of interest. STATISTICAL TESTS: Group comparison of the biomarkers using Mann-Whitney U tests; correlation between the biomarkers assessed using Spearman's rank correlation coefficient and linear regression with goodness-of-fit; fibrosis stage differentiation using receiver operating characteristic curve (ROC) analysis. P-value < 0.05 was considered statistically significant. RESULTS: Average T1rho was 41.76 ± 2.94 msec for F0 and 41.15 ± 3.73 msec for F1-2 (P = 0.60). T1rho showed nonsignificant correlation with either liver fibrosis (ρ = -0.07; P = 0.61) or FF (ρ = -0.14; P = 0.35) but indicated a negative correlation with LIC (ρ = -0.66). MPF was 4.73 ± 0.45% and 5.65 ± 0.81% for F0 and F1-2 participants, respectively. MPF showed a positive correlation with liver fibrosis (ρ = 0.59), and no significant correlations with LIC (ρ = 0.02; P = 0.89) or FF (ρ = 0.05; P = 0.72). The area under the ROC curve was 0.85 (95% confidence interval [CI] 0.75-0.95) and 0.55 (95% CI 0.39-0.71; P = 0.55) for MPF and T1rho to discriminate between F0 and F1-2 fibrosis, respectively. DATA CONCLUSION: MPF-SL has the potential to diagnose early-stage liver fibrosis and does not appear to be confounded by either LIC or FF. LEVEL OF EVIDENCE: 3 TECHNICAL EFFICACY STAGE: 3.


Subject(s)
Liver Cirrhosis , Protons , Humans , Retrospective Studies , Liver Cirrhosis/diagnostic imaging , Liver Cirrhosis/pathology , Magnetic Resonance Imaging/methods , Liver/diagnostic imaging , Liver/pathology , Fibrosis , Macromolecular Substances , Biomarkers
2.
Liver Int ; 42(1): 149-160, 2022 01.
Article in English | MEDLINE | ID: mdl-34610207

ABSTRACT

BACKGROUND & AIMS: How adiposity influences the effect of genetic variants on non-alcoholic fatty liver disease (NAFLD) in the Asian population remains unclear. We aimed to study the association between genetic risk variants and susceptibility/severity of NAFLD in the lean, overweight and obese individuals. METHODS: Nine hundred and four community subjects underwent proton-magnetic resonance spectroscopy and transient elastography examination. Lean (<23 kg/m2 ), overweight (23-24.9 kg/m2 ) and obesity (≥25 kg/m2 ) were defined according to the body mass index cut-offs for Asians. NAFLD was defined as intrahepatic triglycerides ≥5%. PNPLA3, TM6SF2, MBOAT7 and 9 other gene polymorphisms were analysed by rhAMPTM SNP assays. RESULTS: Five hundred and twenty-nine (58.5%), 162 (17.9%) and 213 (23.6%) subjects were lean, overweight and obese, respectively. The prevalence of NAFLD was 12.4%, 41.4% and 59.1% in the three groups (P < .001). Amongst those with NAFLD, lean subjects (30.3%) were more likely to carry the PNPLA3 rs738409 GG genotype than overweight (17.9%) and obese subjects (17.4%) (P = .003). Compared with the CC genotype, the GG genotype was associated with the greatest increase in the risk of NAFLD in lean subjects (odds ratio [OR] 6.04), compared with overweight (OR 3.43, 95% CI [1.06, 11.14]) and obese subjects (OR 2.51, 95% CI [0.93, 6.78]). Additionally, the TM6SF2 rs58542926 TT genotype was associated with reduced serum triglycerides only in lean subjects. A gene-BMI effect was not observed for the other gene polymorphisms. CONCLUSIONS: The PNPLA3 rs738409 gene polymorphism has a greater effect on liver fat in Asian lean individuals than in overweight or obese ones.


Subject(s)
Non-alcoholic Fatty Liver Disease , Genetic Predisposition to Disease , Genotype , Humans , Lipase/genetics , Liver/pathology , Membrane Proteins/genetics , Non-alcoholic Fatty Liver Disease/complications , Non-alcoholic Fatty Liver Disease/epidemiology , Non-alcoholic Fatty Liver Disease/genetics , Polymorphism, Single Nucleotide
3.
J Cell Mol Med ; 24(18): 10705-10713, 2020 09.
Article in English | MEDLINE | ID: mdl-32783366

ABSTRACT

Expression of ATP-binding cassette B5 (ABCB5) has been demonstrated to confer chemoresistance, enhance cancer stem cell properties and associate with poor prognosis in hepatocellular carcinoma (HCC). The aim of this study was to evaluate the genetic variations of ABCB5 in HCC patients with reference to healthy individuals and the clinicopathological significance. A pilot study has examined 20 out of 300 pairs HCC and paralleled blood samples using conventional sequencing method to cover all exons and exon/intron regions to investigate whether there will be novel variant sequence and mutation event. A total of 300 HCC and 300 healthy blood DNA samples were then examined by Sequenom MassARRAY genotyping and pyrosequencing for 38 SNP and 1 INDEL in ABCB5. Five novel SNPs were identified in ABCB5. Comparison of DNA from blood samples of HCC and healthy demonstrated that ABCB5 SNPs rs75494098, rs4721940 and rs10254317 were associated with HCC risk. Specific ABCB5 variants were associated with aggressive HCC features. SNP rs17143212 was significantly associated with ABCB5 expression level. Nonetheless, the paralleled blood and tumour DNA sequences from HCC patients indicated that ABCB5 mutation in tumours was not common and corroborated the TCGA data sets. In conclusion, ABCB5 genetic variants had significant association with HCC risk and aggressive tumour properties.


Subject(s)
ATP Binding Cassette Transporter, Subfamily B/genetics , Carcinoma, Hepatocellular/genetics , Liver Neoplasms/genetics , Animals , Asian People/genetics , Carcinoma, Hepatocellular/ethnology , DNA, Neoplasm/genetics , Disease-Free Survival , Exons/genetics , Genetic Predisposition to Disease , Genotype , Humans , INDEL Mutation , Introns/genetics , Kaplan-Meier Estimate , Liver Neoplasms/ethnology , Mutation , Neoplasms/genetics , Pilot Projects , Polymorphism, Single Nucleotide , Proportional Hazards Models , RNA, Messenger/biosynthesis , RNA, Neoplasm/biosynthesis , Risk , Sequence Alignment , Sequence Homology, Nucleic Acid , Species Specificity , Vertebrates/genetics
4.
J Pathol ; 251(1): 74-86, 2020 05.
Article in English | MEDLINE | ID: mdl-32162306

ABSTRACT

Serrated polyps are a clinically and molecularly heterogeneous group of lesions that can contribute to the development of colorectal cancers (CRCs). However, the molecular mechanism underlying the development of serrated lesions is still not well understood. Here, we combined multiple approaches to analyze the genetic alterations in 86 colorectal adenomas (including 35 sessile serrated lesions, 15 traditional adenomas, and 36 conventional adenomatous polyps). We also investigated the in vitro and in vivo oncogenic properties of a novel variant of the NCOA4-RET fusion gene. Molecular profiling revealed that sessile serrated lesions and traditional serrated adenomas have distinct clinicopathological and molecular features. Moreover, we identified receptor tyrosine kinase translocations exclusively in sessile serrated lesions (17%), and the observation was validated in a separate cohort of 34 sessile serrated lesions (15%). The kinase fusions as well as the BRAF and KRAS mutations were mutually exclusive to each other. Ectopic expression of a novel variant of the NCOA4-RET fusion gene promoted cell proliferation in vitro and in vivo, and the proliferation was significantly suppressed by RET kinase inhibitors. All of these underscored the importance of mitogen-activated protein kinase (MAPK) pathway activation in the serrated pathway of colorectal tumorigenesis. In addition, we demonstrated that the kinase fusion may occur early in the precursor lesion and subsequent loss of TP53 may drives the transformation to carcinoma during serrated tumorigenesis. In conclusion, we identified kinase fusions as a significant alternative driver of the serrated pathway in colorectal cancer development, and detecting their presence may serve as a biomarker for the diagnosis of sessile serrated lesions. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Subject(s)
Colonic Neoplasms/pathology , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , Receptor Protein-Tyrosine Kinases/genetics , Adenoma/genetics , Adenoma/pathology , Animals , Colonic Neoplasms/genetics , Humans , Hyperplasia/genetics , Hyperplasia/pathology , Mice , Mutation/genetics , Proto-Oncogene Proteins B-raf/genetics , ras Proteins/genetics , ras Proteins/metabolism
5.
J Pathol ; 249(2): 166-172, 2019 10.
Article in English | MEDLINE | ID: mdl-31168847

ABSTRACT

Lymphoepithelioma-like hepatocellular carcinoma (LEL-HCC) is a distinct variant of HCC that is characterized by dense tumor-infiltrating lymphocytes (TILs). Patients with LEL-HCC also show better clinical outcomes compared to conventional HCC (c-HCC), which is commonly presented with low TIL. Emerging evidence has begun to highlight tumor-intrinsic genetic abnormalities in the tumor-host immune interfaces. However, genome-wide characterization of LEL-HCC remains largely unexplored. Here, we defined the genomic landscape of 12 LEL-HCC using whole-exome sequencing, and further underpinned those genetic alterations related to an immune active microenvironment by comparing findings to 15 c-HCC that were sequenced in parallel. Overall, the mutational load between LEL-HCC and c-HCC was similar. Interestingly, SNV incidences of specific genes (CTNNB1, AXIN1, NOTCH1, and NOTCH2) were significantly higher in c-HCC than LEL-HCC, suggesting a plausible link between activated Wnt/ß-catenin and Notch signaling pathways and immune avoidance. Marked focal amplification of chromosome 11q13.3 was prevalent in LEL-HCC. Using The Cancer Genome Atlas dataset, we further established oncogenes expressed from chromosome 11q13.3 (CCND1, FGF19, and FGF4) to be strongly associated with the immune checkpoint signature (CD274, PDCD1, BTLA, CTLA4, HAVCR2, IDO1, and LAG3). Our results have illustrated for the first time the somatic landscape of LEL-HCC, and highlighted molecular alterations that could be exploited in combinatory therapy with checkpoint inhibitors in targeting HCC. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.


Subject(s)
Biomarkers, Tumor/genetics , Carcinoma, Hepatocellular/genetics , Liver Neoplasms/genetics , Lymphocytes, Tumor-Infiltrating/pathology , Aged , Carcinoma, Hepatocellular/immunology , Carcinoma, Hepatocellular/pathology , DNA Copy Number Variations , Female , Gene Amplification , Gene Dosage , Genetic Predisposition to Disease , Humans , Liver Neoplasms/immunology , Liver Neoplasms/pathology , Lymphocytes, Tumor-Infiltrating/immunology , Male , Middle Aged , Mutation , Phenotype , Signal Transduction , Tumor Microenvironment , Exome Sequencing
6.
Hepatology ; 70(3): 1011-1025, 2019 09.
Article in English | MEDLINE | ID: mdl-30637779

ABSTRACT

Alternative splicing (AS) allows generation of cell type-specific mRNA transcripts and contributes to hallmarks of cancer. Genome-wide analysis for AS in human hepatocellular carcinoma (HCC), however, is limited. We sought to obtain a comprehensive AS landscape in HCC and define tumor-associated variants. Single-molecule real-time long-read RNA sequencing was performed on patient-derived HCC cells, and presence of splice junctions was defined by SpliceMap-LSC-IDP algorithm. We obtained an all-inclusive map of annotated AS variants and further discovered 362 alternative spliced variants that are not previously reported in any database (neither RefSeq nor GENCODE). They were mostly derived from intron retention and early termination codon with an in-frame open reading frame in 81.5%. We corroborated many of these predicted unannotated and annotated variants to be tumor specific in an independent cohort of primary HCC tumors and matching nontumoral liver. Using the combined Sanger sequencing and TaqMan junction assays, unique and common expressions of spliced variants including enzyme regulators (ARHGEF2, SERPINH1), chromatin modifiers (DEK, CDK9, RBBP7), RNA-binding proteins (SRSF3, RBM27, MATR3, YBX1), and receptors (ADRM1, CD44v8-10, vitamin D receptor, ROR1) were determined in HCC tumors. We further focused functional investigations on ARHGEF2 variants (v1 and v3) that arise from the common amplified site chr.1q22 of HCC. Their biological significance underscores two major cancer hallmarks, namely cancer stemness and epithelial-to-mesenchymal transition-mediated cell invasion and migration, although v3 is consistently more potent than v1. Conclusion: Alternative isoforms and tumor-specific isoforms that arise from aberrant splicing are common during the liver tumorigenesis. Our results highlight insights gained from the analysis of AS in HCC.


Subject(s)
Carcinoma, Hepatocellular/genetics , Gene Expression Regulation, Neoplastic/genetics , Liver Neoplasms/genetics , Oncogene Proteins/genetics , Receptor Tyrosine Kinase-like Orphan Receptors/genetics , Sequence Analysis, RNA/methods , Alternative Splicing , Carcinogenesis/genetics , Carcinoma, Hepatocellular/pathology , Chromosomal Proteins, Non-Histone/genetics , Genome-Wide Association Study , Humans , Liver Neoplasms/pathology , Poly-ADP-Ribose Binding Proteins/genetics , Protein Isoforms/genetics , RNA Splicing , Sensitivity and Specificity , Tumor Cells, Cultured , Exome Sequencing
7.
J Pathol ; 244(4): 394-407, 2018 04.
Article in English | MEDLINE | ID: mdl-29230817

ABSTRACT

Nasopharyngeal carcinoma (NPC) is a highly invasive epithelial malignancy that is prevalent in southern China and Southeast Asia. It is consistently associated with latent Epstein-Barr virus (EBV) infection. In NPC, miR-BARTs, the EBV-encoded miRNAs derived from BamH1-A rightward transcripts, are abundantly expressed and contribute to cancer development by targeting various cellular and viral genes. In this study, we establish a comprehensive transcriptional profile of EBV-encoded miRNAs in a panel of NPC patient-derived xenografts and an EBV-positive NPC cell line by small RNA sequencing. Among the 40 miR-BARTs, predominant expression of 22 miRNAs was consistently detected in these tumors. Among the abundantly expressed EBV-miRNAs, BART5-5p, BART7-3p, BART9-3p, and BART14-3p could negatively regulate the expression of a key DNA double-strand break (DSB) repair gene, ataxia telangiectasia mutated (ATM), by binding to multiple sites on its 3'-UTR. Notably, the expression of these four miR-BARTs represented more than 10% of all EBV-encoded miRNAs in tumor cells, while downregulation of ATM expression was commonly detected in all of our tested sequenced samples. In addition, downregulation of ATM was also observed in primary NPC tissues in both qRT-PCR (16 NP and 45 NPC cases) and immunohistochemical staining (35 NP and 46 NPC cases) analysis. Modulation of ATM expression by BART5-5p, BART7-3p, BART9-3p, and BART14-3p was demonstrated in the transient transfection assays. These findings suggest that EBV uses miRNA machinery as a key mechanism to control the ATM signaling pathway in NPC cells. By suppressing these endogenous miR-BARTs in EBV-positive NPC cells, we further demonstrated the novel function of miR-BARTs in inhibiting Zta-induced lytic reactivation. These findings imply that the four viral miRNAs work co-operatively to modulate ATM activity in response to DNA damage and to maintain viral latency, contributing to the tumorigenesis of NPC. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.


Subject(s)
Ataxia Telangiectasia Mutated Proteins/genetics , Epstein-Barr Virus Infections/virology , Herpesvirus 4, Human/genetics , MicroRNAs/genetics , Nasopharyngeal Carcinoma/genetics , Nasopharyngeal Neoplasms/genetics , RNA, Viral/genetics , 3' Untranslated Regions , Animals , Ataxia Telangiectasia Mutated Proteins/biosynthesis , Binding Sites , Cell Line, Tumor , DNA Damage , Enzyme Repression , Epstein-Barr Virus Infections/diagnosis , Female , Gene Expression Regulation, Neoplastic , Heterografts , Host-Pathogen Interactions , Humans , Male , Mice, Nude , Middle Aged , Nasopharyngeal Carcinoma/enzymology , Nasopharyngeal Carcinoma/pathology , Nasopharyngeal Carcinoma/virology , Nasopharyngeal Neoplasms/enzymology , Nasopharyngeal Neoplasms/pathology , Nasopharyngeal Neoplasms/virology , Transcriptome , Virus Latency
8.
J Pathol ; 243(4): 418-430, 2017 12.
Article in English | MEDLINE | ID: mdl-28862757

ABSTRACT

CCCTC-binding factor (CTCF) is a DNA-binding protein that interacts with a large number of highly divergent target sequences throughout the genome. It is implicated in a variety of functions, including chromatin organization and transcriptional control. The functional role of CTCF in tumour pathogenesis remains elusive. We showed that CTCF is frequently upregulated in a subset of primary hepatocellular carcinomas (HCCs) as compared with non-tumoural liver. Overexpression of CTCF was associated with shorter disease-free survival of patients. Short hairpin RNA (shRNA)-mediated suppression of CTCF inhibited cell proliferation, motility and invasiveness in HCC cell lines; these effects were correlated with prominent reductions in the expression of telomerase reverse transcriptase (TERT), the shelterin complex member telomerase repeat-binding factor 1, and forkhead box protein M1 (FOXM1). In contrast, upregulation of CTCF was positively correlated with FOXM1 and TERT expression in clinical HCC biopsies. Depletion of CTCF resulted in reduced motility and invasiveness in HCC cells that could be reversed by ectopic expression of FOXM1, suggesting that FOXM1 is one of the important downstream effectors of CTCF in HCC. Reporter gene analysis suggested that depletion of CTCF is associated with reduced FOXM1 and TERT promoter activity. Chromatin immunoprecipitation (ChIP)-polymerase chain reaction (PCR) analysis further revealed occupancy of the FOXM1 promoter by CTCF in vivo. Importantly, depletion of CTCF by shRNA significantly inhibited tumour progression and metastasis in HCC mouse models. Our work uncovered a novel functional role of CTCF in HCC pathogenesis, which suggests that targeting CTCF could be further explored as a potential therapeutic strategy for HCC. © 2017 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.


Subject(s)
CCCTC-Binding Factor/metabolism , Carcinoma, Hepatocellular/metabolism , Cell Proliferation , Forkhead Box Protein M1/metabolism , Liver Neoplasms/metabolism , Animals , Binding Sites , CCCTC-Binding Factor/genetics , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/secondary , Carcinoma, Hepatocellular/therapy , Cell Movement , Disease-Free Survival , Female , Forkhead Box Protein M1/genetics , Gene Expression Regulation, Neoplastic , Hep G2 Cells , Humans , Kaplan-Meier Estimate , Liver Neoplasms/genetics , Liver Neoplasms/pathology , Liver Neoplasms/therapy , Mice, Inbred BALB C , Mice, Nude , Neoplasm Invasiveness , Promoter Regions, Genetic , RNA Interference , Signal Transduction , Telomerase/genetics , Telomerase/metabolism , Telomere/genetics , Telomere/metabolism , Telomere Homeostasis , Time Factors , Transcription, Genetic , Transfection , Tumor Burden
10.
J Hepatol ; 60(4): 809-15, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24291241

ABSTRACT

BACKGROUND & AIMS: Liver biopsy is the gold standard for diagnosing non-alcoholic fatty liver disease (NAFLD) but with practical constraints. Phosphorus magnetic resonance spectroscopy ((31)P-MRS) allows in vivo assessment of hepatocellular metabolism and has shown potential for biochemical differentiation in diffuse liver disease. Our aims were to describe spectroscopic signatures in biopsy-proven NAFLD and to determine diagnostic performance of (31)P-MRS for non-alcoholic steatohepatitis (NASH). METHODS: (31)P-MRS was performed in 151 subjects, comprised of healthy controls (n=19) and NAFLD patients with non-NASH (n=37) and NASH (n=95). Signal intensity ratios for phosphomonoesters (PME) including phosphoethanolamine (PE), phosphodiesters (PDE) including glycerophosphocholine (GPC), total nucleotide triphosphate (NTP) including α-NTP, and inorganic phosphate (Pi), expressed relative to total phosphate (TP) or [PME+PDE] and converted to percentage, were obtained. RESULTS: Compared to controls, both NAFLD groups had increased PDE/TP (p<0.001) and decreased Pi/TP (p=0.011). Non-NASH patients showed decreased PE/[PME+PDE] (p=0.048), increased GPC/[PME+PDE] (p<0.001), and normal NTP/TP and α-NTP/TP. Whereas, NASH patients had normal PE/[PME+PDE] and GPC/[PME+PDE], but decreased NTP/TP (p=0.004) and α-NTP/TP (p<0.001). The latter was significantly different between non-NASH and NASH (p=0.047) and selected as discriminating parameter, with area under the receiver-operating characteristics curve of 0.71 (95% confidence interval, 0.62-0.79). An α-NTP/TP cutoff of 16.36% gave 91% sensitivity and cutoff of 10.57% gave 91% specificity for NASH. CONCLUSIONS: (31)P-MRS shows distinct biochemical changes in different NAFLD states, and has fair diagnostic accuracy for NASH.


Subject(s)
Magnetic Resonance Spectroscopy/methods , Non-alcoholic Fatty Liver Disease/diagnosis , Non-alcoholic Fatty Liver Disease/metabolism , Phosphorus/metabolism , Adult , Case-Control Studies , Ethanolamines/metabolism , Female , Glycerylphosphorylcholine/metabolism , Humans , Male , Middle Aged , Non-alcoholic Fatty Liver Disease/pathology , Nucleotides/metabolism , Phosphates/metabolism
11.
J Hepatol ; 58(6): 1165-73, 2013 Jun.
Article in English | MEDLINE | ID: mdl-23376363

ABSTRACT

BACKGROUND & AIMS: 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.


Subject(s)
Carcinoma, Hepatocellular/genetics , High-Throughput Nucleotide Sequencing , Liver Neoplasms/genetics , RNA, Small Interfering/genetics , RNA, Untranslated/genetics , Transcriptome , Adult , Aged , Carcinoma, Hepatocellular/mortality , Female , Gene Expression Regulation, Neoplastic , Humans , Liver Neoplasms/mortality , Male , MicroRNAs/physiology , Middle Aged
12.
Carcinogenesis ; 33(6): 1134-41, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22431718

ABSTRACT

Profiling of microRNA expression in human cancers has highlighted downregulation of miR-145 as a common event in epithelial malignancies. Here, we describe recurrent underexpression of miR-145 in hepatocellular carcinoma (HCC) and the identification of a biological pathway by which miR-145 exerts its functional effects in liver tumorigenesis. In a cohort of 80 HCC patients, quantitative reverse transcription polymerase chain reaction corroborated reduced miR-145 expression in 50% of tumors, which also correlated with a shorter disease-free survival of patients. One HCC tumor analyzed with low endogenous miR-145 was propagated as cell line. This in vitro model HKCI-C2 maintained low miR-145 level and upon restoration of miR-145 expression, a consistent inhibitory effect on cell viability and proliferation was readily found. Flow cytometric analysis indicated that miR-145 re-expression could induce G(2)-M cell cycle arrest and apoptosis. Multiple in silico algorithms predicted that miR-145 could target a number of genes along the insulin-like growth factor (IGF) signaling, including insulin receptor substrate (IRS1)-1, IRS2 and insulin-like growth factor 1 receptor. We found protein expression of these putative targets was concordantly downregulated in the presence of miR-145. Luciferase reporter assay further verified direct target association of miR-145 to specific sites of the IRS1 and IRS2 3'-untranslated regions. Subsequent analysis also affirmed miR-145 modulation on the IGF signaling cascade by reducing its downstream mediator, namely the active ß-catenin level. Taken together, our study shows for the first time the pleiotropic effect of miR-145 in targeting multiple components of the oncogenic IGF signaling pathway in HCC.


Subject(s)
Carcinoma, Hepatocellular/metabolism , Liver Neoplasms/metabolism , MicroRNAs/genetics , MicroRNAs/metabolism , Somatomedins/metabolism , Apoptosis , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/pathology , Cell Proliferation , Cell Survival , Cells, Cultured , Disease-Free Survival , G2 Phase Cell Cycle Checkpoints , Gene Expression Regulation, Neoplastic , Humans , Insulin Receptor Substrate Proteins/metabolism , Liver/pathology , Liver Neoplasms/genetics , Liver Neoplasms/pathology , Receptor, IGF Type 1/metabolism , Signal Transduction/genetics , beta Catenin/biosynthesis
13.
Clin Cancer Res ; 16(3): 867-75, 2010 Feb 01.
Article in English | MEDLINE | ID: mdl-20103675

ABSTRACT

PURPOSE: This study aims to profile the expressions of 156 microRNAs (miRNA) in hepatocellular carcinoma (HCC) and to characterize the functions of miR-222, the most significantly upregulated candidate identified. EXPERIMENTAL DESIGN: miRNA expression profile in HCC tumors, matching adjacent cirrhotic livers, and cell lines was conducted using quantitative PCR. Common miR-222 upregulations were further validated in a larger cohort of tumors. The functional effects of miR-222 inhibition on HCC cell lines were examined. The downstream modulated pathways and target of miR-222 were investigated by coupling gene expression profiling and pathway analysis, and by in silico prediction, respectively. Luciferase reporter assay was done to confirm target interaction. RESULTS: We identified a 40-miRNA signature that could discriminate tumors from adjacent cirrhotic liver tissue, and further corroborated common miR-222 overexpression in tumors relative to its premalignant counterpart (55.3%; P < 0.0001). Increased miR-222 expression correlated significantly with advanced stage HCC and with the shorter disease-free survival of patients (P < or = 0.01). Inhibition of miR-222 in Hep3B and HKCI-9 significantly retarded cell motility (P < 0.05). Further investigations suggested that AKT signaling was the major pathway influenced by miR-222. A consistent reduction of AKT phosphorylation in Hep3B and HKCI-9 was shown following miR-222 suppression. The protein phosphatase 2A subunit B (PPP2R2A) was predicted as a putative miR-222 target in silico. We found that miR-222 inhibition could augment the tumor protein level and restore luciferase activity in reporter construct containing the PPP2R2A 3' untranslated region (P = 0.0066). CONCLUSIONS: Our study showed that miR-222 overexpression is common in HCC and could confer metastatic potentials in HCC cells, possibly through activating AKT signaling.


Subject(s)
Carcinoma, Hepatocellular/genetics , Cell Movement , Liver Neoplasms/genetics , MicroRNAs/metabolism , Proto-Oncogene Proteins c-akt/metabolism , Carcinoma, Hepatocellular/pathology , Disease Progression , Humans , Liver Cirrhosis/complications , Liver Cirrhosis/genetics , Liver Neoplasms/pathology , Signal Transduction/genetics , Up-Regulation
14.
J Pathol ; 220(3): 348-60, 2010 Feb.
Article in English | MEDLINE | ID: mdl-19927314

ABSTRACT

Homozygous deletion screening has been widely utilized to define tumour suppressor genes (TSGs) in cancers. Although these biallelic deletions are infrequent, their identification has facilitated the discovery of many important TSGs. We have systematically examined the genome of hepatocellular carcinoma (HCC), a highly malignant tumour that is rapidly fatal, for the presence of homozygous deletions. Array-CGH analysis on early passage of HCC cultures and cell lines led us to identify six homozygous deleted (HD) regions. A high concordance between array-CGH and expression of HD genes was demonstrated, where crystallin Lambda1 (CRYL1; located on chromosome 13q12.11) displayed the most frequent down-regulation. We found that reduced mRNA expression of CRYL1 was common in HCC tumours when compared with their adjacent non-tumoural liver (p = 0.0097). Significant associations could also be drawn between repressed CRYL1 and advanced tumour staging, increased tumour size, and shorter disease-free survival of patients (p < 0.037). Moreover, homozygous deletions on CRYL1 could be detected in 36% of HCC cases, where recurrent HDs were identified on exons 1, 5, and 8. Examination of other causal events suggested histone deacetylation and promoter hypermethylation to be likely inactivating mechanisms as well. Re-expression of CRYL1 in the SK-Hep1 cell line, where biallelic loss of CRYL1 was found, induced profound inhibition of cellular proliferation and cell growth (p < 0.0015). By Annexin V staining, CRYL1 restoration readily increased pro-apoptotic cells with an induction of PARP cleavage. Flow cytometry further revealed that CRYL1 could prolong the G(2)-M phase, possibly through interruption of the Cdc2/cyclin B pathway. Given that regional chromosome 13q12-q14 loss is a causal genomic event in HCC tumourigenesis, our finding may have implications for identifying a novel TSG CRYL1 within this important locus.


Subject(s)
Carcinoma, Hepatocellular/metabolism , Crystallins/biosynthesis , Liver Neoplasms/metabolism , Neoplasm Proteins/biosynthesis , Adult , Aged , Aged, 80 and over , Carcinoma, Hepatocellular/diagnosis , Carcinoma, Hepatocellular/pathology , Cell Cycle/physiology , Comparative Genomic Hybridization/methods , Crystallins/genetics , Crystallins/physiology , Down-Regulation , Female , Humans , Liver Neoplasms/diagnosis , Liver Neoplasms/pathology , Male , Middle Aged , Neoplasm Proteins/genetics , Polymerase Chain Reaction/methods , Prognosis , RNA, Messenger/genetics , RNA, Neoplasm/genetics , Survival Analysis , Tumor Cells, Cultured
15.
J Gastroenterol Hepatol ; 24(6): 1002-7, 2009 Jun.
Article in English | MEDLINE | ID: mdl-19457152

ABSTRACT

BACKGROUND AND AIMS: The proposed cut-off values for the degree of fibrosis as assessed by liver stiffness measurement (LSM) might not be applicable in severe acute exacerbation of chronic hepatitis B (CHB). We aimed to assess the effect of necroinflammatory activity on LSM in this condition. METHODS: We prospectively recruited consecutive patients with severe acute exacerbation of CHB (alanine aminotransferase or ALT > 10x upper limit of normal). The relationship of ALT levels and LSM were serially assessed and liver biopsy was carried out after ALT normalization. RESULTS: Eleven patients (10 male, median age 43 years) were followed up for 25 weeks; nine patients received antiviral therapy. Overall, LSM was positively correlated with ALT levels (r = 0.67, P < 0.001). At initial presentation, the median serum ALT and LSM was 1136 (581-2210) IU/L and 26.3 (11.1-33.3) kPa. A progressive reduction in LSM was observed during subsequent visits in parallel with the reduction of ALT levels. At the last visit, the median ALT was 27 (11-52) IU/L and LSM was 7.7 (4.7-10.8) kPa. Among the five patients who had liver biopsy carried out at week 25, four patients had F2 fibrosis (LSM 5.7-8.1 kPa) and one patient had F3 fibrosis (LSM 8.6 kPa). CONCLUSIONS: LSM using transient elastography with the current proposed cut-off values might misdiagnose liver cirrhosis in patients suffering from severe acute exacerbation of CHB. LSM should be assessed after normalization of ALT levels in order to accurately assess the degree of fibrosis.


Subject(s)
Elasticity Imaging Techniques/methods , Hepatitis B, Chronic/complications , Hepatitis B, Chronic/diagnostic imaging , Liver Cirrhosis/diagnostic imaging , Adult , Chi-Square Distribution , Female , Hepatitis B, Chronic/physiopathology , Humans , Liver Cirrhosis/physiopathology , Liver Function Tests , Male , Prospective Studies
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