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Nasti A, Okumura M, Takeshita Y, Ho TTB, Sakai Y, Sato TA, Nomura C, Goto H, Nakano Y, Urabe T, Nakamura S, Tamura T, Matsubara K, Takamura T, Kaneko S. The declining insulinogenic index correlates with inflammation and metabolic dysregulation in non-obese individuals assessed by blood gene expression. Diabetes Res Clin Pract 2024; 208:111090. [PMID: 38216088 DOI: 10.1016/j.diabres.2024.111090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 12/19/2023] [Accepted: 01/04/2024] [Indexed: 01/14/2024]
Abstract
AIMS Diabetes onset is difficult to predict. Since decreased insulinogenic index (IGI) is observed in prediabetes, and blood gene expression correlates with insulin secretion, candidate biomarkers can be identified. METHODS We collected blood from 96 participants (54 males, 42 females) in 2008 (age: 52.5 years) and 2016 for clinical and gene expression analyses. IGI was derived from values of insulin and glucose at fasting and at 30 min post-OGTT. Two subgroups were identified based on IGI variation: "Minor change in IGI" group with absolute value variation between -0.05 and +0.05, and "Decrease in IGI" group with a variation between -20 and -0.05. RESULTS Following the comparison of "Minor change in IGI" and "Decrease in IGI" groups at time 0 (2008), we identified 77 genes correlating with declining IGI, related to response to lipid, carbohydrate, and hormone metabolism, response to stress and DNA metabolic processes. Over the eight years, genes correlating to declining IGI were related to inflammation, metabolic and hormonal dysregulation. Individuals with minor change in IGI, instead, featured homeostatic and regenerative responses. CONCLUSIONS By blood gene expression analysis of non-obese individuals, we identified potential gene biomarkers correlating to declining IGI, associated to a pathophysiology of inflammation and metabolic dysregulation.
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Affiliation(s)
- Alessandro Nasti
- Information-Based Medicine Development, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8641, Japan.
| | - Miki Okumura
- Department of Endocrinology and Metabolism, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Yumie Takeshita
- Department of Endocrinology and Metabolism, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Tuyen Thuy Bich Ho
- Information-Based Medicine Development, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8641, Japan
| | - Yoshio Sakai
- Department of Gastroenterology, Kanazawa University Hospital, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8641, Japan; Sakai Internal Medicine Clinic, Nonoichi, Ishikawa 921-8825, Japan
| | | | - Chiaki Nomura
- Department of Endocrinology and Metabolism, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Hisanori Goto
- Department of Endocrinology and Metabolism, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Yujiro Nakano
- Department of Endocrinology and Metabolism, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Takeshi Urabe
- Department of Gastroenterology, Public Central Hospital of Matto Ishikawa, 3-8 Kuramitsu, Hakusan, Ishikawa 924-8588, Japan
| | | | - Takuro Tamura
- Research and Development Center for Precision Medicine, University of Tsukuba, Tsukuba 305-8550, Japan
| | | | - Toshinari Takamura
- Department of Endocrinology and Metabolism, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Shuichi Kaneko
- Information-Based Medicine Development, Kanazawa University, Graduate School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8641, Japan; Department of Gastroenterology, Kanazawa University Hospital, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8641, Japan.
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Liu Y, Zhang H, Xu Y, Liu YZ, Al-Adra DP, Yeh MM, Zhang Z. Five Critical Gene-Based Biomarkers With Optimal Performance for Hepatocellular Carcinoma. Cancer Inform 2023; 22:11769351231190477. [PMID: 37577174 PMCID: PMC10413891 DOI: 10.1177/11769351231190477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most fatal cancers in the world. There is an urgent need to understand the molecular background of HCC to facilitate the identification of biomarkers and discover effective therapeutic targets. Published transcriptomic studies have reported a large number of genes that are individually significant for HCC. However, reliable biomarkers remain to be determined. In this study, built on max-linear competing risk factor models, we developed a machine learning analytical framework to analyze transcriptomic data to identify the most miniature set of differentially expressed genes (DEGs). By analyzing 9 public whole-transcriptome datasets (containing 1184 HCC samples and 672 nontumor controls), we identified 5 critical differentially expressed genes (DEGs) (ie, CCDC107, CXCL12, GIGYF1, GMNN, and IFFO1) between HCC and control samples. The classifiers built on these 5 DEGs reached nearly perfect performance in identification of HCC. The performance of the 5 DEGs was further validated in a US Caucasian cohort that we collected (containing 17 HCC with paired nontumor tissue). The conceptual advance of our work lies in modeling gene-gene interactions and correcting batch effect in the analytic framework. The classifiers built on the 5 DEGs demonstrated clear signature patterns for HCC. The results are interpretable, robust, and reproducible across diverse cohorts/populations with various disease etiologies, indicating the 5 DEGs are intrinsic variables that can describe the overall features of HCC at the genomic level. The analytical framework applied in this study may pave a new way for improving transcriptome profiling analysis of human cancers.
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Affiliation(s)
- Yongjun Liu
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Heping Zhang
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Yuqing Xu
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Yao-Zhong Liu
- Department of Biostatistics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - David P Al-Adra
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Matthew M Yeh
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
- Department of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Zhengjun Zhang
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Biostatistics and Medical Informatics, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
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3
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Chiang CC, Yeh H, Lim SN, Lin WR. Transcriptome analysis creates a new era of precision medicine for managing recurrent hepatocellular carcinoma. World J Gastroenterol 2023; 29:780-799. [PMID: 36816628 PMCID: PMC9932421 DOI: 10.3748/wjg.v29.i5.780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/23/2022] [Accepted: 01/10/2023] [Indexed: 02/06/2023] Open
Abstract
The high incidence of hepatocellular carcinoma (HCC) recurrence negatively impacts outcomes of patients treated with curative intent despite advances in surgical techniques and other locoregional liver-targeting therapies. Over the past few decades, the emergence of transcriptome analysis tools, including real-time quantitative reverse transcription PCR, microarrays, and RNA sequencing, has not only largely contributed to our knowledge about the pathogenesis of recurrent HCC but also led to the development of outcome prediction models based on differentially expressed gene signatures. In recent years, the single-cell RNA sequencing technique has revolutionized our ability to study the complicated crosstalk between cancer cells and the immune environment, which may benefit further investigations on the role of different immune cells in HCC recurrence and the identification of potential therapeutic targets. In the present article, we summarized the major findings yielded with these transcriptome methods within the framework of a causal model consisting of three domains: primary cancer cells; carcinogenic stimuli; and tumor microenvironment. We provided a comprehensive review of the insights that transcriptome analyses have provided into diagnostics, surveillance, and treatment of HCC recurrence.
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Affiliation(s)
- Chun-Cheng Chiang
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, United States
| | - Hsuan Yeh
- School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States
| | - Siew-Na Lim
- Department of Neurology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
| | - Wey-Ran Lin
- College of Medicine, Chang Gung University, Taoyuan 333, Taiwan
- Department of Gastroenterology and Hepatology, Linkou Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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Cavalluzzo B, Mauriello A, Ragone C, Manolio C, Tornesello ML, Buonaguro FM, Tvingsholm SA, Hadrup SR, Tagliamonte M, Buonaguro L. Novel Molecular Targets for Hepatocellular Carcinoma. Cancers (Basel) 2021; 14:140. [PMID: 35008303 PMCID: PMC8750630 DOI: 10.3390/cancers14010140] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/17/2021] [Accepted: 12/22/2021] [Indexed: 12/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of death from cancer globally. Indeed, only a few treatments are available, most of which are effective only for the early stages of the disease. Therefore, there is an urgent needing for potential markers for a specifically targeted therapy. Candidate proteins were selected from datasets of The Human Protein Atlas, in order to identify specific tumor-associated proteins overexpressed in HCC samples associated with poor prognosis. Potential epitopes were predicted from such proteins, and homology with peptides derived from viral proteins was assessed. A multiparametric validation was performed, including recognition by PBMCs from HCC-patients and healthy donors, showing a T-cell cross-reactivity with paired epitopes. These results provide novel HCC-specific tumor-associated antigens (TAAs) for immunotherapeutic anti-HCC strategies potentially able to expand pre-existing virus-specific CD8+ T cells with superior anticancer efficacy.
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Affiliation(s)
- Beatrice Cavalluzzo
- Innovative Immunological Models Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (B.C.); (A.M.); (C.R.); (C.M.); (M.T.)
| | - Angela Mauriello
- Innovative Immunological Models Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (B.C.); (A.M.); (C.R.); (C.M.); (M.T.)
| | - Concetta Ragone
- Innovative Immunological Models Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (B.C.); (A.M.); (C.R.); (C.M.); (M.T.)
| | - Carmen Manolio
- Innovative Immunological Models Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (B.C.); (A.M.); (C.R.); (C.M.); (M.T.)
| | - Maria Lina Tornesello
- Molecular Biology and Viral Oncogenesis Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (M.L.T.); (F.M.B.)
| | - Franco M. Buonaguro
- Molecular Biology and Viral Oncogenesis Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (M.L.T.); (F.M.B.)
| | - Siri Amanda Tvingsholm
- T-Cells and Cancer, Experimental & Translational Immunology (XTI), Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.A.T.); (S.R.H.)
| | - Sine Reker Hadrup
- T-Cells and Cancer, Experimental & Translational Immunology (XTI), Health Technology, Technical University of Denmark, 2800 Kongens Lyngby, Denmark; (S.A.T.); (S.R.H.)
| | - Maria Tagliamonte
- Innovative Immunological Models Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (B.C.); (A.M.); (C.R.); (C.M.); (M.T.)
| | - Luigi Buonaguro
- Innovative Immunological Models Unit, Istituto Nazionale Tumori-IRCCS-“Fond G. Pascale”, 80131 Naples, Italy; (B.C.); (A.M.); (C.R.); (C.M.); (M.T.)
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Yang Y, Ma Y, Yuan M, Peng Y, Fang Z, Wang J. Identifying the biomarkers and pathways associated with hepatocellular carcinoma based on an integrated analysis approach. Liver Int 2021; 41:2485-2498. [PMID: 34033190 DOI: 10.1111/liv.14972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 02/13/2023]
Abstract
BACKGROUND AND AIMS Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death worldwide. The molecular mechanism underlying HCC is still unclear. In this study, we conducted a comprehensive analysis to explore the genes, pathways and their interactions involved in HCC. METHODS We analysed the gene expression datasets corresponding to 488 samples from 10 studies on HCC and identified the genes differentially expressed in HCC samples. Then, the genes were compared against Phenolyzer and GeneCards to screen those potentially associated with HCC. The features of the selected genes were explored by mapping them onto the human protein-protein interaction network, and a subnetwork related to HCC was constructed. Hub genes in this HCC specific subnetwork were identified, and their relevance with HCC was investigated by survival analysis. RESULTS We identified 444 differentially expressed genes (177 upregulated and 267 downregulated) related to HCC. Functional enrichment analysis revealed that pathways like p53 signalling and chemical carcinogenesis were eriched in HCC genes. In the subnetwork related to HCC, five disease modules were detected. Further analysis identified six hub genes from the HCC specific subnetwork. Survival analysis showed that the expression levels of these genes were negatively correlated with survival rate of HCC patients. CONCLUSIONS Based on a systems biology framework, we identified the genes, pathways, as well as the disease specific network related to HCC. We also found novel biomarkers whose expression patterns were correlated with progression of HCC, and they could be candidates for further investigation.
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Affiliation(s)
- Yichen Yang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China.,Tianjin Medical University Cancer Institute & Hospital, Tianjin, China
| | - Yuequn Ma
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Meng Yuan
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Yonglin Peng
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Zhonghai Fang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Ju Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
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Abstract
Hepatitis D virus (HDV) is a small, defective RNA virus that depends on hepatitis B virus (HBV) for virion assembly and transmission. It replicates within the nucleus of hepatocytes and interacts with several cellular proteins. Chronic hepatitis D is a severe and progressive disease, leading to cirrhosis in up to 80% of cases. A high proportion of patients die of liver decompensation or hepatocellular carcinoma (HCC), but the lack of large prospective studies has made it difficult to precisely define the rate of these long-term complications. In particular, the question of whether HDV is an oncogenic virus has been a matter of debate. Studies conducted over the past decade provided evidence that HDV is associated with a significantly higher risk of developing HCC compared to HBV monoinfection. However, the mechanisms whereby HDV promotes liver cancer remain elusive. Recent data have demonstrated that the molecular profile of HCC-HDV is unique and distinct from that of HBV-HCC, with an enrichment of upregulated genes involved in cell-cycle/DNA replication, and DNA damage and repair, which point to genome instability as an important mechanism of HDV hepatocarcinogenesis. These data suggest that HBV and HDV promote carcinogenesis by distinct molecular mechanisms despite the obligatory dependence of HDV on HBV.
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7
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Identification of the possible therapeutic targets in the insulin-like growth factor 1 receptor pathway in a cohort of Egyptian hepatocellular carcinoma complicating chronic hepatitis C type 4. Drug Target Insights 2020; 14:1-11. [PMID: 33132693 PMCID: PMC7597224 DOI: 10.33393/dti.2020.1548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/20/2020] [Indexed: 11/24/2022] Open
Abstract
Background: Molecular targeted drugs are the first line of treatment of advanced hepatocellular carcinoma (HCC) due to its chemo- and radioresistant nature. HCC has several well-documented etiologic factors that drive hepatocarcinogenesis through different molecular pathways. Currently, hepatitis C virus (HCV) is a leading cause of HCC. Therefore, we included a unified cohort of HCV genotype 4-related HCCs to study the expression levels of genes involved in the insulin-like growth factor 1 receptor (IGF1R) pathway, which is known to be involved in all aspects of cancer growth and progression. Aim: Determine the gene expression patterns of IGF1R pathway genes in a cohort of Egyptian HCV-related HCCs. Correlate them with different patient/tumor characteristics. Determine the activity status of involved pathways. Methods: Total ribonucleic acid (RNA) was extracted from 32 formalin-fixed paraffin-embedded tissues of human HCV-related HCCs and 6 healthy liver donors as controls. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) using RT2 Profiler PCR Array for Human Insulin Signaling Pathway was done to determine significantly up- and downregulated genes with identification of most frequently coregulated genes, followed by correlation of gene expression with different patient/tumor characteristics. Finally, canonical pathway analysis was performed using the Ingenuity Pathway Analysis software. Results: Six genes – AEBP1, AKT2, C-FOS, PIK3R1, PRKCI, SHC1 – were significantly overexpressed. Thirteen genes – ADRB3, CEBPA, DUSP14, ERCC1, FRS3, IGF2, INS, IRS1, JUN, MTOR, PIK3R2, PPP1CA, RPS6KA1 – were significantly underexpressed. Several differentially expressed genes were related to different tumor/patient characteristics. Nitric oxide and reactive oxygen species production pathway was significantly activated in the present cohort, while the growth hormone signaling pathway was inactive. Conclusions: The gene expression patterns identified in this study may serve as possible therapeutic targets in HCV-related HCCs. The most frequently coregulated genes may serve to guide combined molecular targeted therapies. The IGF1R pathway showed evidence of inactivity in the present cohort of HCV-related HCCs, so targeting this pathway in therapy may not be effective.
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8
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Kaur H, Dhall A, Kumar R, Raghava GPS. Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. Front Genet 2020; 10:1306. [PMID: 31998366 PMCID: PMC6967266 DOI: 10.3389/fgene.2019.01306] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
The high mortality rate of hepatocellular carcinoma (HCC) is primarily due to its late diagnosis. In the past, numerous attempts have been made to design genetic biomarkers for the identification of HCC; unfortunately, most of the studies are based on small datasets obtained from a specific platform or lack reasonable validation performance on the external datasets. In order to identify a universal expression-based diagnostic biomarker panel for HCC that can be applicable across multiple platforms, we have employed large-scale transcriptomic profiling datasets containing a total of 2,316 HCC and 1,665 non-tumorous tissue samples. These samples were obtained from 30 studies generated by mainly four types of profiling techniques (Affymetrix, Illumina, Agilent, and High-throughput sequencing), which are implemented in a wide range of platforms. Firstly, we scrutinized overlapping 26 genes that are differentially expressed in numerous datasets. Subsequently, we identified a panel of three genes (FCN3, CLEC1B, and PRC1) as HCC biomarker using different feature selection techniques. Three-genes-based HCC biomarker identified HCC samples in training/validation datasets with an accuracy between 93 and 98%, Area Under Receiver Operating Characteristic curve (AUROC) in a range of 0.97 to 1.0. A reasonable performance, i.e., AUROC 0.91–0.96 achieved on validation dataset containing peripheral blood mononuclear cells, concurred their non-invasive utility. Furthermore, the prognostic potential of these genes was evaluated on TCGA-LIHC and GSE14520 cohorts using univariate survival analysis. This analysis revealed that these genes are prognostic indicators for various types of the survivals of HCC patients (e.g., Overall Survival, Progression-Free Survival, Disease-Free Survival). These genes significantly stratified high-risk and low-risk HCC patients (p-value <0.05). In conclusion, we identified a universal platform-independent three-genes-based biomarker that can predict HCC patients with high precision and also possess significant prognostic potential. Eventually, we developed a web server HCCpred based on the above study to facilitate scientific community (http://webs.iiitd.edu.in/raghava/hccpred/).
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Affiliation(s)
- Harpreet Kaur
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Rajesh Kumar
- Bioinformatics Center, CSIR-Institute of Microbial Technology, Chandigarh, India.,Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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Diaz G, Engle RE, Tice A, Melis M, Montenegro S, Rodriguez-Canales J, Hanson J, Emmert-Buck MR, Bock KW, Moore IN, Zamboni F, Govindarajan S, Kleiner DE, Farci P. Molecular Signature and Mechanisms of Hepatitis D Virus-Associated Hepatocellular Carcinoma. Mol Cancer Res 2018; 16:1406-1419. [PMID: 29858376 DOI: 10.1158/1541-7786.mcr-18-0012] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 04/19/2018] [Accepted: 05/24/2018] [Indexed: 12/15/2022]
Abstract
There is limited data on the molecular mechanisms whereby hepatitis D virus (HDV) promotes liver cancer. Therefore, serum and liver specimens obtained at the time of liver transplantation from well-characterized patients with HDV-HCC (n = 5) and with non-HCC HDV cirrhosis (n = 7) were studied using an integrated genomic approach. Transcriptomic profiling was performed using laser capture-microdissected (LCM) malignant and nonmalignant hepatocytes, tumorous and nontumorous liver tissue from patients with HDV-HCC, and liver tissue from patients with non-HCC HDV cirrhosis. HDV-HCC was also compared with hepatitis B virus (HBV) HBV-HCC alone, and hepatitis C virus (HCV) HCV-HCC. HDV malignant hepatocytes were characterized by an enrichment of upregulated transcripts associated with pathways involved in cell-cycle/DNA replication, damage, and repair (Sonic Hedgehog, GADD45, DNA-damage-induced 14-3-3σ, cyclins and cell-cycle regulation, cell cycle: G2-M DNA-damage checkpoint regulation, and hereditary breast cancer). Moreover, a large network of genes identified functionally relate to DNA repair, cell cycle, mitotic apparatus, and cell division, including 4 cancer testis antigen genes, attesting to the critical role of genetic instability in this tumor. Besides being overexpressed, these genes were also strongly coregulated. Gene coregulation was high not only when compared with nonmalignant hepatocytes, but also to malignant hepatocytes from HBV-HCC alone or HCV-HCC. Activation and coregulation of genes critically associated with DNA replication, damage, and repair point to genetic instability as an important mechanism of HDV hepatocarcinogenesis. This specific HDV-HCC trait emerged also from the comparison of the molecular pathways identified for each hepatitis virus-associated HCC. Despite the dependence of HDV on HBV, these findings suggest that HDV and HBV promote carcinogenesis by distinct molecular mechanisms.Implications: This study identifies a molecular signature of HDV-associated hepatocellular carcinoma and suggests the potential for new biomarkers for early diagnostics. Mol Cancer Res; 16(9); 1406-19. ©2018 AACR.
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Affiliation(s)
- Giacomo Diaz
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Ronald E Engle
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Ashley Tice
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Marta Melis
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Stephanie Montenegro
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Jaime Rodriguez-Canales
- Laser Capture Microdissection Core Facility, Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Jeffrey Hanson
- Laser Capture Microdissection Core Facility, Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Michael R Emmert-Buck
- Laser Capture Microdissection Core Facility, Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Kevin W Bock
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Ian N Moore
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institutes of Allergy and Infectious Diseases, NIH, Bethesda, Maryland
| | - Fausto Zamboni
- Liver Transplantation Center, Brotzu Hospital, Cagliari, Italy
| | - Sugantha Govindarajan
- Department of Pathology, Rancho Los Amigos Hospital, University of Southern California, Downey, California
| | - David E Kleiner
- Laboratory of Pathology, National Cancer Institute, NIH, Bethesda, Maryland
| | - Patrizia Farci
- Hepatic Pathogenesis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland.
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10
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Inokawa Y, Inaoka K, Sonohara F, Hayashi M, Kanda M, Nomoto S. Molecular alterations in the carcinogenesis and progression of hepatocellular carcinoma: Tumor factors and background liver factors. Oncol Lett 2016; 12:3662-3668. [PMID: 27900050 DOI: 10.3892/ol.2016.5141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 08/19/2016] [Indexed: 12/17/2022] Open
Abstract
Although hepatocellular carcinoma (HCC) is associated with poor prognosis worldwide, the molecular mechanisms underlying the carcinogenesis and progression of this disease remain unclear. Several tumor characteristics have previously been demonstrated to be prognostic factors of survival following hepatic resection, or the recurrence of HCC or other types of cancer. Comparisons of normal tissues and HCC tumor tissues have revealed the presence of numerous molecular alterations in HCC, including genetic and epigenetic mechanisms, particularly mutations in certain genes and DNA methylation in the promoter regions of tumor-suppressor genes. A number of studies have previously used array analysis to detect variations in the expression levels of cancer-associated genes and microRNAs, and in DNA methylation. However, an investigation of HCC tumor tissues may not determine the effect of noncancerous liver tissues (background liver) in patients with HCC. As HCC may recur multicentrically following resection, a damaged or chronically diseased HCC background liver may be considered as a pre-cancerous organ. Therefore, the influence of the background liver on HCC requires further study. Detailed studies regarding the background liver may be essential for the improved understanding of the carcinogenesis and progression of this malignancy; however only a few studies have investigated the microenvironment of the HCC background liver. The present review discusses prior molecular studies of hepatocarcinogenesis that focus on HCC and background liver tissues.
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Affiliation(s)
- Yoshikuni Inokawa
- Department of Surgery, Aichi Gakuin University School of Dentistry, Nagoya 464-8651, Japan; Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kenichi Inaoka
- Department of Surgery, Aichi Gakuin University School of Dentistry, Nagoya 464-8651, Japan; Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Fuminori Sonohara
- Department of Surgery, Aichi Gakuin University School of Dentistry, Nagoya 464-8651, Japan; Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Masamichi Hayashi
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Mitsuro Kanda
- Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Shuji Nomoto
- Department of Surgery, Aichi Gakuin University School of Dentistry, Nagoya 464-8651, Japan; Department of Gastroenterological Surgery (Surgery II), Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
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11
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Nambiar PR, Boutin SR, Raja R, Rosenberg DW. Global Gene Expression Profiling: A Complement to Conventional Histopathologic Analysis of Neoplasia. Vet Pathol 2016; 42:735-52. [PMID: 16301570 DOI: 10.1354/vp.42-6-735] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Transcriptional profiling of entire tumors has yielded considerable insight into the molecular mechanisms of heterogeneous cell populations within different types of neoplasms. The data thus acquired can be further refined by microdissection methods that enable the analyses of subpopulations of neoplastic cells. Separation of the various components of a neoplasm (i.e., stromal cells, inflammatory infiltrates, and blood vessels) has been problematic, primarily because of a paucity of tools for accurate microdissection. The advent of laser capture microdissection combined with powerful tools of linear amplification of RNA and high-throughput microarray-based assays have allowed the transcriptional mapping of intricate and highly complex networks within pure populations of neoplastic cells. With this approach, specific “molecular signatures” can be assigned to tumors of distinct or even similar histomorphology, thereby aiding the desired objective of pattern recognition, tumor classification, and prognostication. This review highlights the potential benefits of global gene expression profiling of tumor cells as a complement to conventional histopathologic analyses.
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Affiliation(s)
- P R Nambiar
- Division of Comparative Medicine, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139,USA.
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12
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Genomic-Wide Analysis with Microarrays in Human Oncology. MICROARRAYS 2015; 4:454-73. [PMID: 27600234 PMCID: PMC4996403 DOI: 10.3390/microarrays4040454] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/08/2015] [Accepted: 10/13/2015] [Indexed: 12/19/2022]
Abstract
DNA microarray technologies have advanced rapidly and had a profound impact on examining gene expression on a genomic scale in research. This review discusses the history and development of microarray and DNA chip devices, and specific microarrays are described along with their methods and applications. In particular, microarrays have detected many novel cancer-related genes by comparing cancer tissues and non-cancerous tissues in oncological research. Recently, new methods have been in development, such as the double-combination array and triple-combination array, which allow more effective analysis of gene expression and epigenetic changes. Analysis of gene expression alterations in precancerous regions compared with normal regions and array analysis in drug-resistance cancer tissues are also successfully performed. Compared with next-generation sequencing, a similar method of genome analysis, several important differences distinguish these techniques and their applications. Development of novel microarray technologies is expected to contribute to further cancer research.
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13
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Carrasco-Avino G, Schiano TD, Ward SC, Thung SN, Fiel MI. Primary sclerosing cholangitis: detailed histologic assessment and integration using bioinformatics highlights arterial fibrointimal hyperplasia as a novel feature. Am J Clin Pathol 2015; 143:505-13. [PMID: 25780002 DOI: 10.1309/ajcpvkfviprbxqr2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES Liver biopsy diagnosis of primary sclerosing cholangitis (PSC) is difficult. We performed a detailed histologic analysis of PSC cases using novel bioinformatics analysis to identify histologic features that may be useful in its diagnosis. METHODS PSC liver explants were examined and compared with primary biliary cirrhosis and hepatitis C explants to act as controls. Demographic, macroscopic, and histologic variables were analyzed using both conventional statistics and an integrative bioinformatics approach, significance analysis of microarrays (SAM), and hierarchical clustering analysis (HCA). RESULTS The PSC group was younger and had distinctive PSC features, including bile duct scars, onion-skin fibrosis, and arterial fibrointimal hyperplasia. SAM allowed the integration of variables by comparing PSC and control groups, whereas HCA was able to correctly categorize each group. CONCLUSIONS This study demonstrates characteristic PSC histology as well as arterial hyperplasia to be distinctive features that may aid in PSC diagnosis and be confirmed by bioinformatics.
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Affiliation(s)
| | - Thomas D. Schiano
- Division of Liver Diseases and Recanati-Miller Transplant Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Stephen C. Ward
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Swan N. Thung
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - M. Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY
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14
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SERPINB3 is associated with TGF-β1 and cytoplasmic β-catenin expression in hepatocellular carcinomas with poor prognosis. Br J Cancer 2014; 110:2708-15. [PMID: 24809782 PMCID: PMC4037839 DOI: 10.1038/bjc.2014.246] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 12/11/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is one of the most important sanitary problems for its prevalence and poor prognosis. To date, no information is available on the prognostic value of the ov-serpin SERPINB3, detected in primary liver cancer but not in normal liver. The aim of the study was to analyse SERPINB3 expression in liver cancer in relation with molecular signatures of poor prognosis and with clinical outcome. Methods: Liver tumours of 97 patients were analysed in parallel for SERPINB3, TGF-β and β-catenin. In a subgroup of 67 patients with adequate clinical follow-up, the correlation of molecular findings with clinical outcome was also carried out. Results: High SERPINB3 levels were detectable in 22% of the patients. A significant correlation of this serpin with TGF-β at transcription and protein level was observed, whereas for β-catenin a strong correlation was found only at post-transcription level. These findings were in agreement with transcriptome data meta-analysis, showing accumulation of SERPINB3 in the poor-prognosis subclass (S1). High levels of this serpin were significantly associated with early tumour recurrence and high SERPINB3 was the only variable significantly associated with time to recurrence at multivariate analysis. Conclusions: SERPINB3 is overexpressed in the subset of the most aggressive HCCs.
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15
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Caboux E, Paciencia M, Durand G, Robinot N, Wozniak MB, Galateau-Salle F, Byrnes G, Hainaut P, Le Calvez-Kelm F. Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples. PLoS One 2013; 8:e79826. [PMID: 24278187 PMCID: PMC3835918 DOI: 10.1371/journal.pone.0079826] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/03/2013] [Indexed: 12/31/2022] Open
Abstract
The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as “warm ischemia”. Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC) and 3 lung carcinomas (LC) cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN) revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of −3.5%/hr (95% CI: −7.0%/hr to 0.1%/hr; p = 0.054). In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5) and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1) was identified (FDR <0.05). Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.
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Affiliation(s)
- Elodie Caboux
- Laboratory Services and Biobank, International Agency for Research on Cancer, Lyon, France
| | - Maria Paciencia
- Department of Pathology, Centre Hospitalier Universitaire de Caen, Caen, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Nivonirina Robinot
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Magdalena B. Wozniak
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | | | - Graham Byrnes
- Biostatistics Group, International Agency for Research on Cancer, Lyon, France
| | - Pierre Hainaut
- International Agency for Research on Cancer, Lyon, France
- International Prevention Research Institute, Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
- * E-mail:
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Brokalaki EI, Weber F, Sotiropoulos GC, Daoudaki M, Cicinnati VR, Beckebaum S. Claudin-7 expression in hepatocellular carcinoma. Transplant Proc 2013; 44:2737-40. [PMID: 23146509 DOI: 10.1016/j.transproceed.2012.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND The importance of adhesion molecules for local invasion by neoplastic cells and development of metastasis has been confirmed by numerous studies over the past decade. Claudins are integral parts of tight junctions. The aim of the present study was to examine the significance of the expression of claudin-7 messenger RNA (mRNA) as a prognostic factor for hepatocellular carcinoma (HCC). PATIENTS AND METHODS We examined liver tumor and nontumor tissues from 20 HCC patients who underwent resection or liver transplantation. RESULTS A significant increase in the expression of claudin-7 was observed in tumor versus nontumor tissues. There was no significant correlation between the expression profile of claudin-7 mRNA and patient demographic data, the presence of cirrhosis, or the histological stage of tumor differentiation or vascular invasion. Survival analysis showed a trend toward a better prognosis among patients with overexpression of claudin-7 in tumor tissues.
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Affiliation(s)
- E I Brokalaki
- Department of General, Visceral and Transplantation Surgery, University Hospital Essen, Essen, Germany.
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Ueda T, Honda M, Horimoto K, Aburatani S, Saito S, Yamashita T, Sakai Y, Nakamura M, Takatori H, Sunagozaka H, Kaneko S. Gene expression profiling of hepatitis B- and hepatitis C-related hepatocellular carcinoma using graphical Gaussian modeling. Genomics 2013; 101:238-48. [PMID: 23485556 DOI: 10.1016/j.ygeno.2013.02.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 02/09/2013] [Accepted: 02/11/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Gene expression profiling of hepatocellular carcinoma (HCC) and background liver has been studied extensively; however, the relationship between the gene expression profiles of different lesions has not been assessed. METHODS We examined the expression profiles of 34 HCC specimens (17 hepatitis B virus [HBV]-related and 17 hepatitis C virus [HCV]-related) and 71 non-tumor liver specimens (36 chronic hepatitis B [CH-B] and 35 chronic hepatitis C [CH-C]) using an in-house cDNA microarray consisting of liver-predominant genes. Graphical Gaussian modeling (GGM) was applied to elucidate the interactions of gene clusters among the HCC and non-tumor lesions. RESULTS In CH-B-related HCC, the expression of vascular endothelial growth factor-family signaling and regulation of T cell differentiation, apoptosis, and survival, as well as development-related genes was up-regulated. In CH-C-related HCC, the expression of ectodermal development and cell proliferation, wnt receptor signaling, cell adhesion, and defense response genes was also up-regulated. Many of the metabolism-related genes were down-regulated in both CH-B- and CH-C-related HCC. GGM analysis of the HCC and non-tumor lesions revealed that DNA damage response genes were associated with AP1 signaling in non-tumor lesions, which mediates the expression of many genes in CH-B-related HCC. In contrast, signal transducer and activator of transcription 1 and phosphatase and tensin homolog were associated with early growth response protein 1 signaling in non-tumor lesions, which potentially promotes angiogenesis, fibrogenesis, and tumorigenesis in CH-C-related HCC. CONCLUSIONS Gene expression profiling of HCC and non-tumor lesions revealed the predisposing changes of gene expression in HCC. This approach has potential for the early diagnosis and possible prevention of HCC.
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Affiliation(s)
- Teruyuki Ueda
- Department of Gastroenterology, Graduate School of Medicine, Kanazawa University, Kanazawa, Takara-Machi 13-1, Kanazawa 920-8641, Japan
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Mizuno H, Honda M, Shirasaki T, Yamashita T, Yamashita T, Mizukoshi E, Kaneko S. Heterogeneous nuclear ribonucleoprotein A2/B1 in association with hTERT is a potential biomarker for hepatocellular carcinoma. Liver Int 2012; 32:1146-55. [PMID: 22372738 DOI: 10.1111/j.1478-3231.2012.02778.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 02/02/2012] [Indexed: 01/06/2023]
Abstract
BACKGROUND The heterogeneous nature of hepatocellular carcinoma (HCC) and the lack of appropriate biomarkers have hampered patient prognosis and treatment stratification. To identify a new prognostic biomarker that is related to human telomerase reverse transcriptase (hTERT) in HCC, we employed a unique proteomics approach using liquid chromatograph-mass spectrometry/mass spectrometry (LC-MS/MS) after gel filtration purification of liver tissue. METHODS Protein lysates from HCC and cirrhotic liver tissue were subjected to gel filtration using high performance liquid chromatography. The telomerase complex was identified at a molecular mass of 350 kDa in parallel with telomerase activity. These fractionated lysates of 350 kDa were analyzed by LC-MS/MS. The relation of the identified marker and prognosis was statistically examined in surgically resected HCC patients. RESULTS We identified 24 differentially expressed proteins in HCC. One of these proteins, heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNP A2/B1), was further analyzed by immunoprecipitation assay using tissue and cell line samples and found to interact with hTERT. Moreover small interfering RNA against hnRNP A2/B1 suppressed telomerase activity, and immunohistochemical examination showed that the enhanced nuclear and cytoplasmic hnRNP A2/B1 expression in HCC was significantly associated with histological grade of tumor differentiation and microvascular invasion of HCC. Furthermore, survival analysis of 74 HCC patients who received curative surgical treatment showed that hnRNP A2/B1 expression is an independent prognostic factor for patient survival. CONCLUSIONS Heterogeneous nuclear ribonucleoprotein A2/B1, an hTERT-associated protein, is a potential prognostic biomarker for HCC patients and might be a therapeutic target of HCC.
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Affiliation(s)
- Hideki Mizuno
- Department of Gastroenterology, Kanazawa University Graduate School of Medicine, Kanazawa, Japan
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Wong C, Ng IOL. Genomics of Hepatocellular Carcinoma. PRIMARY LIVER CANCER 2012:45-78. [DOI: 10.1007/978-3-642-28702-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
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Fatima G, Mathan G, Kumar V. The HBx protein of hepatitis B virus regulates the expression, intracellular distribution and functions of ribosomal protein S27a. J Gen Virol 2011; 93:706-715. [PMID: 22158882 DOI: 10.1099/vir.0.035691-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The pleiotropic HBx protein of hepatitis B virus is linked functionally to the development of hepatocellular carcinoma (HCC) via effectors and signalling pathways of the host. To identify such effectors in a macrocarcinogenic environment, a PCR-based cDNA subtraction analysis was carried out in the X15-myc oncomouse model of HCC. Altogether, 19 categories of genes, mainly involved in protein biosynthesis and the electron-transport chain, were found to be upregulated in the liver of these mice. Ribosomal protein S27a (RPS27a), which is a natural fusion protein of N-terminal ubiquitin and C-terminal extension protein (CEP), topped the list of expressed genes, with >20-fold higher expression compared with its normal level. Sustained and elevated expression of RPS27a in the mouse liver and its moderate expression in cell culture in the presence of HBx suggested an indirect role of RPS27a in hepatocarcinogenesis. Nevertheless, a remarkable change in the intracellular distribution of ubiquitin from cytoplasm to late-endosomal lysosomes, and of CEP from nucleoli to the perinucleolar region/nuclear foci, was observed in the presence of HBx. RPS27a accelerated the progression of the cell cycle and cooperated with HBx in this process. Further, the knockdown of RPS27a expression by RNA interference in an HBx microenvironment led to retarded cell-cycle progression and reduced cell size. Thus, these results suggest strongly that RPS27a could be an effector of HBx-mediated hepatocarcinogenesis.
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Affiliation(s)
- Grace Fatima
- Virology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Ganeshan Mathan
- Virology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vijay Kumar
- Virology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
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Chen MH, Yang WLR, Lin KT, Liu CH, Liu YW, Huang KW, Chang PMH, Lai JM, Hsu CN, Chao KM, Kao CY, Huang CYF. Gene expression-based chemical genomics identifies potential therapeutic drugs in hepatocellular carcinoma. PLoS One 2011; 6:e27186. [PMID: 22087264 PMCID: PMC3210146 DOI: 10.1371/journal.pone.0027186] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 10/11/2011] [Indexed: 12/17/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive tumor with a poor prognosis. Currently, only sorafenib is approved by the FDA for advanced HCC treatment; therefore, there is an urgent need to discover candidate therapeutic drugs for HCC. We hypothesized that if a drug signature could reverse, at least in part, the gene expression signature of HCC, it might have the potential to inhibit HCC-related pathways and thereby treat HCC. To test this hypothesis, we first built an integrative platform, the "Encyclopedia of Hepatocellular Carcinoma genes Online 2", dubbed EHCO2, to systematically collect, organize and compare the publicly available data from HCC studies. The resulting collection includes a total of 4,020 genes. To systematically query the Connectivity Map (CMap), which includes 6,100 drug-mediated expression profiles, we further designed various gene signature selection and enrichment methods, including a randomization technique, majority vote, and clique analysis. Subsequently, 28 out of 50 prioritized drugs, including tanespimycin, trichostatin A, thioguanosine, and several anti-psychotic drugs with anti-tumor activities, were validated via MTT cell viability assays and clonogenic assays in HCC cell lines. To accelerate their future clinical use, possibly through drug-repurposing, we selected two well-established drugs to test in mice, chlorpromazine and trifluoperazine. Both drugs inhibited orthotopic liver tumor growth. In conclusion, we successfully discovered and validated existing drugs for potential HCC therapeutic use with the pipeline of Connectivity Map analysis and lab verification, thereby suggesting the usefulness of this procedure to accelerate drug repurposing for HCC treatment.
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Affiliation(s)
- Ming-Huang Chen
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Wu-Lung R. Yang
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
| | - Kuan-Ting Lin
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Chia-Hung Liu
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Yu-Wen Liu
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Kai-Wen Huang
- Department of Surgery & Hepatitis Research Center, National Taiwan University Hospital, National Taiwan University, Taipei, Taiwan
| | - Peter Mu-Hsin Chang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Jin-Mei Lai
- Department of Life Science, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Chun-Nan Hsu
- Institute of Information Science, Academia Sinica, Taipei, Taiwan
- Information Sciences Institute, University of Southern California, Marina del Rey, California, United States of America
| | - Kun-Mao Chao
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Cheng-Yan Kao
- Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Biomedical Electronic and Bioinformatics, National Taiwan University, Taipei, Taiwan
| | - Chi-Ying F. Huang
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
- Institute of Biopharmaceutical Sciences, National Yang-Ming University, Taipei, Taiwan
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Jung S, Lee S, Lee J, Li C, Ohk JY, Jeong HK, Lee S, Kim S, Choi Y, Kim S, Lee H, Lee MS. Protein expression pattern in response to ionizing radiation in MCF-7 human breast cancer cells. Oncol Lett 2011; 3:147-154. [PMID: 22740871 DOI: 10.3892/ol.2011.444] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2011] [Accepted: 09/26/2011] [Indexed: 01/06/2023] Open
Abstract
Breast cancer is one of the most common types of cancer in women and is highly treatable by radiotherapy. However, repeated exposure to radiation results in tumor cell resistance. Understanding the molecular mechanisms involved in the response of tumors to γ-irradiation is important for improving radiotherapy. For this reason, we aimed to identify radiation-responsive genes at the protein level. In the present study, we observed differentially expressed proteins using 2D-PAGE and MALDI-TOF-MS for the global analysis of protein expression patterns in response to ionizing radiation (IR). When the expression patterns of proteins were compared to a control gel, numerous spots were found that differed greatly. Among them, 11 spots were found to be significantly different. One set of proteins (GH2, RGS17, BAK1, CCNH, TSG6, RAD51B, IGFBP1 and CASP14) was upregulated and another set of proteins (C1QRF, PLSCR2 and p34(SE1-1)) was downregulated after exposure to γ-rays. These proteins are known to be related to cell cycle control, apoptosis, DNA repair, cell proliferation and other signaling pathways.
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Affiliation(s)
- Samil Jung
- Research Center for Women's Diseases, Sookmyung Women's University, Seoul
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Wang K, Liu J, Yan ZL, Li J, Shi LH, Cong WM, Xia Y, Zou QF, Xi T, Shen F, Wang HY, Wu MC. Overexpression of aspartyl-(asparaginyl)-beta-hydroxylase in hepatocellular carcinoma is associated with worse surgical outcome. Hepatology 2010; 52:164-73. [PMID: 20578260 DOI: 10.1002/hep.23650] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
UNLABELLED The association between the overexpression of aspartyl-(asparaginyl)-beta-hydroxylase (AAH) and the invasiveness of hepatocellular carcinoma (HCC) in vitro has been reported. However, the prognostic value of AAH expression in HCC remains unclear. The purpose of this study was to investigate the relationship between AAH expression, tumor recurrence, and patient survival. We identified AAH as the most overexpressed gene in HCC by way of complementary DNA microarray hybridization. A prospective study of 233 patients undergoing curative resection indicated that AAH expression was an independent factor affecting recurrence (hazard ratio [HR] 3.161, 95% confidence interval [CI] 2.115-4.724, P < 0.001) and survival (HR 2.712, 95% CI 1.734-4.241, P < 0.001). Patients with AAH overexpression had a poorer prognosis than those with AAH underexpression (P < 0.001 for both recurrence and survival). In Barcelona Clinic Liver Cancer stage A patients with AAH overexpression or underexpression, the tumor recurrence and survival rates were also statistically different (45% and 85% versus16% and 33% in 1- and 3-year cumulative recurrence rates, respectively; 73% and 37% versus 90% and 80% in 1- and 3-year survival rates, respectively; P < 0.001 for both). Furthermore, in stage A patients with tumors measuring < or =5 cm in diameter, the time to recurrence was 26.7 +/- 1.6 versus 51.9 +/- 2.8 months, and the 1- and 3- year survival rates were 97% and 52% versus 100% and 90% in AAH overexpression and underexpression patients, respectively (P < 0.001 for both). CONCLUSION AAH overexpression in HCC is strongly correlated with worse surgical outcome, and this molecule likely provides a more precise prognostic predictor in early stage HCCs.
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Affiliation(s)
- Kui Wang
- Department of Comprehensive Treatment, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, P. R. China
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Hodo Y, Hashimoto SI, Honda M, Yamashita T, Suzuki Y, Sugano S, Kaneko S, Matsushima K. Comprehensive gene expression analysis of 5'-end of mRNA identified novel intronic transcripts associated with hepatocellular carcinoma. Genomics 2010; 95:217-23. [PMID: 20096344 DOI: 10.1016/j.ygeno.2010.01.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 12/31/2009] [Accepted: 01/14/2010] [Indexed: 01/23/2023]
Abstract
To elucidate the molecular feature of human hepatocellular carcinoma (HCC), we performed 5'-end serial analysis of gene expression (5'SAGE), which allows genome-wide identification of transcription start sites in addition to quantification of mRNA transcripts. Three 5'SAGE libraries were generated from normal human liver (NL), non-B, non-C HCC tumor (T), and background non-tumor tissues (NT). We obtained 226,834 tags from these libraries and mapped them to the genomic sequences of a total of 8,410 genes using RefSeq database. We identified several novel transcripts specifically expressed in HCC including those mapped to the intronic regions. Among them, we confirmed the transcripts initiated from the introns of a gene encoding acyl-coenzyme A oxidase 2 (ACOX2). The expression of these transcript variants were up-regulated in HCC and showed a different pattern compared with that of ordinary ACOX2 mRNA. The present results indicate that the transcription initiation of a subset of genes may be distinctively altered in HCC, which may suggest the utility of intronic RNAs as surrogate tumor markers.
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Affiliation(s)
- Yuji Hodo
- Department of Gastroentelorogy, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa, Japan
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Midorikawa Y, Sugiyama Y, Aburatani H. Molecular targets for liver cancer therapy: From screening of target genes to clinical trials. Hepatol Res 2010; 40:49-60. [PMID: 19788683 DOI: 10.1111/j.1872-034x.2009.00583.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cancer arises from the accumulation of genetic alterations, and the inactivation of oncogenes, or recovery of suppressor genes, are promising strategies for cancer treatment. Genome-based drug research starts with identification of target genes and is accomplished by exploitation of target-based drugs such as monoclonal antibodies, small molecules and antisense drugs. Recently, clinical trials for treatment of advanced hepatocellular carcinoma (HCC) have been performed, and the effectiveness of sorafenib, an oral multikinase inhibitor of the vascular endothelial growth factor receptor and Ras kinase, has been demonstrated. In addition to known target genes, microarray technology has enabled us to constitute novel therapeutic targets, and many researchers have applied this technology in studies of HCC and have identified candidate target genes, validated to affect cell growth. In addition, promoter arrays for whole-genome epigenetic aberration analysis, ChIP-chip analysis using tiling arrays, and high-throughput sequencing systems have been applied to drug discovery. To elucidate the status of therapeutic target genes in vivo, development of diagnostic markers for stratification of patients is a pressing need. Here, we review recent advances in microarray technology for liver cancer, discuss the innovations and approaches to therapeutic target discovery, and present data regarding the outcome of gene target therapy using monoclonal antibodies and molecular diagnostic markers in our laboratory.
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Affiliation(s)
- Yutaka Midorikawa
- Department of Surgery, Teikyo University School of Medicine University Hospital, Mizonokuchi, Kawasaki
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Nomoto S, Kanda M, Okamura Y, Nishikawa Y, Qiyong L, Fujii T, Sugimoto H, Takeda S, Nakao A. Epidermal growth factor-containing fibulin-like extracellular matrix protein 1, EFEMP1, a novel tumor-suppressor gene detected in hepatocellular carcinoma using double combination array analysis. Ann Surg Oncol 2009; 17:923-32. [PMID: 19898900 DOI: 10.1245/s10434-009-0790-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2009] [Indexed: 11/18/2022]
Abstract
BACKGROUND Although hepatocellular carcinoma (HCC) is one of the commonest cancers worldwide, the underlying molecular mechanisms contributing to hepatocarcinogenesis are still not clear. METHODS In this study, we performed double array analysis, consisting of both expression profiling and karyotyping analysis using single-nucleotide polymorphism (SNP) array, of the same HCC sample from a 68-year-old woman with chronic hepatitis type C, and attempted to find a novel tumor-suppressor gene as a prognostic marker for HCC. RESULTS According to the results of expression array, EFEMP1 gene, which has a role as an angiostatic molecule, showed decreased expression in tumor tissue. The copy number of chromosome 2, where EFEMP1 exists, 2p16, did not show chromosomal deletion. We found many CpG islands in the promoter region of EFEMP1 gene. Reactivation of EFEMP1 expression was seen on 5-aza-2'-deoxycytidine (5-aza-dC) treatment using HCC cell lines, and 24 of 48 (50%) HCC samples showed promoter hypermethylation. In the 24 methylated cases, most of the values of EFEMP1 gene expression examined by real-time reverse-transcription polymerase chain reaction (RT-PCR) in tumor tissues were significantly decreased (P = 0.0004). Intriguingly, EFEMP1 hypermethylation was significantly correlated with worse prognosis (P = 0.0271). CONCLUSION Double array analysis revealed a novel tumor-suppressor gene, EFEMP1, for hepatocellular carcinoma. The mechanism for downregulation of EFEMP1 expression was closely associated with promoter hypermethylation. Promoter methylation of EFEMP1 gene was a marker of a worse prognosis in hepatocellular carcinoma.
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Affiliation(s)
- Shuji Nomoto
- Department of Surgery II, Graduate School of Medicine, Nagoya University, Nagoya, Japan.
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De Giorgi V, Monaco A, Worchech A, Tornesello M, Izzo F, Buonaguro L, Marincola FM, Wang E, Buonaguro FM. Gene profiling, biomarkers and pathways characterizing HCV-related hepatocellular carcinoma. J Transl Med 2009; 7:85. [PMID: 19821982 PMCID: PMC2768694 DOI: 10.1186/1479-5876-7-85] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Accepted: 10/12/2009] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Hepatitis C virus (HCV) infection is a major cause of hepatocellular carcinoma (HCC) worldwide. The molecular mechanisms of HCV-induced hepatocarcinogenesis are not yet fully elucidated. Besides indirect effects as tissue inflammation and regeneration, a more direct oncogenic activity of HCV can be postulated leading to an altered expression of cellular genes by early HCV viral proteins. In the present study, a comparison of gene expression patterns has been performed by microarray analysis on liver biopsies from HCV-positive HCC patients and HCV-negative controls. METHODS Gene expression profiling of liver tissues has been performed using a high-density microarray containing 36'000 oligos, representing 90% of the human genes. Samples were obtained from 14 patients affected by HCV-related HCC and 7 HCV-negative non-liver-cancer patients, enrolled at INT in Naples. Transcriptional profiles identified in liver biopsies from HCC nodules and paired non-adjacent non-HCC liver tissue of the same HCV-positive patients were compared to those from HCV-negative controls by the Cluster program. The pathway analysis was performed using the BRB-Array- Tools based on the "Ingenuity System Database". Significance threshold of t-test was set at 0.001. RESULTS Significant differences were found between the expression patterns of several genes falling into different metabolic and inflammation/immunity pathways in HCV-related HCC tissues as well as the non-HCC counterpart compared to normal liver tissues. Only few genes were found differentially expressed between HCV-related HCC tissues and paired non-HCC counterpart. CONCLUSION In this study, informative data on the global gene expression pattern of HCV-related HCC and non-HCC counterpart, as well as on their difference with the one observed in normal liver tissues have been obtained. These results may lead to the identification of specific biomarkers relevant to develop tools for detection, diagnosis, and classification of HCV-related HCC.
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Affiliation(s)
- Valeria De Giorgi
- Molecular Biology and Viral Oncogenesis & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples - Italy
- Department of Chemistry, University of Naples "Federico II", Naples, Italy
| | - Alessandro Monaco
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD -USA
| | - Andrea Worchech
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD -USA
- Genelux Corporation, Research and Development, San Diego Science Center, San Diego, CA, USA
- Department of Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - MariaLina Tornesello
- Molecular Biology and Viral Oncogenesis & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples - Italy
| | - Francesco Izzo
- Div. of Surgery "D", Ist. Naz. Tumori "Fond. G. Pascale", Naples - Italy
| | - Luigi Buonaguro
- Molecular Biology and Viral Oncogenesis & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples - Italy
| | - Francesco M Marincola
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD -USA
| | - Ena Wang
- Infectious Disease and Immunogenetics Section (IDIS), Department of Transfusion Medicine, Clinical Center and Trans-NIH Center for Human Immunology (CHI), National Institutes of Health, Bethesda, MD -USA
| | - Franco M Buonaguro
- Molecular Biology and Viral Oncogenesis & AIDS Refer. Center, Ist. Naz. Tumori "Fond. G. Pascale", Naples - Italy
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Oh NS, Park JS, Jeon YJ, Oh JH, Jeong SY, Yang JO, Park YW, Yoo HS, Kim NS. Generation of expression clone set for functional proteomics of human gastric and liver cancers. Exp Biol Med (Maywood) 2009; 234:1220-9. [PMID: 19596826 DOI: 10.3181/0812-rm-371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Two thousand sixty-eight multi-purpose expression clones for the 326 candidate genes related to gastric or liver cancers were constructed using the Gateway system. These clones can be expressed as His, Glutathione-S-transferase (GST) or Enhanced version of the green fluorescent protein (EGFP) fusion proteins in E. coli, insect cells or mammalian cells. For the 246 E. coli expression clones, the GST fusion proteins had greater expression efficiency and solubility than the His fusion proteins. Approximately 20% of the expressed proteins had unexpected molecular weights. A detailed sequence analysis of these clones revealed frameshift mutations resulting from insertion, deletion or substitution of nucleotides. The results indicate that these changes in the candidate genes may affect the occurrence of gastric or liver cancers. In addition, when 105 proteins, which were expressed in E. coli at very low or undetectable levels, were expressed in insect cells, 76% of the proteins were expressed very well and most were soluble. We also found that most of the 30 proteins prepared using EGFP mammalian expression clones were localized to cellular compartments expected by Gene ontology (GO) and this localization was unaffected if the EGFP-fusion was at the N-terminal or C-terminal region of the protein. Antibody production and subcellular localization analysis of the candidate genes as well as a screen of genes involved in carcinogenesis pathways are currently in progress using these expression clones. These studies provide a valuable resource for developing a better understanding of the molecular mechanism of carcinogenesis in both gastric and liver cancer and would be very helpful in diagnosis and therapeutic predictions.
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Affiliation(s)
- Nang-Soo Oh
- Laboratory of Human Genomics, Genome Research Center, KRIBB, Daejeon 305-806, Korea
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Chen YR, Sekine K, Nakamura K, Yanai H, Tanaka M, Miyajima A. Y-box binding protein-1 down-regulates expression of carbamoyl phosphate synthetase-I by suppressing CCAAT enhancer-binding protein-alpha function in mice. Gastroenterology 2009; 137:330-40. [PMID: 19272383 DOI: 10.1053/j.gastro.2009.02.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2008] [Revised: 02/09/2009] [Accepted: 02/17/2009] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Carbamoyl phosphate synthetase-I (CPS1) is a key enzyme in the urea cycle and patients with defects in the function or expression of CPS1 suffer from hyperammonemia. CPS1 is expressed in the liver at neonatal and adult stages in a CCAAT enhancer-binding protein-alpha (C/EBPalpha)-dependent manner. Despite expression of C/EBPalpha, CPS1 is not expressed in fetal liver, indicating an additional factor is involved in the regulation of CPS1 expression. The aim of this study was to elucidate the mechanism of CPS1 expression. METHODS Microarray was performed to find Y-box binding protein-1 (YB-1) that was expressed in mouse fetal liver. The role of YB-1 in CPS1 expression was investigated by overexpression of YB-1 in mouse fetal liver culture and luciferase reporter assays using the CPS1 promoter. Chromatin immunoprecipitation assay was used to examine recruitment of YB-1 to the CPS1 promoter in vivo. RESULTS Expression of YB-1 and CPS1 was inversely correlated in vivo, and YB-1 inhibited CPS1 expression and ammonia clearance in fetal liver culture. Although YB-1 was not expressed in adult liver, acute liver injury up-regulated YB-1 and down-regulated CPS1, accompanying an increase of the serum ammonia level. YB-1 inhibited C/EBPalpha-induced transcription from the CPS1 promoter via the Y-box near the C/EBPalpha-binding site. Chromatin immunoprecipitation assays demonstrated that YB-1 was recruited to the CPS1 promoter in fetal and injured adult liver, but not in normal adult liver. CONCLUSIONS YB-1 is a key regulator of ammonia detoxification by negatively regulating CPS1 expression via suppression of C/EBPalpha function.
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Affiliation(s)
- Yen-Rong Chen
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Japan
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Furuta K, Sato S, Yamauchi T, Ozawa T, Harada M, Kakumu S. Intrahepatic gene expression profiles in chronic hepatitis B and autoimmune liver disease. J Gastroenterol 2009; 43:866-74. [PMID: 19012040 DOI: 10.1007/s00535-008-2237-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 06/08/2008] [Indexed: 02/04/2023]
Abstract
BACKGROUND DNA microarray technology has enabled genomewide analysis of gene transcript levels, yielding insight into the molecular nature of liver disease. METHODS We compared gene expression of liver biopsy specimens in 16 patients with different stages of chronic hepatitis B, five with autoimmune hepatitis (AIH), five with primary biliary cirrhosis (PBC), and six with druginduced hepatitis. RESULTS Of 21 073 genes, 424 showed different expression in a particular disease group on analysis of variance. Genes associated with extracellular matrix, cell growth, and DNA repair were noted in the advanced fibrotic stage of chronic hepatitis B (B-3), while gene expression regarding complement activation and the innate immune response decreased. When we compared gene expression at the relatively early stage in each disease group with pathway analysis, pathways relating to chemotaxis and cell homeostasis were selected in chronic hepatitis B. In PBC, gene expression relating to structural constituents and contractions of muscle such as actin and myosin were enhanced, in contrast to the downregulation of genes relating to protein binding in AIH. A hierarchical clustering analysis of hepatitis B genes defined five clusters. Generally, the transcripts upregulated according to disease progression were associated with signaling pathway/transcription, including tumor-associated calcium signal transducer 1 and chemokine ligand 19, and with cell communication, such as collagen. In two groups, all transcripts were downregulated; transcripts related to chemokine ligands and metallothionein were further depressed in B-3. CONCLUSIONS Analysis of gene expression in liver may be useful for understanding features of distinct liver diseases and for guiding disease progression, particularly in chronic hepatitis B.
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Affiliation(s)
- Keiko Furuta
- Department of Internal Medicine, Division of Gastroenterology, Aichi Medical University School of Medicine, Aichi-gun, Japan
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Yamashita T, Honda M, Takatori H, Nishino R, Minato H, Takamura H, Ohta T, Kaneko S. Activation of lipogenic pathway correlates with cell proliferation and poor prognosis in hepatocellular carcinoma. J Hepatol 2009; 50:100-10. [PMID: 19008011 DOI: 10.1016/j.jhep.2008.07.036] [Citation(s) in RCA: 145] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2008] [Revised: 07/01/2008] [Accepted: 07/23/2008] [Indexed: 12/13/2022]
Abstract
BACKGROUND/AIMS Metabolic dysregulation is one of the risk factors for the development of hepatocellular carcinoma (HCC). We investigated the activated metabolic pathway in HCC to identify its role in HCC growth and mortality. METHODS Gene expression profiles of HCC tissues and non-cancerous liver tissues were obtained by serial analysis of gene expression. Pathway analysis was performed to characterize the metabolic pathway activated in HCC. Suppression of the activated pathway by RNA interference was used to evaluate its role in HCC in vitro. Relation of the pathway activation and prognosis was statistically examined. RESULTS A total of 289 transcripts were up- or down-regulated in HCC compared with non-cancerous liver (P<0.005). Pathway analysis revealed that the lipogenic pathway regulated by sterol regulatory element binding factor 1 (SREBF1) was activated in HCC, which was validated by real-time RT-PCR. Suppression of SREBF1 induced growth arrest and apoptosis whereas overexpression of SREBF1 enhanced cell proliferation in human HCC cell lines. SREBF1 protein expression was evaluated in 54 HCC samples by immunohistochemistry, and Kaplan-Meier survival analysis indicated that SREBF1-high HCC correlated with high mortality. CONCLUSIONS The lipogenic pathway is activated in a subset of HCC and contributes to cell proliferation and prognosis.
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Affiliation(s)
- Taro Yamashita
- Department of Gastroenterology, Kanazawa University Graduate School of Medical Science, 13-1 Takara-Machi, Kanazawa 920-8641, Japan
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Mas VR, Maluf DG, Archer KJ, Yanek K, Kong X, Kulik L, Freise CE, Olthoff KM, Ghobrial RM, McIver P, Fisher R. Genes involved in viral carcinogenesis and tumor initiation in hepatitis C virus-induced hepatocellular carcinoma. Mol Med 2008; 15:85-94. [PMID: 19098997 DOI: 10.2119/molmed.2008.00110] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 12/11/2008] [Indexed: 11/06/2022] Open
Abstract
The role of chronic hepatitis C virus (HCV) in the pathogenesis of HCV-associated hepatocellular carcinoma (HCC) remains controversial. To understand the transition from benign to malignant, we studied the gene expression patterns in liver tissues at different stages, including normal, cirrhosis, and different HCC stages. We studied 108 liver tissue samples obtained from 88 distinct patients (41 HCV-cirrhotic tissues, 17 HCV-cirrhotic tissues from patients with HCC, and 47 HCV-HCC tissues). Differentially expressed genes (DEG) were studied by use of high-density oligonucleotide arrays. Among probe sets identified as differentially expressed via the F test, all pairwise comparisons were performed. Cirrhotic tissues with and without concomitant HCC were further evaluated, and a classifier was used to predict whether the tissue type was associated with HCC. Differential expression profiles were analyzed using Interaction Networks and Functional Analysis. Characteristic gene signatures were identified when normal tissue was compared with cirrhosis, cirrhosis with early HCC, and normal with HCC. Pathway analysis classified the cellular and biological functions of the DEG as related to cellular growth and proliferation, cell death and inflammatory disease in cirrhosis; cell death, cell cycle, DNA replication, and immune response in early HCCs; and cell death, cell growth and proliferation, cell cycle, and DNA repair in advanced HCCs. Characteristic gene signatures were identified at different stages of HCV-HCC progression. A set of genes were identified to predict whether the cirrhotic tissue was associated with HCC.
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Affiliation(s)
- Valeria R Mas
- Division of Transplantation, Department of Surgery, Virginia Commonwealth University, Richmond, Virginia, USA.
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Skawran B, Steinemann D, Becker T, Buurman R, Flik J, Wiese B, Flemming P, Kreipe H, Schlegelberger B, Wilkens L. Loss of 13q is associated with genes involved in cell cycle and proliferation in dedifferentiated hepatocellular carcinoma. Mod Pathol 2008; 21:1479-89. [PMID: 18820673 DOI: 10.1038/modpathol.2008.147] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Dedifferentiation of hepatocellular carcinoma implies aggressive clinical behavior and is associated with an increasing number of genomic alterations, eg deletion of 13q. Genes directly or indirectly deregulated due to these genomic alterations are mainly unknown. Therefore this study compares array comparative genomic hybridization and whole genome gene expression data of 23 well, moderately, or poorly dedifferentiated hepatocellular carcinoma, using unsupervised hierarchical clustering. Dedifferentiated carcinoma clearly branched off from well and moderately differentiated carcinoma (P<0.001 chi(2)-test). Within the dedifferentiated group, 827 genes were upregulated and 33 genes were downregulated. Significance analysis of microarrays for hepatocellular carcinoma with and without deletion of 13q did not display deregulation of any gene located in the deleted region. However, 531 significantly upregulated genes were identified in these cases. A total of 6 genes (BIC, CPNE1, RBPMS, RFC4, RPSA, TOP2A) were among the 20 most significantly upregulated genes both in dedifferentiated carcinoma and in carcinoma with loss of 13q. These genes are involved in cell-cycle control and proliferation. Of 33 downregulated genes in the dedifferentiated subgroup, 4 metallothioneins had the lowest fold change, most probably mediated through inactivation of C/EBPalpha by the PI3K/AKT cascade. In conclusion dedifferentiation of hepatocellular carcinoma is associated with upregulation of genes involved in cell-cycle control and proliferation. Notably, a significant portion of these genes is also upregulated in carcinoma with deletion of 13q. As no downregulated genes were identified and microRNAs (mir-621, mir-16-1, mir-15a) are located within the deleted region of 13q and may be lost, we speculate that these miRNAs may induce the upregulation of critical cell-cycle control genes.
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Affiliation(s)
- Britta Skawran
- Institute of Cell and Molecular Pathology, Hannover Medical School, Hannover, Germany
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Abstract
Hepatocellular carcinoma (HCC) typically has poor prognosis, because it is often diagnosed at an advanced stage. Heterogeneous phenotypic and genetic traits of affected individuals and a wide range of risk factors have classified it a complex disease. HCC is not amenable to standard chemotherapy and is resistant to radiotherapy. In most cases, surgical resection and liver transplantation remain the only curative treatment options. Therefore, development of novel, effective therapies is of prime importance. Extensive research over the past decade has identified a number of molecular biomarkers as well as cellular networks and signaling pathways affected in liver cancer. Recent studies using a combination of "omics" technologies, microRNA studies, combinatorial chemistry, and bioinformatics are providing new insights into the gene expression and protein profiles during various stages of the disease. In this review, we discuss the contribution of these newer approaches toward an understanding of molecular mechanisms of HCC and for the development of novel cancer therapeutics.
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Radiology, Cell Biology and Development, University of Minnesota Medical School, Minneapolis, MN, USA.
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Wong CH, Chan SKP, Chan HLY, Tsui SKW, Feitelson M. The Molecular Diagnosis of Hepatitis B Virus-Associated Hepatocellular Carcinoma. Crit Rev Clin Lab Sci 2008; 43:69-101. [PMID: 16531275 DOI: 10.1080/10408360500410407] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hepatitis B virus (HBV) infection is the major cause of hepatocellular carcinoma (HCC) worldwide. The pathogenesis of HBV-associated HCC has been studied extensively, and molecular changes during malignant transformation have been identified. It has been proposed that the insertion of HBV DNA into the human genome results in chromosomal instability and inactivation of tumor suppressor genes. Transactivation of oncogenes, inactivation of tumor suppressor genes, and alteration of the cell cycle by HBV proteins are also involved in the progression of hepatocellular carcinogenesis. Traditional clinical examinations of HCC, such as biopsy, computer tomography, ultrasonic imaging, and detection of such biomarkers as a-fetoprotein, are currently the "gold standard" in diagnosis. These tests diagnose HCC only in the late stages of disease. This limitation has greatly reduced the chance of survival of HCC patients. To resolve this problem, new biomarkers that can diagnose HCC in earlier stages are necessary. Based on recent molecular studies of the effects of HBV on cellular transformation, differentially expressed biomarkers of HBV infection have been elucidated. With the analyses of the HBV replication profile, the viral load (HBV DNA levels) of patients, and the viral protein expression, the severity of hepatitis in the preneoplastic stages can be assessed. In the future, with the molecular profiles identified by genomic and proteomic approaches, stage-specific biomarkers should be identified to monitor the progression and prognosis of HCC.
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Affiliation(s)
- Chi-Hang Wong
- Center for Emerging Infectious Diseases, The Chinese University, Hong Kong, Shatin, N.T., Hong Kong SAR, China
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Nishino R, Honda M, Yamashita T, Takatori H, Minato H, Zen Y, Sasaki M, Takamura H, Horimoto K, Ohta T, Nakanuma Y, Kaneko S. Identification of novel candidate tumour marker genes for intrahepatic cholangiocarcinoma. J Hepatol 2008; 49:207-16. [PMID: 18490072 DOI: 10.1016/j.jhep.2008.03.025] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Revised: 03/10/2008] [Accepted: 03/24/2008] [Indexed: 01/07/2023]
Abstract
BACKGROUND/AIMS Specific markers are required for early detection and diagnosis of intrahepatic cholangiocarcinoma (ICC); however, the tumour markers currently in use are not specific for ICC. METHODS We compared an ICC cDNA library with that of hepatocellular carcinoma (HCC) by serial analysis of gene expression (SAGE). The expression patterns in each were confirmed by quantitative real-time reverse transcriptase-polymerase chain reaction (RT-PCR), immunoblotting and immunohistochemical analysis of 74 samples including 16 ICC samples. RESULTS A comparison of the two libraries revealed distinct gene expression patterns for each type of liver cancer. In addition to the known tumour markers, we detected nine novel genes associated with ICC. By comparing the mean transcript abundance in the ICC library with those in other libraries, including gastric, colon, prostate and breast cancer, together with our RT-PCR results, we identified three genes as specific markers of ICC: biglycan, insulin-like growth factor-binding protein 5 and claudin-4. Immunoblotting and immunohistochemical analyses showed that claudin-4 was highly expressed in ICC. Moreover, discrimination analysis revealed that a combination of these genes could be used to distinguish ICC from HCC or metastatic adenocarcinoma. CONCLUSIONS We identified novel marker genes of ICC that are potentially useful for the diagnosis of liver cancer.
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Affiliation(s)
- Ryuhei Nishino
- Department of Gastroenterology, Kanazawa University Graduate School of Medical Science, Kanazawa University, 13-1 Takara-Machi, Kanazawa 920-8641, Japan
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Furuta K, Sato S, Yamauchi T, Kakumu S. Changes in intrahepatic gene expression profiles from chronic hepatitis to hepatocellular carcinoma in patients with hepatitis C virus infection. Hepatol Res 2008; 38:673-82. [PMID: 18328064 DOI: 10.1111/j.1872-034x.2008.00328.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AIM DNA microarray technology has enabled genome-wide analysis of gene transcript levels, which has yielded insight into the molecular nature of hepatitis C virus infection. However, little insight into the molecular nature of the early to advanced stages of chronic liver disease has as yet been obtained. METHODS We compared the gene expression profiles of liver biopsy specimens from 14 patients at different stages of chronic hepatitis C. We also evaluated the liver tissue of hepatocellular carcinoma and its surrounding region obtained surgically in seven patients with hepatitis C virus infection. RESULTS Of 21 073 genes, 582 genes showed significant changes in expression levels across the disease group. Twenty-eight samples from six disease groups clustered according to the histological classification except for 4 samples. A heat map produced by hierarchical clustering revealed nine clusters where gene expression profiles were changed in abundance. Among 44 genes which changed twofold or more in transcript abundance, transcripts from chronic hepatitis tended to be upregulated, and gradually downregulated according to disease progression toward hepatocellular carcinoma in five of nine clusters. In chronic hepatitis, transcripts relating to metabolism and immune response were upregulated, while in hepatocellular carcinoma, transcripts associated with cell cycle, growth, proliferation, apoptosis and signaling pathway were upregulated. CONCLUSION Disease progression in hepatitis C virus-infected patients appeared to be associated with changes in gene expression profiles in the liver consistent with plausible functional categories, although we should confirm these findings using larger samples.
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Affiliation(s)
- Keiko Furuta
- Department of Gastroenterology, Aichi Medical University School of Medicine, Aichi, Japan
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Li Y, Qin X, Cui J, Dai Z, Kang X, Yue H, Zhang Y, Su J, Cao J, Ou C, Yang C, Duan X, Yue H, Liu Y. Proteome analysis of aflatoxin B1-induced hepatocarcinogenesis in tree shrew (Tupaia belangeri chinensis) and functional identification of candidate protein peroxiredoxin II. Proteomics 2008; 8:1490-501. [PMID: 18318006 DOI: 10.1002/pmic.200700229] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
In order to explore the proteins responsible for hepatocellular carcinoma (HCC), aflatoxin B(1)-induced hepatocarcinogenesis in tree shrew (Tupaia belangeri chinensis) was analyzed with 2-DE and MS. By comparing HCC samples with their own precancerous biopsies and HCC-surrounding tissues, a group of candidate proteins that differentially expressed in HCC were obtained. Peroxiredoxin (Prx) II, one of the candidates with distinct alteration, was further investigated and validated. Western blot and RT-PCR assays confirmed the overexpression of Prx II in both tree shrew and human HCC tissues. RNA interference for silencing Prx II was employed subsequently to explore the function and underlying mechanism of Prx II on liver cancer cell line Hep3B. Results showed the cell proliferation and clone formation decreased obviously when Prx II expression was inhibited, while the flow cytometer analysis showed the percentage of cell apoptosis enhanced. Inhibition of Prx II expression also obviously increased the generation of ROS and malondialdehyde, both are the products from peroxidation. These results imply the important role of Prx II in hepatocarcinogenesis, possibly through its function in regulating peroxidation and hereby to provide a favorable microenvironment for cancer cell surviving and progressing.
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Affiliation(s)
- Yuan Li
- Department of Experimental Pathology, Guangxi Cancer Institute, Nanning, China.
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Gene expression profiling in hepatocellular carcinoma: upregulation of genes in amplified chromosome regions. Mod Pathol 2008; 21:505-16. [PMID: 18277965 DOI: 10.1038/modpathol.3800998] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cytogenetics of hepatocellular carcinoma and adenoma have revealed gains of chromosome 1q as a significant differentiating factor. However, no studies are available comparing these amplification events with gene expression. Therefore, gene expression profiling was performed on tumours cytogenetically well characterized by array-based comparative genomic hybridisation. For this approach analysis was carried out on 24 hepatocellular carcinoma and 8 hepatocellular adenoma cytogenetically characterised by array-based comparative genomic hybridisation. Expression profiles of mRNA were determined using a genome-wide microarray containing 43,000 spots. Hierarchical clustering analysis branched all hepatocellular adenoma from hepatocellular carcinoma. Significance analysis of microarray demonstrated 722 dysregulated genes in hepatocellular carcinoma. Gene set enrichment analysis detected groups of upregulated genes located in chromosome bands 1q22-42 seen also as the most frequently gained regions by comparative genomic hybridisation. Comparison of significance analysis of microarray and gene set enrichment analysis narrowed down the number of dysregulated genes to 18, with 7 genes localised on 1q22 (SCAMP3, IQGAP3, PYGO2, GPATC4, ASH1L, APOA1BP, and CCT3). In hepatocellular adenoma 26 genes in bands 11p15, 11q12, and 12p13 were upregulated. However, the respective chromosome bands were not gained in hepatocellular adenoma. Expression analysis and comparative genomic hybridisation identified an upregulation of genes in amplified regions of 1q. These results may serve to further narrow down the number of candidate driver genes in hepatocarcinogenesis.
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Iizuka N, Hamamoto Y, Tsunedomi R, Oka M. Translational microarray systems for outcome prediction of hepatocellular carcinoma. Cancer Sci 2008; 99:659-65. [PMID: 18377418 PMCID: PMC11159982 DOI: 10.1111/j.1349-7006.2008.00751.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA microarray technology has revolutionized our understanding of the molecular basis of hepatocellular carcinoma (HCC), one of the most fatal human cancers with a high recurrence rate. Many researchers have used DNA microarray technology to reclassify HCC with respect to metastatic potential and to develop predictors for the outcome of HCC. However, developed predictors have reached the level only of small retrospective studies, and their current status is far from that required for clinical use. This is due to the lack of transparent data, the high cost and data instability associated with the high dimensionality of the technique, the infancy of bioinformatics, and the complicated nature of recurrent HCC. This comprehensive review summarizes: (i) class comparison studies to identify genes or pathways involved in HCC metastasis (ii) class discovery studies that have resulted in the identification of a new molecular subclass of HCC with respect to metastasis, and (iii) class prediction studies to develop multidimensional predictors for HCC outcome. We also discuss issues that need to be addressed so that the power of array-based predictors can be estimated prospectively in large independent cohorts of HCC patients.
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Affiliation(s)
- Norio Iizuka
- Departments of Surgery II, Yamaguchi University Graduate School of Medicine, 10101 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
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Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer and the third leading cause of cancer death worldwide. Hepatocarcinogenesis is a multistep process evolving from normal through chronic hepatitis/cirrhosis and dysplastic nodules to HCC. With advances in molecular methods, there is a growing understanding of the molecular mechanisms in hepatocarcinogenesis. Hepatocarcinogenesis is strongly linked to increases in allelic losses, chromosomal changes, gene mutations, epigenetic alterations and alterations in molecular cellular pathways. Some of these alterations are accompanied by a stepwise increase in the different pathological disease stages in hepatocarcinogenesis. Overall, a detailed understanding of the underlying molecular mechanisms involved in the progression of HCC is of fundamental importance to the development of effective prevention and treatment regimes for HCC.
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Affiliation(s)
- Chun-Ming Wong
- SH Ho Foundation Research Laboratory, Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
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Saffroy R, Pham P, Reffas M, Takka M, Lemoine A, Debuire B. New perspectives and strategy research biomarkers for hepatocellular carcinoma. Clin Chem Lab Med 2008; 45:1169-79. [PMID: 17635075 DOI: 10.1515/cclm.2007.262] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. Cirrhosis caused by hepatitis B virus, hepatitis C virus or chronic alcohol intake is associated with major risk. Systematic screening for HCC of asymptomatic patients with cirrhosis is needed for earlier detection of small tumors requiring treatment (liver transplantation, surgical resection, percutaneous techniques). The recommended screening strategy among cirrhotic patients is based on regular liver ultrasonography associated with serum alpha-fetoprotein (AFP) assay. As the performance of AFP is not satisfactory, additional tumoral markers are proposed (des-gamma-carboxyprothrombin, glycosylated AFP-L3 fraction). Currently, diagnosis of HCC in cirrhotic patients includes non-invasive tests (imaging after contrast administration, AFP assay); diagnostic biopsy is performed when imaging is limited. After treatment, tumor recurrence is assessed by regular follow-up (AFP assay and imaging). Despite the lack of accurate markers, recent developments in genomic and proteomic approaches will allow the discovery of new biomarkers for primary tumors, as well as for recurrence. This review summarizes the current state of biomarkers for screening, diagnosis and follow-up of HCC, and highlights new perspectives in the field.
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Affiliation(s)
- Raphaël Saffroy
- Service de Biochimie, Biologie Moléculaire et Toxicologie, Hôpital Universitaire Paul Brousse, Université Paris-Sud, UMR-S602, Villejuif, INSERM, Villejuif, France.
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Bureau C, Péron JM, Bouisson M, Danjoux M, Selves J, Bioulac-Sage P, Balabaud C, Torrisani J, Cordelier P, Buscail L, Vinel JP. Expression of the transcription factor Klf6 in cirrhosis, macronodules, and hepatocellular carcinoma. J Gastroenterol Hepatol 2008; 23:78-86. [PMID: 18171345 DOI: 10.1111/j.1440-1746.2007.05234.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND AND AIMS Macronodules (MN) occurring in cirrhosis are considered to be precursor lesions for hepatocellular carcinoma (HCC). However, early molecular events in hepatocellular carcinogenesis are poorly understood. The aim of this study was to compare gene expression profiling between cirrhotic tissues, MN, and HCC, to identify genes early involved in liver carcinogenesis. METHODS Tissues were obtained from explanted livers: nine cirrhosis, 10 MN, and seven HCC. Total RNAs were extracted by RNeasy and reverse transcribed with labelled [(33)P]-alpha ATP. Hybridations were performed on Atlas Human Cancer 1.2 membranes (1176 genes). RESULTS A two-way hierarchical clustering algorithm successfully isolated specific gene expression profiles when comparing MN, cirrhosis, and HCC. A total of 16 and 14 genes were up- and down-expressed, respectively, in HCC as compared to cirrhotic tissues. The molecular signature of MN was characterized by the down-expression of 23 and 42 genes as compared to cirrhosis and HCC, respectively. Among them, Klf6 was down-expressed in all MN samples whereas it was over-expressed in cirrhosis and HCC. This result was confirmed at RNA level by quantitative real time-polymerase chain reaction and at protein level by Western blotting. However, no mutation in the exon 2 of Klf6 was detected. CONCLUSION We identified a molecular signature of MN characterized by a down-expression of several genes. One of them, Klf6 was found to be down-expressed in all MN without evidence of somatic mutations in the exon 2. This gene could be involved at an early stage of hepatocarcinogenesis.
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Affiliation(s)
- Christophe Bureau
- INSERM U858, Fédération Digestive Purpan, CHU Toulouse, Toulouse, France.
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Mas VR, Fisher RA, Archer KJ, Yanek KC, Williams B, Dumur CI, Maluf DG. Genes Associated With Progression and Recurrence of Hepatocellular Carcinoma in Hepatitis C Patients Waiting and Undergoing Liver Transplantation: Preliminary Results. Transplantation 2007; 83:973-81. [PMID: 17460570 DOI: 10.1097/01.tp.0000258643.05294.0b] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Liver transplantation (LT) represents a curative treatment for small hepatocellular carcinoma (HCC). Potentially curable higher-stage HCC patients are denied LT due to the lack of cancer markers that predict progression and recurrence. METHODS Thirty-eight candidates for LT with hepatitis C virus (HCV) cirrhosis and HCC were studied. Gene expression (Gexp) analysis of tumor samples was performed using microarrays. RESULTS Twenty patients underwent transplantation, 13 progressed while waiting for transplantation, 4 are alive awaiting transplantation, and 1 died without progression while waiting for LT. Differences in GExp among patients who underwent LT or did not progress (n=25) versus those whose disease progressed while waiting for LT (n=13) were assessed. Thus, 54 probe sets (Pset) were significantly differentially expressed. Among LT patients, 10 Psets were differentially expressed between LT patients with the same explanted stage that recurred (n=5) versus LT patients who did not recur (n=5). Ninety-eight Psets were significantly associated with survival at the alpha=0.005 level. CONCLUSIONS Here, we have identified genes associated with HCC progression in HCV-HCC patients awaiting LT transplantation. A limited number of genes were related to overall survival and cancer-free survival after LT. Incorporation of these molecular markers could help to improve organ allocation for HCV-HCC patients.
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Affiliation(s)
- Valeria R Mas
- Division of Transplantation, Department of Surgery, Virginia Commonwealth University, Richmond, VA 23298-0057, USA
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Budhu A, Chen Y, Kim JW, Forgues M, Valerie K, Harris CC, Wang XW. Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins. Carcinogenesis 2007; 28:1552-60. [PMID: 17404395 DOI: 10.1093/carcin/bgm075] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a fatal disease and hepatitis B and C viruses (HBV and HCV) are considered as major causative factors for the development of HCC. We have conducted gene expression profiling studies to search for potential target genes responsible for HCV-mediated HCC. Adenoviruses encoding core (HCV structural protein), NS3 and NS5A [HCV non-structural (NS) proteins] were generated and infected individually or together in freshly isolated primary human hepatocytes. An adenovirus harboring the oncogenic HBV protein, HBx, was included for comparison. A microarray platform of over 22,000 human oligos was analyzed to seek out significant differentially expressed genes among these viral proteins. We also compared these gene expression profiles with those obtained from HCV-infected liver samples from chronic liver disease (CLD) patients and HCV-related HCC. We found that HCV-related proteins largely induce unique genes when compared with HBx. In particular, interferon-inducible gene 27 (IFI27) was highly expressed in HCV or core-infected hepatocytes and HCV-related CLD or HCC, but was not significantly expressed in HBx-infected hepatocytes or HBV-related CLD or HCC, indicating that IFI27 may play a role in HCV-mediated HCC. In conclusion, our results suggest that HBV and HCV promote HCC development mainly through different mechanisms.
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Affiliation(s)
- A Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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Abstract
One of the most aggressive cancers is hepatocellular carcinoma, which is associated with a very poor patient outcome due to a high recurrence rate and metastatic spread. NM23, the first metastasis suppressor gene to be identified, has been widely studied in human cancers. However, conflicting results have been obtained depending on the tumor type and the evaluation protocol. The current knowledge of NM23 as a diagnostic and/or prognostic marker in hepatocellular carcinoma is reviewed herein. Most studies demonstrate an inverse association between the expression of NM23-H1 and the metastatic potential, which is not observed with the closely related NM23-H2 isoform. Transfection of metastatic hepatoma cells with NM23 reduced their metastatic potential, as for other tumor cell lines. The demonstration of a causative role of NM23 in metastatic dissemination in a mouse model of hepatocarcinoma suggests that hepatocarcinoma-derived cells could be good models for the analysis of the molecular mechanisms involved in NM23 action.
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Affiliation(s)
- Mathieu Boissan
- INSERM U680, Faculté de Médecine, Université P. et M. Curie (UPMC-Paris 6), 27 rue Chaligny, Paris, F-75012, France
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Midorikawa Y, Makuuchi M, Tang W, Aburatani H. Microarray-based analysis for hepatocellular carcinoma: From gene expression profiling to new challenges. World J Gastroenterol 2007; 13:1487-92. [PMID: 17461438 PMCID: PMC4146888 DOI: 10.3748/wjg.v13.i10.1487] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Accumulation of mutations and alterations in the expression of various genes result in carcinogenesis, and the development of microarray technology has enabled us to identify the comprehensive gene expression alterations in oncogenesis. Many studies have applied this technology for hepatocellular carcinoma (HCC), and identified a number of candidate genes useful as biomarkers in cancer staging, prediction of recurrence and prognosis, and treatment selection. Some of these target molecules have been used to develop new serum diagnostic markers and therapeutic targets against HCC to benefit patients. Previously, we compared gene expression profiling data with classification based on clinicopathological features, such as hepatitis viral infection or liver cancer progression. The next era of gene expression analysis will require systematic integration of expression profiles with other types of biological information, such as genomic locus, gene function, and sequence information. We have reported integration between expression profiles and locus information, which is effective in detecting structural genomic abnormalities, such as chromosomal gains and losses, in which we showed that gene expression profiles are subject to chromosomal bias. Furthermore, array-based comparative genomic hybridization analysis and allelic dosage analysis using genotyping arrays for HCC were also reviewed, with comparison of conventional methods.
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Affiliation(s)
- Yutaka Midorikawa
- Hepato-Biliary-Pancreatic Surgery Division, Department of Surgery, The University of Tokyo, Tokyo 113-8655, Japan.
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Expression profiling of liver cell lines expressing entire or parts of hepatitis C virus open reading frame. Hepatology 2007. [DOI: 10.1002/hep.1840360620] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
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Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). BMC Bioinformatics 2007; 8:66. [PMID: 17326819 PMCID: PMC1828168 DOI: 10.1186/1471-2105-8-66] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2006] [Accepted: 02/27/2007] [Indexed: 02/02/2023] Open
Abstract
Background The significant advances in microarray and proteomics analyses have resulted in an exponential increase in potential new targets and have promised to shed light on the identification of disease markers and cellular pathways. We aim to collect and decipher the HCC-related genes at the systems level. Results Here, we build an integrative platform, the Encyclopedia of Hepatocellular Carcinoma genes Online, dubbed EHCO , to systematically collect, organize and compare the pileup of unsorted HCC-related studies by using natural language processing and softbots. Among the eight gene set collections, ranging across PubMed, SAGE, microarray, and proteomics data, there are 2,906 genes in total; however, more than 77% genes are only included once, suggesting that tremendous efforts need to be exerted to characterize the relationship between HCC and these genes. Of these HCC inventories, protein binding represents the largest proportion (~25%) from Gene Ontology analysis. In fact, many differentially expressed gene sets in EHCO could form interaction networks (e.g. HBV-associated HCC network) by using available human protein-protein interaction datasets. To further highlight the potential new targets in the inferred network from EHCO, we combine comparative genomics and interactomics approaches to analyze 120 evolutionary conserved and overexpressed genes in HCC. 47 out of 120 queries can form a highly interactive network with 18 queries serving as hubs. Conclusion This architectural map may represent the first step toward the attempt to decipher the hepatocarcinogenesis at the systems level. Targeting hubs and/or disruption of the network formation might reveal novel strategy for HCC treatment.
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