1
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Kim Y, Kang BE, Gariani K, Gariani J, Lee J, Kim HJ, Lee CW, Schoonjans K, Auwerx J, Ryu D. Loss of hepatic Sirt7 accelerates diethylnitrosamine (DEN)-induced formation of hepatocellular carcinoma by impairing DNA damage repair. BMB Rep 2024; 57:98-103. [PMID: 38303560 PMCID: PMC10910089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/16/2023] [Accepted: 12/07/2023] [Indexed: 02/03/2024] Open
Abstract
The mammalian sirtuin family (SIRT1-SIRT7) has shown diverse biological roles in the regulation and maintenance of genome stability under genotoxic stress. SIRT7, one of the least studied sirtuin, has been demonstrated to be a key factor for DNA damage response (DDR). However, conflicting results have proposed that Sirt7 is an oncogenic factor to promote transformation in cancer cells. To address this inconsistency, we investigated properties of SIRT7 in hepatocellular carcinoma (HCC) regulation under DNA damage and found that loss of hepatic Sirt7 accelerated HCC progression. Specifically, the number, size, and volume of hepatic tumor colonies in diethylnitrosamine (DEN) injected Sirt7-deficient liver were markedly enhanced. Further, levels of HCC progression markers and pro-inflammatory cytokines were significantly elevated in the absence of hepatic Sirt7, unlike those in the control. In chromatin, SIRT7 was stabilized and colocalized to damage site by inhibiting the induction of γH2AX under DNA damage. Together, our findings suggest that SIRT7 is a crucial factor for DNA damage repair and that hepatic loss-of-Sirt7 can promote genomic instability and accelerate HCC development, unlike early studies describing that Sirt7 is an oncogenic factor [BMB Reports 2024; 57(2): 98-103].
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Affiliation(s)
- Yuna Kim
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Baeki E. Kang
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea, Gwangju 61005, Korea
| | - Karim Gariani
- Service of Endocrinology, Diabetes, Nutrition and Therapeutic Patient Education, Geneva University Hospitals, Geneva 1205, Korea
| | - Joanna Gariani
- Department of Radiology, Hirslanden Grangettes Clinic, Geneva 1224, Switzerland, Gwangju 61005, Korea
| | - Junguee Lee
- Department of Pathology, Konyang University, Daejeon 35365, Korea, Gwangju 61005, Korea
| | - Hyun-Jin Kim
- Department of Physiology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea, Gwangju 61005, Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
| | - Kristina Schoonjans
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne 1015, Switzerland, Gwangju 61005, Korea
| | - Johan Auwerx
- Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne, Lausanne 1015, Switzerland, Gwangju 61005, Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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2
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Imamura T, Okamura Y, Ohshima K, Uesaka K, Sugiura T, Yamamoto Y, Ashida R, Ohgi K, Nagashima T, Yamaguchi K. Molecular characterization-based multi-omics analyses in primary liver cancer using the Japanese version of the genome atlas. JOURNAL OF HEPATO-BILIARY-PANCREATIC SCIENCES 2023; 30:269-282. [PMID: 35918906 DOI: 10.1002/jhbp.1223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/12/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Primary liver cancer (PLC) is classified into hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC), and combined hepatocellular and intrahepatic cholangiocarcinoma (CHC). We investigated the genomic landscape of PLC according to the histological classification and established a cross-histological molecular subtyping for PLC by a multi-omics analysis. METHODS We analyzed 265 PLC cases with whole-exome sequencing and DNA copy number analyses and 251 cases with gene expression profiling. RESULTS The cohort included HCC (n = 223, 84%), ICC (n = 34, 13%), and CHC (n = 8, 3%). Mutation analyses identified histological type-specific driver genes, such as CTNNB1 in HCC and KRAS, IDH1, and PIK3CA in ICC, and ARID1A and KMT2C in CHC. The tumor suppressor gene TP53 mutation was detected in 21.1% of HCC, 16.1% of ICC, and 25.0% of CHC cases. Other well-characterized tumor suppressor genes included RB1, which was mutated in 2.8% of HCC and 3.2% of ICC; and PTEN, which was mutated in 1.4% of HCC, 3.2% of ICC, and 12.5% of CHC cases. DNA copy number analyses identified focal amplifications, with NUF2 (1q23.3) the most frequently detected as an amplified gene in all 3 types (HCC, 3.8%; CHC, 12.5%, ICC, 3.2%). Molecular subtyping for PLC based on the multi-omics analysis identified three subtypes, one of which was associated with recurrence after resection and amplified genes located at chromosome 8q. CONCLUSIONS Our dataset serves as a fundamental resource for genomic medicine for PLC in Japan and identified amplified genes located at chromosome 8q as promising therapeutic targets for the subgroup with a poor prognosis.
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Affiliation(s)
- Taisuke Imamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yukiyasu Okamura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan.,Division of Digestive Surgery, Department of Surgery, Nihon University School of Medicine, Tokyo, Japan
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Katsuhiko Uesaka
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Teiichi Sugiura
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yusuke Yamamoto
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Ryo Ashida
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Katsuhisa Ohgi
- Division of Hepato-Biliary-Pancreatic Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan.,SRL, Inc., Tokyo, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center Hospital and Research Institute, Shizuoka, Japan
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3
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Liu W, Yin C, Liu Y. Circular RNA circ_0091579 Promotes Hepatocellular Carcinoma Proliferation, Migration, Invasion, and Glycolysis Through miR-490-5p/CASC3 Axis. Cancer Biother Radiopharm 2020; 36:863-878. [PMID: 32673066 DOI: 10.1089/cbr.2019.3472] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is one of the most common malignancies with high invasion and metastasis capacities. Circular RNAs (circRNAs) were evidenced to take part in the progression of multifarious cancers, including HCC. However, the role of circ_0091579 in HCC progression has not been fully described. This study aimed to explore the function of circ_0091579 and its potential regulatory mechanism in the progression of HCC. Materials and Methods: The expression of circ_0091579, microRNA-490-5p (miR-490-5p), and cancer susceptibility candidate 3 (CASC3) in HCC tissues and cells was detected by quantitative real-time polymerase chain reaction. The circular characteristic and stability of circ_0091579 were verified by RNase R digestion and actinomycin D reaction assays. Cell proliferation, migration, and invasion were determined by methyl thiazolyl tetrazolium assay and Transwell assay, respectively. The level of glycolysis was evaluated by glucose consumption and lactate production. The levels of proteins were examined by Western blot. The interaction between miR-490-5p and circ_0091579 or CASC3 was certified by Dual-luciferase reporter assay. Results: circ_0091579 and CASC3 were upregulated, while miR-490-5p was downregulated in HCC tissues and cells. Silencing of either circ_0091579 or CASC3 suppressed cell proliferation, migration, invasion, and glycolysis in HCC cells. Moreover, miR-490-5p was verified to directly bind to circ_0091579 and CASC3. Circ_0091579 upregulated CASC3 by sponging miR-490-5p in HCC cells to promote cell proliferation, invasion, and migration. Conclusion: circ_0091579 promoted cell proliferation, migration, invasion, and glycolysis partially through miR-490-5p/CASC3 axis in HCC cells.
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Affiliation(s)
- Wei Liu
- Department of Laboratory, Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Changbin Yin
- Department of Laboratory, Luhe Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yue Liu
- Department of Research and Development Center, DAAN Gene Co., Ltd. of Sun Yat-Sen University, Guangzhou, China
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4
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Cao J, Qiu J, Wang X, Lu Z, Wang D, Feng H, Li X, Liu Q, Pan H, Han X, Wei J, Liu S, Wang L. Identification of microRNA-124 in regulation of Hepatocellular carcinoma through BIRC3 and the NF-κB pathway. J Cancer 2018; 9:3006-3015. [PMID: 30210622 PMCID: PMC6134807 DOI: 10.7150/jca.25956] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 06/09/2018] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) being proved to be involved in the carcinogenesis of numerous tumors. MicroRNA-124 (miR-124), identified as a tumor suppressor, has been demonstrated to exert pivotal roles in multiple processes of tumorigenesis. The present study demonstrated that miR-124 was low-expressed in human hepatocellular carcinoma (HCC) tissues and cell lines. In addition, overexpression of miR-124 through infected with miR-124 lentivirus inhibited the proliferation and migration of HCC in vitro and tumorigenesis in vivo, whereas inhibition of miR-124 expression can reverse the process. Moreover, Baculoviral IAP Repeat Containing 3 (BIRC3) was identified as a target gene of miR-124. The BIRC3 mRNA expression was increased in HCC tissues and negatively correlated with miR-124 expression. Knockdown of BIRC3 recovered the miR-124-induced inhibiting effect on HCC progression. Furthermore, we found that up-regulation of miR-124 significantly inhibited p-P65, p-IκBα and c-Myc proteins expression. However, the effect of miR-124 up-regulation on HCC development was partly reversed by BIRC3 restoration. In conclusion, our data proved that miR-124 inhibits the proliferation and migration of HCC at least partly through targeting BIRC3 and regulating NF-κB signaling pathway, and it may be a therapeutic target for HCC prognosis.
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Affiliation(s)
- Jia Cao
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Department of Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Jing Qiu
- Qingdao Municipal Hospital, Department of stomatology, Qingdao, 266071, China
| | - Xi Wang
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Department of Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - ZhenHui Lu
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - Danni Wang
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Department of Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - HuiMin Feng
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Department of Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - XiaoHan Li
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Department of Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - QiaoQiao Liu
- Qingdao Municipal Hospital, Department of stomatology, Qingdao, 266071, China
| | - HuaZheng Pan
- The Affiliated Hospital of Qingdao University, Medical Animal Lab, Qingdao, 266003, China
| | - XueBo Han
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China
| | - Jun Wei
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
| | - ShiHai Liu
- The Affiliated Hospital of Qingdao University, Medical Animal Lab, Qingdao, 266003, China
| | - LiBin Wang
- Ningxia Medical University, Clinical Medicine College, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Department of Beijing National Biochip Research Center Sub-Center in Ningxia, Yinchuan, 750004, China.,The General Hospital of Ningxia Medical University, Yinchuan, 750004, China
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5
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Xu L, Dai W, Li J, He L, Wang F, Xia Y, Chen K, Li S, Liu T, Lu J, Zhou Y, Wang Y, Guo C. Methylation-regulated miR-124-1 suppresses tumorigenesis in hepatocellular carcinoma by targeting CASC3. Oncotarget 2018; 7:26027-41. [PMID: 27029030 PMCID: PMC5041962 DOI: 10.18632/oncotarget.8266] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 03/08/2016] [Indexed: 12/27/2022] Open
Abstract
This study was to investigate the roles and mechanisms of miR-124-1 in hepatocellular carcinoma (HCC). We analyzed the expression of miR-124-1 in human HCC tissues and cell lines. Luciferase reporter assays were used to analyze the target of miR-124-1. Human HCC cell lines were transduced with lentiviruses expressing miR-124-1, and proliferation and colony formation were analyzed. The growth of human HCC cells overexpressing miR-124-1 was assessed in nude mice. The expression of p38-MAPK, JNK, ERK and related signaling molecules was detected by western blotting and immunohistochemistry. Our results showed that miR-124-1 levels were reduced in HCC tissues and cell lines compared with those in adjacent non-cancer tissues and normal liver cell lines respectively. Downregulation of miR-124-1 in HCC cell lines were attributed to hypermethylation of its promoter region. Overexpression of miR-124-1 inhibited HCC cell proliferation in vitro, whereas miR-124-1 was correlated with clinicopathological parameters of HCC patients. HCC cell-mediated overexpression of miR-124-1 in nude mice suppressed tumor growth. Cancer susceptibility candidate 3 (CASC3) was identified as a direct target of miR-124-1 by computational analysis and experimental assays. MiR-124-1-mediated downregulation of CASC3 resulted in the inactivation of p38-MAPK, JNK and ERK. Our findings provide potential new targets for the prevention or treatment of HCC.
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Affiliation(s)
- Ling Xu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.,Department of Gastroenterology, Shanghai Tongren Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Weiqi Dai
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - JingJing Li
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Lei He
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Fan Wang
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yujing Xia
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Kan Chen
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Sainan Li
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Tong Liu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Jie Lu
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yingqun Zhou
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Yugang Wang
- Department of Gastroenterology, Shanghai Tongren Hospital, Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Chuanyong Guo
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
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6
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Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor LA, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I. Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes. Oncotarget 2018; 9:9137-9155. [PMID: 29507679 PMCID: PMC5823624 DOI: 10.18632/oncotarget.24070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/02/2018] [Indexed: 12/30/2022] Open
Abstract
In many cancers, significantly down- or upregulated genes are found within chromosomal regions with DNA copy number alteration opposite to the expression changes. Generally, this paradox has been overlooked as noise, but can potentially be a consequence of interference of epigenetic regulatory mechanisms, including microRNA-mediated control of mRNA levels. To explore potential associations between microRNAs and paradoxes in non-small-cell lung cancer (NSCLC) we curated and analyzed lung adenocarcinoma (LUAD) data, comprising gene expressions, copy number aberrations (CNAs) and microRNA expressions. We integrated data from 1,062 tumor samples and 241 normal lung samples, including newly-generated array comparative genomic hybridization (aCGH) data from 63 LUAD samples. We identified 85 “paradoxical” genes whose differential expression consistently contrasted with aberrations of their copy numbers. Paradoxical status of 70 out of 85 genes was validated on sample-wise basis using The Cancer Genome Atlas (TCGA) LUAD data. Of these, 41 genes are prognostic and form a clinically relevant signature, which we validated on three independent datasets. By meta-analysis of results from 9 LUAD microRNA expression studies we identified 24 consistently-deregulated microRNAs. Using TCGA-LUAD data we showed that deregulation of 19 of these microRNAs explains differential expression of the paradoxical genes. Our results show that deregulation of paradoxical genes is crucial in LUAD and their expression pattern is maintained epigenetically, defying gene copy number status.
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Affiliation(s)
- Tomas Tokar
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Chiara Pastrello
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Varune R Ramnarine
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,The Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Kenneth J Craddock
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Larrisa A Pikor
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Emily A Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Simon Vary
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Mathematical Institute, University of Oxford, Oxford, United Kingdom.,Faculty of Mathematics, Physics and Informatics, Comenius University, Bratislava, Slovakia
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Wan L Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Department of Computer Science, University of Toronto, Toronto, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
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7
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Tornesello ML, Buonaguro L, Izzo F, Buonaguro FM. Molecular alterations in hepatocellular carcinoma associated with hepatitis B and hepatitis C infections. Oncotarget 2018; 7:25087-102. [PMID: 26943571 PMCID: PMC5041890 DOI: 10.18632/oncotarget.7837] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 02/20/2016] [Indexed: 02/07/2023] Open
Abstract
Chronic infections with hepatitis B (HBV) and hepatitis C viruses (HCV) are the leading cause of cirrhosis and hepatocellular carcinoma (HCC) worldwide. Both viruses encode multifunctional regulatory proteins activating several oncogenic pathways, which induce accumulation of multiple genetic alterations in the infected hepatocytes. Gene mutations in HBV- and HCV-induced HCCs frequently impair the TP53, Wnt/b-catenin, RAS/RAF/MAPK kinase and AKT/mTOR pathways, which represent important anti-cancer targets. In this review, we highlight the molecular mechanisms underlying the pathogenesis of primary liver cancer, with particular emphasis on the host genetic variations identified by high-throughput technologies. In addition, we discuss the importance of genetic alterations, such as mutations in the telomerase reverse transcriptase (TERT) promoter, for the diagnosis, prognosis, and tumor stratification for development of more effective treatment approaches.
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Affiliation(s)
- Maria Lina Tornesello
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Luigi Buonaguro
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Francesco Izzo
- Hepato-Biliary Surgery Department, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
| | - Franco M Buonaguro
- Molecular Biology and Viral Oncology Unit, Department of Research, Istituto Nazionale Tumori "Fondazione G. Pascale" - IRCCS, Napoli, Italy
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8
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Jiang M, Zeng Q, Dai S, Liang H, Dai F, Xie X, Lu K, Gao C. Comparative analysis of hepatocellular carcinoma and cirrhosis gene expression profiles. Mol Med Rep 2016; 15:380-386. [PMID: 27959423 PMCID: PMC5355740 DOI: 10.3892/mmr.2016.6021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/11/2016] [Indexed: 01/24/2023] Open
Abstract
Gene expression data of hepatocellular carcinoma (HCC) was compared with that of cirrhosis (C) to identify critical genes in HCC. A total of five gene expression data sets were downloaded from Gene Expression Omnibus. HCC and healthy samples were combined as dataset HCC, whereas cirrhosis samples were included in dataset C. A network was constructed for dataset HCC with the package R for performing Weighted Gene Co-expression Network Analysis. Modules were identified by cluster analysis with the packages flashClust and dynamicTreeCut. Hub genes were screened out by calculating connectivity. Functional annotations were assigned to the hub genes using the Database for Annotation, Visualization and Integration Discovery, and functional annotation networks were visualized with Cytoscape. Following the exclusion of outlier samples, 394 HCC samples and 47 healthy samples were included in dataset HCC and 233 cirrhosis samples were included in dataset C. A total of 6 modules were identified in the weighted gene co-expression network of dataset HCC (blue, brown, turquoise, green, red and yellow). Modules blue, brown and turquoise had high preservation whereas module yellow exhibited the lowest preservation. These modules were associated with transcription, mitosis, cation transportation, cation homeostasis, secretion and regulation of cyclase activity. Various hub genes of module yellow were cytokines, including chemokine (C-C motif) ligand 22 and interleukin-19, which may be important in the development of HCC. Gene expression profiles of HCC were compared with those of cirrhosis and numerous critical genes were identified, which may contribute to the progression of HCC. Further studies on these genes may improve the understanding of HCC pathogenesis.
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Affiliation(s)
- Mingming Jiang
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army, Quanzhou, Fujian 362000, P.R. China
| | - Qingfang Zeng
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army, Quanzhou, Fujian 362000, P.R. China
| | - Suiping Dai
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army, Quanzhou, Fujian 362000, P.R. China
| | - Huixia Liang
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army, Quanzhou, Fujian 362000, P.R. China
| | - Fengying Dai
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army, Quanzhou, Fujian 362000, P.R. China
| | - Xueling Xie
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army, Quanzhou, Fujian 362000, P.R. China
| | - Kunlin Lu
- Department of Obstetrics and Gynecology, The 180th Hospital of Chinese People's Liberation Army, Quanzhou, Fujian 362000, P.R. China
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China
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9
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Zhang J, Cheng J, Zeng Z, Wang Y, Li X, Xie Q, Jia J, Yan Y, Guo Z, Gao J, Yao M, Chen X, Lu F. Comprehensive profiling of novel microRNA-9 targets and a tumor suppressor role of microRNA-9 via targeting IGF2BP1 in hepatocellular carcinoma. Oncotarget 2016; 6:42040-52. [PMID: 26547929 PMCID: PMC4747208 DOI: 10.18632/oncotarget.5969] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 10/09/2015] [Indexed: 01/01/2023] Open
Abstract
MicroRNA-9 (miR-9) dysregulation is implicated in a variety of human malignancies including hepatocellular carcinoma (HCC), but its role remains contradictory. In this study, we explored the expression and methylation status of miR-9 in HCC samples, as well as the tumor-related functions of miR-9 in vitro. Bioinformatics analysis, array-based RNA expression profile, and literature retrieval were used to identify miR-9 targets in HCC. The potential downstream candidates were then validated by luciferase reporter assay, real-time quantitative PCR, and western blot or enzyme linked immunosorbent assay (ELISA). The expression status and clinicopathologic significances of miR-9 target genes in clinical samples were further explored. The results showed that miR-9 was frequently downregulated in primary HCC. Its silencing was largely contributed by a high frequency (42.5%) of mir-9-1 hypermethylation, which was correlated with bigger tumor size (P = 0.0234). In vitro functional studies revealed that miR-9 restoration retarded HCC cell proliferation and migration. IL-6, AP3B1, TC10, ONECUT2, IGF2BP1, MYO1D, and ANXA2 were confirmed to be miR-9 targets in HCC. Among them, ONECUT2, IGF2BP1, and ANXA2 were confirmed to be aberrantly upregulated in HCC. Moreover, upregulation of ONECUT2, IGF2BP1, and IL-6 were significantly associated with poor post-surgery prognosis (P = 0.0458, P = 0.0037 and P = 0.0461, respectively). Mechanically, miR-9 plays a tumor suppressive role partially through a functional miR-9/IGF2BP1/AKT&ERK axis. Our study suggests that miR-9 functions as a tumor suppressor in HCC progression by inhibiting a series of target genes, including the newly validated miR-9/IGF2BP1/AKT&ERK axis, thus providing potential therapeutic targets and novel prognostic biomarkers for HCC patients.
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Affiliation(s)
- Jiangbo Zhang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jin Cheng
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.,Institute of Sports Medicine, Beijing Key Laboratory of Sports Injuries, Peking University Third Hospital, Beijing 100191, China
| | - Zhenzhen Zeng
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yongfeng Wang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiaojun Li
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Qing Xie
- Department of Clinical Laboratory, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
| | - Junqiao Jia
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ying Yan
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Zhengyang Guo
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jian Gao
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Mingjie Yao
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiangmei Chen
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fengmin Lu
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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10
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Tan L, Meier T, Kuhlmann M, Xie F, Baier C, Zhu Z, Cong WM, Wilkens L. Distinct set of chromosomal aberrations in childhood hepatocellular carcinoma is correlated to hepatitis B virus infection. Cancer Genet 2016; 209:87-96. [PMID: 26837720 DOI: 10.1016/j.cancergen.2015.12.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 11/25/2015] [Accepted: 12/20/2015] [Indexed: 02/07/2023]
Abstract
Hepatocellular carcinoma (HCC) is rarely observed in children and adolescents, but it is reported to be correlated with hepatitis B virus (HBV+) infections. This correlation is not easily explained, because in adults, HBV infections lead to the development of HCC only after decades, not within a few years. In HBV+ adulthood HCC, distinct chromosomal imbalances have been observed. Similar analyses have not been reported for childhood HCC. Here, we investigated whether chromosomal changes were associated with childhood HCC. We analysed formalin-fixed paraffin-embedded (FFPE) samples derived from 17 patients, 0-18 years old, who underwent partial hepatectomies due to HBV+ or HBV- associated HCC. In parallel, in 15 cases, we also analysed non-neoplastic liver tissues adjacent to the HCC. All samples were analysed with high resolution, microarray-based, comparative genomic hybridisation (aCGH). Overall, genomic aberrations in childhood HCC resembled those reported for adulthood HCC. In HBV+ HCC samples, chromosomes 1, 6, 7, 9, 17, 19, and 22 were significantly changed compared to those in HBV- HCC samples. Most interestingly, aberrations for chromosomes 7, 8, 9, 11, and 19 were also observed in corresponding non-neoplastic samples. A specific set of chromosomal abnormalities, including gains in chromosomes 8q, 9q, 11q, and 19, was significantly enriched in HBV+ compared to HBV- non-neoplastic tissues. In childhood HCC, HBV+ was correlated to increased chromosomal instability and specific chromosomal imbalances. A subset of aberrations might be essential in HCC carcinogenesis because they occurred in adjacent, non-neoplastic tissues. In particular, the gain in chromosome 19 appeared to be highly important.
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Affiliation(s)
- Lu Tan
- Tumor Immunology and Gene Therapy Center, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China; Institute of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China; Institute Pathology, University Bonn, Germany
| | - Tatiana Meier
- Institute of Pathology, Nordstadtkrankenhaus (Klinikum Region Hannover), Hannover, Germany
| | - Mareike Kuhlmann
- Institute of Pathology, Nordstadtkrankenhaus (Klinikum Region Hannover), Hannover, Germany
| | - Feng Xie
- Department of Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Claas Baier
- Institute of Pathology, Nordstadtkrankenhaus (Klinikum Region Hannover), Hannover, Germany
| | - Zhen Zhu
- Institute of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Wen-Ming Cong
- Institute of Pathology, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - Ludwig Wilkens
- Institute of Pathology, Nordstadtkrankenhaus (Klinikum Region Hannover), Hannover, Germany; Institute of Human Genetics, Medical School Hannover, Germany.
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11
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Vincent-Chong VK, Salahshourifar I, Razali R, Anwar A, Zain RB. Immortalization of epithelial cells in oral carcinogenesis as revealed by genome-wide array comparative genomic hybridization: A meta-analysis. Head Neck 2015; 38 Suppl 1:E783-97. [PMID: 25914319 DOI: 10.1002/hed.24102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2015] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This purpose of this meta-analysis study was to identify the most frequent and potentially significant copy number alteration (CNA) in oral carcinogenesis. METHODS Seven oral squamous cell carcinoma (OSCC)-related publications, corresponding to 312 samples, were identified for this meta-analysis. The data were analyzed in a 4-step process that included the genome assembly coordination of multiple platforms, assignment of chromosomal position anchors, calling gains and losses, and functional annotation analysis. RESULTS Gains were more frequent than losses in the entire dataset. High-frequency gains were identified in chromosomes 5p, 14q, 11q, 7p, 17q, 20q, 8q, and 3q, whereas high-frequency losses were identified in chromosomes 3p, 8p, 6p, 18q, and 4q. Ingenuity pathway analysis showed that the top biological function was associated with immortalization of the epithelial cells (p = 1.93E-04). CONCLUSION This study has identified multiple recurrent CNAs that are involved in various biological annotations associated with oral carcinogenesis. © 2015 Wiley Periodicals, Inc. Head Neck 38: E783-E797, 2016.
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Affiliation(s)
- Vui King Vincent-Chong
- Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia.,Department of Oro-maxillofacial Surgical and Medical Sciences, Faculty of Dentistry, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia
| | - Iman Salahshourifar
- Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia
| | - Rozaimi Razali
- Sengenics Sdn Bhd, High Impact Research (HIR) Building, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia
| | - Arif Anwar
- Sengenics Sdn Bhd, High Impact Research (HIR) Building, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia
| | - Rosnah Binti Zain
- Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia.,Department of Oro-maxillofacial Surgical and Medical Sciences, Faculty of Dentistry, University of Malaya, Lembah Pantai, Kuala Lumpur, Malaysia
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12
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Zhao Z, Chen GY, Long J, Li H, Huang J. Genomic losses at 5q13.2 and 8p23.1 in dysplastic hepatocytes are common events in hepatitis B virus-related hepatocellular carcinoma. Oncol Lett 2015; 9:2839-2846. [PMID: 26137157 DOI: 10.3892/ol.2015.3140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 03/24/2015] [Indexed: 12/30/2022] Open
Abstract
Chromosomal loci with genomic imbalances are frequently identified in hepatocellular carcinoma (HCC). Greater than two-thirds of hepatitis B virus (HBV)-related HCCs originate from liver cirrhosis following a duration of up to two decades. However, it is unclear whether these genomic imbalances occur and accumulate in dysplastic hepatocytes of the cirrhotic liver during the progression from regenerated nodules to preneoplastic lesions, including dysplastic nodules (DN). In the present study, high-grade DNs (HGDNs) of HBV-related liver cirrhosis were screened to identify loci with genomic imbalances, and the frequency of the identified loci in a group of HCCs was analyzed in order to determine whether there may be a genetic link between liver cirrhosis and HCC. Genomic DNA was extracted from six HGDNs of two cases of HBV-related liver cirrhosis and subjected to array comparative genomic hybridization (CGH) analysis with a NimbleGen 720K microarray. Loci with the most frequently observed genomic imbalances in DNs were further analyzed in 83 cases of HCC by differential polymerase chain reaction (PCR) and quantitative PCR. The array CGH analysis revealed that the majority of genomic imbalances in the HGDNs were genomic losses of small segments, with loss of heterozygosity (LOH) at 5q13.2 and 8p23.1 identified most frequently. Of the 83 HCC cases, 30 (36.1%) cases were identified with LOH at 5q13.2, where known tumor-associated genes are located, including general transcription factor IIH subunit 2 (GTF2H2), baculoviral IAP repeat-containing protein 1 (BIRC1) and occludin (OCLN). LOH frequency at 8p23.1 in HCC was 61.29% (D8S1130) and 68.4% (D8S503) respectively, similar to the results obtained in previous studies. In conclusion, the results of the present study provided evidence that genomic losses at 5q13.2 and 8p23.1 identified in dysplastic hepatocytes of the cirrhotic liver are common events in HCC. HCC-associated chromosomal abnormalities may occur and accumulate in preneoplastic lesions of liver cirrhosis.
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Affiliation(s)
- Zhang Zhao
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Guang-Yong Chen
- Department of Pathology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China
| | - Jiang Long
- Minimally Invasive Hepatobiliary Cancer Center, Beijing You-An Hospital, Capital Medical University, Beijing 100069, P.R. China
| | - Hai Li
- Department of Hepatopancreatobiliary and Splenic Medicine, Affiliated Hospital of Medical College of Chinese People's Armed Police Force, Tianjin 300192, P.R. China
| | - Jian Huang
- Liver Research Center, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, P.R. China ; Beijing Key Laboratory of Traditional Medicine in Liver Cirrhosis, National Clinical Research Center of Digestive Disease, Beijing 100050, P.R. China
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13
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Liu YJ, Zhou Y, Yeh MM. Recurrent genetic alterations in hepatitis C-associated hepatocellular carcinoma detected by genomic microarray: a genetic, clinical and pathological correlation study. Mol Cytogenet 2014; 7:81. [PMID: 25469175 PMCID: PMC4251858 DOI: 10.1186/s13039-014-0081-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/26/2014] [Indexed: 01/30/2023] Open
Abstract
Background In the US, approximately 50% of hepatocellular carcinoma (HCC) is caused by hepatitis-C virus (HCV) infection. The molecular mechanism of a malignant transformation of hepatocyte induced by HCV infection is still largely unclear. There are several clinical and pathological staging systems for HCC, but none of them include biological parameters as predictors for prognosis and there has not been a standardized molecular classification of HCC. To understand the underlying pathogenic genetic alterations in HCV-associated HCC and aid in molecular classification of HCC and patient prognosis, microarray analysis of DNA copy number alterations in HCC were conducted using whole genome microarray with DNA from formalin-fixed paraffin-embedded (FFPE) specimens of both cancer tissues and paired nearby cirrhotic non-neoplastic tissues. Results Our results show that the most common chromosomal aberrations (>5 Mb) observed in HCC were chromosomal gains of 1q (80%), 8q (60%), 7q (40%), 5p (33%), 7p (33%), Xq (33%), 5q (27%), and Xp (20%), as well as chromosome losses of 17p (40%), 4q21.21-q26 (33%), 8p (33%), 1p36.11-pter (20%), and 9p (20%). Statistically significant smaller copy number alterations (3.9 kb to 644 kb) were identified using STAC algorithm, including losses of FGFR3, RECQL4, NOTCH1, PTEN, TSC2, and/or ASPSCR1 and gains of ETV1and/or MAF. Correlation analysis between genetic data and pathological data showed that gain of 1q21.1-q23.2 and gain of 8q11.1q13.1 are significantly associated with grade 2–4 and moderately or poorly differentiated HCCs, and gain of chromosome 5q was significantly associated with HCCs with vascular invasion, while gain of chromosome 7q is significantly associated with stage I HCCs. Conclusions This study has provided a detailed map of genomic aberrations occurring in HCV-associated HCC and has suggested candidate genes. In addition, gene enrichment analysis on the recurrent abnormal regions indicated NF- kappaB and BMP signaling pathways in HCC development and progression. This study demonstrated that genomic microarray test can be used to distinguish HCC from non- neoplastic cirrhotic nodules and to identify prognostic factors associated with HCC progression using pathologically characterized FFPE samples. Our data support the utility of genomic microarray test for the diagnosis, risk stratification, and pathogenic studies of HCC.
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Affiliation(s)
- Yajuan J Liu
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Box 357470, Seattle, WA 98195 USA
| | - Yang Zhou
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Box 357470, Seattle, WA 98195 USA
| | - Matthew M Yeh
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Box 357470, Seattle, WA 98195 USA
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14
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Kamieniak MM, Rico D, Milne RL, Muñoz-Repeto I, Ibáñez K, Grillo MA, Domingo S, Borrego S, Cazorla A, García-Bueno JM, Hernando S, García-Donas J, Hernández-Agudo E, Y Cajal TR, Robles-Díaz L, Márquez-Rodas I, Cusidó M, Sáez R, Lacambra-Calvet C, Osorio A, Urioste M, Cigudosa JC, Paz-Ares L, Palacios J, Benítez J, García MJ. Deletion at 6q24.2-26 predicts longer survival of high-grade serous epithelial ovarian cancer patients. Mol Oncol 2014; 9:422-36. [PMID: 25454820 PMCID: PMC5528660 DOI: 10.1016/j.molonc.2014.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 09/12/2014] [Accepted: 09/25/2014] [Indexed: 12/15/2022] Open
Abstract
Standard treatments for advanced high-grade serous ovarian carcinomas (HGSOCs) show significant side-effects and provide only short-term survival benefits due to disease recurrence. Thus, identification of novel prognostic and predictive biomarkers is urgently needed. We have used 42 paraffin-embedded HGSOCs, to evaluate the utility of DNA copy number alterations, as potential predictors of clinical outcome. Copy number-based unsupervised clustering stratified HGSOCs into two clusters of different immunohistopathological features and survival outcome (HR = 0.15, 95%CI = 0.03-0.81; Padj = 0.03). We found that loss at 6q24.2-26 was significantly associated with the cluster of longer survival independently from other confounding factors (HR = 0.06, 95%CI = 0.01-0.43, Padj = 0.005). The prognostic value of this deletion was validated in two independent series, one consisting of 36 HGSOCs analyzed by fluorescent in situ hybridization (P = 0.04) and another comprised of 411 HGSOCs from the Cancer Genome Atlas study (TCGA) (HR = 0.67, 95%CI = 0.48-0.93, Padj = 0.019). In addition, we confirmed the association of low expression of the genes from the region with longer survival in 799 HGSOCs (HR = 0.74, 95%CI = 0.61-0.90, log-rank P = 0.002) and 675 high-FIGO stage HGSOCs (HR = 0.76, 95%CI = 0.61-0.96, log-rank P = 0.02) available from the online tool KM-plotter. Finally, by integrating copy number, RNAseq and survival data of 296 HGSOCs from TCGA we propose a few candidate genes that can potentially explain the association. Altogether our findings indicate that the 6q24.2-26 deletion is an independent marker of favorable outcome in HGSOCs with potential clinical value as it can be analyzed by FISH on tumor sections and guide the selection of patients towards more conservative therapeutic strategies in order to reduce side-effects and improve quality of life.
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Affiliation(s)
- Marta M Kamieniak
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Daniel Rico
- Structural Computational Biology Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3 28029, Madrid, Spain
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne 3004, Australia; Center for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street Carlton, Melbourne 3010, Victoria, Australia
| | - Ivan Muñoz-Repeto
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Kristina Ibáñez
- Structural Computational Biology Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3 28029, Madrid, Spain
| | - Miguel A Grillo
- Molecular Cytogenetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Samuel Domingo
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain
| | - Salud Borrego
- Departments of Genetics, Reproduction, and Fetal Medicine, IBIS, University Hospital Virgen del Rocio/CSIC/University of Seville, Avda. Manuel Siurot, s/n., 41013 Sevilla, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Alicia Cazorla
- Pathology Department, Fundación Jiménez Díaz, Avda. Reyes Católicos, 2, 28040 Madrid, Spain
| | - José M García-Bueno
- Oncology Department, Hospital General de Albacete, Calle Hermanos Falco, 37, 02006 Albacete, Spain
| | - Susana Hernando
- Oncology Department, Fundación Hospital Alcorcón, Calle Valdelaguna, 1, 28922 Alcorcón, Spain
| | - Jesús García-Donas
- Medical Oncology Service, Oncologic Center Clara Campal, Calle Oña, 10, 28050 Madrid, Spain
| | - Elena Hernández-Agudo
- Breast Cancer Clinical Research Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Teresa Ramón Y Cajal
- Medical Oncology Service, Hospital Sant Pau, Carrer de Sant Quintí, 89, 08026 Barcelona, Spain
| | - Luis Robles-Díaz
- Familial Cancer Unit and Medical Oncology Department, Hospital 12 de Octubre, Avda de Córdoba, s/n, 28041 Madrid, Spain
| | - Ivan Márquez-Rodas
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón, Universidad Complutense, Calle Doctor Esquerdo, 46, 28007 Madrid, Spain
| | - Maite Cusidó
- Obstetrics and Gynecology Department, Institut Universitari Dexeus, Carrer de Sabino Arana, 5, 08028 Barcelona, Spain
| | - Raquel Sáez
- Laboratory of Genetics, Hospital Donostia, Calle Doctor Begiristain, 117, 20080 San Sebastián, Spain
| | - Carmen Lacambra-Calvet
- Department of Internal Medicine, Hospital Severo Ochoa, Avd. de Orellana, s/n., 28911 Madrid, Spain
| | - Ana Osorio
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Miguel Urioste
- Familial Cancer Clinical Unit, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Juan C Cigudosa
- Molecular Cytogenetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029 Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - Luis Paz-Ares
- Medical Oncology Department, University Hospital Virgen del Rocio, Avda. Manuel Siurot s/n., 41013 Sevilla, Spain
| | - José Palacios
- Pathology Department, Hospital Universitario Ramón y Cajal, Ctra. de Colmenar Viejo, km. 9,100, 28034 Madrid, Spain
| | - Javier Benítez
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain
| | - María J García
- Human Genetics Group, Spanish National Cancer Research Center (CNIO), C/ Melchor Fernández Almagro 3, 28029, Madrid, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), Spain.
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15
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Takai A, Dang HT, Wang XW. Identification of drivers from cancer genome diversity in hepatocellular carcinoma. Int J Mol Sci 2014; 15:11142-60. [PMID: 24955791 PMCID: PMC4100204 DOI: 10.3390/ijms150611142] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 06/12/2014] [Accepted: 06/16/2014] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancers with a dismal outcome. The complicated molecular pathogenesis of HCC caused by tumor heterogeneity makes it difficult to identify druggable targets useful for treating HCC patients. One approach that has a potential for the improvement of patient prognosis is the identification of cancer driver genes that play a critical role in the development of HCC. Recent technological advances of high-throughput methods, such as gene expression profiles, DNA copy number alterations and somatic mutations, have expanded our understanding of the comprehensive genetic profiles of HCC. Integrative analysis of these omics profiles enables us to classify the molecular subgroups of HCC patients. As each subgroup classified according to genetic profiles has different clinical features, such as recurrence rate and prognosis, the tumor subclassification tools are useful in clinical practice. Furthermore, a global genetic analysis, including genome-wide RNAi functional screening, makes it possible to identify cancer vulnerable genes. Identification of common cancer driver genes in HCC leads to the development of an effective molecular target therapy.
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Affiliation(s)
- Atsushi Takai
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Hien T Dang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Xin W Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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16
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Abstract
Liver cancer is the third leading cause of cancer-related death worldwide. Advances in sequencing technologies have enabled the examination of liver cancer genomes at high resolution; somatic mutations, structural alterations, HBV integration, RNA editing and retrotransposon changes have been comprehensively identified. Furthermore, integrated analyses of trans-omics data (genome, transcriptome and methylome data) have identified multiple critical genes and pathways implicated in hepatocarcinogenesis. These analyses have uncovered potential therapeutic targets, including growth factor signalling, WNT signalling, the NFE2L2-mediated oxidative pathway and chromatin modifying factors, and paved the way for new molecular classifications for clinical application. The aetiological factors associated with liver cancer are well understood; however, their effects on the accumulation of somatic changes and the influence of ethnic variation in risk factors still remain unknown. The international collaborations of cancer genome sequencing projects are expected to contribute to an improved understanding of risk evaluation, diagnosis and therapy for this cancer.
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Affiliation(s)
- Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan
| | - Hiroyuki Aburatani
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1, Komaba, Meguro-ku, Tokyo 153-8904, Japan
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17
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Involvement of DNA damage response pathways in hepatocellular carcinoma. BIOMED RESEARCH INTERNATIONAL 2014; 2014:153867. [PMID: 24877058 PMCID: PMC4022277 DOI: 10.1155/2014/153867] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 01/23/2014] [Accepted: 03/25/2014] [Indexed: 12/16/2022]
Abstract
Hepatocellular carcinoma (HCC) has been known as one of the most lethal human malignancies, due to the difficulty of early detection, chemoresistance, and radioresistance, and is characterized by active angiogenesis and metastasis, which account for rapid recurrence and poor survival. Its development has been closely associated with multiple risk factors, including hepatitis B and C virus infection, alcohol consumption, obesity, and diet contamination. Genetic alterations and genomic instability, probably resulted from unrepaired DNA lesions, are increasingly recognized as a common feature of human HCC. Dysregulation of DNA damage repair and signaling to cell cycle checkpoints, known as the DNA damage response (DDR), is associated with a predisposition to cancer and affects responses to DNA-damaging anticancer therapy. It has been demonstrated that various HCC-associated risk factors are able to promote DNA damages, formation of DNA adducts, and chromosomal aberrations. Hence, alterations in the DDR pathways may accumulate these lesions to trigger hepatocarcinogenesis and also to facilitate advanced HCC progression. This review collects some of the most known information about the link between HCC-associated risk factors and DDR pathways in HCC. Hopefully, the review will remind the researchers and clinicians of further characterizing and validating the roles of these DDR pathways in HCC.
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18
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Shi HY, Lee KT, Lee HH, Ho WH, Sun DP, Wang JJ, Chiu CC. Comparison of artificial neural network and logistic regression models for predicting in-hospital mortality after primary liver cancer surgery. PLoS One 2012; 7:e35781. [PMID: 22563399 PMCID: PMC3338531 DOI: 10.1371/journal.pone.0035781] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 03/21/2012] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Since most published articles comparing the performance of artificial neural network (ANN) models and logistic regression (LR) models for predicting hepatocellular carcinoma (HCC) outcomes used only a single dataset, the essential issue of internal validity (reproducibility) of the models has not been addressed. The study purposes to validate the use of ANN model for predicting in-hospital mortality in HCC surgery patients in Taiwan and to compare the predictive accuracy of ANN with that of LR model. METHODOLOGY/PRINCIPAL FINDINGS Patients who underwent a HCC surgery during the period from 1998 to 2009 were included in the study. This study retrospectively compared 1,000 pairs of LR and ANN models based on initial clinical data for 22,926 HCC surgery patients. For each pair of ANN and LR models, the area under the receiver operating characteristic (AUROC) curves, Hosmer-Lemeshow (H-L) statistics and accuracy rate were calculated and compared using paired T-tests. A global sensitivity analysis was also performed to assess the relative significance of input parameters in the system model and the relative importance of variables. Compared to the LR models, the ANN models had a better accuracy rate in 97.28% of cases, a better H-L statistic in 41.18% of cases, and a better AUROC curve in 84.67% of cases. Surgeon volume was the most influential (sensitive) parameter affecting in-hospital mortality followed by age and lengths of stay. CONCLUSIONS/SIGNIFICANCE In comparison with the conventional LR model, the ANN model in the study was more accurate in predicting in-hospital mortality and had higher overall performance indices. Further studies of this model may consider the effect of a more detailed database that includes complications and clinical examination findings as well as more detailed outcome data.
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Affiliation(s)
- Hon-Yi Shi
- Department of Healthcare Administration and Medical Informatics, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - King-Teh Lee
- Department of Healthcare Administration and Medical Informatics, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hao-Hsien Lee
- Department of Surgery, Chi Mei Medical Center, Liouying, Taiwan
| | - Wen-Hsien Ho
- Department of Healthcare Administration and Medical Informatics, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ding-Ping Sun
- Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
| | - Jhi-Joung Wang
- Department of Medical Research, Chi Mei Medical Center, Tainan, Taiwan
| | - Chong-Chi Chiu
- Department of Surgery, Chi Mei Medical Center, Liouying, Taiwan
- Department of Surgery, Chi Mei Medical Center, Tainan, Taiwan
- Department of Surgery, Taipei Medical University, Taipei, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
- * E-mail:
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