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Csak T, Bala S, Lippai D, Satishchandran A, Catalano D, Kodys K, Szabo G. microRNA-122 regulates hypoxia-inducible factor-1 and vimentin in hepatocytes and correlates with fibrosis in diet-induced steatohepatitis. Liver Int 2015; 35:532-41. [PMID: 25040043 PMCID: PMC4289469 DOI: 10.1111/liv.12633] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 07/06/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS miR-122 is the most abundant miRNA in the liver particularly in hepatocytes where it targets cholesterol metabolism. Steatosis, a key component of non-alcoholic fatty liver disease, is regulated by hypoxia-inducible factor-1α (HIF-1α). Here, we hypothesized that reduced miR-122 has a pathogenic role in steatohepatitis. METHODS miR-122 and its target genes were evaluated in mouse livers and/or isolated hepatocytes after methionine-choline-deficient (MCD) or methionine-choline-supplemented (MCS) diet. RESULTS Liver and hepatocyte miR-122 expression was significantly decreased in steatohepatitis. A maximum reduction in miR-122 occurred at the fibrosis stage (8 weeks of MCD diet). MAP3K3, a miR-122 target gene, was induced at all stages of non-alcoholic steatohepatitis (NASH; 3-8 weeks) only at the mRNA level. Increased NF-κB activation was found in MCD diet-fed mice and MAP3K3 regulated the NF-κB DNA binding in naive hepatocytes. HIF-1α mRNA and DNA binding and expression of the HIF-1α target gene, profibrotic lysyl oxidase, was increased in advanced steatohepatitis (8 weeks). In addition, increase in vimentin and Sirius red staining (liver fibrosis) was found at 8 weeks of MCD diet. Using miR-122 overexpression and inhibition approaches, we confirmed that HIF-1α, vimentin and MAP3K3 are novel miR-122 targets in hepatocytes. We report transcriptional repression of miR-122 in NASH. Decreased liver miR-122 was associated with elevated circulating miR-122 in both exosome-rich and protein-rich serum fractions. CONCLUSIONS Our novel data suggest that decreased liver miR-122 contributes to upregulation of modulators of tissue remodelling (HIF-1α, vimentin and MAP3K3) and might play a role in NASH-induced liver fibrosis.
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Affiliation(s)
- Timea Csak
- Department of Medicine; University of Massachusetts Medical School; Worcester MA USA
| | - Shashi Bala
- Department of Medicine; University of Massachusetts Medical School; Worcester MA USA
| | - Dora Lippai
- Department of Medicine; University of Massachusetts Medical School; Worcester MA USA
| | | | - Donna Catalano
- Department of Medicine; University of Massachusetts Medical School; Worcester MA USA
| | - Karen Kodys
- Department of Medicine; University of Massachusetts Medical School; Worcester MA USA
| | - Gyongyi Szabo
- Department of Medicine; University of Massachusetts Medical School; Worcester MA USA
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Abstract
Alcoholic liver disease (ALD) is characterized by hepatocyte damage, inflammatory cell activation and increased intestinal permeability leading to the clinical manifestations of alcoholic hepatitis. Selected members of the family of microRNAs are affected by alcohol, resulting in an abnormal miRNA profile in the liver and circulation in ALD. Increasing evidence suggests that mRNAs that regulate inflammation, lipid metabolism and promote cancer are affected by excessive alcohol administration in mouse models of ALD. This communication highlights recent findings in miRNA expression and functions as they relate to the pathogenesis of ALD. The cell-specific distribution of miRNAs, as well as the significance of circulating extracellular miRNAs, is discussed as potential biomarkers. Finally, the prospects of miRNA-based therapies are evaluated in ALD.
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Affiliation(s)
- Gyongyi Szabo
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Abhishek Satishchandran
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
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103
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Villena JA. New insights into PGC-1 coactivators: redefining their role in the regulation of mitochondrial function and beyond. FEBS J 2015; 282:647-72. [DOI: 10.1111/febs.13175] [Citation(s) in RCA: 252] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 10/31/2014] [Accepted: 12/10/2014] [Indexed: 12/25/2022]
Affiliation(s)
- Josep A. Villena
- Laboratory of Metabolism and Obesity; Vall d'Hebron-Institut de Recerca; Universitat Autònoma de Barcelona; Spain
- CIBERDEM (CIBER de Diabetes y Enfermedades Metabólicas Asociadas); Instituto de Salud Carlos III; Barcelona Spain
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104
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Zamanian–Azodi M, Rezaei–Tavirani M, Hasanzadeh H, Rahmati Rad S, Dalilan S. Introducing biomarker panel in esophageal, gastric, and colon cancers; a proteomic approach. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2015; 8:6-18. [PMID: 25584171 PMCID: PMC4285927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 11/18/2014] [Indexed: 10/26/2022]
Abstract
Cancer research is an attractive field in molecular biology and medicine. By applying large-scale tools such as advanced genomics and proteomics, cancer diagnosis and treatment have been improved greatly. Cancers of esophagus, gastric, and colon accounted for major health problem globally. Biomarker panel could bring out the accuracy for cancer evaluation tests as it can suggest a group of candidate molecules specified to particular malignancy in a way that distinguishing malignant tumors from benign, differentiating from other diseases, and identifying each stages with high specificity and sensitivity. In this review, a systematic search of unique protein markers reported by several proteomic literatures are classified in their specific cancer type group as novel panels for feasible accurate malignancy diagnosis and treatment. About thousands of introduced proteins were studied; however, a small number of them belonged to a specific kind of malignancy. In conclusion, despite the fact that combinatorial biomarkers appear to be hopeful, more evaluation of them is crucial to achieve the suitable biomarker panel for clinical application. This effort needs more investigations and researches for finding a specific and sensitive panel.
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Affiliation(s)
- Mona Zamanian–Azodi
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei–Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Hasanzadeh
- Department of Medical Physics, Semnan University of Medical Sciences, Semnan, Iran
| | - Sara Rahmati Rad
- Department of Cell and Molecular Biology, Faculty of Science, University of Tehran, Tehran, Iran
| | - Sona Dalilan
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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105
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Novák J, Olejníčková V, Tkáčová N, Santulli G. Mechanistic Role of MicroRNAs in Coupling Lipid Metabolism and Atherosclerosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 887:79-100. [PMID: 26662987 PMCID: PMC4871243 DOI: 10.1007/978-3-319-22380-3_5] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs, miRs) represent a group of powerful and versatile posttranscriptional regulators of gene expression being involved in the fine control of a plethora of physiological and pathological processes. Besides their well-established crucial roles in the regulation of cell cycle, embryogenesis or tumorigenesis, these tiny molecules have also been shown to participate in the regulation of lipid metabolism. In particular, miRs orchestrate cholesterol and fatty acids synthesis, transport, and degradation and low-density and high-density lipoprotein (LDL and HDL) formation. It is thus not surprising that they have also been reported to affect the development and progression of several lipid metabolism-related disorders including liver steatosis and atherosclerosis. Mounting evidence suggests that miRs might represent important "posttranscriptional hubs" of lipid metabolism, which means that one miR usually targets 3'-untranslated regions of various mRNAs that are involved in different steps of one precise metabolic/signaling pathway, e.g., one miR targets mRNAs of enzymes important for cholesterol synthesis, degradation, and transport. Therefore, changes in the levels of one key miR affect various steps of one pathway, which is thereby promoted or inhibited. This makes miRs potent future diagnostic and even therapeutic tools for personalized medicine. Within this chapter, the most prominent microRNAs involved in lipid metabolism, e.g., miR-27a/b, miR-33/33*, miR-122, miR-144, or miR-223, and their intracellular and extracellular functions will be extensively discussed, in particular focusing on their mechanistic role in the pathophysiology of atherosclerosis. Special emphasis will be given on miR-122, the first microRNA currently in clinical trials for the treatment of hepatitis C and on miR-223, the most abundant miR in lipoprotein particles.
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Affiliation(s)
- Jan Novák
- 2nd Department of Internal Medicine, St. Anne's University Hospital and Faculty of Medicine, Masaryk University, Brno, Czech Republic.
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Kamenice 5-building A18, Brno, 62500, Czech Republic.
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5-building A20, Brno, 62500, Czech Republic.
| | - Veronika Olejníčková
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5-building A20, Brno, 62500, Czech Republic
| | - Nikola Tkáčová
- Department of Physiology, Faculty of Medicine, Masaryk University, Kamenice 5-building A20, Brno, 62500, Czech Republic
| | - Gaetano Santulli
- Columbia University Medical Center, New York Presbyterian Hospital —Manhattan, New York, NY, USA; “Federico II” University Hospital, Naples, Italy
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106
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Chan B, Manley J, Lee J, Singh SR. The emerging roles of microRNAs in cancer metabolism. Cancer Lett 2015; 356:301–8. [DOI: 10.1016/j.canlet.2014.10.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 10/09/2014] [Indexed: 12/13/2022]
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107
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Su CH, Lin Y, Cai L. Genetic factors, viral infection, other factors and liver cancer: an update on current progress. Asian Pac J Cancer Prev 2014; 14:4953-60. [PMID: 24175758 DOI: 10.7314/apjcp.2013.14.9.4953] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Primary liver cancer is one of the most common cancers at the global level, accounting for half of all cancers in some undeveloped countries. This disease tends to occur in livers damaged through alcohol abuse, or chronic infection with hepatitis B and C, on a background of cirrhosis. Various cancer-causing substances are associated with primary liver cancer, including certain pesticides and such chemicals as vinyl chloride and arsenic. The strong association between HBV infection and liver cancer is well documented in epidemiological studies. It is generally acknowledged that the virus is involved through long term chronic infection, frequently associated with cirrhosis, suggesting a nonspecific mechanism triggered by the immune response. Chronic inflammation of liver, continuous cell death, abnormal cell growth, would increase the occurrence rate of genetic alterations and risk of disease. However, the statistics indicated that only about one fifth of HBV carries would develop HCC in lifetime, suggesting that individual variation in genome would also influence the susceptibility of HCC. The goal of this review is to highlight present level of knowledge on the role of viral infection and genetic variation in the development of liver cancer.
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Affiliation(s)
- Cheng-Hao Su
- Department of Emergency Countermeasure and Information Management, Xiamen Center for Disease Control and Prevention, Xiamen, China E-mail :
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108
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Wong CCL, Au SLK, Tse APW, Xu IMJ, Lai RKH, Chiu DKC, Wei LL, Fan DNY, Tsang FHC, Lo RCL, Wong CM, Ng IOL. Switching of pyruvate kinase isoform L to M2 promotes metabolic reprogramming in hepatocarcinogenesis. PLoS One 2014; 9:e115036. [PMID: 25541689 PMCID: PMC4277479 DOI: 10.1371/journal.pone.0115036] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 11/18/2014] [Indexed: 12/31/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is an aggressive tumor, with a high mortality rate due to late symptom presentation and frequent tumor recurrences and metastasis. It is also a rapidly growing tumor supported by different metabolic mechanisms; nevertheless, the biological and molecular mechanisms involved in the metabolic reprogramming in HCC are unclear. In this study, we found that pyruvate kinase M2 (PKM2) was frequently over-expressed in human HCCs and its over-expression was associated with aggressive clinicopathological features and poor prognosis of HCC patients. Furthermore, knockdown of PKM2 suppressed aerobic glycolysis and cell proliferation in HCC cell lines in vitro. Importantly, knockdown of PKM2 hampered HCC growth in both subcutaneous injection and orthotopic liver implantation models, and reduced lung metastasis in vivo. Of significance, PKM2 over-expression in human HCCs was associated with a down-regulation of a liver-specific microRNA, miR-122. We further showed that miR-122 interacted with the 3UTR of the PKM2 gene. Re-expression of miR-122 in HCC cell lines reduced PKM2 expression, decreased glucose uptake in vitro, and suppressed HCC tumor growth in vivo. Our clinical data and functional studies have revealed a novel biological mechanism involved in HCC metabolic reprogramming.
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Affiliation(s)
- Carmen Chak-Lui Wong
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, HKSAR
| | | | - Aki Pui-Wah Tse
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
| | - Iris Ming-Jing Xu
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
| | - Robin Kit-Ho Lai
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
| | | | - Larry Lai Wei
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
| | | | | | - Regina Cheuk-Lam Lo
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, HKSAR
| | - Chun-Ming Wong
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, HKSAR
| | - Irene Oi-Lin Ng
- Department of Pathology, The University of Hong Kong, Hong Kong, HKSAR
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, HKSAR
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109
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Yang J, Han S, Huang W, Chen T, Liu Y, Pan S, Li S. A meta-analysis of microRNA expression in liver cancer. PLoS One 2014; 9:e114533. [PMID: 25490558 PMCID: PMC4260848 DOI: 10.1371/journal.pone.0114533] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 11/10/2014] [Indexed: 12/15/2022] Open
Abstract
MicroRNA (miRNA) played an important role in the progression of liver cancer and its diagnostic and prognostic values have been frequently studied. However, different microarray techniques and small sample size led to inconsistent findings in previous studies. We performed a comprehensive meta-analysis of a total of 357 tumor and 283 noncancerous samples from 12 published miRNA expression studies using robust rank aggregation method. As a result, we identified a statistically significant meta-signature of five upregulated (miR-221, miR-222, miR-93, miR-21 and miR-224) and four downregulated (miR-130a, miR-195, miR-199a and miR-375) miRNAs. We then conducted miRNA target prediction and pathway enrichment analysis to find what biological process these miRNAs might affect. We found that most of the pathways were frequently associated with cell signaling and cancer pathogenesis. Thus these miRNAs may involve in the onset and progression of liver cancer and serve as potential diagnostic and therapeutic targets of this malignancy.
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Affiliation(s)
- Jingcheng Yang
- First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Shuai Han
- First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Wenwen Huang
- First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Ting Chen
- Department of Management Information System, College of Computer and Information Engineering, Guangxi Teachers Education University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Yang Liu
- First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Shangling Pan
- Department of Pathophysiology, Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
| | - Shikang Li
- First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, China
- * E-mail:
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110
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Kim JH, Sohn BH, Lee HS, Kim SB, Yoo JE, Park YY, Jeong W, Lee SS, Park ES, Kaseb A, Kim BH, Kim WB, Yeon JE, Byun KS, Chu IS, Kim SS, Wang XW, Thorgeirsson SS, Luk JM, Kang KJ, Heo J, Park YN, Lee JS. Genomic predictors for recurrence patterns of hepatocellular carcinoma: model derivation and validation. PLoS Med 2014; 11:e1001770. [PMID: 25536056 PMCID: PMC4275163 DOI: 10.1371/journal.pmed.1001770] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 11/07/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Typically observed at 2 y after surgical resection, late recurrence is a major challenge in the management of hepatocellular carcinoma (HCC). We aimed to develop a genomic predictor that can identify patients at high risk for late recurrence and assess its clinical implications. METHODS AND FINDINGS Systematic analysis of gene expression data from human liver undergoing hepatic injury and regeneration revealed a 233-gene signature that was significantly associated with late recurrence of HCC. Using this signature, we developed a prognostic predictor that can identify patients at high risk of late recurrence, and tested and validated the robustness of the predictor in patients (n = 396) who underwent surgery between 1990 and 2011 at four centers (210 recurrences during a median of 3.7 y of follow-up). In multivariate analysis, this signature was the strongest risk factor for late recurrence (hazard ratio, 2.2; 95% confidence interval, 1.3-3.7; p = 0.002). In contrast, our previously developed tumor-derived 65-gene risk score was significantly associated with early recurrence (p = 0.005) but not with late recurrence (p = 0.7). In multivariate analysis, the 65-gene risk score was the strongest risk factor for very early recurrence (<1 y after surgical resection) (hazard ratio, 1.7; 95% confidence interval, 1.1-2.6; p = 0.01). The potential significance of STAT3 activation in late recurrence was predicted by gene network analysis and validated later. We also developed and validated 4- and 20-gene predictors from the full 233-gene predictor. The main limitation of the study is that most of the patients in our study were hepatitis B virus-positive. Further investigations are needed to test our prediction models in patients with different etiologies of HCC, such as hepatitis C virus. CONCLUSIONS Two independently developed predictors reflected well the differences between early and late recurrence of HCC at the molecular level and provided new biomarkers for risk stratification. Please see later in the article for the Editors' Summary.
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Affiliation(s)
- Ji Hoon Kim
- Department of Systems Biology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Kleberg Center for Molecular Markers, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Bo Hwa Sohn
- Department of Systems Biology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Kleberg Center for Molecular Markers, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Hyun-Sung Lee
- Department of Systems Biology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Kleberg Center for Molecular Markers, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Sang-Bae Kim
- Department of Systems Biology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Kleberg Center for Molecular Markers, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Jeong Eun Yoo
- Department of Pathology and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Yun-Yong Park
- ASAN Institute for Life Sciences, Asan Medical Center, Department of Medicine, University of Ulsan College of Medicine, Seoul, Korea
| | - Woojin Jeong
- Department of Life Sciences, Division of Life and Pharmaceutical Sciences, Center for Cell Signaling and Drug Discovery Research, Ewha Womans University, Seoul, Korea
| | - Sung Sook Lee
- Department of Hematology-Oncology, Inje University Haeundae Paik Hospital, Busan, Korea
| | - Eun Sung Park
- Institute for Medical Convergence, Yonsei University College of Medicine, Seoul, Korea
| | - Ahmed Kaseb
- Department of GI Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Baek Hui Kim
- Department of Pathology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Wan Bae Kim
- Department of Surgery, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Jong Eun Yeon
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - Kwan Soo Byun
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Korea University College of Medicine, Seoul, Korea
| | - In-Sun Chu
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Sung Soo Kim
- Department of Biochemistry and Molecular Biology, Medical Research Center and Biomedical Science Institute, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Snorri S. Thorgeirsson
- Laboratory of Experimental Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John M. Luk
- Department of Pharmacology, National University of Singapore, Singapore
| | - Koo Jeong Kang
- Department of Surgery, Keimyung University School of Medicine, Daegu, Korea
| | - Jeonghoon Heo
- Departments of Molecular Biology and Immunology, Kosin University College of Medicine, Busan, Korea
| | - Young Nyun Park
- Department of Pathology and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul, Korea
| | - Ju-Seog Lee
- Department of Systems Biology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Kleberg Center for Molecular Markers, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
- Department of Biochemistry and Molecular Biology, Medical Research Center and Biomedical Science Institute, School of Medicine, Kyung Hee University, Seoul, Korea
- * E-mail:
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111
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Yu C, Xue J, Zhu W, Jiao Y, Zhang S, Cao J. Warburg meets non-coding RNAs: the emerging role of ncRNA in regulating the glucose metabolism of cancer cells. Tumour Biol 2014; 36:81-94. [DOI: 10.1007/s13277-014-2875-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/18/2014] [Indexed: 12/26/2022] Open
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Prognostic marker microRNA-125b inhibits tumorigenic properties of hepatocellular carcinoma cells via suppressing tumorigenic molecule eIF5A2. Dig Dis Sci 2014; 59:2477-87. [PMID: 24811246 DOI: 10.1007/s10620-014-3184-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 04/21/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) belong to a group of small non-coding RNA with differential expression in tumors, including hepatocellular carcinoma (HCC). AIM This study investigates the involvement of miR-125b in HCC. METHODS Clinical analysis of miR-125b was performed using data derived from miRNA profiling and qPCR. Phenotypic changes of liver cell lines were examined after ectopic miR-125b expression. Lastly, bioinformatics analysis coupled with luciferase reporter assay was used to reveal the cellular target of miR-125b. RESULTS A down-regulation of miR-125b was found in HCC tumors and cultured cells. Patients having tumors with ≥twofold reduction in miR-125b compared to adjacent non-tumor tissues contributed to 23 out of 49 HCC cases (46.9 %), while this down-regulation was usually found in patients with tumor venous infiltration and recurrence. miR-125b expression was also negatively correlated with increased serum AFP level and poor overall survival of patients. Ectopic expression of miR-125b led to alleviated tumor phenotypes of HCC cells. Among the 110 bioinformatically predicated candidates, 31 of them negatively correlated with miR-125b in HCC tumors for which one of them named eukaryotic translation initiation factor 5A2 (eIF5A2), known also as a liver oncofetal molecule, was validated to be a direct target of miR-125b in HCC. CONCLUSIONS This study has evidenced for the negative correlation of tumor miR-125b expression with poor prognosis of HCC patients. Expression of miR-125b can reverse the tumorigenic properties of cultured HCC cells via suppressing the tumorigenic molecule eIF5A2, thus postulating restoration of miR-125b level as a way to counteract liver tumorigenesis.
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113
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The role of micro-RNAs in hepatocellular carcinoma: from molecular biology to treatment. Molecules 2014; 19:6393-406. [PMID: 24853455 PMCID: PMC6271763 DOI: 10.3390/molecules19056393] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 05/02/2014] [Accepted: 05/15/2014] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide and the third leading cause of cancer deaths. microRNAs (miRNAs) are evolutionary conserved small non-coding RNA that negatively regulate gene expression and protein translation. Recent evidences have shown that they are involved in many biological processes, from development and cell-cycle regulation to apoptosis. miRNAs can behave as tumor suppressor or promoter of oncogenesis depending on the cellular function of their targets. Moreover, they are frequently dysregulated in HCC. In this review we summarize the latest findings of miRNAs regulation in HCC and their role as potentially diagnostic and prognostic biomarkers for HCC. We highlight development of miRNAs as potential therapeutic targets for HCC.
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114
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Synergistic effect of MiR-146a mimic and cetuximab on hepatocellular carcinoma cells. BIOMED RESEARCH INTERNATIONAL 2014; 2014:384121. [PMID: 24895573 PMCID: PMC4033429 DOI: 10.1155/2014/384121] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Revised: 02/01/2014] [Accepted: 03/25/2014] [Indexed: 12/15/2022]
Abstract
Previously, we found that the expression of microRNA-146a (miR-146a) was downregulated in hepatocellular carcinoma (HCC) formalin-fixed paraffin-embedded (FFPE) tissues compared to the adjacent noncancerous hepatic tissues. In the current study, we have explored the in vitro effect of miR-146a on the malignant phenotypes of HCC cells. MiR-146a mimic could suppress cell growth and increase cellular apoptosis in HCC cell lines HepG2, HepB3, and SNU449, as assessed by spectrophotometry, fluorimetry, and fluorescence microscopy, respectively. Furthermore, western blot showed that miR-146a mimic downregulated EGFR, ERK1/2, and stat5 signalings. These effects were less potent compared to that of a siRNA targeting EGFR, a known target gene of miR-146a. Moreover, miR-146a mimic could enhance the cell growth inhibition and apoptosis induction impact of various EGFR targeting agents. The most potent combination was miR-146a mimic with cetuximab, presenting a synergistic effect. In conclusion, miR-146a plays a vital role in the cell growth and apoptosis of HCC cells and inducing miR-146a level might be a critical targeted molecular therapy strategy for HCC.
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115
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Abstract
BACKGROUND Aberrant expression of microRNA-146a (miR-146a) has been found in several classes of cancers. However, its expression and clinicopathological contribution in hepatocellular carcinoma (HCC) has not been fully elucidated. OBJECTIVE To explore the clinicopathological significance of the miR-146a level in HCC formalin-fixed paraffin-embedded (FFPE) tissue. METHODS Eighty-five HCC samples and their para-cancerous normal liver tissues were collected. Total mRNA including miRNA was extracted, and miR-146a expression was determined using real-time RT-PCR. Furthermore, the correlation between the miR-146a expression and clinicopathological parameters was investigated. RESULTS MicroRNA-146a expression in HCC tissues was lower compared with that in adjacent non-cancerous hepatic tissues. MicroRNA-146a expression was also related to clinical TNM stage, metastasis, portal vein tumor embolus, and number of tumor nodes. CONCLUSIONS Down-regulation of miR-146a is related to HCC carcinogenesis and deterioration of HCC. MicroRNA-146a may act as a suppressor miRNA of HCC, and it is therefore a potential prognostic biomarker for HCC patients.
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Affiliation(s)
- Minhua Rong
- Research Department, Affiliated Cancer Hospital, Guangxi Medical University, 71 Hedi Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Rongquan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Yiwu Dang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, 6 Shuangyong Road, Nanning, Guangxi Zhuang Autonomous Region 530021, P. R. China
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116
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Jin JC, Zhang X, Jin XL, Qian CS, Jiang H, Ruan Y. MicroRNA‑122 regulation of the morphology and cytoarchitecture of hepatoma carcinoma cells. Mol Med Rep 2014; 9:1376-80. [PMID: 24504483 DOI: 10.3892/mmr.2014.1930] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 01/16/2014] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are a large family of post‑transcriptional regulators of gene expression that control a number of developmental and cellular processes in eukaryotic organisms and are ~23 nucleotides in length. miRNA‑122 is an abundant liver‑specific miRNA, implicated in fatty acid and cholesterol metabolism, as well as in hepatitis C viral replication and is frequently suppressed in primary hepatocellular carcinomas. In the current study, the Hep3B cell line with stable overexpression of miR‑122 was successfully established through gene transfection methods and drug screening. miR‑122 was observed to alter cell morphology in vitro by stable overexpression in Hep3B cells. This alteration was viewed by light microscopy and transmission electron microscopy. These alterations included increases in the cell volume, the appearance of lipid granules and vacuoles, thickening of nuclear membrane, swelling of the mitochondria, cytoplasm vacuolization and a more prominent nucleolus. Furthermore, the study provided novel evidence that miR‑122 function was dependent upon its expression level. In addition, it was observed to negatively regulate mitochondria.
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Affiliation(s)
- Ji-Chun Jin
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Yanbian University, Yanji, Jilin 133000, P.R. China
| | - Xian Zhang
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Yanbian University, Yanji, Jilin 133000, P.R. China
| | - Xing-Lin Jin
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Yanbian University, Yanji, Jilin 133000, P.R. China
| | - Chang-Shi Qian
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Yanbian University, Yanji, Jilin 133000, P.R. China
| | - Hao Jiang
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Yanbian University, Yanji, Jilin 133000, P.R. China
| | - Yang Ruan
- Department of Hepatopancreatobiliary Surgery, Affiliated Hospital of Yanbian University, Yanji, Jilin 133000, P.R. China
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117
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Liu AM, Xu Z, Shek FH, Wong KF, Lee NP, Poon RT, Chen J, Luk JM. miR-122 targets pyruvate kinase M2 and affects metabolism of hepatocellular carcinoma. PLoS One 2014; 9:e86872. [PMID: 24466275 PMCID: PMC3900676 DOI: 10.1371/journal.pone.0086872] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 12/16/2013] [Indexed: 12/13/2022] Open
Abstract
In contrast to normal differentiated cells that depend on mitochondrial oxidative phosphorylation for energy production, cancer cells have evolved to utilize aerobic glycolysis (Warburg's effect), with benefit of providing intermediates for biomass production. MicroRNA-122 (miR-122) is highly expressed in normal liver tissue regulating a wide variety of biological processes including cellular metabolism, but is reduced in hepatocellular carcinoma (HCC). Overexpression of miR-122 was shown to inhibit cancer cell proliferation, metastasis, and increase chemosensitivity, but its functions in cancer metabolism remains unknown. The present study aims to identify the miR-122 targeted genes and to investigate the associated regulatory mechanisms in HCC metabolism. We found the ectopic overexpression of miR-122 affected metabolic activities of HCC cells, evidenced by the reduced lactate production and increased oxygen consumption. Integrated gene expression analysis in a cohort of 94 HCC tissues revealed miR-122 level tightly associated with a battery of glycolytic genes, in which pyruvate kinase (PK) gene showed the strongest anti-correlation coefficient (Pearson r = -0.6938, p = <0.0001). In addition, reduced PK level was significantly associated with poor clinical outcomes of HCC patients. We found isoform M2 (PKM2) is the dominant form highly expressed in HCC and is a direct target of miR-122, as overexpression of miR-122 reduced both the mRNA and protein levels of PKM2, whereas PKM2 re-expression abrogated the miR-122-mediated glycolytic activities. The present study demonstrated the regulatory role of miR-122 on PKM2 in HCC, having an implication of therapeutic intervention targeting cancer metabolic pathways.
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MESH Headings
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Blotting, Western
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Carrier Proteins/antagonists & inhibitors
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Proliferation
- Female
- Gene Expression Profiling
- Glycolysis
- Humans
- Immunoenzyme Techniques
- Lactic Acid/metabolism
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Male
- Membrane Proteins/antagonists & inhibitors
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- MicroRNAs/genetics
- Middle Aged
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/pathology
- Neoplasm Staging
- Oligonucleotide Array Sequence Analysis
- Oxygen Consumption
- Prognosis
- RNA, Messenger/genetics
- RNA, Small Interfering/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Survival Rate
- Thyroid Hormones/genetics
- Thyroid Hormones/metabolism
- Tumor Cells, Cultured
- Thyroid Hormone-Binding Proteins
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Affiliation(s)
- Angela M. Liu
- Department of Pharmacology, National University of Singapore, Singapore
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Zhi Xu
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Felix H. Shek
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Kwong-Fai Wong
- Cancer Science Institute, National University of Singapore, Singapore
| | - Nikki P. Lee
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Ronnie T. Poon
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - John M. Luk
- Department of Pharmacology, National University of Singapore, Singapore
- Department of Surgery, National University Health System, Singapore
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
- Cancer Science Institute, National University of Singapore, Singapore
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong
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Wang G, Dong X, Tian W, Lu Y, Hu J, Liu Y, Yuchi J, Wu X. Evaluation of miR-122-regulated suicide gene therapy for hepatocellular carcinoma in an orthotopic mouse model. Chin J Cancer Res 2014; 25:646-55. [PMID: 24385691 DOI: 10.3978/j.issn.1000-9604.2013.11.07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/24/2013] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Intratumoral administration of adenoviral vector encoding herpes simplex virus (HSV) thymidine kinase (TK) gene (Ad-TK) followed by systemic ganciclovir (GCV) is an effective approach in treating experimental hepatocellular carcinoma (HCC). However, hepatotoxicity due to unwanted vector spread and suicide gene expression limited the application of this therapy. miR-122 is an abundant, liver-specific microRNA whose expression is decreased in human primary HCC and HCC-derived cell lines. These different expression profiles provide an opportunity to induce tumor-specific gene expression by miR-122 regulation. METHODS By inserting miR-122 target sequences (miR-122T) in the 3' untranslated region (UTR) of TK gene, we constructed adenovirus (Ad) vectors expressing miR-122-regulated TK (Ad-TK-122T) and report genes. After intratumoral administration of Ad vectors into an orthotopic miR-122-deficient HCC mouse model, we observed the miR-122-regulated transgene expression and assessed the antitumor activity and safety of Ad-TK-122T. RESULTS Insertion of miR-122T specifically down-regulated transgene expression in vitro and selectively protected the miR-122-positive cells from killing by TK/GCV treatment. Insertion of miR-122T led to significant reduction of tansgene expression in the liver without inhibition of its expression in tumors in vivo, resulting in an 11-fold improvement of tumor-specific transgene expression. Intratumoral injection of Ad vectors mediated TK/GCV system led to a vector dosage-dependent regression of tumor. The insertion of miR-122T does not influence the antitumor effects of suicide gene therapy. Whereas mice administrated with Ad-TK showed severe lethal hepatotoxicity at the effective therapeutic dose, no liver damage was found in Ad-TK-122T group. CONCLUSIONS miR-122-regulated TK expression achieved effective anti-tumor effects and increased the safety of intratumoral delivery of adenovirus-mediated TK/GCV gene therapy for miR-122-deficient HCC.
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Affiliation(s)
- Gang Wang
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaoyan Dong
- Beijing FivePlus Molecular Medicine Institute, Beijing 100176, China
| | - Wenhong Tian
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China; ; School of Life Science, Jilin University, Changchun 130012, China
| | - Yue Lu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jianyan Hu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yunfan Liu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jie Yuchi
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaobing Wu
- Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China; ; Beijing Yizhuang International Biomedical Investment & Management Co., Ltd., Beijing 100111, China
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119
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Lim L, Balakrishnan A, Huskey N, Jones KD, Jodari M, Ng R, Song G, Riordan J, Anderton B, Cheung ST, Willenbring H, Dupuy A, Chen X, Brown D, Chang AN, Goga A. MicroRNA-494 within an oncogenic microRNA megacluster regulates G1/S transition in liver tumorigenesis through suppression of mutated in colorectal cancer. Hepatology 2014; 59:202-15. [PMID: 23913442 PMCID: PMC3877416 DOI: 10.1002/hep.26662] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Accepted: 07/26/2013] [Indexed: 12/30/2022]
Abstract
UNLABELLED Hepatocellular carcinoma (HCC) is associated with poor survival for patients and few effective treatment options, raising the need for novel therapeutic strategies. MicroRNAs (miRNAs) play important roles in tumor development and show deregulated patterns of expression in HCC. Because of the liver's unique affinity for small nucleic acids, miRNA-based therapy has been proposed in the treatment of liver disease. Thus, there is an urgent need to identify and characterize aberrantly expressed miRNAs in HCC. In our study, we profiled miRNA expression changes in de novo liver tumors driven by MYC and/or RAS, two canonical oncogenes activated in a majority of human HCCs. We identified an up-regulated miRNA megacluster comprised of 53 miRNAs on mouse chromosome 12qF1 (human homolog 14q32). This miRNA megacluster is up-regulated in all three transgenic liver models and in a subset of human HCCs. An unbiased functional analysis of all miRNAs within this cluster was performed. We found that miR-494 is overexpressed in human HCC and aids in transformation by regulating the G1 /S cell cycle transition through targeting of the Mutated in Colorectal Cancer tumor suppressor. miR-494 inhibition in human HCC cell lines decreases cellular transformation, and anti-miR-494 treatment of primary MYC-driven liver tumor formation significantly diminishes tumor size. CONCLUSION Our findings identify a new therapeutic target (miR-494) for the treatment of HCC.
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Affiliation(s)
- Lionel Lim
- Department of Cell & Tissue Biology, University of California San FranciscoSan Francisco, CA,Department of Medicine, University of California San FranciscoSan Francisco, CA,Address reprint requests to: Andrei Goga, M.D., Ph.D., Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, Box 0512, San Francisco, CA 94143-0512. E-mail: ; fax: 415-476-1128
| | - Asha Balakrishnan
- Department of Medicine, University of California San FranciscoSan Francisco, CA,Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical SchoolHannover, Germany,Address reprint requests to: Andrei Goga, M.D., Ph.D., Department of Cell & Tissue Biology, University of California San Francisco, 513 Parnassus Avenue, Box 0512, San Francisco, CA 94143-0512. E-mail: ; fax: 415-476-1128
| | - Noelle Huskey
- Department of Cell & Tissue Biology, University of California San FranciscoSan Francisco, CA,Department of Medicine, University of California San FranciscoSan Francisco, CA
| | - Kirk D Jones
- Department of Pathology, University of California San FranciscoSan Francisco, CA
| | - Mona Jodari
- Department of Cell & Tissue Biology, University of California San FranciscoSan Francisco, CA
| | - Raymond Ng
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San FranciscoSan Francisco, CA
| | - Guisheng Song
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San FranciscoSan Francisco, CA
| | - Jesse Riordan
- Anatomy and Cell Biology, University of IowaIowa City, IA
| | - Brittany Anderton
- Department of Cell & Tissue Biology, University of California San FranciscoSan Francisco, CA,Department of Medicine, University of California San FranciscoSan Francisco, CA
| | - Siu-Tim Cheung
- Department of Surgery, The University of Hong KongHong Kong
| | - Holger Willenbring
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San FranciscoSan Francisco, CA,Liver Center, University of California San FranciscoSan Francisco, CA
| | - Adam Dupuy
- Anatomy and Cell Biology, University of IowaIowa City, IA
| | - Xin Chen
- Liver Center, University of California San FranciscoSan Francisco, CA,Department of Bioengineering and Therapeutic Sciences, University of California San FranciscoSan Francisco, CA
| | | | | | - Andrei Goga
- Department of Cell & Tissue Biology, University of California San FranciscoSan Francisco, CA,Department of Medicine, University of California San FranciscoSan Francisco, CA,Liver Center, University of California San FranciscoSan Francisco, CA
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120
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iSubgraph: integrative genomics for subgroup discovery in hepatocellular carcinoma using graph mining and mixture models. PLoS One 2013; 8:e78624. [PMID: 24223834 PMCID: PMC3817163 DOI: 10.1371/journal.pone.0078624] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 09/13/2013] [Indexed: 11/24/2022] Open
Abstract
The high tumor heterogeneity makes it very challenging to identify key tumorigenic pathways as therapeutic targets. The integration of multiple omics data is a promising approach to identify driving regulatory networks in patient subgroups. Here, we propose a novel conceptual framework to discover patterns of miRNA-gene networks, observed frequently up- or down-regulated in a group of patients and to use such networks for patient stratification in hepatocellular carcinoma (HCC). We developed an integrative subgraph mining approach, called iSubgraph, and identified altered regulatory networks frequently observed in HCC patients. The miRNA and gene expression profiles were jointly analyzed in a graph structure. We defined a method to transform microarray data into graph representation that encodes miRNA and gene expression levels and the interactions between them as well. The iSubgraph algorithm was capable to detect cooperative regulation of miRNAs and genes even if it occurred only in some patients. Next, the miRNA-mRNA modules were used in an unsupervised class prediction model to discover HCC subgroups via patient clustering by mixture models. The robustness analysis of the mixture model showed that the class predictions are highly stable. Moreover, the Kaplan-Meier survival analysis revealed that the HCC subgroups identified by the algorithm have different survival characteristics. The pathway analyses of the miRNA-mRNA co-modules identified by the algorithm demonstrate key roles of Myc, E2F1, let-7, TGFB1, TNF and EGFR in HCC subgroups. Thus, our method can integrate various omics data derived from different platforms and with different dynamic scales to better define molecular tumor subtypes. iSubgraph is available as MATLAB code at http://www.cs.umd.edu/~ozdemir/isubgraph/.
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121
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Abstract
NAFLD affects a large proportion of the US population and its incidence and prevalence are increasing to epidemic proportions around the world. As with other liver diseases that cause cirrhosis, NAFLD increases the risk of liver cancer, a disease with poor outcomes and limited therapeutic options. The incidences of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma are also rising, and HCC is now the leading cause of obesity-related cancer deaths in middle-aged men in the USA. In this Review, we summarize the correlations between liver cancer and NAFLD-related cirrhosis, and the role of the metabolic syndrome in the development of liver cancer from diverse aetiologies, including HCV-mediated cirrhosis. Recent advances in understanding the progression of NAFLD to HCC from preclinical models will also be discussed. Targeted genetic manipulation of certain metabolic or stress-response pathways, including one-carbon metabolism, NF-κB, PTEN and microRNAs, has been valuable in elucidating the pathways that regulate carcinogenesis in NAFLD. Although tremendous advances have occurred in the identification of diagnostic and therapeutic opportunities to reduce the progression of NAFLD, considerable gaps in our knowledge remain with regard to the mechanisms by which NAFLD and its risk factors promote liver cancer.
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Affiliation(s)
- Gregory A Michelotti
- Division of Gastroenterology, Department of Medicine, Duke University Medical Center, 595 LaSalle Street, Snyderman Building, Suite 1073, Durham, NC 27710, USA
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122
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Shah N, Nelson JE, Kowdley KV. MicroRNAs in Liver Disease: Bench to Bedside. J Clin Exp Hepatol 2013; 3:231-42. [PMID: 25755505 PMCID: PMC3940370 DOI: 10.1016/j.jceh.2013.09.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRs) are small non-coding RNAs that negatively regulate gene expression by pairing with partially complementary target sequences in the 3'UTRs of mRNAs to promote degradation and/or block translation. Aberrant miR expression is associated with development of multiple diseases including hepatic diseases. The role of miRs in the regulation of gene expression and rapid progress in the field of microRNA research are resulting in momentum toward development of diagnostic markers and novel therapeutic strategies for human liver diseases. Recent studies provide clear evidence that miRs are abundant in the liver and modulate a diverse spectrum of biological functions, thereby supporting an association between alterations of miR homeostasis and pathological liver diseases. Here we review the role of miRs in liver as their physiological and pathological importance has been demonstrated in metabolism, immunity, viral hepatitis, oncogenesis, fatty liver diseases (alcoholic and non-alcoholic), drug-induced liver injury, fibrosis as well as acute liver failure.
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Key Words
- ALD, alcoholic liver disease
- ALF, acute liver failure
- DILI, drug-induced liver injury
- HBV, hepatitis B virus
- HCC, hepatocellular carcinoma
- HCV, hepatitis C virus
- HSC, hepatic stellate cell
- IFN, interferon
- NAFLD, non-alcoholic fatty liver disease
- NASH, non-alcoholic steatohepatitis
- PPAR γ, peroxisome proliferator-activated receptor γ
- TGF, transforming growth factor
- TNF, tumor necrosis factor
- UTR, untranslated region
- down-regulation
- liver
- miR-122
- miRs/miRNA, microRNA
- microRNA
- up-regulation
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Affiliation(s)
- Nihar Shah
- Liver Center of Excellence, Digestive Disease Institute, Virginia Mason Medical Center, Seattle, WA, United States
| | - James E. Nelson
- Benaroya Research Institute, Virginia Mason Medical Center, Seattle, WA, United States
| | - Kris V. Kowdley
- Liver Center of Excellence, Digestive Disease Institute, Virginia Mason Medical Center, Seattle, WA, United States,Benaroya Research Institute, Virginia Mason Medical Center, Seattle, WA, United States,Address for correspondence: Kris V. Kowdley, MD, 1201 9th Ave., Seattle, WA 98101, United States. Tel.: +1 (206) 287 1083; fax: +1 (206) 341 1934.
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123
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Shi B, Abrams M, Sepp-Lorenzino L. Expression of asialoglycoprotein receptor 1 in human hepatocellular carcinoma. J Histochem Cytochem 2013; 61:901-9. [PMID: 23979840 DOI: 10.1369/0022155413503662] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Human hepatocellular carcinoma (HCC) is the fifth most common cancer in the world. Currently, surgical resection is the only effective treatment for HCC if the tumor is resectable. Small molecule, biologics and siRNA anti-cancer drugs have been explored for the treatment of HCC. Selective targeting to tumor tissue rather than normal liver in HCC patients is still a challenge. Galactosamine-mediated targeting delivery of anti-cancer drugs in the liver has been tested because its receptor, asialoglycoprotein receptor 1 (ASGPR1), is expressed in the liver and not in other human tissues. We examined ASGPR1 expression levels by immunohistochemistry in HCC with different grades. Guidance for a targeting delivery strategy for anti-cancer drugs to HCC is suggested in this report.
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Affiliation(s)
- Bin Shi
- Department of In Vivo Pharmacology - Oncology, Merck Research Laboratories, Merck & Co., Inc., West Point, PA (BS)
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124
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Xu K, Mao X, Mehta M, Cui J, Zhang C, Mao F, Xu Y. Elucidation of how cancer cells avoid acidosis through comparative transcriptomic data analysis. PLoS One 2013; 8:e71177. [PMID: 23967163 PMCID: PMC3743895 DOI: 10.1371/journal.pone.0071177] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 06/27/2013] [Indexed: 12/31/2022] Open
Abstract
The rapid growth of cancer cells fueled by glycolysis produces large amounts of protons in cancer cells, which tri mechanisms to transport them out, hence leading to increased acidity in their extracellular environments. It has been well established that the increased acidity will induce cell death of normal cells but not cancer cells. The main question we address here is: how cancer cells deal with the increased acidity to avoid the activation of apoptosis. We have carried out a comparative analysis of transcriptomic data of six solid cancer types, breast, colon, liver, two lung (adenocarcinoma, squamous cell carcinoma) and prostate cancers, and proposed a model of how cancer cells utilize a few mechanisms to keep the protons outside of the cells. The model consists of a number of previously, well or partially, studied mechanisms for transporting out the excess protons, such as through the monocarboxylate transporters, V-ATPases, NHEs and the one facilitated by carbonic anhydrases. In addition we propose a new mechanism that neutralizes protons through the conversion of glutamate to γ-aminobutyrate, which consumes one proton per reaction. We hypothesize that these processes are regulated by cancer related conditions such as hypoxia and growth factors and by the pH levels, making these encoded processes not available to normal cells under acidic conditions.
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Affiliation(s)
- Kun Xu
- Computational Systems Biology Lab, University of Georgia, Athens, Georgia, United States of America
- Department of Statistics, University of Georgia, Athens, Georgia, United States of America
| | - Xizeng Mao
- Computational Systems Biology Lab, University of Georgia, Athens, Georgia, United States of America
| | - Minesh Mehta
- Computational Systems Biology Lab, University of Georgia, Athens, Georgia, United States of America
- Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio, United States of America
| | - Juan Cui
- Computational Systems Biology Lab, University of Georgia, Athens, Georgia, United States of America
| | - Chi Zhang
- Computational Systems Biology Lab, University of Georgia, Athens, Georgia, United States of America
| | - Fenglou Mao
- Computational Systems Biology Lab, University of Georgia, Athens, Georgia, United States of America
| | - Ying Xu
- Computational Systems Biology Lab, University of Georgia, Athens, Georgia, United States of America
- Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- College of Computer Science and Technology, Jilin University, Changchun, Jilin, China
- * E-mail:
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125
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Bienertova-Vasku J, Sana J, Slaby O. The role of microRNAs in mitochondria in cancer. Cancer Lett 2013; 336:1-7. [DOI: 10.1016/j.canlet.2013.05.001] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 04/30/2013] [Accepted: 05/03/2013] [Indexed: 02/06/2023]
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126
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Genetics and epigenetics of liver cancer. N Biotechnol 2013; 30:381-4. [DOI: 10.1016/j.nbt.2013.01.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 01/23/2013] [Accepted: 01/25/2013] [Indexed: 02/07/2023]
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127
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Wang T, Gu J, Yuan J, Tao R, Li Y, Li S. Inferring pathway crosstalk networks using gene set co-expression signatures. MOLECULAR BIOSYSTEMS 2013; 9:1822-8. [PMID: 23591523 DOI: 10.1039/c3mb25506a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Constructing molecular interaction networks in cells is important for understanding the underlying mechanisms of biological processes. Except for single gene analysis, several gene set-based methods have been proposed to infer pathway crosstalk by analyzing large-scale gene expression data. But most of them take all pathway genes as a whole to infer the crosstalk. Biological evidence suggests that the pathway crosstalk usually occurs between some subsets rather than the whole sets of pathway genes. In this study, we propose a novel method, sGSCA (signature-based gene set co-expression analysis) which can use the co-expression correlations between subsets of pathway genes to infer the pathway crosstalk networks. The method applies sparse canonical correlation analysis (sCCA) to measure the pathway level co-expression and simultaneously obtain the subsets or signature genes that contribute to the co-expression of pathways. On simulated datasets, sGSCA can efficiently detect pathway crosstalk and the corresponding highly correlated signature genes. We applied sGSCA to two cancer gene expression datasets (one for hepatocellular cancer and the other for lung cancer). In the inferred networks, we found several important pathway crosstalks related to the cancers. The identified signature genes also show high enrichment for the cancer related genes. sGSCA can infer pathway crosstalk networks using large-scale gene expression data, and should be a useful tool for systematically studying the molecular mechanisms of complex diseases on both pathway and gene levels at the same time.
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Affiliation(s)
- Ting Wang
- Bioinformatics Division/Center for Synthetic and Systems Biology, Tsinghua National Laboratory for Information Science and Technology (TNLIST), Department of Automation, Tsinghua University, Beijing, 100084, China.
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Zhang G, Yang P, Guo P, Miele L, Sarkar FH, Wang Z, Zhou Q. Unraveling the mystery of cancer metabolism in the genesis of tumor-initiating cells and development of cancer. Biochim Biophys Acta Rev Cancer 2013; 1836:49-59. [PMID: 23523716 DOI: 10.1016/j.bbcan.2013.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2013] [Revised: 03/06/2013] [Accepted: 03/11/2013] [Indexed: 01/01/2023]
Abstract
Robust anaerobic metabolism plays a causative role in the origin of cancer cells; however, the oncogenic metabolic genes, factors, pathways, and networks in genesis of tumor-initiating cells (TICs) have not yet been systematically summarized. In addition, the mechanisms of oncogenic metabolism in the genesis of TICs are enigmatic. In this review, we discussed multiple cancer metabolism-related genes (MRGs) that are overexpressed in TICs and are responsible for inducing pluripotent stem cells. Moreover, we summarized that oncogenic metabolic genes and onco-metabolites induce metabolic reprogramming, which switches normal mitochondrial oxidative phosphorylation to cancer anaerobic metabolism, triggers epigenetic, genetic, and environmental alterations, drives the generation of TICs, and boosts the development of cancer. Importantly, cancer metabolism is controlled by positive and negative metabolic regulators. Positive oncogenic metabolic regulators, including key oncogenic metabolic genes, onco-metabolites, hypoxia, and an acidic environment, promote oncogenic metabolic reprogramming and anaerobic metabolism. However, dysfunction of negative metabolic regulators, including defects in p53, PTEN, and LKB1-AMPK-mTOR pathways, enhances cancer metabolism. Loss of the metabolic balance results in oncogenic metabolic reprogramming, genesis of TICs, and tumorigenesis. Collectively, this review provides new insight into the role and mechanism of these oncogenic metabolisms in the genesis of TICs and tumorigenesis. Accordingly, targeting key oncogenic genes, onco-metabolites, pathways, networks, and the acidic cancer microenvironment appears to be an attractive strategy for novel anti-tumor treatment.
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Affiliation(s)
- Gaochuan Zhang
- Department of Bioinformatics, School of Biology and Basic Medical Sciences, Medical College, Soochow University, Suzhou, Jiangsu 215123, PR China
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129
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Xiao Y, Ping Y, Fan H, Xu C, Guan J, Zhao H, Li Y, Lv Y, Jin Y, Wang L, Li X. Identifying dysfunctional miRNA-mRNA regulatory modules by inverse activation, cofunction, and high interconnection of target genes: a case study of glioblastoma. Neuro Oncol 2013; 15:818-28. [PMID: 23516263 DOI: 10.1093/neuonc/not018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Accumulating evidence demonstrates that complex diseases may arise from cooperative effects of multiple dysfunctional miRNAs. Thus, identifying abnormal functions cooperatively regulated by multiple miRNAs is useful for understanding the pathogenesis of complex diseases. METHODS In this study, we proposed a multistep method to identify dysfunctional miRNA-mRNA regulatory modules (dMiMRMs) in a specific disease, in which a group of miRNAs cooperatively regulate a group of target genes involved in a specific function. We identified dysfunctional miRNAs, which were differentially expressed and inversely regulated most of their target genes, by integrating paired miRNA and mRNA expression profiles and miRNA target information. Then, we identified cooperative functional units, in each of which a pair of miRNAs cooperatively repressed function-enriched and highly interconnected target genes. Finally, the cooperative functional units were assembled into dMiMRMs. RESULTS We applied our method to glioblastoma (GBM) and identified GBM-associated dMiMRMs at the population, subtype, and individual levels. We identified 5 common dMiMRMs using all GBM samples, 3 of which were associated with the prognosis in patients with GBM and were better predictors of prognosis than were miRNAs or mRNAs alone. By applying our approach to GBM subtypes, we found consistent dMiMRMs across GBM subtypes, and some subtype-specific dMiMRMs were observed. Furthermore, personalized dMiMRMs were identified, suggesting significant individual differences in different patients with GBM. CONCLUSIONS Our method provides the capability to identify miRNA-mediated dysfunctional mechanisms underlying complex diseases.
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Affiliation(s)
- Yun Xiao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
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130
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Aravalli RN. Development of MicroRNA Therapeutics for Hepatocellular Carcinoma. Diagnostics (Basel) 2013; 3:170-91. [PMID: 26835673 PMCID: PMC4665582 DOI: 10.3390/diagnostics3010170] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 03/01/2013] [Accepted: 03/11/2013] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common form of liver cancer and is the third leading cause of cancer-related deaths worldwide. Treatment options for HCC are very limited, as it is often diagnosed at a late stage. Recent studies have demonstrated that microRNAs (miRNAs), a class of non-coding RNAs, are aberrantly expressed in HCC. Some of these were shown to be functionally involved in carcinogenesis and tumor progression, suggesting that miRNAs can serve as novel molecular targets for HCC therapy. Several promising studies have recently demonstrated the therapeutic potential of miRNAs in animal models and in reducing the viral load in hepatitis C patients. In this review, these advances and strategies for modulating miRNAs for in vivo therapeutic delivery and replacement therapy are discussed.
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Affiliation(s)
- Rajagopal N Aravalli
- Department of Radiology, University of Minnesota Medical School, MMC 292 Mayo Memorial Building, 420 Delaware Street S.E., Minneapolis, MN 55455, USA.
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131
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Rong M, Chen G, Dang Y. Increased miR-221 expression in hepatocellular carcinoma tissues and its role in enhancing cell growth and inhibiting apoptosis in vitro. BMC Cancer 2013; 13:21. [PMID: 23320393 PMCID: PMC3551704 DOI: 10.1186/1471-2407-13-21] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Accepted: 01/11/2013] [Indexed: 02/07/2023] Open
Abstract
Background MiR-221 is over-expressed in human hepatocellular carcinoma (HCC), but its clinical significance and function in HCC remains uncertain. The aim of the study was to investigate the relationship between miR-221 overexpression and clinicopathological parameters in HCC formalin-fixed paraffin-embedded (FFPE) tissues, and the effect of miR-221 inhibitor and mimic on different HCC cell lines in vitro. Methods MiR-221 expression was detected using real time RT-qPCR in FFPE HCC and the adjacent noncancerous liver tissues. The relationship between miR-221 level and clinicopathological features was also analyzed. Furthermore, miR-221 inhibitor and mimic were transfected into HCC cell lines HepB3, HepG2 and SNU449. The effects of miR-221 on cell growth, cell cycle, caspase activity and apoptosis were also investigated by spectrophotometry, fluorimetry, fluorescence microscopy and flow cytometry, respectively. Results The relative expression of miR-221 in clinical TNM stages III and IV was significantly higher than that in the stages I and II. The miR-221 level was also upregulated in the metastatic group compared to the nonmetastatic group. Furthermore, miR-221 over-expression was related to the status of tumor capsular infiltration in HCC clinical samples. Functionally, cell growth was inhibited, cell cycle was arrested in G1/S-phase and apoptosis was increased by miR-221 inhibitor in vitro. Likewise, miR-221 mimic accelerated the cell growth. Conclusions Expression of miR-221 in FFPE tissues could provide predictive significance for prognosis of HCC patients. Moreover, miR-221 inhibitor could be useful to suppress proliferation and induce apoptosis in HCC cells. Thus miR-221 might be a critical targeted therapy strategy for HCC.
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Affiliation(s)
- Minhua Rong
- Research Department, Affiliated Cancer Hospital, Guangxi Medical University, 71 Hedi Road, Nanning, Guangxi Zhuang Autonomous Region 530021, PR China.
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132
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Elfimova N, Schlattjan M, Sowa JP, Dienes HP, Canbay A, Odenthal M. Circulating microRNAs: promising candidates serving as novel biomarkers of acute hepatitis. Front Physiol 2012; 3:476. [PMID: 23267332 PMCID: PMC3527896 DOI: 10.3389/fphys.2012.00476] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 12/05/2012] [Indexed: 11/13/2022] Open
Abstract
Acute liver failure as life threatening condition comprises a difficult diagnostic situation to evaluate potential outcomes and therapeutic options. Thus, prognostic indicators are urgently needed for evaluation of progression of liver injury, clinical outcome, prognosis, and for therapeutic response. Recently, circulating microRNA, in particular miR-122, was described as a potential biomarker of acute liver injury after intoxication of mice. Circulating microRNA (miRNA) molecules are very stable and RNase-resistant due to protein aggregation and vesicle enclosure. Since miRNA species are known to be associated with chronic liver damage or with liver cancer, circulating miRNA patterns are suggested to serve also as reporters for progression of acute liver failure. miRNA profiling analyses using PCR arrays or next generation sequencing, may achieve identification of miRNA species that are linked to the rapid progression of acute liver injury, to the outcome of liver failure, or to the therapeutic response. Therefore, circulating miRNAs are promising, non-invasive biomarkers of future diagnostic approaches. However, normalisation of circulating miRNA levels is essential and further standardisation of miRNA quantification assays is needed.
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Affiliation(s)
- Natalia Elfimova
- Laboratory of Molecular Hepatology, Institute for Pathology, University Hospital of Cologne Cologne, Germany
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133
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Zeng L, Yu J, Huang T, Jia H, Dong Q, He F, Yuan W, Qin L, Li Y, Xie L. Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma. BMC Genomics 2012; 13 Suppl 8:S14. [PMID: 23282077 PMCID: PMC3535701 DOI: 10.1186/1471-2164-13-s8-s14] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most fatal cancers in the world, and metastasis is a significant cause to the high mortality in patients with HCC. However, the molecular mechanism behind HCC metastasis is not fully understood. Study of regulatory networks may help investigate HCC metastasis in the way of systems biology profiling. Methods By utilizing both sequence information and parallel microRNA(miRNA) and mRNA expression data on the same cohort of HBV related HCC patients without or with venous metastasis, we constructed combinatorial regulatory networks of non-metastatic and metastatic HCC which contain transcription factor(TF) regulation and miRNA regulation. Differential regulation patterns, classifying marker modules, and key regulatory miRNAs were analyzed by comparing non-metastatic and metastatic networks. Results Globally TFs accounted for the main part of regulation while miRNAs for the minor part of regulation. However miRNAs displayed a more active role in the metastatic network than in the non-metastatic one. Seventeen differential regulatory modules discriminative of the metastatic status were identified as cumulative-module classifier, which could also distinguish survival time. MiR-16, miR-30a, Let-7e and miR-204 were identified as key miRNA regulators contributed to HCC metastasis. Conclusion In this work we demonstrated an integrative approach to conduct differential combinatorial regulatory network analysis in the specific context venous metastasis of HBV-HCC. Our results proposed possible transcriptional regulatory patterns underlying the different metastatic subgroups of HCC. The workflow in this study can be applied in similar context of cancer research and could also be extended to other clinical topics.
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Affiliation(s)
- Lingyao Zeng
- School of Life Science and Technology, Tongji University, Shanghai 200092, PR China
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134
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Cellular and molecular mechanisms of hepatocellular carcinoma: an update. Arch Toxicol 2012; 87:227-47. [PMID: 23007558 DOI: 10.1007/s00204-012-0931-2] [Citation(s) in RCA: 166] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 08/27/2012] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary malignant tumor that accounts for ~80 % of all liver cancer cases worldwide. It is a multifactorial disease caused by a variety of risk factors and often develops in the background of underlying cirrhosis. A number of cellular phenomena, such as tumor microenvironment, inflammation, oxidative stress, and hypoxia act in concert with various molecular events to facilitate tumor initiation, progression, and metastasis. The emergence of microRNAs and molecular-targeted therapies adds a new dimension in our efforts to combat this deadly disease. Intense research in this multitude of areas has led to significant progress in our understanding of cellular processes and molecular mechanisms that occur during multistage events that lead to hepatocarcinogenesis. In this review, we discuss the current knowledge of HCC, focusing mainly on advances that have occurred during the past 5 years and on the development of novel therapeutics for liver cancer.
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135
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Yan Z, Shah PK, Amin SB, Samur MK, Huang N, Wang X, Misra V, Ji H, Gabuzda D, Li C. Integrative analysis of gene and miRNA expression profiles with transcription factor-miRNA feed-forward loops identifies regulators in human cancers. Nucleic Acids Res 2012; 40:e135. [PMID: 22645320 PMCID: PMC3458521 DOI: 10.1093/nar/gks395] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 04/08/2012] [Accepted: 04/15/2012] [Indexed: 12/31/2022] Open
Abstract
We describe here a novel method for integrating gene and miRNA expression profiles in cancer using feed-forward loops (FFLs) consisting of transcription factors (TFs), miRNAs and their common target genes. The dChip-GemiNI (Gene and miRNA Network-based Integration) method statistically ranks computationally predicted FFLs by their explanatory power to account for differential gene and miRNA expression between two biological conditions such as normal and cancer. GemiNI integrates not only gene and miRNA expression data but also computationally derived information about TF-target gene and miRNA-mRNA interactions. Literature validation shows that the integrated modeling of expression data and FFLs better identifies cancer-related TFs and miRNAs compared to existing approaches. We have utilized GemiNI for analyzing six data sets of solid cancers (liver, kidney, prostate, lung and germ cell) and found that top-ranked FFLs account for ∼20% of transcriptome changes between normal and cancer. We have identified common FFL regulators across multiple cancer types, such as known FFLs consisting of MYC and miR-15/miR-17 families, and novel FFLs consisting of ARNT, CREB1 and their miRNA partners. The results and analysis web server are available at http://www.canevolve.org/dChip-GemiNi.
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Affiliation(s)
- Zhenyu Yan
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Parantu K. Shah
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Samir B. Amin
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Mehmet K. Samur
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Norman Huang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xujun Wang
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Vikas Misra
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongbin Ji
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Dana Gabuzda
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Cheng Li
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA, Department of Biostatistics and Medical Informatics, Akdeniz University, Antalya, Turkey, Department of Bioinformatics, Tongji University, Shanghai, China, Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, MA 02215, USA and State Key Laboratory of Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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Androsavich JR, Chau BN, Bhat B, Linsley PS, Walter NG. Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver. RNA (NEW YORK, N.Y.) 2012; 18:1510-26. [PMID: 22740638 PMCID: PMC3404372 DOI: 10.1261/rna.033308.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2012] [Accepted: 05/23/2012] [Indexed: 05/27/2023]
Abstract
MicroRNAs (miRNAs) bind to mRNAs and fine-tune protein output by affecting mRNA stability and/or translation. miR-21 is a ubiquitous, highly abundant, and stress-responsive miRNA linked to several diseases, including cancer, fibrosis, and inflammation. Although the RNA silencing activity of miR-21 in diseased cells has been well documented, the roles of miR-21 under healthy cellular conditions are not well understood. Here, we show that pharmacological inhibition or genetic deletion of miR-21 in healthy mouse liver has little impact on regulation of canonical seed-matched mRNAs and only a limited number of genes enriched in stress response pathways. These surprisingly weak and selective regulatory effects on known and predicted target mRNAs contrast with those of other abundant liver miRNAs such as miR-122 and let-7. Moreover, miR-21 shows greatly reduced binding to polysome-associated target mRNAs compared to miR-122 and let-7. Bioinformatic analysis suggests that reduced thermodynamic stability of seed pairing and target binding may contribute to this deficiency of miR-21. Significantly, these trends are reversed in human cervical carcinoma (HeLa) cells, where miRNAs including miR-21 show enhanced target binding within polysomes and where miR-21 triggers strong degradative activity toward target mRNAs. Taken together, our results suggest that, under normal cellular conditions in liver, miR-21 activity is maintained below a threshold required for binding and silencing most of its targets. Consequently, enhanced association with polysome-associated mRNA is likely to explain in part the gain of miR-21 function often found in diseased or stressed cells.
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Affiliation(s)
- John R. Androsavich
- Department of Chemistry
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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137
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Martignetti L, Laud-Duval K, Tirode F, Pierron G, Reynaud S, Barillot E, Delattre O, Zinovyev A. Antagonism pattern detection between microRNA and target expression in Ewing's sarcoma. PLoS One 2012; 7:e41770. [PMID: 22848594 PMCID: PMC3404966 DOI: 10.1371/journal.pone.0041770] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/26/2012] [Indexed: 01/05/2023] Open
Abstract
MicroRNAs (miRNAs) have emerged as fundamental regulators that silence gene expression at the post-transcriptional and translational levels. The identification of their targets is a major challenge to elucidate the regulated biological processes. The overall effect of miRNA is reflected on target mRNA expression, suggesting the design of new investigative methods based on high-throughput experimental data such as miRNA and transcriptome profiles. We propose a novel statistical measure of non-linear dependence between miRNA and mRNA expression, in order to infer miRNA-target interactions. This approach, which we name antagonism pattern detection, is based on the statistical recognition of a triangular-shaped pattern in miRNA-target expression profiles. This pattern is observed in miRNA-target expression measurements since their simultaneously elevated expression is statistically under-represented in the case of miRNA silencing effect. The proposed method enables miRNA target prediction to strongly rely on cellular context and physiological conditions reflected by expression data. The procedure has been assessed on synthetic datasets and tested on a set of real positive controls. Then it has been applied to analyze expression data from Ewing’s sarcoma patients. The antagonism relationship is evaluated as a good indicator of real miRNA-target biological interaction. The predicted targets are consistently enriched for miRNA binding site motifs in their 3′UTR. Moreover, we reveal sets of predicted targets for each miRNA sharing important biological function. The procedure allows us to infer crucial miRNA regulators and their potential targets in Ewing’s sarcoma disease. It can be considered as a valid statistical approach to discover new insights in the miRNA regulatory mechanisms.
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138
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Tsai WC, Hsu SD, Hsu CS, Lai TC, Chen SJ, Shen R, Huang Y, Chen HC, Lee CH, Tsai TF, Hsu MT, Wu JC, Huang HD, Shiao MS, Hsiao M, Tsou AP. MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. J Clin Invest 2012; 122:2884-97. [PMID: 22820290 DOI: 10.1172/jci63455] [Citation(s) in RCA: 640] [Impact Index Per Article: 53.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 06/12/2012] [Indexed: 12/13/2022] Open
Abstract
MicroRNA-122 (miR-122), which accounts for 70% of the liver's total miRNAs, plays a pivotal role in the liver. However, its intrinsic physiological roles remain largely undetermined. We demonstrated that mice lacking the gene encoding miR-122a (Mir122a) are viable but develop temporally controlled steatohepatitis, fibrosis, and hepatocellular carcinoma (HCC). These mice exhibited a striking disparity in HCC incidence based on sex, with a male-to-female ratio of 3.9:1, which recapitulates the disease incidence in humans. Impaired expression of microsomal triglyceride transfer protein (MTTP) contributed to steatosis, which was reversed by in vivo restoration of Mttp expression. We found that hepatic fibrosis onset can be partially attributed to the action of a miR-122a target, the Klf6 transcript. In addition, Mir122a(-/-) livers exhibited disruptions in a range of pathways, many of which closely resemble the disruptions found in human HCC. Importantly, the reexpression of miR-122a reduced disease manifestation and tumor incidence in Mir122a(-/-) mice. This study demonstrates that mice with a targeted deletion of the Mir122a gene possess several key phenotypes of human liver diseases, which provides a rationale for the development of a unique therapy for the treatment of chronic liver disease and HCC.
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Affiliation(s)
- Wei-Chih Tsai
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
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139
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Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers. Mol Syst Biol 2012; 8:594. [PMID: 22806142 PMCID: PMC3421440 DOI: 10.1038/msb.2012.24] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 05/25/2012] [Indexed: 12/14/2022] Open
Abstract
A common inflammatome signature, as well as disease-specific expression patterns, was identified from 11 different rodent inflammatory disease models. Causal regulatory networks and the drivers of the inflammatome signature were uncovered and validated. ![]()
Representative inflammatome gene signatures, as well as disease model-specific gene signatures, were identified from 12 gene expression profiling data sets derived from 9 different tissues isolated from 11 rodent inflammatory disease models. The inflammatome signature is highly enriched for immune response-related genes, disease causal genes, and drug targets. Regulatory relationships among the inflammatome signature genes were examined in over 70 causal networks derived from a number of large-scale genetic studies of multiple diseases, and the potential key drivers were uncovered and validated prospectively. Over 70% of the inflammatome signature genes and over 50% of the key driver genes have not been reported in previous studies of common signatures in inflammatory conditions.
Common inflammatome gene signatures as well as disease-specific signatures were identified by analyzing 12 expression profiling data sets derived from 9 different tissues isolated from 11 rodent inflammatory disease models. The inflammatome signature significantly overlaps with known drug targets and co-expressed gene modules linked to metabolic disorders and cancer. A large proportion of genes in this signature are tightly connected in tissue-specific Bayesian networks (BNs) built from multiple independent mouse and human cohorts. Both the inflammatome signature and the corresponding consensus BNs are highly enriched for immune response-related genes supported as causal for adiposity, adipokine, diabetes, aortic lesion, bone, muscle, and cholesterol traits, suggesting the causal nature of the inflammatome for a variety of diseases. Integration of this inflammatome signature with the BNs uncovered 151 key drivers that appeared to be more biologically important than the non-drivers in terms of their impact on disease phenotypes. The identification of this inflammatome signature, its network architecture, and key drivers not only highlights the shared etiology but also pinpoints potential targets for intervention of various common diseases.
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140
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Srivastava S, Wong KF, Ong CW, Huak CY, Yeoh KG, Teh M, Luk JM, Salto-Tellez M. A morpho-molecular prognostic model for hepatocellular carcinoma. Br J Cancer 2012; 107:334-9. [PMID: 22713659 PMCID: PMC3394972 DOI: 10.1038/bjc.2012.230] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is the third common cause of cancer-related deaths and its prognostication is still suboptimal. The aim of this study was to establish a new prognostication algorithm for HCC. Methods: In all, 13 biomarkers related to the etiopathogenesis of HCC were evaluated by immunohistochemistry using tissue microarrays containing 121 primary HCC resection cases, and validated in subsequent cohort of 85 HCC cases. The results were compared with Affymetrix Gene Chip Human Genome U133Plus microarray data in a separate cohort of 228 HCC patients. Results: On immunohistochemical evaluation and multivariate Cox regression analysis p53, alpha fetaprotein (AFP), CD44 and CD31, tumour size and vascular invasion, were significant predictors for worse survival in HCC patients. A morpho-molecular prognostic model (MMPM) was constructed and it was a significant independent predictor for overall survival (OS) and relapse-free survival (RFS) (P<0.000). The OS and RFS of HCClow was higher (104 and 78 months) as compared with HCChigh (73 and 43 months) (P<0.0001for OS and RFS). Hepatocellular carcinoma patients with higher stage (III+IV), >5 cm tumour size, positive vascular invasion and satellitosis belonged to HCChigh group. The validation group reproduced the same findings. Gene expression analysis confirmed that 7 of the 12 biomarkers were overexpressed in >50% of tumour samples and significant overexpression in tumour samples was observed in AFP, CD31, CD117 and Ki-67 genes. Conclusion: The MMPM, based on the expression of selected proteins and clinicopathological parameters, can be used to classify HCC patients between good vs poor prognosis and high vs low risk of recurrence following hepatic resection.
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Affiliation(s)
- S Srivastava
- Cancer Science Institute, National University of Singapore, Singapore
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Gu Z, Liu J, Cao K, Zhang J, Wang J. Centrality-based pathway enrichment: a systematic approach for finding significant pathways dominated by key genes. BMC SYSTEMS BIOLOGY 2012; 6:56. [PMID: 22672776 PMCID: PMC3443660 DOI: 10.1186/1752-0509-6-56] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 05/24/2012] [Indexed: 12/18/2022]
Abstract
Background Biological pathways are important for understanding biological mechanisms. Thus, finding important pathways that underlie biological problems helps researchers to focus on the most relevant sets of genes. Pathways resemble networks with complicated structures, but most of the existing pathway enrichment tools ignore topological information embedded within pathways, which limits their applicability. Results A systematic and extensible pathway enrichment method in which nodes are weighted by network centrality was proposed. We demonstrate how choice of pathway structure and centrality measurement, as well as the presence of key genes, affects pathway significance. We emphasize two improvements of our method over current methods. First, allowing for the diversity of genes’ characters and the difficulty of covering gene importance from all aspects, we set centrality as an optional parameter in the model. Second, nodes rather than genes form the basic unit of pathways, such that one node can be composed of several genes and one gene may reside in different nodes. By comparing our methodology to the original enrichment method using both simulation data and real-world data, we demonstrate the efficacy of our method in finding new pathways from biological perspective. Conclusions Our method can benefit the systematic analysis of biological pathways and help to extract more meaningful information from gene expression data. The algorithm has been implemented as an R package CePa, and also a web-based version of CePa is provided.
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Affiliation(s)
- Zuguang Gu
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing, 210093, China
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142
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Hu J, Xu Y, Hao J, Wang S, Li C, Meng S. MiR-122 in hepatic function and liver diseases. Protein Cell 2012; 3:364-71. [PMID: 22610888 DOI: 10.1007/s13238-012-2036-3] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Accepted: 02/22/2012] [Indexed: 02/06/2023] Open
Abstract
As the most abundant liver-specific microRNA, microRNA-122 (miR-122) is involved in various physiological processes in hepatic function as well as in liver pathology. There is now compelling evidence that miR-122, as a regulator of gene networks and pathways in hepatocytes, plays a central role in diverse aspects of hepatic function and in the progress of liver diseases. This liver-enriched transcription factors-regulated miRNA promotes differentiation of hepatocytes and regulates lipid metabolism. With regard to liver diseases, miR-122 was shown to stimulate hepatitis C virus (HCV) replication through a unique and unusual interaction with two binding sites in the 5'-UTR of HCV genome to mediate the stability of the viral RNA, whereas inhibit the expression and replication of hepatitis B virus (HBV) by a miR-122-cylin G1/p53-HBV enhancer regulatory pathway. In addition, miR-122 acts as a suppressor of cell proliferation and malignant transformation of hepatocytes with remarkable tumor inhibition activity. Notably, a clinical trial targeting miR-122 with the anti-miR-122 oligonucleotides miravirsen, the first miRNA targeted drug, has been initiated for treatment of HCV infection. With further understanding of the comprehensive roles of miR-122 in hepatic functions and the mechanisms involved in miR-122 down-regulation in chronic hepatitis or hepatocellular carcinoma, miR-122 appears to be a promising candidate for effective therapeutic approaches against tumor and infectious diseases.
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Affiliation(s)
- Jun Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China
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143
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Gu Z, Zhang C, Wang J. Gene regulation is governed by a core network in hepatocellular carcinoma. BMC SYSTEMS BIOLOGY 2012; 6:32. [PMID: 22548756 PMCID: PMC3403900 DOI: 10.1186/1752-0509-6-32] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 05/01/2012] [Indexed: 01/29/2023]
Abstract
Background Hepatocellular carcinoma (HCC) is one of the most lethal cancers worldwide, and the mechanisms that lead to the disease are still relatively unclear. However, with the development of high-throughput technologies it is possible to gain a systematic view of biological systems to enhance the understanding of the roles of genes associated with HCC. Thus, analysis of the mechanism of molecule interactions in the context of gene regulatory networks can reveal specific sub-networks that lead to the development of HCC. Results In this study, we aimed to identify the most important gene regulations that are dysfunctional in HCC generation. Our method for constructing gene regulatory network is based on predicted target interactions, experimentally-supported interactions, and co-expression model. Regulators in the network included both transcription factors and microRNAs to provide a complete view of gene regulation. Analysis of gene regulatory network revealed that gene regulation in HCC is highly modular, in which different sets of regulators take charge of specific biological processes. We found that microRNAs mainly control biological functions related to mitochondria and oxidative reduction, while transcription factors control immune responses, extracellular activity and the cell cycle. On the higher level of gene regulation, there exists a core network that organizes regulations between different modules and maintains the robustness of the whole network. There is direct experimental evidence for most of the regulators in the core gene regulatory network relating to HCC. We infer it is the central controller of gene regulation. Finally, we explored the influence of the core gene regulatory network on biological pathways. Conclusions Our analysis provides insights into the mechanism of transcriptional and post-transcriptional control in HCC. In particular, we highlight the importance of the core gene regulatory network; we propose that it is highly related to HCC and we believe further experimental validation is worthwhile.
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Affiliation(s)
- Zuguang Gu
- The State Key Laboratory of Pharmaceutical Biotechnology and Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, School of Life Science, Nanjing University, Nanjing 210093, China
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144
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Kim YH, Liang H, Liu X, Lee JS, Cho JY, Cheong JH, Kim H, Li M, Downey TJ, Dyer MD, Sun Y, Sun J, Beasley EM, Chung HC, Noh SH, Weinstein JN, Liu CG, Powis G. AMPKα modulation in cancer progression: multilayer integrative analysis of the whole transcriptome in Asian gastric cancer. Cancer Res 2012; 72:2512-21. [PMID: 22434430 DOI: 10.1158/0008-5472.can-11-3870] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gastric cancer is the most common cancer in Asia and most developing countries. Despite the use of multimodality therapeutics, it remains the second leading cause of cancer death in the world. To identify the molecular underpinnings of gastric cancer in the Asian population, we applied an RNA-sequencing approach to gastric tumor and noncancerous specimens, generating 680 million informative short reads to quantitatively characterize the entire transcriptome of gastric cancer (including mRNAs and miRNAs). A multilayer analysis was then developed to identify multiple types of transcriptional aberrations associated with different stages of gastric cancer, including differentially expressed mRNAs, recurrent somatic mutations, and key differentially expressed miRNAs. Through this approach, we identified the central metabolic regulator AMP-activated protein kinase (AMPK)α as a potential functional target in Asian gastric cancer. Furthermore, we experimentally showed the translational relevance of this gene as a potential therapeutic target for early-stage gastric cancer in Asian patients. Together, our findings not only provide a valuable information resource for identifying and elucidating the molecular mechanisms of Asian gastric cancer, but also represent a general integrative framework to develop more effective therapeutic targets.
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Affiliation(s)
- Yon Hui Kim
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiuping Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,USA
| | - Ju-Seog Lee
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jae Yong Cho
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-749, Korea
| | - Jae-Ho Cheong
- Department of Surgery, Yonsei University College of Medicine, Seoul 120-749, Korea
| | - Hoguen Kim
- Department of Pathology, Yonsei University College of Medicine, Seoul 120-749, Korea
| | - Min Li
- Partek Inc., St. Louis, MO 63141, USA
| | | | | | | | - Jingtao Sun
- Life Technologies, Foster City, CA 94404, USA
| | | | - Hyun Cheol Chung
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul 120-749, Korea
| | - Sung Hoon Noh
- Department of Surgery, Yonsei University College of Medicine, Seoul 120-749, Korea
| | - John N Weinstein
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chang-Gong Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,USA
| | - Garth Powis
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030,USA
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145
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Jin Y, Yu Q, Zhou D, Chen L, Huang X, Xu G, Huang J, Gao X, Gao Y, Shen L. The mitochondrial DNA 9-bp deletion polymorphism is a risk factor for hepatocellular carcinoma in the Chinese population. Genet Test Mol Biomarkers 2012; 16:330-4. [PMID: 22283196 DOI: 10.1089/gtmb.2011.0208] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide. Although molecular biology of carcinogenesis and tumor progression of HCC has been increasingly understood with intense research in recent years, the molecular and cellular mechanisms of HCC pathogenesis are still poorly understood. In the present study, a case-control study including 390 HCC patients and 431 healthy controls was conducted to investigate the association of HCC susceptibility with the mitochondrial DNA (mtDNA) 9-bp deletion polymorphism in Chinese population. Chi-square testing showed that frequencies of 9-bp one repeat or two repeats were significantly different between HCC and control groups. Carriage of 9-bp one repeat fragment was associated with a significantly increased risk of developing HCC (odds ratio=1.48, 95% confidence interval: 1.03-2.14, p=0.027). Stratification analysis further showed that the differences between cases and controls were more obvious in drinkers than nondrinkers. Computational modeling of the 9-bp deletion polymorphism suggests that the mtDNA sequence without the 9-bp deletion polymorphism lies within a predicted binding site (seed region) for hsa-miR-519c-5p and hsa-miR-526a. Our data suggested that the 9-bp deletion polymorphism in mitochondria may influence HCC risk, likely through specific microRNA-mediated regulation, which was possibly involved in the pathogenesis of HCC. The replication of our studies in other populations with larger sample size is warranted.
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Affiliation(s)
- Yiqi Jin
- Department of Vascular/Interventional Radiology, Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Suzhou, P.R. China
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146
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Liu AM, Yao TJ, Wang W, Wong KF, Lee NP, Fan ST, Poon RTP, Gao C, Luk JM. Circulating miR-15b and miR-130b in serum as potential markers for detecting hepatocellular carcinoma: a retrospective cohort study. BMJ Open 2012; 2:e000825. [PMID: 22403344 PMCID: PMC3308260 DOI: 10.1136/bmjopen-2012-000825] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Serum α-fetoprotein (AFP) is the most commonly used biomarker for screening hepatocellular carcinoma (HCC) but fails to detect about half of the patients. Thus, we investigated if circulating microRNAs (miRNAs) could outperform AFP for HCC detection. DESIGN A retrospective cohort study. SETTING Two clinical centres in China. PARTICIPANTS The exploration phase included 96 patients with HCC who received primary curative hepatectomy, and the validation phase included 29 hepatitis B carriers, 57 patients with HCC and 30 healthy controls. MAIN OUTCOME MEASURES Expression of miRNAs was measured by real-time quantitative reverse transcription-PCR. Areas under receiver operating characteristic curves were used to determine the feasibility of using serum miRNA concentration as a diagnostic marker for defining HCC. A multivariate logistic regression analysis was used to evaluate performances of combined serum miRNAs. RESULTS In the exploration phase, miRNA profiling on resected tumour/adjacent non-tumour tissues identified miR-15b, miR-21, miR-130b and miR-183 highly expressed in tumours. These miRNAs were also detectable in culture supernatants of HCC cell lines and in serum samples of patients. Remarkably, these serum miRNAs were markedly reduced after surgery, indicating the tumour-derived source of these circulating miRNAs. In a cross-centre validation study, combined miR-15b and miR-130b demonstrated as a classifier for HCC detection, yielding a receiver operating characteristic curve area of 0.98 (98.2% sensitivity and 91.5% specificity). The detection sensitivity of the classifier in a subgroup of HCCs with low AFP (<20 ng/ml) was 96.7%. The classifier also identified early-stage HCC cases that could not be detected by AFP. CONCLUSION The combined miR-15b and miR-130b classifier is a serum biomarker with clinical value for HCC screening.
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Affiliation(s)
- Angela M Liu
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
- Department of Surgery, National University of Singapore, Singapore, Singapore
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Tzy-Jyun Yao
- Clinical Trials Center, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Wei Wang
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
| | - Kwong-Fai Wong
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
| | - Nikki P Lee
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Sheung Tat Fan
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Ronnie T P Poon
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
| | - Chunfang Gao
- Department of Laboratory Medicine, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
| | - John M Luk
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Hong Kong, Hong Kong
- Department of Pharmacology, National University of Singapore, Singapore, Singapore
- Department of Surgery, National University of Singapore, Singapore, Singapore
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
- Roche R&D Center (China) Ltd., Department of Oncology, Shanghai, China
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147
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Wong KF, Luk JM. Discovery of lamin B1 and vimentin as circulating biomarkers for early hepatocellular carcinoma. Methods Mol Biol 2012; 909:295-310. [PMID: 22903723 DOI: 10.1007/978-1-61779-959-4_19] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The recent advancements in proteomic technologies have reconstituted our research strategies over different type of liver diseases including hepatocellular carcinoma (HCC). Combined analyses on HCC proteome and clinicopathological data of patients have allowed identification of many promising biomarkers that can be further developed into noninvasive diagnostic assays for cancer surveillance. Capitalizing our established proteomic platform primarily based on two-dimensional polyacrylamide gel electrophoresis (2DE) and MALDI-TOF/TOF mass spectrometry, our groups have identified lamin B1 (LMNB1) and vimentin (VIM) as promising biomarkers for detection of early HCC. Protein levels of both biomarkers were significantly elevated in cancerous tissues when compared to the controls in disease-free and cirrhotic liver subjects. Further investigation of the circulating LMNB1 mRNA level in patients' blood samples by standard PCR showed 76% sensitivity and 82% specificity for detection of early HCC. In parallel, an ELISA assay for measuring circulating vimentin level in patients' serum samples could detect small HCC at 40.91% sensitivity and 87.5% specificity. The candidate biomarkers were evaluated with the diagnostic performance of α-fetoprotein (AFP) for HCC. In this article, we address the current protocols for HCC biomarker discovery, ranging from clinical sample preparation, 2DE proteomic profiling and informatics analysis, and assay development and clinical validation study. Focus is emphasized on the methods for sample preservation and low-abundance protein enrichment.
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Affiliation(s)
- Kwong-Fai Wong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
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148
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Budhu A, Wang XW. MicroRNAs and Gastroenterological Cancers. DRUG DISCOVERY TODAY. DISEASE MECHANISMS 2011; 8:e95-e102. [PMID: 22582080 PMCID: PMC3349158 DOI: 10.1016/j.ddmec.2011.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
MicroRNAs are small noncoding RNAs that control gene expression. In doing so, they functionally contribute to the maintenance of cellular processes as well as several important features related to cancer development and progression such as cell growth control, differentiation and apoptosis. In fact, recent studies have shown that microRNAs are suitable and effective cancer-related biomarkers since they display altered expression profiles in cancers versus normal tissue. In addition, microRNAs have been associated with cancer progression and outcome. In this review, the current state of knowledge microRNA expression and function in relation to gastroenterological cancers will be addressed. Moreover, the mechanisms to alter their expression and the potential application of microRNAs in clinical settings will also be highlighted. Finally, the challenges involved in translating microRNA research to the clinic will be discussed.
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Affiliation(s)
- Anuradha Budhu
- Liver Carcinogenesis Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, U.S.A
| | - Xin W Wang
- Liver Carcinogenesis Section, Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, U.S.A
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149
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Modulation of the unfolded protein response is the core of microRNA-122-involved sensitivity to chemotherapy in hepatocellular carcinoma. Neoplasia 2011; 13:590-600. [PMID: 21750653 DOI: 10.1593/neo.11422] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Revised: 04/28/2011] [Accepted: 04/29/2011] [Indexed: 12/22/2022] Open
Abstract
The loss of microRNA-122 (miR-122) expression correlates to many characteristic properties of hepatocellular carcinoma (HCC) cells, including clonogenic survival, anchorage-independent growth, migration, invasion, epithelial-mesenchymal transition, and tumorigenesis. However, all of these findings do not sufficiently explain the oncogenic potential of miR-122. In the current study, we used two-dimensional differential in-gel electrophoresis to measure changes in the expression of thousands of proteins in response to the inhibition of miR-122 in human hepatoma cells. Several proteins that were upregulated on miR-122 inhibition were involved in the unfolded protein response (UPR) pathway. The overexpression of miR-122 resulted in the repression of UPR pathway activation. Therefore, miR-122 may act as an inhibitor of the chaperone gene expression and negatively regulate the UPR pathway in HCC. We further showed that the miR-122 inhibitor enhanced the stability of the 26S proteasome non-ATPase regulatory subunit 10 (PSMD10) through the up-regulation of its target gene cyclin-dependent kinase 4 (CDK4). This process may activate the UPR pathway to prevent chemotherapy-mediated tumor cell apoptosis. The current study suggests that miR-122 negatively regulates the UPR through the CDK4-PSMD10 pathway. The down-regulation of miR-122 activated the CDK4-PSMD10-UPR pathway to decrease tumor cell anticancer drug-mediated apoptosis. We identified a new HCC therapeutic target and proclaimed the potential risk of the therapeutic use of miR-122 silencing.
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150
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Kasinski AL, Slack FJ. Epigenetics and genetics. MicroRNAs en route to the clinic: progress in validating and targeting microRNAs for cancer therapy. Nat Rev Cancer 2011; 11:849-64. [PMID: 22113163 PMCID: PMC4314215 DOI: 10.1038/nrc3166] [Citation(s) in RCA: 779] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In normal cells multiple microRNAs (miRNAs) converge to maintain a proper balance of various processes, including proliferation, differentiation and cell death. miRNA dysregulation can have profound cellular consequences, especially because individual miRNAs can bind to and regulate multiple mRNAs. In cancer, the loss of tumour-suppressive miRNAs enhances the expression of target oncogenes, whereas increased expression of oncogenic miRNAs (known as oncomirs) can repress target tumour suppressor genes. This realization has resulted in a quest to understand the pathways that are regulated by these miRNAs using in vivo model systems, and to comprehend the feasibility of targeting oncogenic miRNAs and restoring tumour-suppressive miRNAs for cancer therapy. Here we discuss progress in using mouse models to understand the roles of miRNAs in cancer and the potential for manipulating miRNAs for cancer therapy as these molecules make their way towards clinical trials.
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Affiliation(s)
- Andrea L Kasinski
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
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