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Application of miRNA Biomarkers in Predicting Overall Survival Outcomes for Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5249576. [PMID: 36147635 PMCID: PMC9485713 DOI: 10.1155/2022/5249576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/25/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022]
Abstract
Background With the development of research, the importance of microRNAs (miRNAs) in the occurrence, metastasis, and prognosis of lung adenocarcinoma (LUAD) has attracted extensive attention. This study is aimed at predicting overall survival (OS) results through bioinformatics to identify novel miRNA biomarkers and hub genes. Materials and Methods The data of LUAD-related miRNA and mRNA samples was downloaded from The Cancer Genome Atlas (TCGA) database. Upon screening and pretreatment of initial data, TCGA data were analyzed using R platform and a series of analytical tools to identify biomarkers with high specificity and sensitivity. Results 7 miRNAs and 13 hub genes that had strong relation to the overall surviving status were identified in patients with LUAD. The expression of seven miRNAs (hsa-miR-19a-3p, hsa-miR-126-5p, hsa-miR-556-3p, hsa-miR-671-5p, hsa-miR-937-3p, hsa-miR-4664-3p, and hsa-miR-4746-5p) could apparently improve the OS rate of patient with LUAD. The 13 hub genes, namely, CCT6A, CDK5R1, CEP55, DNAJB4, EGLN3, HDGF, HOXC8, LIMD1, MKI67, PCP4L1, PPIL1, SCAI, and STK32A, showed a correlation with the OS status. Conclusion 7 miRNAs were identified as novel biomarkers for the prognosis of patients with LUAD. This study offered a deeper comprehension of LUAD treatment and prognosis from the molecular level and helped enhance the understanding of the pathogenesis and potential molecular events of LUAD.
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Youssef SS, Elfiky A, Nabeel MM, Shousha HI, Elbaz T, Omran D, Marie MS, Elzahry MA, Abul-Fotouh A, Hashem A, Guda MF, Abdelaziz AO. Assessment of circulating levels of microRNA-326, microRNA-424, and microRNA-511 as biomarkers for hepatocellular carcinoma in Egyptians. World J Hepatol 2022; 14:1562-1575. [PMID: 36157872 PMCID: PMC9453463 DOI: 10.4254/wjh.v14.i8.1562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/14/2022] [Accepted: 07/31/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the fifth most common cancer. Differential expression of microRNAs (miRNAs)-326, miRNA-424, and miRNA-511 has been associated with the diagnosis and prognosis of HCC in different populations. However, limited information is available regarding their expression in Egyptian HCC patients.
AIM To assess the role of circulating miRNAs-326, miRNA-424, and miRNA-511 in Egyptian HCC patients.
METHODS This prospective observational study included 70 HCC patients and 25 healthy controls. The circulating levels of these three miRNAs were evaluated by real-time PCR. Receiver operating characteristic curve analysis was used to test the diagnostic accuracy of microRNA expression levels.
RESULTS All miRNAs were differentially expressed in HCC patients; miRNAs326 and miRNA-424 were upregulated, while miRNA-511 was downregulated. Both miRNA-326 and miRNA-424 showed sensitivity and specificity of 97%, 71.4%, and 52%, 60%, respectively, to differentiate HCC from controls. Moreover, miRNA-326 was associated with survival and could differentiate between Child grades (A vs B); miRNA-424 significantly differentiated early vs intermediate stages of HCC; while miRNA-511 was significantly correlated with response to modified Response Evaluation Criteria in Solid Tumors (mRECIST).
CONCLUSION We conclude that miRNA-326, miRNA-424, and miRNA-511 have diagnostic and prognostic roles in Egyptian patients with hepatitis C virus-related HCC and should be considered for better disease management.
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Affiliation(s)
- Samar Samir Youssef
- Department of Microbial Biotechnology, National Research Centre, Cairo 1211, Egypt
| | - Asmaa Elfiky
- Department of Environmental and Occupational Medicine, National Research Centre, Cairo 1211, Egypt
| | - Mohamed M Nabeel
- Department of Endemic Medicine and Hepatogastroenterology, Faculty of Medicine, Cairo University, Cairo 11562 Egypt
| | - Hend Ibrahim Shousha
- Department of Endemic Medicine and Hepatogastroenterology, Faculty of Medicine, Cairo University, Cairo 11562 Egypt
| | - Tamer Elbaz
- Department of Endemic Medicine and Hepatogastroenterology, Faculty of Medicine, Cairo University, Cairo 11562 Egypt
| | - Dalia Omran
- Department of Endemic Medicine, Faculty of Medicine, Cairo University, Cairo 1256, Egypt
| | - Mohammad Saeed Marie
- Department of Endemic Medicine and Hepatogastroenterology, Faculty of Medicine, Cairo University, Cairo 11562 Egypt
| | - Mohammad A Elzahry
- Department of Endemic Medicine, Faculty of Medicine, Cairo University, Cairo 1256, Egypt
| | - Amr Abul-Fotouh
- Department of Endemic Medicine, Faculty of Medicine, Cairo University, Cairo 1256, Egypt
| | - Ahmed Hashem
- Department of Endemic Medicine, Faculty of Medicine, Cairo University, Cairo 1256, Egypt
| | | | - Ashraf O Abdelaziz
- Department of Endemic Medicine and Hepatogastroenterology, Faculty of Medicine, Cairo University, Cairo 11562 Egypt
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Yu G, Mu H, Fang F, Zhou H, Li H, Wu Q, Xiong Q, Cui Y. LRP1B mutation associates with increased tumor mutation burden and inferior prognosis in liver hepatocellular carcinoma. Medicine (Baltimore) 2022; 101:e29763. [PMID: 35777027 PMCID: PMC9239668 DOI: 10.1097/md.0000000000029763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Liver hepatocellular carcinoma (LIHC) is the most common primary liver cancer and the main cause of death in patients with cirrhosis. LRP1B is found to involve in a variety of cancers, but the association of LRP1B mutation with tumor mutation burden (TMB) and prognosis of LIHC is rarely studied. METHODS AND RESULTS Herein, we analyzed the somatic mutation data of 364 LIHC patients from The Cancer Genome Atlas (TCGA) and found that LRP1B showed elevated mutation rate. Calculation of the TMB in LRP1B mutant and LRP1B wild-type groups showed that LRP1B mutant group had higher TMB compared with that in LRP1B wild-type group. Then survival analysis was performed and the survival curve showed that LRP1B mutation was associated with poor survival outcome, and this association remained to be significant after adjusting for multiple confounding factors including age, gender, tumor stage, mutations of BRCA1, BRCA2, and POLE. CONCLUSION Collectively, our results revealed that LRP1B mutation was related to high TMB value and poor prognosis in LIHC, indicating that LRP1B mutation is probably helpful for the selection of immunotherapy and prognosis prediction in LIHC.
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Affiliation(s)
- Ge Yu
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
| | - Han Mu
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
| | - Feng Fang
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
| | - Hongyuan Zhou
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
| | - Huikai Li
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
| | - Qiang Wu
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
| | - Qingqing Xiong
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
| | - Yunlong Cui
- Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Tianjin, China
- *Correspondence: Yunlong Cui, Department of Hepatobiliary Cancer, Tianjin Cancer Institute & Hospital, Tianjin Medical University, Huanhuxi Road, Tiyuanbei, Hexi District, Tianjin, PR China (e-mail: )
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4
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Zhao J, Yu H, Han T, Zhu X. Prognosis Value of microRNA-3677-3p in Lung Adenocarcinoma and Its Regulatory Effect on Tumor Progression. Cancer Manag Res 2021; 13:9261-9270. [PMID: 34955656 PMCID: PMC8694712 DOI: 10.2147/cmar.s330357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/19/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Lung adenocarcinomas (LUAD) was the most common subtype of lung cancer, and may result in a poor prognosis. This study was designed to explore the role of miR-3677-3p in LUAD and discuss in what way it functions in LUAD. Materials and Methods We used RT-qPCR method to detect the expression levels of miR-3677-3p in 105 pairs of LUAD tissues and noncancerous tissues, as also as in LUAD cells. We used χ 2 test to analyze the correlation between miR-3677-3p level and the clinical data. The prognosis significance of miR-3677-3p was inferred with Kaplan-Meier and multivariate Cox regression assays. Biological functions of LUAD cells were accessed by cell counting kit-8, transwell migration and invasion assay. The target gene of miR-3677-3p was investigated by luciferase activity assay. Results miR-3677-3p represented an ascendant expression in LUAD tissue specimens and cells. miR-3677-3p expression was associated with the TNM stage and with solitary metastasis. Over-expression of miR-3677-3p can shorten the overall survival period of LUAD patients when compared with low expression. Knockdown of miR-3677-3p suppressed the biology function of NSCLC cells including proliferation, migration, and invasion. KLF12 was a target gene of miR-3677-3p. Conclusion miR-3677-3p represents as a potential prognostic biomarker for LUAD. miR-3677-3p can promote LUAD progression by targeting KLF12.
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Affiliation(s)
- Jian Zhao
- Third Department of Thoracic Surgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, People's Republic of China
| | - Hanbing Yu
- Third Department of Thoracic Surgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, People's Republic of China
| | - Tianci Han
- Third Department of Thoracic Surgery, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, People's Republic of China
| | - Xiangyu Zhu
- Department of General Medicine, Liaoning Cancer Hospital and Institute, Shenyang, Liaoning, People's Republic of China
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5
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Shi T, Iwama H, Fujita K, Kobara H, Nishiyama N, Fujihara S, Goda Y, Yoneyama H, Morishita A, Tani J, Yamada M, Nakahara M, Takuma K, Masaki T. Evaluating the Effect of Lenvatinib on Sorafenib-Resistant Hepatocellular Carcinoma Cells. Int J Mol Sci 2021; 22:13071. [PMID: 34884875 PMCID: PMC8657692 DOI: 10.3390/ijms222313071] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 11/29/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the major causes of cancer-related deaths worldwide. Sorafenib has been used as a first-line systemic treatment for over a decade. However, resistance to sorafenib limits patient response and presents a major hurdle during HCC treatment. Lenvatinib has been approved as a first-line systemic treatment for advanced HCC and is the first agent to achieve non-inferiority against sorafenib. Therefore, in the present study, we evaluated the inhibition efficacy of lenvatinib in sorafenib-resistant HCC cells. Only a few studies have been conducted on this topic. Two human HCC cell lines, Huh-7 and Hep-3B, were used to establish sorafenib resistance, and in vitro and in vivo studies were employed. Lenvatinib suppressed sorafenib-resistant HCC cell proliferation mainly by inducing G1 cell cycle arrest through ERK signaling. Hep-3B sorafenib-resistant cells showed partial cross-resistance to lenvatinib, possibly due to the contribution of poor autophagic responsiveness. Overall, the findings suggest that the underlying mechanism of lenvatinib in overcoming sorafenib resistance in HCC involves FGFR4-ERK signaling. Lenvatinib may be a suitable second-line therapy for unresectable HCC patients who have developed sorafenib resistance and express FGFR4.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Carcinoma, Hepatocellular/blood supply
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/mortality
- Carcinoma, Hepatocellular/pathology
- Cell Line, Tumor
- Cell Movement/genetics
- Cell Proliferation/drug effects
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Liver Neoplasms/blood supply
- Liver Neoplasms/drug therapy
- Liver Neoplasms/mortality
- Liver Neoplasms/pathology
- Mice, Inbred BALB C
- MicroRNAs/genetics
- Neovascularization, Pathologic/drug therapy
- Neovascularization, Pathologic/genetics
- Phenylurea Compounds/pharmacology
- Quinolines/pharmacology
- Sorafenib/pharmacology
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Tingting Shi
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Hisakazu Iwama
- Life Science Research Center, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan;
| | - Koji Fujita
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Hideki Kobara
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Noriko Nishiyama
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Shintaro Fujihara
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Yasuhiro Goda
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Hirohito Yoneyama
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Asahiro Morishita
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Joji Tani
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Mari Yamada
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Mai Nakahara
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Kei Takuma
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
| | - Tsutomu Masaki
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki 761-0793, Japan; (K.F.); (H.K.); (N.N.); (S.F.); (Y.G.); (H.Y.); (A.M.); (J.T.); (M.Y.); (M.N.); (K.T.)
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Mao HX, Chen BW, Wang J, Ma CY, Gan YC, Qiu KJ. miR-3677-5p promotes the proliferation, migration and invasion of hepatocellular carcinoma cells and is associated with prognosis. Exp Ther Med 2021; 22:780. [PMID: 34055079 PMCID: PMC8145920 DOI: 10.3892/etm.2021.10212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 01/28/2021] [Indexed: 11/26/2022] Open
Abstract
MicroRNA (miRNA/miR)-3677 has been indicated to be negatively associated with the survival of patients with hepatocellular carcinoma (HCC) based on The Cancer Genome Atlas database. However, as a novel miRNA, the role of miR-3677-5p in HCC has remained to be elucidated. In the present study, the expression of miR-3677-5p was assessed in HCC tissues and cell lines using reverse transcription-quantitative PCR. Survival analysis was performed using Kaplan-Meier curves. Furthermore, the prognostic significance of miR-3677-5p was evaluated using Cox regression analysis. The effects of miR-3677-5p on cell proliferation, as well as migration and invasion capacities, were analyzed using Cell Counting Kit-8, crystal violet and Transwell assays. The results demonstrated that the level of miR-3677-5p expression was upregulated in human HCC tissues and cell lines and that miR-3677-5p expression was closely associated with tumor size, TNM stage and vascular invasion. Furthermore, high miR-3677-5p expression was significantly associated with unfavorable clinical prognosis for patients with HCC. Overexpression of miR-3677-5p was indicated to significantly promote the proliferation, migration and invasion of HCC cells, whereas knockdown of miR-3677-5p was observed to have an inhibitory effect. In conclusion, the present study demonstrated that miR-3677-5p acts as an oncogene that has a critical role in the regulation of HCC proliferation and progression. Hence, miR-3677-5p may serve as a valuable prognostic biomarker and may be developed as a promising therapeutic target for HCC.
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Affiliation(s)
- Hai-Xiang Mao
- Department of Pancreatic and Hepatobiliary Surgery, Ningbo Medical Treatment Center, Lihuili Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Bai-Wen Chen
- Department of Pancreatic and Hepatobiliary Surgery, Ningbo Medical Treatment Center, Lihuili Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Jie Wang
- Department of Pancreatic and Hepatobiliary Surgery, Ningbo Medical Treatment Center, Lihuili Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Chen-Yang Ma
- Department of Pancreatic and Hepatobiliary Surgery, Ningbo Medical Treatment Center, Lihuili Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Yi-Chao Gan
- Department of Pancreatic and Hepatobiliary Surgery, Ningbo Medical Treatment Center, Lihuili Hospital, Ningbo, Zhejiang 315000, P.R. China
| | - Kai-Jie Qiu
- Department of Pancreatic and Hepatobiliary Surgery, Ningbo Medical Treatment Center, Lihuili Hospital, Ningbo, Zhejiang 315000, P.R. China
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7
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Sathipati SY, Ho SY. Identification of the miRNA signature associated with survival in patients with ovarian cancer. Aging (Albany NY) 2021; 13:12660-12690. [PMID: 33910165 PMCID: PMC8148489 DOI: 10.18632/aging.202940] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/23/2021] [Indexed: 12/22/2022]
Abstract
Ovarian cancer is a major gynaecological malignant tumor associated with a high mortality rate. Identifying survival-related variants may improve treatment and survival in patients with ovarian cancer. In this work, we proposed a support vector regression (SVR)-based method called OV-SURV, which is incorporated with an inheritable bi-objective combinatorial genetic algorithm for feature selection to identify a miRNA signature associated with survival in patients with ovarian cancer. There were 209 patients with miRNA expression profiles and survival information of ovarian cancer retrieved from The Cancer Genome Atlas database. OV-SURV achieved a mean correlation coefficient of 0.77±0.01and a mean absolute error of 0.69±0.02 years using 10-fold cross-validation. Analysis of the top ranked miRNAs revealed that the miRNAs, hsa-let-7f, hsa-miR-1237, hsa-miR-98, hsa-miR-933, and hsa-miR-889, were significantly associated with the survival in patients with ovarian cancer. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that four of these miRNAs, hsa-miR-182, hsa-miR-34a, hsa-miR-342, and hsa-miR-1304, were highly enriched in fatty acid biosynthesis, and the five miRNAs, hsa-let-7f, hsa-miR-34a, hsa-miR-342, hsa-miR-1304, and hsa-miR-24, were highly enriched in fatty acid metabolism. The prediction model with the identified miRNA signature consisting of prognostic biomarkers can benefit therapeutic decision making of ovarian cancer.
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Affiliation(s)
- Srinivasulu Yerukala Sathipati
- Center for Precision Medicine Research, Marshfield Clinic Research Institute, Marshfield, WI 54449, USA.,Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Shinn-Ying Ho
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
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8
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An Integrating Immune-Related Signature to Improve Prognosis of Hepatocellular Carcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2020; 2020:8872329. [PMID: 33204302 PMCID: PMC7655255 DOI: 10.1155/2020/8872329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/26/2020] [Accepted: 10/15/2020] [Indexed: 01/27/2023]
Abstract
Growing evidence suggests that the superiority of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) could act as biomarkers for cancer prognosis. However, the prognostic marker for hepatocellular carcinoma with high accuracy and sensitivity is still lacking. In this research, a retrospective, cohort-based study of genome-wide RNA-seq data of patients with hepatocellular carcinoma was carried out, and two protein-coding genes (GTPBP4, TREM-1) and one lncRNA (LINC00426) were sorted out to construct an integrative signature to predict the prognosis of patients. The results show that both the AUC and the C-index of this model perform well in TCGA validation dataset, cross-platform GEO validation dataset, and different subsets divided by gender, stage, and grade. The expression pattern and functional analysis show that all three genes contained in the model are associated with immune infiltration, cell proliferation, invasion, and metastasis, providing further confirmation of this model. In summary, the proposed model can effectively distinguish the high- and low-risk groups of hepatocellular carcinoma patients and is expected to shed light on the treatment of hepatocellular carcinoma and greatly improve the patients' prognosis.
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Tomesz A, Szabo L, Molnar R, Deutsch A, Darago R, Mathe D, Budan F, Ghodratollah N, Varjas T, Nemeth B, Kiss I. Effect of 7,12-Dimethylbenz(α)anthracene on the Expression of miR-330, miR-29a, miR-9-1, miR-9-3 and the mTORC1 Gene in CBA/Ca Mice. In Vivo 2020; 34:2337-2343. [PMID: 32871758 DOI: 10.21873/invivo.12046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND/AIM Development of malignant tumors is preceded by molecular biological events. Our aim was to establish an assay panel by using miRNAs and other genes for the rapid screening of potential carcinogens or chemopreventive agents. MATERIALS AND METHODS Six male and 6 female CBA/Ca mice received 20 mg/bwkg 7,12-dimethylbenz(α)anthracene (DMBA) intraperitoneally, and 24 h later RNA was isolated from parenchymal organs. Expression of miR-330, miR-29a, miR-9-1, miR-9-3 and mTORC1 was analysed by real time polymerase chain reaction and compared to non-treated controls. RESULTS DMBA caused significant alterations in the expression of the studied genes. The most profound changes were the strongly elevated miR-9-3 and mTORC1 expressions in female mice in all organs studied. CONCLUSION miR-9-3 and mTORC1 expression in female mice were found to be the most suitable biomarkers for rapid identification of possible carcinogenic effects.
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Affiliation(s)
- Andras Tomesz
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary .,Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Laszlo Szabo
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary.,Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Richard Molnar
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary.,Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Arpad Deutsch
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Richard Darago
- Doctoral School of Health Sciences, Faculty of Health Sciences, University of Pécs, Pécs, Hungary
| | - Domokos Mathe
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
| | - Ferenc Budan
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary.,Institute of Environmental Engineering, University of Pannonia, Veszprém, Hungary
| | | | - Timea Varjas
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Balazs Nemeth
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Istvan Kiss
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
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Boubaker G, Strempel S, Hemphill A, Müller N, Wang J, Gottstein B, Spiliotis M. Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice. PLoS Negl Trop Dis 2020; 14:e0007640. [PMID: 32442168 PMCID: PMC7244097 DOI: 10.1371/journal.pntd.0007640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 03/05/2020] [Indexed: 12/15/2022] Open
Abstract
We present a comprehensive analysis of the hepatic miRNA transcriptome at one month post-infection of experimental primary alveolar echinococcosis (AE), a parasitic infection caused upon ingestion of E. multilocularis eggs. Liver tissues were collected from infected and non-infected C57BL/6 mice, then small RNA libraries were prepared for next-generation sequencing (NGS). We conducted a Stem-loop RT-qPCR for validation of most dysregulated miRNAs. In infected mice, the expression levels of 28 miRNAs were significantly altered. Of these, 9 were up-regulated (fold change (FC) ≥ 1.5) and 19 were down-regulated (FC ≤ 0.66) as compared to the non-infected controls. In infected livers, mmu-miR-148a-3p and mmu-miR-101b-3p were 8- and 6-fold down-regulated, respectively, and the expression of mmu-miR-22-3p was reduced by 50%, compared to non-infected liver tissue. Conversely, significantly higher hepatic levels were noted for Mus musculus (mmu)-miR-21a-5p (FC = 2.3) and mmu-miR-122-5p (FC = 1.8). In addition, the relative mRNA expression levels of five genes (vegfa, mtor, hif1-α, fasn and acsl1) that were identified as targets of down-regulated miRNAs were significantly enhanced. All the five genes exhibited a higher expression level in livers of E. multilocularis infected mice compared to non-infected mice. Finally, we studied the issue related to functionally mature arm selection preference (5p and/or 3p) from the miRNA precursor and showed that 9 pre-miRNAs exhibited different arm selection preferences in normal versus infected liver tissues. In conclusion, this study provides first evidence that miRNAs are regulated early in primary murine AE. Our findings raise intriguing questions such as (i) how E. multilocularis affects hepatic miRNA expression;(ii) what are the alterations in miRNA expression patterns in more advanced AE-stages; and (iii) which hepatic cellular, metabolic and/or immunologic processes are modulated through altered miRNAs in AE. Thus, further research on the regulation of miRNAs during AE is needed, since miRNAs constitute an attractive potential option for development of novel therapeutic approaches against AE. Various infectious diseases in humans have been associated with altered expression patterns of microRNAs (miRNAs), a class of small non-coding RNAs involved in negative regulation of gene expression. Herein, we revealed that significant alteration of miRNAs expression occurred in murine liver subsequently to experimental infection with E. multilocularis eggs when compared to non-infected controls. At the early stage of murine AE, hepatic miRNAs were mainly down-regulated. Respective target genes of the most extensively down-regulated miRNAs were involved in angiogenesis and fatty acid synthesis. Furthermore, we found higher mRNA levels of three angiogenic and two lipogenic genes in E. multilocularis infected livers compared to non-infected controls. Angiogenesis and fatty acid biosynthesis may be beneficial for development of the E. multilocularis metacestodes. In fact the formation of new blood vessels in the periparasitic area may ensure that parasites are supplied with oxygen and nutrients and get rid of waste products. Additionally, E. multilocularis is not able to undertake de novo fatty acid synthesis, thus lipids must be scavenged from its host. More research on the regulation of the hepatic miRNA transcriptome at more advanced stages of AE is needed.
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Affiliation(s)
- Ghalia Boubaker
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Department of Clinical Biology B, Laboratory of Parasitology and Mycology, University of Monastir, Monastir, Tunisia
- * E-mail: (GB); (BG)
| | | | - Andrew Hemphill
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Norbert Müller
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Junhua Wang
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
| | - Bruno Gottstein
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
- Institute of Infectious Diseases, Faculty of Medicine, University of Berne, Berne, Switzerland
- * E-mail: (GB); (BG)
| | - Markus Spiliotis
- Department of Infectious Diseases and Pathobiology, Institute of Parasitology, University of Bern, Bern, Switzerland
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11
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Liang JJ, Wang JY, Zhang TJ, An GS, Ni JH, Li SY, Jia HT. MiR-509-3-5p-NONHSAT112228.2 Axis Regulates p21 and Suppresses Proliferation and Migration of Lung Cancer Cells. Curr Top Med Chem 2020; 20:835-846. [DOI: 10.2174/1568026620666200306102713] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/24/2019] [Accepted: 12/06/2019] [Indexed: 12/19/2022]
Abstract
Background:
Although the involvement of individual microRNA and lncRNA in the regulation
of p21 expression has largely been evidenced, less is known about the roles of functional interactions
between miRNAs and lncRNAs in p21 expression. Our previous work demonstrated that miR-509-
3-5p could block cancer cell growth.
Methods:
To gain an insight into the role of miR-509-3-5p in the regulation of p21 expression, we performed
in silico prediction and showed that miR-509-3-5p might target the NONHSAT112228.2, a
sense-overlapping lncRNA transcribed by a non-code gene overlapping with p21 gene. Mutation and
luciferase report analysis suggested that miR-509-3-5p could target NONHSAT112228.2, thereby blocking
its expression. Consistently, NONHSAT112228.2 expression was inversely correlated with both
miR-509-3-5p and p21 expression in cancer cells. Ectopic expression of miR-509-3-5p and knockdown
of NONHSAT112228.2 both promoted proliferation and migration of cancer cells.
Results:
Interestingly, high-expression of NONHSAT112228.2 accompanied by low-expression of p21
was observed in lung cancer tissues and associated with lower overall survival.
Conclusion:
Taken together, our study found a new regulatory pathway of p21, in which MiR-509-3-5p
functionally interacts with NONHSAT112228.2 to release p21 expression. MiR-509-3-5p—
NONHSAT112228.2 regulatory axis can inhibit the proliferation and migration of lung cancer cells.
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Affiliation(s)
- Jing-Jing Liang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Jun-Yi Wang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Tong-Jia Zhang
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Guo-Shun An
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ju-Hua Ni
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Shu-Yan Li
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Hong-Ti Jia
- Department of Biochemistry and Molecular Biology, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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12
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Yao C, Ruan JW, Zhu YR, Liu F, Wu HM, Zhang Y, Jiang Q. The therapeutic value of the SphK1-targeting microRNA-3677 in human osteosarcoma cells. Aging (Albany NY) 2020; 12:5399-5410. [PMID: 32203055 PMCID: PMC7138565 DOI: 10.18632/aging.102961] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022]
Abstract
Sphingosine kinase 1 (SphK1) is a potential therapeutic target for human osteosarcoma (OS). SphK1-targeting microRNAs (miRNAs) could have important therapeutic value for OS. We discovered that micorRNA-3677 (miR-3677) is a SphK1-targeting miRNA, inhibiting OS cell progression. The results of RNA-Pull down assay confirmed direct binding between biotinylated-miR-3677 and SphK1 mRNA in primary human OS cells. In established and primary human OS cells forced overexpression of miR-3677, by a lentiviral construct, decreased SphK1 3’-UTR (untranslated region) activity and downregulated SphK1 expression. Both were however enhanced with miR-3677 inhibition in OS cells. Function studies demonstrated that OS cell growth, proliferation and migration were inhibited with miR-3677 overexpression, but augmented with miR-3677 inhibition. MiR-3677 overexpression-induced anti-OS cell activity was reversed with re-expression of the 3’-UTR-depleted SphK1. Additionally, in SphK1 knockout OS cells (by CRISPR/Cas9 strategy), altering miR-3677 expression failed to further alter cell functions. Finally, we show that miR-3677 expression was significantly downregulated in primary human OS tissues, correlating with SphK1 mRNA upregulation. We conclude that targeting SphK1 by miR-3677 inhibits human OS cell progression.
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Affiliation(s)
- Chen Yao
- Department of Orthopedics, Nanjing Drum Tower Hospital of Nanjing Medical University, Nanjing, China.,Department of Orthopedics, Affiliated Hospital of Nanjing University of TCM, Jiangsu Province Hospital of TCM, Nanjing, China
| | - Jian-Wei Ruan
- Department of Orthopedics, Taizhou Municipal Hospital, Taizhou, China
| | - Yun-Rong Zhu
- Department of Orthopedics, The Affiliated Jiangyin Hospital of Medical College of Southeast University, Jiangyin, China
| | - Fei Liu
- Department of Orthopedics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Hui-Ming Wu
- Department of Orthopedics, Affiliated Hospital of Nanjing University of TCM, Jiangsu Province Hospital of TCM, Nanjing, China
| | - Yan Zhang
- Department of Radiotherapy and Oncology, Affiliated Kunshan Hospital of Jiangsu University, Kunshan, China
| | - Qing Jiang
- Department of Orthopedics, Nanjing Drum Tower Hospital of Nanjing Medical University, Nanjing, China
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13
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Dai X, Huang R, Hu S, Zhou Y, Sun X, Gui P, Yu Z, Zhou P. A novel miR-0308-3p revealed by miRNA-seq of HBV-positive hepatocellular carcinoma suppresses cell proliferation and promotes G1/S arrest by targeting double CDK6/Cyclin D1 genes. Cell Biosci 2020; 10:24. [PMID: 32128112 PMCID: PMC7047384 DOI: 10.1186/s13578-020-00382-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/31/2020] [Indexed: 02/07/2023] Open
Abstract
Background Persistent infection with hepatitis B virus (HBV) accounts for the majority of hepatocellular carcinoma (HCC), but the molecular mechanisms underlying liver carcinogenesis are still not completely understood. Increasing evidence demonstrates that microRNAs (miRNAs) play significant functional roles in virus–host interactions. The aim of this study was to explore differentially expressed miRNA profiles and investigate the molecular mechanism of miR-0308-3p in HBV-positive HCC carcinogenesis. Methods High-throughput sequencing was used to detect novel miRNAs in three samples of HBV-positive HCC tissue compared to matched HBV-negative HCC tissue. The Cancer Genome Atlas (TCGA) database was used to mine miRNAs related to HBV-positive HCC. Bioinformatics analyses were conducted to predict the miRNAs’ possible biological and pathway regulatory functions. Quantitative polymerase chain reaction (qPCR) was then applied to evaluate the expression levels of randomly selected miRNAs. CCK-8 was used to measure cell proliferation and cell cycles were analyzed using flow cytometry. A dual luciferase reporter gene assay was used to confirm the downstream targets of miR-0308-3p. Results In total, there were 34 overlapping miRNAs in both our miRNA-seq data and the TCGA database. We found two overlapping miRNAs in both the HBV-positive HCC samples and the TCGA database, and 205 novel pre-miRNA sequences were predicted. miR-522 and miR-523 were markedly overexpressed in HBV-positive HCC and were associated with a significantly poorer long-term prognosis (miR-522, HR 2.19, 95% CI 1.33–3.6, p = 0.0015; miR-523HR 1.5, 95% CI 1–2.44, p = 0.0047). Of note, we found that the novel miR-0308-3p was markedly downregulated in HBV-positive HCC samples and HCC cancer cell lines compared with HBV-negative HCC samples and adjacent normal hepatic tissue. Moreover, elevated expression of miR-0308-3p was found to inhibit proliferation of cancer cells by promoting G1/S cell cycle arrest but did not influence the apoptosis of cancer cells. A dual luciferase reporter activity assay identified that miR-0308-3p acted directly on the target sequence of the CDK6 and Cyclin D1 mRNA 3ʹUTR to suppress CDK6 and Cyclin D1 expression. Conclusions MiR-0308-3p upregulation dramatically suppressed HCC cell proliferation and induced G1/S cell cycle arrest by directly targeting CDK6/Cyclin D1. These findings reveal a novel molecular mechanism for activation of G1/S arrest in HCC and may prove clinically useful for developing new therapeutic targets.
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Affiliation(s)
- Xiaoming Dai
- 1The First Affiliated Hospital, University of South China, 69 Chuanshan Road, Hengyang, 421001 Hunan People's Republic of China
| | - Ruixue Huang
- 2Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Sai Hu
- 3Institute for Chemical Carcinogenesis, State Key Laboratory of Respiratory, Guangzhou Medical University, Guangzhou, 511436 People's Republic of China
| | - Yao Zhou
- 2Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, 410078 China
| | - Xiaoya Sun
- 3Institute for Chemical Carcinogenesis, State Key Laboratory of Respiratory, Guangzhou Medical University, Guangzhou, 511436 People's Republic of China
| | - Pucheng Gui
- 1The First Affiliated Hospital, University of South China, 69 Chuanshan Road, Hengyang, 421001 Hunan People's Republic of China
| | - Zijian Yu
- 1The First Affiliated Hospital, University of South China, 69 Chuanshan Road, Hengyang, 421001 Hunan People's Republic of China
| | - Pingkun Zhou
- 3Institute for Chemical Carcinogenesis, State Key Laboratory of Respiratory, Guangzhou Medical University, Guangzhou, 511436 People's Republic of China.,Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, 27 Taiping Road, Haidian District, Beijing, 100850 People's Republic of China
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14
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Lv Y, Duanmu J, Fu X, Li T, Jiang Q. Identifying a new microRNA signature as a prognostic biomarker in colon cancer. PLoS One 2020; 15:e0228575. [PMID: 32049961 PMCID: PMC7015317 DOI: 10.1371/journal.pone.0228575] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 01/17/2020] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The aim was to identify a novel prognostic miRNA signature for colon cancer (CC) in silico. METHODS Data on the expression of miRNAs and relevant clinical information for 407 patients were obtained from The Cancer Genome Atlas (TCGA), and the samples were randomly split into a validation set (n = 203) and training set (n = 204). The differential expression of miRNAs between normal tissues and patients with CC was analyzed. We detected a miRNA expression signature in the training dataset by using a Cox proportional hazard regression model. Then, we verified the signature in the validation set. Association of the miRNA signature with overall survival was assessed in the validation cohort and combined cohort by log-rank test and based on Kaplan-Meier curves. The receiver operating characteristic and disease-free survival analyses were performed to evaluate the miRNA signature of CC in the combined cohort. Multivariate and univariate Cox analyses related to survival for the miRNA signature were performed, and a nomogram was built as a prognostic model for CC. To explore the function of target genes of the miRNA signature, Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used. RESULTS Between the matched normal tissues and colon cancer tissues, 267 differentially expressed miRNAs were detected, and a single-factor CoxPH model showed that 13 miRNAs were related to overall survival in the training cohort. Then, a five-miRNA signature was identified using a CoxPH regression model with multiple factors. The five-miRNA signature had significant prognostic value in the training cohort and was validated in the validation cohort and combined cohort. A total of 193 target genes of the miRNA signature were identified. According to the results of functional analysis of the target genes, the signaling pathways MAPK, AMPK and PI3K-Akt, focal adhesion, and microRNAs in cancer were remarkably enriched. CONCLUSION A five-miRNA signature had increased prognostic value for CC, which may provide important biological insights for the discovery and development of molecular predictors to improve the prognosis of patients with CC.
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Affiliation(s)
- Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Jinzhong Duanmu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Xiaorui Fu
- Queen Mary School, Medical Department, Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Taiyuan Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
| | - Qunguang Jiang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, People's Republic of China
- * E-mail:
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15
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Pan C, Luo J, Zhang J. Computational Identification of RNA-Seq Based miRNA-Mediated Prognostic Modules in Cancer. IEEE J Biomed Health Inform 2020; 24:626-633. [DOI: 10.1109/jbhi.2019.2911528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Ziogas IA, Sioutas G, Mylonas KS, Tsoulfas G. Role of MicroRNA in the Diagnosis and Management of Hepatocellular Carcinoma. Microrna 2020; 9:25-40. [PMID: 31218966 DOI: 10.2174/2211536608666190619155406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/11/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Hepatocellular Carcinoma (HCC) is one of the most common malignant tumors in the world and comes third in cancer-induced mortality. The need for improved and more specific diagnostic methods that can detect early-stage disease is immense, as it is amenable to curative modalities, while advanced HCC is associated with low survival rates. microRNA (miRNA) expression is deregulated in HCC and this can be implemented both diagnostically and therapeutically. OBJECTIVE To provide a concise review on the role of miRNA in diagnosis, prognosis, and treatment of HCC. METHODS We conducted a comprehensive review of the PubMed bibliographic database. RESULTS Multiple miRNAs are involved in the pathogenesis of HCC. Measurement of the levels of these miRNAs either in tumor tissue or in the blood constitutes a promising diagnostic, as well as prognostic tool. OncomiRs are miRNAs that promote tumorigenesis, thus inhibiting them by administering antagomiRs is a promising treatment option. Moreover, replacement of the depleted miRNAs is another potential therapeutic approach for HCC. Modification of miRNA levels may also regulate sensitivity to chemotherapeutic agents. CONCLUSION miRNA play a pivotal role in HCC pathogenesis and once the underlying mechanisms are elucidated, they will become part of everyday clinical practice against HCC.
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Affiliation(s)
- Ioannis A Ziogas
- Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Surgery Working Group, Society of Junior Doctors, Athens, Greece
| | - Georgios Sioutas
- Surgery Working Group, Society of Junior Doctors, Athens, Greece
- Medical School, Democritus University of Thrace, Alexandroupolis, Greece
| | - Konstantinos S Mylonas
- Surgery Working Group, Society of Junior Doctors, Athens, Greece
- Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgios Tsoulfas
- 1st Department of Surgery, Aristotle University of Thessaloniki, Thessaloniki, Greece
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17
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Peng LN, Deng XY, Gan XX, Zhang JH, Ren GH, Shen F, Feng JH, Cai WS, Xu B. Targeting of TLE3 by miR-3677 in human breast cancer promotes cell proliferation, migration and invasion. Oncol Lett 2019; 19:1409-1417. [PMID: 32002031 PMCID: PMC6960393 DOI: 10.3892/ol.2019.11241] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 11/07/2019] [Indexed: 02/07/2023] Open
Abstract
Numerous studies have indicated an important function of microRNAs (miRs) in breast cancer (BC) progression, oncogenesis and metastasis. However, the function of miR-3677, which has been revealed to be upregulated in BC [The Cancer Genome Atlas (TCGA) data], has not been investigated to date. In the present study, miR-3677 was revealed to be upregulated in BC as determined using TCGA. miR-3677 was significantly upregulated in BC tissues and cell lines compared with those noted in adjacent non-cancerous tissues and primary normal breast cells (P<0.05). The overexpression of miR-3677 promoted the cell proliferation, migration and invasion of BC cells. Using bioinformatics algorithms and luciferase assays, a novel target gene for miR-3677, namely transducin-like enhancer of Split3 (TLE3), was identified. Silencing of TLE3 in miR-3677-transfected BC cells suppressed their proliferation and migration. An inverse correlation was observed between miR-3677 and TLE3 expression levels in human BC tissues. In conclusion, the present study demonstrated that miR-3677 promoted BC cell proliferation, migration and invasion by inhibiting TLE3 expression, which provided a novel mechanism and a promising therapeutic target for patients with BC.
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Affiliation(s)
- Li-Na Peng
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China.,Department of General Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Xing-Yan Deng
- Department of General Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China.,Department of Thyroid Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Xiao-Xiong Gan
- Department of General Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Jin-Hui Zhang
- Department of General Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Guang-Hui Ren
- Department of General Surgery, Shenzhen Hospital, Southern Medical University, Shenzhen, Guangdong 518101, P.R. China
| | - Fei Shen
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China.,Department of General Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China.,Department of Thyroid Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Jian-Hua Feng
- Department of General Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Wen-Song Cai
- Department of General Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China.,Department of Thyroid Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
| | - Bo Xu
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, Guangdong 510630, P.R. China.,Department of General Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China.,Department of Thyroid Surgery, Guangzhou First People's Hospital, School of Medicine, South China University of Technology, Guangzhou, Guangdong 510180, P.R. China
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18
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MicroRNAs in Animal Models of HCC. Cancers (Basel) 2019; 11:cancers11121906. [PMID: 31805631 PMCID: PMC6966618 DOI: 10.3390/cancers11121906] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/27/2019] [Accepted: 11/28/2019] [Indexed: 12/11/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related mortality. Molecular heterogeneity and absence of biomarkers for patient allocation to the best therapeutic option contribute to poor prognosis of advanced stages. Aberrant microRNA (miRNA) expression is associated with HCC development and progression and influences drug resistance. Therefore, miRNAs have been assayed as putative biomarkers and therapeutic targets. miRNA-based therapeutic approaches demonstrated safety profiles and antitumor efficacy in HCC animal models; nevertheless, caution should be used when transferring preclinical findings to the clinics, due to possible molecular inconsistency between animal models and the heterogeneous pattern of the human disease. In this context, models with defined genetic and molecular backgrounds might help to identify novel therapeutic options for specific HCC subgroups. In this review, we describe rodent models of HCC, emphasizing their representativeness with the human pathology and their usefulness as preclinical tools for assessing miRNA-based therapeutic strategies.
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19
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Fang S, Guo J, Zhang J, Liu J, Hong S, Yu B, Gao Y, Hu S, Liu H, Sun L, Zhao Y. A P53‐related microRNA model for predicting the prognosis of hepatocellular carcinoma patients. J Cell Physiol 2019; 235:3569-3578. [PMID: 31556110 DOI: 10.1002/jcp.29245] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/26/2019] [Indexed: 12/31/2022]
Affiliation(s)
- Shuang‐Sang Fang
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- School of Traditional Chinese Medicine Beijing University of Chinese Medicine Beijing China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Jin‐Cheng Guo
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- School of Traditional Chinese Medicine Beijing University of Chinese Medicine Beijing China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Jian‐Hua Zhang
- Department of Blood Transfusion Peking University People's Hospital Beijing China
| | - Jin‐Na Liu
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Shuai Hong
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Bo Yu
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Yuhan Gao
- Department of Blood Transfusion Peking University People's Hospital Beijing China
| | - Su‐Pei Hu
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
| | - Hai‐Zhong Liu
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
| | - Liang Sun
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
| | - Yi Zhao
- Hwa Mei Hospital University of Chinese Academy of Sciences Ningbo China
- School of Traditional Chinese Medicine Beijing University of Chinese Medicine Beijing China
- Key Laboratory of Intelligent Information Processing, State Key Laboratory of Computer Architecture, Institute of Computing Technology Chinese Academy of Sciences Beijing China
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20
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Zhu GQ, Yang Y, Chen EB, Wang B, Xiao K, Shi SM, Zhou ZJ, Zhou SL, Wang Z, Shi YH, Fan J, Zhou J, Liu TS, Dai Z. Development and validation of a new tumor-based gene signature predicting prognosis of HBV/HCV-included resected hepatocellular carcinoma patients. J Transl Med 2019; 17:203. [PMID: 31215439 PMCID: PMC6582497 DOI: 10.1186/s12967-019-1946-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/03/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Due to the phenotypic and molecular diversity of hepatocellular carcinomas (HCC), it is still a challenge to determine patients' prognosis. We aim to identify new prognostic markers for resected HCC patients. METHODS 274 patients were retrospectively identified and samples collected from Zhongshan hospital, Fudan University. We analyzed the gene expression patterns of tumors and compared expression patterns with patient survival times. We identified a "9-gene signature" associated with survival by using the coefficient and regression formula of multivariate Cox model. This molecular signature was then validated in three patients cohorts from internal cohort (n = 69), TCGA (n = 369) and GEO dataset (n = 80). RESULTS We identified 9-gene signature consisting of ZC2HC1A, MARCKSL1, PTGS1, CDKN2B, CLEC10A, PRDX3, PRKCH, MPEG1 and LMO2. The 9-gene signature was used, combined with clinical parameters, to fit a multivariable Cox model to the training cohort (concordance index, ci = 0.85), which was successfully validated (ci = 0.86 for internal cohort; ci = 0.78 for in silico cohort). The signature showed improved performance compared with clinical parameters alone (ci = 0.70). Furthermore, the signature predicted patient prognosis than previous gene signatures more accurately. It was also used to stratify early-stage, HBV or HCV-infected patients into low and high-risk groups, leading to significant differences in survival in training and validation (P < 0.001). CONCLUSIONS The 9-gene signature, in which four were upregulated (ZC2HC1A, MARCKSL1, PTGS1, CDKN2B) and five (CLEC10A, PRDX3, PRKCH, MPEG1, LMO2) were downregulated in HCC with poor prognosis, stratified HCC patients into low and high risk group significantly in different clinical settings, including receiving adjuvant transarterial chemoembolization and especially in early stage disease. This new signature should be validated in prospective studies to stratify patients in clinical decisions.
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Affiliation(s)
- Gui-Qi Zhu
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Yi Yang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Er-Bao Chen
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Biao Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Kun Xiao
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Shi-Ming Shi
- Department of Radiation Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zheng-Jun Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Shao-Lai Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Zheng Wang
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Ying-Hong Shi
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jia Fan
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Zhou
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Tian-Shu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhi Dai
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
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21
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Qin L, Huang J, Wang G, Huang J, Wu X, Li J, Yi W, Qin F, Huang D. Integrated analysis of clinical significance and functional involvement of microRNAs in hepatocellular carcinoma. J Cell Physiol 2019; 234:23581-23595. [PMID: 31210353 DOI: 10.1002/jcp.28927] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/21/2019] [Accepted: 05/22/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Li Qin
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Jian Huang
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Guodong Wang
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Jinxin Huang
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Xintian Wu
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Jinzhuan Li
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Weili Yi
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Fuhui Qin
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
| | - Dongning Huang
- Department of Radiation Oncology Liuzhou Worker Hospital Liuzhou Guangxi Province People's Republic of China
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22
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Modulation of the IL-6-Signaling Pathway in Liver Cells by miRNAs Targeting gp130, JAK1, and/or STAT3. MOLECULAR THERAPY. NUCLEIC ACIDS 2019; 16:419-433. [PMID: 31026677 PMCID: PMC6479786 DOI: 10.1016/j.omtn.2019.03.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/22/2019] [Accepted: 03/24/2019] [Indexed: 12/19/2022]
Abstract
Interleukin-6 (IL-6)-type cytokines share the common receptor glycoprotein 130 (gp130), which activates a signaling cascade involving Janus kinases (JAKs) and signal transducer and activator of transcription (STAT) transcription factors. IL-6 and/or its signaling pathway is often deregulated in diseases, such as chronic liver diseases and cancer. Thus, the identification of compounds inhibiting this pathway is of interest for future targeted therapies. We established novel cellular screening systems based on a STAT-responsive reporter gene (Cypridina luciferase). Of a library containing 538 microRNA (miRNA) mimics, several miRNAs affected hyper-IL-6-induced luciferase activities. When focusing on candidate miRNAs specifically targeting 3′ UTRs of signaling molecules of this pathway, we identified, e.g., miR-3677-5p as a novel miRNA affecting protein expression of both STAT3 and JAK1, whereas miR-16-1-3p, miR-4473, and miR-520f-3p reduced gp130 surface expression. Interestingly, combination treatment with 2 or 3 miRNAs targeting gp130 or different signaling molecules of the pathway did not increase the inhibitory effects on phospho-STAT3 levels and STAT3 target gene expression compared to treatment with single mimics. Taken together, we identified a set of miRNAs of potential therapeutic value for cancer and inflammatory diseases, which directly target the expression of molecules within the IL-6-signaling pathway and can dampen inflammatory signal transduction.
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23
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Wei Q, Zhao L, Jiang L, Bi J, Yu Z, Zhao L, Song X, Sun M, Chen Y, Wei M. Prognostic relevance of miR-137 and its liver microenvironment regulatory target gene AFM in hepatocellular carcinoma. J Cell Physiol 2018; 234:11888-11899. [PMID: 30523640 DOI: 10.1002/jcp.27855] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 11/12/2018] [Indexed: 12/27/2022]
Abstract
MiR-137 has been identified as potential hepatocellular carcinoma (HCC) prognostic biomarkers. Highly relevant HCC prognostic biomarkers may be derived from combinations of miR-137 with its target genes involved in the regulation of liver microenvironment. This study aimed at the discovery of such a combination with improved HCC prognosis performance than miR-137 or its target gene alone in a significantly higher number of HCC patients than previous studies. Analysis of the differentially expressed micro RNAs (miRNAs) between cancer and noncancer tissues reconfirmed miR-137 to be among the most relevant prognostic miRNAs and the data of 375 HCC patients and 50 normal cases were from the Cancer Genome Atlas (TCGA) data sets. Target genes were identified by the established search methods and Kaplan-Meier survival analysis of HCC patients was used to evaluate the overall survival (OS) and recurrence-free survival (RFS). Cox proportional hazards regression indicated that the miR-137 and its target gene AFM combination is an independent prognostic factor for the OS and RFS in HCC. In vitro experiments validated that miR-137 could bind to 3'-untranslated region of the AFM and promote the invasion and metastasis of HCC cell lines. The expressions of miR-137 and its liver microenvironment regulatory target gene AFM in combination significantly correlated with HCC progression in a higher number of patients than in previous studies, which suggested their potential as prognostic biomarkers for HCC.
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Affiliation(s)
- Qian Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Longyang Jiang
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Jia Bi
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Zhaojin Yu
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Lan Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Xinyue Song
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Mingli Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
| | - Yuzong Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore, Singapore
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning, China
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Żorniak M, Garczorz W, Wosiewicz P, Marek T, Błaszczyńska M, Waluga M, Kukla M, Kimsa-Furdzik M, Francuz T, Hartleb M. Mucosal miR-3677 is over-expressed in cirrhotic patients with gastric antral vascular ectasia (GAVE). Scand J Gastroenterol 2018; 53:1503-1508. [PMID: 30621516 DOI: 10.1080/00365521.2018.1547922] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Gastric antral vascular ectasia (GAVE) is a rare vasculopathy that associates several diseases, most commonly liver cirrhosis. It usually presents as an occult gastrointestinal bleeding leading to profound iron deficiency anemia. We hypothesized that GAVE is local mucosal pathology dependent on genetic mechanisms, and the purpose of the study was to characterize miRNAs expression in gastric tissue of patients with cirrhosis and GAVE. MATERIALS AND METHODS Thirteen patients with GAVE and cirrhosis and 35 healthy subjects were recruited. Microarray analysis and comparative microRNA study was done by quantitative polymerase chain reaction (qPCR). The microarray scores were grouped with use of the hierarchical clusterization analysis and miRNA target prediction was done with TargetScan 6.2 algorithm and Gene Ontology analysis (DIANA-miRPath). RESULTS Concentration of miR-3677 in GAVE-affected mucosa was higher by 72% in comparison with GAVE-free mucosa of patients with cirrhosis (33.7 vs. 35.6 PCR cycles; p < .001) and by 45% in comparison with normal mucosa (33.7 vs. 34.9 PCR cycles; p < .05). According to Gene Ontology analysis miR-3677 was related to angiopoietin-like protein 4 (ANGPTL4) gene. CONCLUSION GAVE in liver cirrhosis is associated with increased expression of miR-3667 that may be linked with ANGPTL4 gene.
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Affiliation(s)
- Michał Żorniak
- a Department of Gastroenterology and Hepatology , School of Medicine in Katowice, Medical University of Silesia , Katowice , Poland
| | - Wojciech Garczorz
- b Department of Biochemistry, School of Medicine in Katowice , Medical University of Silesia , Katowice , Poland
| | - Piotr Wosiewicz
- a Department of Gastroenterology and Hepatology , School of Medicine in Katowice, Medical University of Silesia , Katowice , Poland
| | - Tomasz Marek
- a Department of Gastroenterology and Hepatology , School of Medicine in Katowice, Medical University of Silesia , Katowice , Poland
| | | | - Marek Waluga
- a Department of Gastroenterology and Hepatology , School of Medicine in Katowice, Medical University of Silesia , Katowice , Poland
| | - Michał Kukla
- a Department of Gastroenterology and Hepatology , School of Medicine in Katowice, Medical University of Silesia , Katowice , Poland
| | - Małgorzata Kimsa-Furdzik
- b Department of Biochemistry, School of Medicine in Katowice , Medical University of Silesia , Katowice , Poland
| | - Tomasz Francuz
- b Department of Biochemistry, School of Medicine in Katowice , Medical University of Silesia , Katowice , Poland
| | - Marek Hartleb
- a Department of Gastroenterology and Hepatology , School of Medicine in Katowice, Medical University of Silesia , Katowice , Poland
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25
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Zhang C, Chen B, Jiao A, Li F, Sun N, Zhang G, Zhang J. miR-663a inhibits tumor growth and invasion by regulating TGF-β1 in hepatocellular carcinoma. BMC Cancer 2018; 18:1179. [PMID: 30486878 PMCID: PMC6264054 DOI: 10.1186/s12885-018-5016-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 10/30/2018] [Indexed: 12/23/2022] Open
Abstract
Background The dysregulation of miR-663a is frequently observed in many human cancers. However, the functional role and precise mechanism of miR-663a have been controversial in hepatocellular carcinoma (HCC) and need to be studied in depth. Methods The expression of miR-663a was detected in human cell lines and HCC tissues by quantitative RT-PCR (qRT-PCR), and data from the Cancer Genome Atlas (TCGA). Cell proliferation was investigated using MTS, EdU, colony formation assays, and xenograft animal experiments, and the cell invasion capacity was evaluated using the transwell assay. The target gene of miR-663a was identified by qRT-PCR, Western blot, and dual-luciferase reporter assays. The clinicopathological features of miR-663a and the correlation between miR-663a and TGF-β1 expression were also investigated in the clinical samples of HCC. Results miR-663a was significantly downregulated in HCC cells relative to immortal normal liver cells, as indicated using qRT-PCR, and the lower expression of miR-663a was also confirmed in HCC tissue samples and the data from TCGA. The expression of miR-663a in HCC tissue samples was statistically significantly associated with size and the number of tumors. In addition, the upregulation of miR-663a inhibited the proliferation and invasion of HCC cells in vitro. Further study showed that miR-663a directly targeted transforming growth factor beta 1 (TGF-β1) to suppress HCC invasion, and that the inhibitory effect of miR-663a on cell invasion could be regulated by TGF-β1. In vivo studies showed that miR-663a significantly inhibited tumor growth. A negative correlation between miR-663a and TGF-β1 expression was also confirmed from the clinical samples of HCC. Conclusions miR-663a acts as a tumor suppressor and exerts a substantial role in inhibiting the proliferation, invasion, and tumorigenesis of HCC by regulating TGF-β1 in vitro and in vivo. These observations indicate that miR-663a may be a suitable diagnostic, therapeutic, and prognostic target for the treatment of HCC. Electronic supplementary material The online version of this article (10.1186/s12885-018-5016-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chengshuo Zhang
- Hepatobiliary Surgery Department and Unit of Organ Transplantation, The First Hospital of China Medical University, 155#, Nanjingbei street, Heping district, Shenyang, Liaoning, People's Republic of China
| | - Baomin Chen
- Hepatobiliary Surgery Department, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510000, People's Republic of China
| | - Ao Jiao
- Hepatobiliary Surgery Department and Unit of Organ Transplantation, The First Hospital of China Medical University, 155#, Nanjingbei street, Heping district, Shenyang, Liaoning, People's Republic of China
| | - Feng Li
- Hepatobiliary Surgery Department and Unit of Organ Transplantation, The First Hospital of China Medical University, 155#, Nanjingbei street, Heping district, Shenyang, Liaoning, People's Republic of China
| | - Ning Sun
- Hepatobiliary Surgery Department and Unit of Organ Transplantation, The First Hospital of China Medical University, 155#, Nanjingbei street, Heping district, Shenyang, Liaoning, People's Republic of China
| | - Guoqing Zhang
- Hepatobiliary Surgery Department, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, People's Republic of China
| | - Jialin Zhang
- Hepatobiliary Surgery Department and Unit of Organ Transplantation, The First Hospital of China Medical University, 155#, Nanjingbei street, Heping district, Shenyang, Liaoning, People's Republic of China.
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26
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Jadideslam G, Ansarin K, Sakhinia E, Alipour S, Pouremamali F, Khabbazi A. The MicroRNA-326: Autoimmune diseases, diagnostic biomarker, and therapeutic target. J Cell Physiol 2018; 233:9209-9222. [PMID: 30078204 DOI: 10.1002/jcp.26949] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 06/13/2018] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are uniquely regulated in healthy, inflamed, activated, cancerous, or other cells and tissues of a pathological state. Many studies confirm that immune dysregulation and autoimmune diseases with inflammation are correlated with various miRNA expression changes in targeted tissues and cells in innate or adaptive immunity. In this review, we will explain the history and classification of epigenetic changes. Next, we will describe the role of miRNAs changes, especially mir-326 in autoimmunity, autoinflammatory, and other pathological conditions. A systematic search of MEDLINE, Embase, and Cochrane Library was presented for all related studies from 1899 to 2017 with restrictions in the English language. In recent years, researchers have concentrated on mostly those roles of miRNA that are correlated with the inflammatory and anti-inflammatory process. Latest studies have proposed a fundamental pathogenic role in cancers and autoinflammatory diseases. Studies have described the role of microRNAs in autoimmunity and autoinflammatory diseases, cancers, and so on. The miRNA-326 expression plays a significant role in autoimmune and other types of diseases.
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Affiliation(s)
- Golamreza Jadideslam
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran.,Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Iran
| | - Khalil Ansarin
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Sakhinia
- Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran.,Department of Medical Genetics, Faculty of Medicine and Tabriz Genetic Analysis Centre (TGAC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahriar Alipour
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran
| | - Farhad Pouremamali
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Khabbazi
- Connective Tissue Diseases Research Center, Tabriz University of Medical Science, Iran
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Zhang H, Wang Z, Ma R, Wu J, Feng J. MicroRNAs as biomarkers for the progression and prognosis of colon carcinoma. Int J Mol Med 2018; 42:2080-2088. [PMID: 30066832 PMCID: PMC6108873 DOI: 10.3892/ijmm.2018.3792] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022] Open
Abstract
Early detection is critical for the treatment of colon carcinoma. However, current biomarkers for its diagnosis and prognosis are insufficient and improvement is required. Aberrantly expressed microRNAs (miRNAs/miRs) in colon carcinoma have been identified to function as potential diagnostic and prognostic biomarkers. In the present study, 245 differentially expressed miRNAs between colon carcinoma and normal tissues were identified by a bioinformatics analysis of a dataset from The Cancer Genome Atlas. A six-miRNA (miR-149, miR-3189, miR-3677, miR-3917, miR-4999 and miR-6854) prognostic prediction system was established, which is able to independently and effectively predict the prognosis of colon carcinoma patients [P<0.001, area under the receiver operating characteristic curve (AUC)=0.763]. Furthermore, the six miRNAs were highly correlated with the tumor-nodes-metastasis (TNM) stage and were able to distinguish between different stages (high vs. low TNM stage, P<0.001). Of note, combination of the six-miRNA signature and TNM stage provides an improved prediction of the patient's prognosis (AUC=0.797). Functional enrichment analysis revealed the possible mechanistic involvement of these predictive miRNAs in cancer-associated biological processes and pathways. Taken together, the present study demonstrated the promising potential of the novel six-miRNA model as an independent factor for the prediction of the progression and prognosis of colon carcinoma.
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Affiliation(s)
- Hui Zhang
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
| | - Zhuo Wang
- Laboratory of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
| | - Rong Ma
- Laboratory of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
| | - Jianzhong Wu
- Laboratory of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
| | - Jifeng Feng
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing, Jiangsu 210000, P.R. China
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28
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Gao C, Zhou C, Zhuang J, Liu L, Liu C, Li H, Liu G, Wei J, Sun C. MicroRNA expression in cervical cancer: Novel diagnostic and prognostic biomarkers. J Cell Biochem 2018; 119:7080-7090. [PMID: 29737570 DOI: 10.1002/jcb.27029] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/06/2018] [Indexed: 12/31/2022]
Abstract
Growing evidence has shown that a large number of miRNAs are abnormally expressed in cervical cancer (CC) tissues and play irreplaceable roles in tumorigenesis, progression, and metastasis. This study aimed to identify new biomarkers and pivotal genes associated with CC prognosis through comprehensive bioinformatics analysis. At first, the data of gene expression microarray (GSE30656) was downloaded from GEO database and differential miRNAs were obtained. Additionally, 4 miRNAs associated with the survival time of patients with CC were screened through TCGA differential data analysis, Kaplan-Meier, and Landmark analysis. Among them, the low expression of miR-188 and high expression of miR-223 correlated with the short survival of CC patients, while the down-regulation of miR-99a and miR-125b was closely related to the 5-year survival rate of patients. Then, based on the correspondence between the differentially expressed genes (DEGs) in CC from the TCGA data and the 4 miRNAs target genes, 58 target genes were screened to perform the analysis of function enrichment and the visualization of protein-protein interaction (PPI) networks. The seven pivotal genes of the PPI network as the target genes of four miRNAs related to prognosis, they were directly or indirectly involved in the development of CC. In this study, based on high-throughput data mining, differentially expressed miRNAs and related target genes were analyzed to provide an effective bioinformatics basis for further understanding of the pathogenesis and prognosis of CC. And the results may be a promising biomarker for the early screening of high-risk populations and early diagnosis of cervical cancer.
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Affiliation(s)
- Chundi Gao
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Chao Zhou
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Jing Zhuang
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Lijuan Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Cun Liu
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Huayao Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, P. R. China
| | - Gongxi Liu
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Junyu Wei
- Departmen of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong, P. R. China.,Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
| | - Changgang Sun
- Department of Oncology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong, P. R. China
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29
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Yang Y, Lu Q, Shao X, Mo B, Nie X, Liu W, Chen X, Tang Y, Deng Y, Yan J. Development Of A Three-Gene Prognostic Signature For Hepatitis B Virus Associated Hepatocellular Carcinoma Based On Integrated Transcriptomic Analysis. J Cancer 2018; 9:1989-2002. [PMID: 29896284 PMCID: PMC5995946 DOI: 10.7150/jca.23762] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/14/2018] [Indexed: 02/07/2023] Open
Abstract
Integration of public genome-wide gene expression data together with Cox regression analysis is a powerful weapon to identify new prognostic gene signatures for cancer diagnosis and prognosis. Hepatitis B virus (HBV) is a major cause of hepatocellular carcinoma (HCC), however, it remains largely unknown about the specific gene prognostic signature of HBV-associated HCC. Using Robust Rank Aggreg (RRA) method to integrate seven whole genome expression datasets, we identified 82 up-regulated genes and 577 down-regulated genes in HBV-associated HCC patients. Combination of several enrichment analysis, univariate and multivariate Cox proportional hazards regression analysis, we revealed that a three-gene (SPP2, CDC37L1, and ECHDC2) prognostic signature could act as an independent prognostic indicator for HBV-associated HCC in both the discovery cohort and the internal testing cohort. Gene set enrichment analysis showed that the high-risk group with lower expression levels of the three genes was enriched in bladder cancer and cell cycle pathway, whereas the low-risk group with higher expression levels of the three genes was enriched in drug metabolism-cytochrome P450, PPAR signaling pathway, fatty acid and histidine metabolisms. This indicates that patients of HBV-associated HCC with higher expression of these three genes may preserve relatively good hepatic cellular metabolism and function, which may also protect HCC patients from persistent drug toxicity in response to various medication. Our findings suggest a three-gene prognostic model that serves as a specific prognostic signature for HBV-associated HCC.
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Affiliation(s)
- Yao Yang
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Qian Lu
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing 102218, China
| | - Xuejun Shao
- Brigade 315th of Territorial Defense Force, Chinese People's Liberation Army Ground Force, Xishuangbanna District, Yunan 666200, China
| | - Banghui Mo
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Xuqiang Nie
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Wei Liu
- Health Physical Examination Center, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Xianhua Chen
- Diagnosis and Treatment Center for Servicemen, Southwest Hospital, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Yuan Tang
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Youcai Deng
- Institute of Materia Medica, College of Pharmacy, Army Medical University (Third Military Medical University), Chongqing 400038, China
| | - Jun Yan
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing 102218, China.,Institute of Hepatobiliary Surgery, Southwest Hospital, Third Military Medical University, Chongqing 400042, China
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Liao X, Zhu G, Huang R, Yang C, Wang X, Huang K, Yu T, Han C, Su H, Peng T. Identification of potential prognostic microRNA biomarkers for predicting survival in patients with hepatocellular carcinoma. Cancer Manag Res 2018; 10:787-803. [PMID: 29713196 PMCID: PMC5912208 DOI: 10.2147/cmar.s161334] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background The aim of the present study was to identify potential prognostic microRNA (miRNA) biomarkers for hepatocellular carcinoma (HCC) prognosis prediction based on a dataset from The Cancer Genome Atlas (TCGA). Materials and methods A miRNA sequencing dataset and corresponding clinical parameters of HCC were obtained from TCGA. Genome-wide univariate Cox regression analysis was used to screen prognostic differentially expressed miRNAs (DEMs), and multivariable Cox regression analysis was used for prognostic signature construction. Comprehensive survival analysis was performed to evaluate the prognostic value of the prognostic signature. Results Five miRNAs were regarded as prognostic DEMs and used for prognostic signature construction. The five-DEM prognostic signature performed well in prognosis prediction (adjusted P < 0.0001, adjusted hazard ratio = 2.249, 95% confidence interval =1.491-3.394), and time-dependent receiver-operating characteristic (ROC) analysis showed an area under the curve (AUC) of 0.765, 0.745, 0.725, and 0.687 for 1-, 2-, 3-, and 5-year HCC overall survival (OS) prediction, respectively. Comprehensive survival analysis of the prognostic signature suggests that the risk score model could serve as an independent factor of HCC and perform better in prognosis prediction than other traditional clinical indicators. Functional assessment of the target genes of hsa-mir-139 and hsa-mir-5003 indicates that they were significantly enriched in multiple biological processes and pathways, including cell proliferation and cell migration regulation, pathways in cancer, and the cyclic adenosine monophosphate (cAMP) signaling pathway. Conclusion Our study indicates that the novel miRNA expression signature may be a potential prognostic biomarker for HCC patients.
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Affiliation(s)
- Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Chengkun Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Ketuan Huang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Tingdong Yu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Chuangye Han
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Hao Su
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
| | - Tao Peng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, People's Republic of China
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Sun H, Shao Y, Huang J, Sun S, Liu Y, Zhou P, Yang H. Prognostic value of microRNA-9 in cancers: a systematic review and meta-analysis. Oncotarget 2018; 7:67020-67032. [PMID: 27563807 PMCID: PMC5341854 DOI: 10.18632/oncotarget.11466] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 08/08/2016] [Indexed: 12/28/2022] Open
Abstract
Recent studies revealed that different microRNA-9 (miR-9) expressions were associated with prognoses of different cancers. We conducted this meta-analysis to evaluate the prognostic value of miR-9. PubMed, Embase, Web of Science, and Cochrane Library (last update by November 30, 2015) were searched for literatures. A total of 17 studies from 16 articles were finally qualified and enrolled in this meta-analysis. Pooled analyses showed that a higher expression of miR-9 might predict poor overall survival (HR: 2.17, 95% CI: 1.39 – 3.41, P < 0.001 (7.23 * 10−4)), disease-free survival (HR: 5.22, 95% CI: 2.17 – 12.53, P < 0.001 (2.21 * 10−4)), and recurrence-free survival (HR: 1.57, 95% CI: 1.32 – 1.85, P < 0.001 (1.80*10−7)) in various carcinomas. However, results of subgroup analyses revealed that down-regulated miR-9 was associated with poor overall survival (HR: 0.45, 95% CI: 0.28 – 0.73, P < 0.001 (1.13*10−3)) and progress-free survival (HR: 0.46, 95% CI: 0.34 – 0.62, P < 0.001 (5.03*10−7)) in ovarian cancer patients. By subgroup analyses we also found that sample collecting time and patients’ origin had little influence on the result of OS. These results indicate that in most cancer types the highly expressed miR-9 is associated with poor survival of patients, whereas the down-regulated miR-9 may predict poor prognosis in patients with ovarian cancer.
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Affiliation(s)
- Han Sun
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, P.R. China
| | - Yingjie Shao
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R. China
| | - Jin Huang
- Department of Radiation Oncology, The Third Affiliated Hospital of Soochow University, Changzhou, 213003, P.R. China
| | - Siwei Sun
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, P.R. China
| | - Yijie Liu
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, P.R. China
| | - Pinghui Zhou
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, P.R. China
| | - Huilin Yang
- Department of Orthopedic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215006, P.R. China
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Gao X, Wu Y, Yu W, Li H. Identification of a seven-miRNA signature as prognostic biomarker for lung squamous cell carcinoma. Oncotarget 2018; 7:81670-81679. [PMID: 27835574 PMCID: PMC5348421 DOI: 10.18632/oncotarget.13164] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 10/19/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Specific biomarkers for outcome prediction of lung squamous cell carcinoma (LUSC) are still lacking. This study assessed the prognostic value of differentially expressed miRNAs of LUSC patients. RESULTS Twelve of the 133 most significantly altered miRNAs were associated with overall survival (OS) across different clinical subclasses of the Cancer Genome Atlas (TCGA) LUSC cohort. A linear prognostic model of seven miRNAs was developed to divide patients into high- and low-risk groups. Patients assigned to the high-risk group exhibited poor OS compared with patients in the low-risk group, which was further validated in the validation cohort and entire LUSC cohort. METHODS MiRNA expression profiles with clinical information of 447 LUSC patients were obtained from TCGA. Most significantly altered miRNAs were identified between tumor and normal samples. Using survival analysis and supervised principal components method, a seven-miRNA signature for prediction of OS of LUSC patients was established. Survival receiver operating characteristic (ROC) analysis was used to assess the performance of survival prediction. The biological relevance of predicted miRNA targets was also analyzed using bioinformatics method. CONCLUSIONS The current study suggests that seven-miRNA signature may have clinical implications in the outcome prediction of LUSC.
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Affiliation(s)
- Xujie Gao
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Yupeng Wu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Wenwen Yu
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
| | - Hui Li
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,Department of Gastrointestinal Cancer Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.,National Clinical Research Center of Cancer, Tianjin, China.,Key Laboratory of Cancer Immunology and Biotherapy, Tianjin, China
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33
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Jin X, Feng CY, Xiang Z, Chen YP, Li YM. CircRNA expression pattern and circRNA-miRNA-mRNA network in the pathogenesis of nonalcoholic steatohepatitis. Oncotarget 2018; 7:66455-66467. [PMID: 27677588 PMCID: PMC5341813 DOI: 10.18632/oncotarget.12186] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 08/31/2016] [Indexed: 02/06/2023] Open
Abstract
The pathogenesis of nonalcoholic steatohepatitis (NASH) is still unclear, where involvement of circRNA is considered for its active role as “miRNA sponge”. Therefore, we aimed to investigate the circRNA expression pattern in NASH and further construct the circRNA-miRNA-mRNA network for in-depth mechanism exploration. Briefly, NASH mice model was established by Methionine and choline deficiency (MCD) diet feeding. Liver circRNA and mRNA profile was initially screened by microarray and ensuing qRT-PCR verification was carried out. The overlapped predicted miRNAs as downstream targets of circRNAs and upstream regulators of mRNAs were verified by qRT-PCR and final circRNA-miRNA-mRNA network was constructed. Gene Ontology (GO) and KEGG pathway analysis were further applied to enrich the huge mRNA microarray data. To sum up, there were 69 up and 63 down regulated circRNAs as well as 2760 up and 2465 down regulated mRNAs in NASH group, comparing with control group. Randomly selected 13 of 14 mRNAs and 2 of 8 circRNAs were successfully verified by qRT-PCR. Through predicted overlapped miRNA verification, four circRNA-miRNA-mRNA pathways were constructed, including circRNA_002581-miR-122-Slc1a5, circRNA_002581- miR-122-Plp2, circRNA_002581-miR-122-Cpeb1 and circRNA_007585-miR-326- UCP2. GO and KEGG pathway analysis also enriched specific mRNAs. Therefore, circRNA profile may serve as candidate for NASH diagnosis and circRNA-miRNA -mRNA pathway may provide novel mechanism for NASH.
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Affiliation(s)
- Xi Jin
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chun-Yan Feng
- Department of Clinical Medicine, Hangzhou Medical College, Hangzhou, China
| | - Zun Xiang
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yi-Peng Chen
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - You-Ming Li
- Department of Gastroenterology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Hu J, Li P, Song Y, Ge YX, Meng XM, Huang C, Li J, Xu T. Progress and prospects of circular RNAs in Hepatocellular carcinoma: Novel insights into their function. J Cell Physiol 2017; 233:4408-4422. [PMID: 28833094 DOI: 10.1002/jcp.26154] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most predominant subjects of liver malignancies, which arouses global concern in the recent years. Advanced studies have found that Circular RNAs (circRNAs) are differentially expressed in HCC, with its regulatory capacity in HCC pathogenesis and metastasis. However, the underlying mechanism remains largely unknown. In this review, we summarized the functions and mechanisms of those aberrantly expressed circRNAs in HCC tissues. We hope to enlighten more comprehensive studies on the detailed mechanisms of circRNAs and explore their potential values in clinic applications. It revealed that hsa_circ_0004018 can be used as a potential biomarker in HCC diagnosis, with its superior sensitivity to alpha-fetoprotein (AFP). Notably, the correlation of circRNA abundance in the proliferation of liver regeneration (LR) has recently been clarified and different circRNA profiles served as candidates for nonalcoholic steatohepatitis (NASH) diagnosis also be discussed. Therefore, the improved understanding of circRNAs in HCC pathogenesis and metastasis proposed a novel basis for the early diagnosis in HCC patients, which provides a useful resource to explore the pathogenesis of HCC.
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Affiliation(s)
- Ji Hu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Peng Li
- Department of Medical, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yang Song
- Department of Pain treatment, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yun-Xuan Ge
- Beijing Institute of Radiation Medicine, Academy of Military Medical Sciences, Beijing, China
| | - Xiao-Ming Meng
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Cheng Huang
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Jun Li
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, China.,Institute for Liver Diseases of Anhui Medical University, Anhui Medical University, Hefei, China
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35
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Prognostic value of microRNAs in hepatocellular carcinoma: a meta-analysis. Oncotarget 2017; 8:107237-107257. [PMID: 29291025 PMCID: PMC5739810 DOI: 10.18632/oncotarget.20883] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 08/29/2017] [Indexed: 12/20/2022] Open
Abstract
Background Numerous articles reported that dysregulated expression levels of miRNAs correlated with survival time of HCC patients. However, there has not been a comprehensive meta-analysis to evaluate the accurate prognostic value of miRNAs in HCC. Design Meta-analysis. Materials and Methods Studies, published in English, estimating expression levels of miRNAs with any survival curves in HCC were identified up until 15 April, 2017 by performing online searches in PubMed, EMBASE, Web of Science and Cochrane Database of Systematic Reviews by two independent authors. The pooled hazard ratios (HR) with 95% confidence intervals (CI) were used to estimate the correlation between miRNA expression and overall survival (OS). Results 54 relevant articles about 16 miRNAs, with 6464 patients, were ultimately included. HCC patients with high expression of tissue miR-9 (HR = 2.35, 95% CI = 1.46–3.76), miR-21 (HR = 1.76, 95% CI = 1.29–2.41), miR-34c (HR = 1.64, 95% CI = 1.05–2.57), miR-155 (HR = 2.84, 95% CI = 1.46–5.51), miR-221 (HR = 1.76, 95% CI = 1.02–3.04) or low expression of tissue miR-22 (HR = 2.29, 95% CI = 1.63–3.21), miR-29c (HR = 1.35, 95% CI = 1.10–1.65), miR-34a (HR = 1.84, 95% CI = 1.30–2.59), miR-199a (HR = 2.78, 95% CI = 1.89–4.08), miR-200a (HR = 2.64, 95% CI = 1.86–3.77), miR-203 (HR = 2.20, 95% CI = 1.61–3.00) have significantly poor OS (P < 0.05). Likewise, HCC patients with high expression of blood miR-21 (HR = 1.73, 95% CI = 1.07–2.80), miR-192 (HR = 2.42, 95% CI = 1.15–5.10), miR-224 (HR = 1.56, 95% CI = 1.14–2.12) or low expression of blood miR-148a (HR = 2.26, 95% CI = 1.11–4.59) have significantly short OS (P < 0.05). Conclusions In conclusion, tissue miR-9, miR-21, miR-22, miR-29c, miR-34a, miR-34c, miR-155, miR-199a, miR-200a, miR-203, miR-221 and blood miR-21, miR-148a, miR-192, miR-224 demonstrate significantly prognostic value. Among them, tissue miR-9, miR-22, miR-155, miR-199a, miR-200a, miR-203 and blood miR-148a, miR-192 are potential prognostic candidates for predicting OS in HCC.
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36
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Zhang SQ, Yang Z, Cai XL, Zhao M, Sun MM, Li J, Feng GX, Feng JY, Ye LH, Niu JQ, Zhang XD. miR-511 promotes the proliferation of human hepatoma cells by targeting the 3'UTR of B cell translocation gene 1 (BTG1) mRNA. Acta Pharmacol Sin 2017; 38:1161-1170. [PMID: 28603285 DOI: 10.1038/aps.2017.62] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 02/27/2017] [Indexed: 12/17/2022] Open
Abstract
Aberrant expression of miR-511 is involved in the development of cancer, but the role of miR-511 in hepatocellular carcinoma (HCC) is not well documented. In this study, we explored the molecular mechanisms of miR-511 in hepatocarcinogenesis. Our results of bioinformatics analysis suggested that B cell translocation gene 1 (BTG1), a member of anti-proliferative gene family, was one of the putative targets of miR-511. The expression levels of miR-511 were significantly higher in 30 clinical HCC tissues than in corresponding peritumor tissues, and were negatively correlated with those of BTG1 in the HCC tissues (r=-0.6105, P<0.01). In human hepatoma cell lines HepG2 and H7402, overexpression of miR-511 dose-dependently inhibited the expression of BTG1, whereas knockdown of miR-511 dose-dependently increased the expression of BTG1. Luciferase reporter gene assays verified that miR-511 targeted the 3'UTR of BTG1 mRNA. In the hepatoma cells, overexpression of miR-511 significantly decreased BTG1-induced G1 phase arrest, which was rescued by overexpression of BTG1. Furthermore, overexpression of miR-511 promoted the proliferation of the hepatoma cells, which was rescued by overexpression of BTG1. Conversely, knockdown of miR-511 inhibited cell proliferation, which was reversed by knockdown of BTG1. In conclusion, miR-511 promotes the proliferation of human hepatoma cells in vitro by targeting the 3'UTR of BTG1 mRNA.
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37
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Li B, Feng W, Luo O, Xu T, Cao Y, Wu H, Yu D, Ding Y. Development and Validation of a Three-gene Prognostic Signature for Patients with Hepatocellular Carcinoma. Sci Rep 2017; 7:5517. [PMID: 28717245 PMCID: PMC5514049 DOI: 10.1038/s41598-017-04811-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/19/2017] [Indexed: 12/25/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the leading cause of cancer-related death worldwide, because recurrence often occurs in most HCC patients undergoing hepatectomy. It is necessary to identify patients with high risk for recurrence and adopt effective therapies. An obstacle to monitor patients at high risk for poor prognosis has been the lack of useful predictive biomarkers. Fortunately, recent progress in system biology allows to screen the biomarkers for HCC prognosis in a high-throughput manner. In this study, we performed systematic Kaplan-Meier survival analysis of the whole mRNA transcriptomics based on the Cancer Genome Atlas project (TCGA) and developed a three-gene prognostic signature composing of three genes UPB1, SOCS2 and RTN3. The model was validated in two independent microarray data sets retrieved from Gene Expression Omnibus (GEO) and the expression pattern of these three predictive genes in HCC was confirmed by western blot and immunohistochemistry with our HCC samples. In conclusion, our results showed that this three-gene signature has prognostic value for HCC patients.
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Affiliation(s)
- Binghua Li
- Department of Hepatobiliary Surgery, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China
| | - Wendu Feng
- Department of Hepatobiliary Surgery, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China
| | - Ouyang Luo
- Department of Hepatobiliary Surgery, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China
| | - Tiancheng Xu
- Department of Hepatobiliary Surgery, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China
| | - Yajuan Cao
- Department of Hepatobiliary Surgery, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China
| | - Hongyan Wu
- Department of Pathology, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China
| | - Decai Yu
- Department of Hepatobiliary Surgery, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China.
| | - Yitao Ding
- Department of Hepatobiliary Surgery, the Affliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, 210093, China.
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Choi M, Min YH, Pyo J, Lee CW, Jang CY, Kim JE. TC Mps1 12, a novel Mps1 inhibitor, suppresses the growth of hepatocellular carcinoma cells via the accumulation of chromosomal instability. Br J Pharmacol 2017; 174:1810-1825. [PMID: 28299790 DOI: 10.1111/bph.13782] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 03/01/2017] [Accepted: 03/05/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND AND PURPOSE Chromosomal instability is not only a hallmark of cancer but also an attractive therapeutic target. A diverse set of mitotic kinases maintains chromosomal stability. One of these is monopolar spindle 1 (Mps1, also known as TTK), which is essential for chromosome alignment and for the spindle assembly checkpoint (SAC). Pharmacological inhibition of Mps1 has been suggested as a cancer therapeutic; however, despite the existence of a novel Mps1 inhibitor, TC Mps1 12, no such studies have been performed. EXPERIMENTAL APPROACH The effects of TC Mps1 12 on cell viability, chromosome alignment, centrosome number, mitotic duration, apoptosis and SAC were determined in hepatocellular carcinoma (HCC) cells. In addition, the association of Mps1 expression with the overall survival of HCC patients was analysed. KEY RESULTS Treatment of human HCC cells with TC Mps1 12 led to chromosome misalignment and missegregation, and disorganization of centrosomes. Even in the presence of these errors, TC Mps1 12-treated cells overrode the SAC, resulting in a shortened mitotic duration and mitotic slippage. This mitotic catastrophe triggered apoptosis and, finally, inhibited the growth of HCC cells. In addition, the expression of the Mps1-encoding TTK gene was associated with poor overall survival of HCC patients. CONCLUSION AND IMPLICATIONS TC Mps1 12 results in the accumulation of chromosomal instabilities and mitotic catastrophe in HCC cells. Overall, these data demonstrate that the inhibition of Mps1 kinase using TC Mps1 12 is a promising therapeutic approach for liver cancer.
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Affiliation(s)
- Minji Choi
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Yoo Hong Min
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Jaehyuk Pyo
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, School of Medicine, Sungkyunkwan University, Suwon, Republic of Korea
| | - Chang-Young Jang
- College of Pharmacy, Sookmyung Women's University, Seoul, Republic of Korea
| | - Ja-Eun Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea.,East-West Medical Research Institute, Kyung Hee University, Seoul, Republic of Korea.,Department of Pharmacology, School of Medicine, Kyung Hee University, Seoul, Republic of Korea
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39
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Zhen Y, Xinghui Z, Chao W, Yi Z, Jinwen C, Ruifang G, Chao Z, Min Z, Chunlei G, Yan F, Lingfang D, Long S, Wenzhi S, Xiaohe L, Rong X. Several microRNAs could predict survival in patients with hepatitis B-related liver cancer. Sci Rep 2017; 7:45195. [PMID: 28322348 PMCID: PMC5359660 DOI: 10.1038/srep45195] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 02/20/2017] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs as biomarkers play an important role in the tumorigenesis process, including hepatocellular carcinomas (HCCs). In this paper, we used The Cancer Genome Atlas (TCGA) database to mine hepatitis B-related liver cancer microRNAs that could predict survival in patients with hepatitis B-related liver cancer. There were 93 cases of HBV-HCC and 49 cases of adjacent normal controls included in the study. Kaplan–Meier survival analysis of a liver cancer group versus a normal control group of differentially expressed genes identified eight genes with statistical significance. Compared with the normal liver cell line, hepatocellular carcinoma cell lines had high expression of 8 microRNAs, albeit at different levels. A Cox proportional hazards regression model for multivariate analysis showed that four genes had a significant difference. We established classification models to distinguish short survival time and long survival time of liver cancers. Eight genes (mir9-3, mir10b, mir31, mir519c, mir522, mir3660, mir4784, and mir6883) were identified could predict survival in patients with HBV-HCC. There was a significant correlation between mir10b and mir31 and clinical stages (p < 0.05). A random forests model effectively estimated patient survival times.
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Affiliation(s)
- Ye Zhen
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China.,School of public health, Taishan Medical University, Tai'an 271016, China.,Department of Infectious Disease, Tai'an Central Hospital, Tai'an 271000, China
| | - Zhao Xinghui
- Laboratory of Vaccine and Antibody Engineering, Beijing Institute of Biotechnology, Beijing 100071, China
| | - Wu Chao
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Zhao Yi
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Chen Jinwen
- Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Gao Ruifang
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Zhang Chao
- College of Information Science and Engineering, Shandong Agriculture University, Tai'an 271000, China
| | - Zhao Min
- Department of Infectious Disease, Tai'an Central Hospital, Tai'an 271000, China
| | - Guo Chunlei
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Fang Yan
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Du Lingfang
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Shen Long
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Shen Wenzhi
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Luo Xiaohe
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China
| | - Xiang Rong
- Department of Tumor Molecular Biology, Nankai University School of Medicine, Tianjin 371000, China.,The 2011 Project Collaborative Innovation Center for Biological Therapy, Nankai University School of Medicine, Tianjin 371000, China.,The International Collaborative Laboratory for Biological Medicine of the Ministry of Education, Nankai University School of Medicine, Tianjin 371000, China
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40
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Yang H, Zhang X, Cai XY, Wen DY, Ye ZH, Liang L, Zhang L, Wang HL, Chen G, Feng ZB. From big data to diagnosis and prognosis: gene expression signatures in liver hepatocellular carcinoma. PeerJ 2017; 5:e3089. [PMID: 28316892 PMCID: PMC5354077 DOI: 10.7717/peerj.3089] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 02/12/2017] [Indexed: 01/27/2023] Open
Abstract
Background Liver hepatocellular carcinoma accounts for the overwhelming majority of primary liver cancers and its belated diagnosis and poor prognosis call for novel biomarkers to be discovered, which, in the era of big data, innovative bioinformatics and computational techniques can prove to be highly helpful in. Methods Big data aggregated from The Cancer Genome Atlas and Natural Language Processing were integrated to generate differentially expressed genes. Relevant signaling pathways of differentially expressed genes went through Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes and Panther pathway enrichment analysis and protein-protein interaction network. The pathway ranked high in the enrichment analysis was further investigated, and selected genes with top priority were evaluated and assessed in terms of their diagnostic and prognostic values. Results A list of 389 genes was generated by overlapping genes from The Cancer Genome Atlas and Natural Language Processing. Three pathways demonstrated top priorities, and the one with specific associations with cancers, ‘pathways in cancer,’ was analyzed with its four highlighted genes, namely, BIRC5, E2F1, CCNE1, and CDKN2A, which were validated using Oncomine. The detection pool composed of the four genes presented satisfactory diagnostic power with an outstanding integrated AUC of 0.990 (95% CI [0.982–0.998], P < 0.001, sensitivity: 96.0%, specificity: 96.5%). BIRC5 (P = 0.021) and CCNE1 (P = 0.027) were associated with poor prognosis, while CDKN2A (P = 0.066) and E2F1 (P = 0.088) demonstrated no statistically significant differences. Discussion The study illustrates liver hepatocellular carcinoma gene signatures, related pathways and networks from the perspective of big data, featuring the cancer-specific pathway with priority, ‘pathways in cancer.’ The detection pool of the four highlighted genes, namely BIRC5, E2F1, CCNE1 and CDKN2A, should be further investigated given its high evidence level of diagnosis, whereas the prognostic powers of BIRC5 and CCNE1 are equally attractive and worthy of attention.
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Affiliation(s)
- Hong Yang
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xin Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Xiao-Yong Cai
- Department of General Surgery, First Affiliated Hospital of Guangxi Medical University (West Branch), Nanning, Guangxi, China
| | - Dong-Yue Wen
- Department of Ultrasonography, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhi-Hua Ye
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Liang Liang
- Department of General Surgery, First Affiliated Hospital of Guangxi Medical University (West Branch), Nanning, Guangxi, China
| | - Lu Zhang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Han-Lin Wang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
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Cao W, Liu JN, Liu Z, Wang X, Han ZG, Ji T, Chen WT, Zou X. A three-lncRNA signature derived from the Atlas of ncRNA in cancer (TANRIC) database predicts the survival of patients with head and neck squamous cell carcinoma. Oral Oncol 2017; 65:94-101. [PMID: 28109476 DOI: 10.1016/j.oraloncology.2016.12.017] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 11/12/2016] [Accepted: 12/17/2016] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Long non-coding RNAs (lncRNAs) have important biological functions and can be used as prognostic biomarkers in cancer. To identify a lncRNA prognostic signature for head and neck squamous cell carcinoma (HNSCC). METHOD We analysed RNA-seq data derived from the TANRIC database to identify a lncRNA prognostic signature model using the orthogonal partial least squares discrimination analysis (OPLS-DA) and 1.5-fold expression change criterion methods. The prognosis prediction model based on the lncRNA signatures and clinical parameters were evaluated using the 5-fold cross validation method. RESULTS A total of 84 out of 3199 lncRNAs were significantly associated with the survival of patients with HNSCC (log-rank test P<0.01). Using the OPLS-DA and 1.5-fold change selection criterion, 5 lncRNAs (KTN1-AS1, LINC00460, GUSBP11, LINC00923 and RP5-894A10.6) were further selected. The prediction power of each combination of the 5 lncRNAs was evaluated through the receiver operating characteristic (ROC) curve and a three-lncRNA panel (KTN1-AS1, LINC00460 and RP5-894A10.6) achieved the highest prognostic prediction power (AUC 0.68, 95% CI 0.60-0.76, P<0.0001) in the cohort. The patients were categorized into high- and low-risk groups based on their three-lncRNA profiles. Patients with high-risk scores had worse overall survival than those with low risk scores in the cohort (log-rank test P=0.0003). Multivariable Cox regression analyses showed that the lncRNA signature and tumour grade were independent prognostic factors for patients with HNSCC. CONCLUSIONS Our findings showed that the three-lncRNA signature might be a novel biomarker for the accurate prognosis prediction of patients with HNSCC.
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Affiliation(s)
- Wei Cao
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Jian-Nan Liu
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Zeqi Liu
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Xu Wang
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China
| | - Ze-Guang Han
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Tong Ji
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
| | - Wan-Tao Chen
- Department of Oral Maxillofacial-Head and Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China; Shanghai Key Laboratory of Stomatology, Shanghai 200011, China.
| | - Xin Zou
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China.
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Fang Z, Zhang L, Liao Q, Wang Y, Yu F, Feng M, Xiang X, Xiong J. Regulation of TRIM24 by miR-511 modulates cell proliferation in gastric cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:17. [PMID: 28114950 PMCID: PMC5259882 DOI: 10.1186/s13046-017-0489-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/05/2017] [Indexed: 12/20/2022]
Abstract
Background Increasing evidence highlights the important roles of tripartite motif containing 24 (TRIM24) in tumor initiation and malignant progression in many tumors, including gastric cancer (GC). Although TRIM24 expression is remarkably upregulated during GC carcinogenesis, the molecular mechanisms underlying TRIM24 dysregulation remain unexplored. Methods In this study, miRNA target prediction tools were applied to explore miRNAs that potentially target TRIM24. Western blot and quantitative reverse-transcriptase PCR (qRT-PCR) were performed to detected TRIM24 and miR-511 expression in GC tissues and cell lines. Dual-luciferase reporter assay was utilized to validate if TRIM24 is a direct target gene of miR-511. CCK-8 assay, cell colony formation assay, EdU incorporation assay and cell cycle analysis were performed to determine whether miR-511-mediated regulation of TRIM24 could affect GC progression. Results In our study, miR-511 was found to be downregulated in GC and an inverse correlation was observed between TRIM24 and miR-511 expression in primary GC tissues and cell lines. Dual-luciferase reporter assay further verified TRIM24 is a direct target of miR-511. Functional assays showed miR-511 overexpression inhibited cell growth, colony formation ability and cell cycle progression. Conversely, inhibition of endogenous miR-511 promoted these phenotypes in GC cells. Moreover, reintroduction of TRIM24 rescued miR-511-induced inhibitory effects on GC cells. Furthermore, miR-511 elicits tumor-suppressive effects through inactivating PI3K/AKT and Wnt/β-catenin pathways by suppressing TRIM24. Conclusions Our results provide the new evidence supporting the tumor-suppressive role of miR-511 in GC by suppressing TRIM24, suggesting that this novel miR-511/TRIM24 axis is critical in the control of gastric cancer tumorigenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13046-017-0489-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ziling Fang
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China
| | - Ling Zhang
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China
| | - Quan Liao
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China
| | - Yi Wang
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China
| | - Feng Yu
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China
| | - Miao Feng
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China
| | - Xiaojun Xiang
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China.
| | - Jianping Xiong
- Department of Oncology, the First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu District, Nanchang, 330006, Jiangxi Province, China.
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Khosla R, Rastogi A, Ramakrishna G, Pamecha V, Mukhopadhyay A, Vasudevan M, Sarin SK, Trehanpati N. EpCAM+ Liver Cancer Stem-Like Cells Exhibiting Autocrine Wnt Signaling Potentially Originate in Cirrhotic Patients. Stem Cells Transl Med 2017; 6:807-818. [PMID: 28176469 PMCID: PMC5442787 DOI: 10.1002/sctm.16-0248] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/18/2016] [Accepted: 09/30/2016] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is believed to originate from cancer stem cells (CSCs). While epithelial cell adhesion molecule (EpCAM) is a marker of normal hepatic stem cells (HSCs), EpCAM+ cells from HCC behave like CSCs. Since HCC mostly develops on a cirrhotic background, we sought to determine whether CSC‐like EpCAM+ cells exist in patients with advanced cirrhosis. Both flow cytometry and immunohistochemistry showed that frequency of EpCAM+ cells in advanced cirrhosis was increased as compared to control. To determine whether increased EpCAM population in advanced cirrhosis harbors any CSC‐like cells, we compared molecular and functional features of EpCAM+ cells from advanced cirrhosis (Ep+CIR; n = 20) with EpCAM+ cells from both HCC (Ep+HCC; n = 20) and noncancerous/noncirrhotic (control) (Ep+NSC; n = 7) liver tissues. Ep+CIRs displayed similarity with Ep+HCC cells including upregulated expression of stemness and Notch pathway genes, enhanced self‐renewal in serial spheroid assay and generation of subcutaneous tumors in nonobese diabetic/severe combined immunodeficiency mice. Moreover, transcriptome and miRNome of Ep+CIRs appeared closer to that of Ep+HCC cells than Ep+NSCs. Interestingly, more than 50% micro RNAs (miRNAs) and transcripts specifically expressed in Ep+HCCs were also expressed in Ep+CIRs. However, none of Ep+NSC specific miRNAs and only 7% Ep+NSC specific transcripts were expressed in Ep+CIRs. Further, according to gene expression and in vitro Wnt inhibition analysis, autocrine Wnt signaling appeared to be a distinct feature of Ep+CIR and Ep+HCC cells, which was absent from Ep+NSCs. EpCAM+ cells in advanced cirrhosis possibly include a population of CSC‐like cells which can be explored for early diagnosis of HCC development. Stem Cells Translational Medicine2017;6:807–818
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Affiliation(s)
- Ritu Khosla
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Archana Rastogi
- Department of Pathology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Gayatri Ramakrishna
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Viniyendra Pamecha
- Department of Liver Transplant and Hepato Pancreato Biliary Surgery, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Ashok Mukhopadhyay
- Stem Cell Biology Laboratory, National Institute of Immunology, New Delhi, India
| | | | - Shiv Kumar Sarin
- Department of Hepatology, Institute of Liver and Biliary Sciences, New Delhi, India
| | - Nirupma Trehanpati
- Department of Molecular and Cellular Medicine, Institute of Liver and Biliary Sciences, New Delhi, India
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Terzi E, Salvatore V, Negrini G, Piscaglia F. Ongoing challenges in the diagnosis of hepatocellular carcinoma. Expert Rev Gastroenterol Hepatol 2016; 10:451-63. [PMID: 26603785 DOI: 10.1586/17474124.2016.1124758] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In 2001, the European Association for the Study of the Liver (EASL) endorsed the possibility of achieving a non-invasive diagnosis of Hepatocellular Carcinoma (HCC) for the first time. Since then, various refinements of the criteria and techniques capable of achieving this diagnosis and the role of plasma and tissue oncomarkers have been reported in the literature and have been accepted to different extents in various geographical areas. Such tools can also potentially imply prognostic significance. The present article critically discusses some of the most relevant and debated challenges which have emerged in this field, including the role of contrast-enhanced ultrasound, and of hepatocyte-specific magnetic resonance contrast agents, the pitfall of transient hepatic attenuation differences, the reliability of biopsy and the status of biomarkers.
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Affiliation(s)
- Eleonora Terzi
- a Division of Internal Medicine, Department of Digestive Disease and Internal Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy
| | - Veronica Salvatore
- a Division of Internal Medicine, Department of Digestive Disease and Internal Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy
| | - Giulia Negrini
- a Division of Internal Medicine, Department of Digestive Disease and Internal Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy
| | - Fabio Piscaglia
- a Division of Internal Medicine, Department of Digestive Disease and Internal Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy
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Zhang Y, Zhou J, Sun M, Sun G, Cao Y, Zhang H, Tian R, Zhou L, Duan L, Chen X, Lun L. Prognostic Value of microRNA-9 in Various Cancers: a Meta-analysis. Pathol Oncol Res 2016; 23:573-582. [PMID: 27844330 PMCID: PMC5487937 DOI: 10.1007/s12253-016-0148-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/09/2016] [Indexed: 10/28/2022]
Abstract
Recently, there are more and more evidences from studies have revealed the association between microRNA-9 (miR-9) expression and outcome in multiple cancers, but inconsistent results have also been reported. It is necessary to rationalize a meta analysis of all available data to clarify the prognostic role of miR-9. Eligible studies were selected through multiple search strategies and the quality was assessed by MOOSE. Data was extracted from studies according to the key statistics index. All analyses were performed using STATA software. Twenty studies were selected in the meta-analysis to evaluate the prognostic role of miR-9 in multiple tumors. MiR-9 expression level was an independent prognostic biomarker for OS in tumor patients using multivariate and univariate analyses. High expression levels of miR-9 was demonstrated to associated with poor overall survival (OS) (HR = 2.23, 95 % CI: 1.56-3.17, P < 0.05) and recurrence free survival/progress free survival (RFS/PFS) (HR = 2.08, 95 % CI: 1.33-3.27, P < 0.05). Subgroup analysis showed that residence region (China and Japan), sample size, cancer type (solid or leukemia), follow-up months and analysis method (qPCR) did not alter the predictive value of miR-9 on OS in various cancers. Furthermore, no significant associations were detected for miR-9 expression and lymph node metastasis or distant metastasis. The present results suggest that promoted miR-9 expression is associated with poor OS in patients with general cancers.
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Affiliation(s)
- Yunyuan Zhang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Jun Zhou
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Meiling Sun
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Guirong Sun
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Yongxian Cao
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Haiping Zhang
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Runhua Tian
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China
| | - Lan Zhou
- College of Laboratory Medicine, Key Laboratory of Laboratory Medical Diagnostics Designated by Chinese Ministry of Education, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Liang Duan
- Department of Laboratory Medicine, the Second Hospital Affiliated to Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Xian Chen
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China.
| | - Limin Lun
- Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao, 266003, People's Republic of China.
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Prioritizing cancer-related microRNAs by integrating microRNA and mRNA datasets. Sci Rep 2016; 6:35350. [PMID: 27734929 PMCID: PMC5062133 DOI: 10.1038/srep35350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/28/2016] [Indexed: 12/29/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs regulating the expression of target genes, and they are involved in cancer initiation and progression. Even though many cancer-related miRNAs were identified, their functional impact may vary, depending on their effects on the regulation of other miRNAs and genes. In this study, we propose a novel method for the prioritization of candidate cancer-related miRNAs that may affect the expression of other miRNAs and genes across the entire biological network. For this, we propose three important features: the average expression of a miRNA in multiple cancer samples, the average of the absolute correlation values between the expression of a miRNA and expression of all genes, and the number of predicted miRNA target genes. These three features were integrated using order statistics. By applying the proposed approach to four cancer types, glioblastoma, ovarian cancer, prostate cancer, and breast cancer, we prioritized candidate cancer-related miRNAs and determined their functional roles in cancer-related pathways. The proposed approach can be used to identify miRNAs that play crucial roles in driving cancer development, and the elucidation of novel potential therapeutic targets for cancer treatment.
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Lin K, Xu T, He BS, Pan YQ, Sun HL, Peng HX, Hu XX, Wang SK. MicroRNA expression profiles predict progression and clinical outcome in lung adenocarcinoma. Onco Targets Ther 2016; 9:5679-5692. [PMID: 27695346 PMCID: PMC5029843 DOI: 10.2147/ott.s111241] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Lung cancer is one of the leading causes of cancer death worldwide. Accumulating evidence has indicated that microRNAs (miRNAs) can be proposed as promising diagnostic and prognostic markers for various cancers. The current study analyzed the miRNA expression profiles of 418 lung adenocarcinoma (LUAD) cases obtained from The Cancer Genome Atlas dataset, with the aim to investigate the relationship of miRNAs with progression and prognosis of LUAD. A total of 185 miRNAs were found to be differentially expressed between LUAD tumor tissues and adjacent normal tissues. Among them, 13, 10, 0, and 10 miRNAs were discovered to be associated with pathologic T, N, M, and Stage, respectively. Interestingly, mir-200 family (mir-200a, mir-200b, and mir-429) was shown to play a critical role in the progression of LUAD. In the multivariate Cox regression analysis, mir-1468 (P=0.009), mir-212 (P=0.026), mir-3653 (P=0.012), and mir-31 (P=0.002) were significantly correlated with recurrence-free survival. With regard to overall survival, mir-551b (P=0.011), mir-3653 (P=0.016), and mir-31 (P=0.001) were proven as independent prognostic markers. In summary, this study identified the cancer-specific miRNAs that may predict the progression and prognosis of LUAD.
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Affiliation(s)
- Kang Lin
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University
| | - Tao Xu
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University
| | - Bang-Shun He
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University
| | - Yu-Qin Pan
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University
| | - Hui-Ling Sun
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University
| | - Hong-Xin Peng
- Medical School, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Xiu-Xiu Hu
- Medical School, Southeast University, Nanjing, Jiangsu, People's Republic of China
| | - Shu-Kui Wang
- Central Laboratory, Nanjing First Hospital, Nanjing Medical University
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Chen Q, Wu F, Wang M, Dong S, Liu Y, Lu Y, Song Y, Zhou Q, Liu P, Luo Y, Su S. Transcriptional Profiling and miRNA-Target Network Analysis Identify Potential Biomarkers for Efficacy Evaluation of Fuzheng-Huayu Formula-Treated Hepatitis B Caused Liver Cirrhosis. Int J Mol Sci 2016; 17:ijms17060883. [PMID: 27271613 PMCID: PMC4926417 DOI: 10.3390/ijms17060883] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 12/28/2022] Open
Abstract
Fuzheng-Huayu (FZHY) formula has been found to have a satisfactory effect on hepatitis B-caused cirrhosis (HBC) treatment. However, the efficacy evaluation of FZHY is often challenging. In this study, a randomized, double-blind and placebo-controlled trial was used to evaluate the therapeutic efficacy of FZHY in HBC treatment. In the trial, 35 medical indexes were detected, and 14 indexes had a statistically-significant difference before compared to after the trial. Importantly, the Child-Pugh score also demonstrated FZHY having therapeutic efficacy. Furthermore, the microRNA (miRNA) profiles of 12 serum samples were detected in FZHY groups, and 112 differential-expressed (DE) miRNAs were determined. Using predicted miRNA targets, 13 kernel miRNAs were identified from the established miRNA-target network. Subsequently, quantitative Real-time Polymerase Chain Reaction (qRT-PCR) was used to validate the expression level of 13 identified miRNAs in the trials. The results showed that nine miRNAs have a statistically-significant difference before compared to after FZHY treatment. By means of a logistic regression model, a miRNA panel with hsa-miR-18a-5p, -326, -1182 and -193b-5p was established, and it can clearly improve the accuracy of the efficacy evaluation of FZHY. This study suggested that the particular miRNAs can act as potential biomarkers and obviously increase the diagnostic accuracy for drug evaluation in HBC treatment progression.
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Affiliation(s)
- Qilong Chen
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
- Laboratory of Epigenetics, Institute of Biomedical Science, Fudan University, Shanghai 200032, China.
| | - Feizhen Wu
- Laboratory of Epigenetics, Institute of Biomedical Science, Fudan University, Shanghai 200032, China.
| | - Mei Wang
- Department of Endocrinology and Metabolism, Shanghai First People's Hospital, Shanghai Jiaotong University, Shanghai 201201, China.
| | - Shu Dong
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Yamin Liu
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Yiyu Lu
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Yanan Song
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Qianmei Zhou
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Ping Liu
- Institute of Liver Disease, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Yunquan Luo
- Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Shibing Su
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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Shen J, Siegel AB, Remotti H, Wang Q, Santella RM. Identifying microRNA panels specifically associated with hepatocellular carcinoma and its different etiologies. ACTA ACUST UNITED AC 2016; 2:151-162. [PMID: 28243631 DOI: 10.20517/2394-5079.2015.66] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AIM Deregulation of microRNAs (miRNAs) expression has been identified in hepatocellular carcinoma (HCC), but few results are consistent. The objective of this study is to investigate "HCC tumor type specific" and "tumor common" miRNA panels. METHODS The authors integrate and analyze clinical, etiologic and miRNA profiles data from 9 types of solid tumors in The Cancer Genome Atlas (TCGA) and HCC data from Columbia University Medical Center (CUMC). RESULTS Levels of 33 miRNAs were significant different between HCC tumor and paired non-tumor tissues (over 2-fold changes) after Bonferroni correction for multiple comparisons, and most (28 miRNAs) were down-regulated in HCC tumors. Using this panel, the authors well classified HCC tumor tissues with 4 misclassifications among 48 paired tissues. Validating this panel in an additional 302 HCC tumor tissues, the authors almost perfectly distinguished tumor from non-tumor tissues with only two misclassifications (99% of HCC tissues correctly classified). Evaluating miRNA profiles in 32 independent HCC paired tissues from CUMC, the authors observed 40 miRNAs significantly deregulated in HCC with over 2-fold changes; 14 overlapped with those identified in TCGA. Subgroup analyses by HCC etiology found that 4 upregulated and 8 downregulated miRNAs were significantly associated with alcohol-related HCC. There were 7 and 4 miRNAs significantly associated with hepatitis B virus- and hepatitis C virus-related HCC, respectively. Data for the first time revealed that miR-24-1, miR-130a and miR-505 were significantly down-regulated only in HCC tumors; miR-142 and miR-455 were significantly down-regulated in HCC, but up-regulated in 5 other solid tumors; suggesting their HCC "tumor type specific" characteristics. A panel of 8 miRNAs was significant in at least 5 tumor types, including HCC, and was identified as "tumor common" marker. CONCLUSION The authors concluded that aberrant miRNA panels have HCC "tumor type specificity" and may be affected by etiologic factors.
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Affiliation(s)
- Jing Shen
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Abby B Siegel
- Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Helen Remotti
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Qiao Wang
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY 10032, USA
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Wu QW. Serpine2, a potential novel target for combating melanoma metastasis. Am J Transl Res 2016; 8:1985-1997. [PMID: 27347308 PMCID: PMC4891413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 11/17/2015] [Indexed: 06/06/2023]
Abstract
Early stages of melanoma can be treated by surgical resection of tumor, but there is still no effective treatment once it is progressed to metastatic phases. Although growing family of both metastasis promoting and metastasis suppressor genes have been reported, the molecular mechanisms governing melanoma metastatic cascade are still not completely understood. Therefore, defining the molecules that govern melanoma metastasis may aid the development of more effective therapeutic strategies for combating cancer. In the present study, we found that Serpin Peptidase Inhibitor 2, Serpine2 was involved in the metastasis of melanoma cells. The requirement of Serpine2 in the migration of melanoma cells was confirmed by gene silencing and over-expression in vitro. Moreover, down-regulation of Serpine2 expression strikingly inhibited melanoma cellular metastasis in vivo. Finally, we found that Serpine2 promotes melanoma metastasis through the glycogen synthesis kinase 3β, GSK-3β signaling pathway. To conclude, our findings suggested a novel mechanism underlying the metastasis of melanoma cells which might serve as a new intervention target for the treatment of melanoma.
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Affiliation(s)
- Qi Wei Wu
- Department of Dermatology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine 1111 Xianxia Road, Shanghai 200336, China
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