1
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Gao Y, Gong Y, Liu Y, Xue Y, Zheng K, Guo Y, Hao L, Peng Q, Shi X. Integrated analysis of transcriptomics and metabolomics in human hepatocellular carcinoma HepG2215 cells after YAP1 knockdown. Acta Histochem 2023; 125:151987. [PMID: 36473310 DOI: 10.1016/j.acthis.2022.151987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/07/2022]
Abstract
Yes-associated protein 1 (YAP1) plays a critical role in hepatocellular carcinoma (HCC). Inhibition of YAP1 expression suppresses HCC progression, but the underlying mechanism is still unclear. In this study, we studied the effects and molecular mechanisms of YAP1 knockdown on the growth and metabolism in human HCC HepG2215 cells. Inhibition of YAP1 expression inhibits the proliferation and metastasis in HepG2215 cells, and differentially expressed genes (DEGs) and metabolites were identified in shYAP1-HepG2215 cells. Further, 805 DEGs, mainly associated with metabolism and particularly lipid metabolism, were identified by transcriptome sequencing analyses in shYAP1-HepG2215 cells. YAP1 knockdown increased albumin (ALB) levels by Protein-protein interaction (PPI) network analyses in HepG2215 cells. Metabolomic profiling identified 37 metabolites with significant differences in the shYAP1 group, and amino acid metabolism generally decreased in the shYAP1 group. Comprehensive analysis of transcriptomics and metabolomics revealed that the ATP-binding cassette (ABC) transporters play a central role after YAP1 knockdown in HepG2215 cells. Therefore, YAP1 knockdown inhibited HCC growth, which affected the metabolism of lipids and amino acids by regulating the expression of ALB and ABC transporters in HepG2215 cells.
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Affiliation(s)
- Yuting Gao
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China; School of Basic Medical Sciences, Shanxi University of Chinese Medicine, Jinzhong 030619, China
| | - Yi Gong
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Yiwei Liu
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Yu Xue
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Kangning Zheng
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Yinglin Guo
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Liyuan Hao
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Qing Peng
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China
| | - Xinli Shi
- Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, China.
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2
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Liu X, Wang C, Yang Q, Yuan Y, Sheng Y, Li D, Ojha SC, Sun C, Deng C. AC093797.1 as a Potential Biomarker to Indicate the Prognosis of Hepatocellular Carcinoma and Inhibits Cell Proliferation, Invasion, and Migration by Reprogramming Cell Metabolism and Extracellular Matrix Dynamics. Front Genet 2021; 12:778742. [PMID: 34925460 PMCID: PMC8678093 DOI: 10.3389/fgene.2021.778742] [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: 09/17/2021] [Accepted: 10/28/2021] [Indexed: 11/13/2022] Open
Abstract
Purpose: The risk signature composed of four lncRNA (AC093797.1, POLR2J4, AL121748.1, and AL162231.4.) can be used to predict the overall survival (OS) of patients with hepatocellular carcinoma (HCC). However, the clinical significance and biological function of AC093797.1 are still unexplored in HCC or other malignant tumors. In this study, we aimed to investigate the biological function of AC093797.1 in HCC and screen the candidate hub genes and pathways related to hepatocarcinogenesis. Methods: RT-qPCR was employed to detect AC093797.1 in HCC tissues and cell lines. The role of AC093797.1 in HCC was evaluated via the cell-counting kit-8, transwell, and wound healing assays. The effects of AC093797.1 on tumor growth in vivo were clarified by nude mice tumor formation experiments. Then, RNA-sequencing and bioinformatics analysis based on subcutaneous tumor tissue was performed to identify the hub genes and pathways associated with HCC. Results: The expression of AC093797.1 decreased in HCC tissues and cell lines, and patients with low expressed AC093797.1 had poor overall survival (OS). AC093797.1 overexpression impeded HCC cell proliferation, invasion, and migration in vitro and suppressed tumor growth in vivo. Compared with the control group, 710 differentially expressed genes (243 upregulated genes and 467 downregulated genes) were filtered via RNA-sequencing, which mainly enriched in amino acid metabolism, extracellular matrix structure constituents, cell adhesion molecules cams, signaling to Ras, and signaling to ERKs. Conclusion: AC093797.1 may inhibit cell proliferation, invasion, and migration in HCC by reprograming cell metabolism or regulating several pathways, suggesting that AC093797.1 might be a potential therapeutic and prognostic marker for HCC patients.
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Affiliation(s)
- Xiaoling Liu
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chenyu Wang
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Qing Yang
- The Department of Gastroenterology, The Second People's Hospital of Neijiang, Neijiang, China
| | - Yue Yuan
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yunjian Sheng
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Decheng Li
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Suvash Chandra Ojha
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Changfeng Sun
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Cunliang Deng
- The Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,The Department of Tuberculosis, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Infection and Immunity, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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3
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Feng L, Wang Y, Wang X, An S, Aizimuaji Z, Tao C, Zhang K, Cheng S, Wu J, Xiao T, Rong W. Integrated analysis of the rhesus monkey liver transcriptome during development and human primary HCC AFP-related gene expression. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 25:406-415. [PMID: 34484865 PMCID: PMC8403716 DOI: 10.1016/j.omtn.2021.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/16/2021] [Indexed: 01/10/2023]
Abstract
Embryonic development and tumorigenesis have a certain degree of similarity. Alpha-fetoprotein (AFP), a protein related to embryonic development, is a well-known biomarker for the diagnosis and prognosis of hepatocellular carcinoma (HCC). In this study, we analyzed the differences in gene expression profiles and molecular mechanisms in human HCC tissues from patients in AFPhigh (serum AFP level ≥ 25 ng/mL) and AFPlow (serum AFP level < 25 ng/mL) groups. The results indicated that AFPhigh HCC has more malignant biological characteristics. Single-sample gene set enrichment analysis (ssGSEA) showed significantly higher levels of genes expressed in dendritic cells, neutrophils, and natural killer cells in the AFPlow group than in the AFPhigh group. Then, we defined a rhesus monkey fetal liver developmental landscape and compared it to the HCC gene expression profile. The gene signatures of AFPhigh HCC tissues were similar to those of early embryonic liver tissues. In this study, we comprehensively analyzed the rhesus monkey liver transcriptome during development and human primary HCC AFP-related gene expression profiles and clarified the function of AFP in the occurrence and development of HCC from the perspective of developmental biology, which might provide a new perspective on the pathogenesis of HCC.
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Affiliation(s)
- Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yaru Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Xijun Wang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Songlin An
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Zulihumaer Aizimuaji
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Changcheng Tao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Kai Zhang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jianxiong Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Corresponding author: Dr. Jianxiong Wu, Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Ting Xiao
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Corresponding author: Dr. Ting Xiao, State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
| | - Weiqi Rong
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Corresponding author: Dr. Weiqi Rong, Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.
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4
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Li J, Li MH, Wang TT, Liu XN, Zhu XT, Dai YZ, Zhai KC, Liu YD, Lin JL, Ge RL, Sun SH, Wang F, Yuan JH. SLC38A4 functions as a tumour suppressor in hepatocellular carcinoma through modulating Wnt/β-catenin/MYC/HMGCS2 axis. Br J Cancer 2021; 125:865-876. [PMID: 34274945 DOI: 10.1038/s41416-021-01490-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/11/2021] [Accepted: 07/08/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Many molecular alterations are shared by embryonic liver development and hepatocellular carcinoma (HCC). Identifying the common molecular events would provide a novel prognostic biomarker and therapeutic target for HCC. METHODS Expression levels and clinical relevancies of SLC38A4 and HMGCS2 were investigated by qRT-PCR, western blot, TCGA and GEO datasets. The biological roles of SLC38A4 were investigated by functional assays. The downstream signalling pathway of SLC38A4 was investigated by qRT-PCR, western blot, immunofluorescence, luciferase reporter assay, TCGA and GEO datasets. RESULTS SLC38A4 silencing was identified as an oncofetal molecular event. DNA hypermethylation contributed to the downregulations of Slc38a4/SLC38A4 in the foetal liver and HCC. Low expression of SLC38A4 was associated with poor prognosis of HCC patients. Functional assays demonstrated that SLC38A4 depletion promoted HCC cellular proliferation, stemness and migration, and inhibited HCC cellular apoptosis in vitro, and further repressed HCC tumorigenesis in vivo. HMGCS2 was identified as a critical downstream target of SLC38A4. SLC38A4 increased HMGCS2 expression via upregulating AXIN1 and repressing Wnt/β-catenin/MYC axis. Functional rescue assays showed that HMGCS2 overexpression reversed the oncogenic roles of SLC38A4 depletion in HCC. CONCLUSIONS SLC38A4 downregulation was identified as a novel oncofetal event, and SLC38A4 was identified as a novel tumour suppressor in HCC.
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Affiliation(s)
- Jie Li
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Ming-Han Li
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Tian-Tian Wang
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Xiao-Ning Liu
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao-Ting Zhu
- Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun-Zhang Dai
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Ke-Chao Zhai
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Yong-da Liu
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Jia-Li Lin
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Rui-Liang Ge
- The Second Department of Liver Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Shu-Han Sun
- Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Fang Wang
- Department of Medical Genetics, Naval Medical University, Shanghai, China.
| | - Ji-Hang Yuan
- Department of Medical Genetics, Naval Medical University, Shanghai, China.
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5
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Unfried JP, Sangro P, Prats-Mari L, Sangro B, Fortes P. The Landscape of lncRNAs in Hepatocellular Carcinoma: A Translational Perspective. Cancers (Basel) 2021; 13:2651. [PMID: 34071216 PMCID: PMC8197910 DOI: 10.3390/cancers13112651] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
LncRNAs are emerging as relevant regulators of multiple cellular processes involved in cell physiology as well as in the development and progression of human diseases, most notably, cancer. Hepatocellular carcinoma (HCC) is a prominent cause of cancer-related death worldwide due to the high prevalence of causative factors, usual cirrhotic status of the tumor-harboring livers and the suboptimal benefit of locoregional and systemic therapies. Despite huge progress in the molecular characterization of HCC, no oncogenic loop addiction has been identified and most genetic alterations remain non-druggable, underscoring the importance of advancing research in novel approaches for HCC treatment. In this context, long non-coding RNAs (lncRNAs) appear as potentially useful targets as they often exhibit high tumor- and tissue-specific expression and many studies have reported an outstanding dysregulation of lncRNAs in HCC. However, there is a limited perspective of the potential role that deregulated lncRNAs may play in HCC progression and aggressiveness or the mechanisms and therapeutic implications behind such effects. In this review, we offer a clarifying landscape of current efforts to evaluate lncRNA potential as therapeutic targets in HCC using evidence from preclinical models as well as from recent studies on novel oncogenic pathways that show lncRNA-dependency.
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Affiliation(s)
- Juan Pablo Unfried
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), 31008 Pamplona, Spain; (L.P.-M.); (P.F.)
| | - Paloma Sangro
- Liver Unit, Clínica Universidad de Navarra (CUN), 31008 Pamplona, Spain;
| | - Laura Prats-Mari
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), 31008 Pamplona, Spain; (L.P.-M.); (P.F.)
| | - Bruno Sangro
- Liver Unit, Clínica Universidad de Navarra (CUN), 31008 Pamplona, Spain;
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), 31008 Pamplona, Spain
| | - Puri Fortes
- Center for Applied Medical Research (CIMA), Department of Gene Therapy and Regulation of Gene Expression, Universidad de Navarra (UNAV), 31008 Pamplona, Spain; (L.P.-M.); (P.F.)
- Navarra Institute for Health Research (IdiSNA), 31008 Pamplona, Spain
- Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), 31008 Pamplona, Spain
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6
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Ma X, Mo M, Tan HJJ, Tan C, Zeng X, Zhang G, Huang D, Liang J, Liu S, Qiu X. LINC02499, a novel liver-specific long non-coding RNA with potential diagnostic and prognostic value, inhibits hepatocellular carcinoma cell proliferation, migration, and invasion. Hepatol Res 2020; 50:726-740. [PMID: 32039538 DOI: 10.1111/hepr.13491] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 01/07/2020] [Accepted: 01/29/2020] [Indexed: 12/14/2022]
Abstract
AIM Liver-specific non-coding RNAs have been reported to play crucial roles in hepatocellular carcinoma (HCC). We investigated the possible biological performance of a novel liver-specific long non-coding RNA, LINC02499, in HCC. METHODS The association between LINC02499 expression and HCC was evaluated based on The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, and then confirmed in a HCC cohort by quantitative real-time polymerase chain reaction. The effects of LINC02499 on HCC cells were verified by gain- and loss-of-function assays. Pathway enrichment analyses were used to explore the potential mechanism of LINC02499 in HCC. RESULTS LINC02499 expression was remarkably decreased in HCC tissues compared to adjacent non-tumor tissues based on TCGA (P < 0.001) and GEO databases (P < 0.001) and our HCC cohort (P < 0.001). Decreased LINC02499 was also significantly associated with poorer overall survival in both the TCGA database (P = 0.009) and our HCC cohort (P = 0.002). Furthermore, the receiver operating characteristic analysis indicated that LINC02499 showed a good performance in HCC diagnosis (area under the curve = 0.879, P < 0.001), and both sensitivity and specificity were 83.8%. In addition, up- and downregulated LINC02499 significantly impacted proliferation, migration, and invasion abilities of HCC cells in vitro. Pathway enrichment analyses revealed that the potential target genes of LINC02499 were involved in "Complement and coagulation cascades" and "Butanoate metabolism" pathways. CONCLUSION LINC02499 could be a potential novel diagnostic and prognostic biomarker for HCC patients, and it could exert a tumor suppressor role in the progression of HCC.
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Affiliation(s)
- Xiaoyun Ma
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Meile Mo
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | | | - Chao Tan
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Xiaoyun Zeng
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Guoqiang Zhang
- Hospital-acquired Infection Control Department, Affiliated Cancer Hospital of Guangxi Medical University, Nanning, China
| | - Dongping Huang
- Department of Sanitary Chemistry, School of Public Health, Guangxi Medical University, Nanning, China
| | - Jun Liang
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Shun Liu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
| | - Xiaoqiang Qiu
- Department of Epidemiology, School of Public Health, Guangxi Medical University, Nanning, China
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7
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An Oncogenic Role for Four-Jointed Box 1 (FJX1) in Nasopharyngeal Carcinoma. DISEASE MARKERS 2019; 2019:3857853. [PMID: 31236144 PMCID: PMC6545767 DOI: 10.1155/2019/3857853] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/07/2019] [Indexed: 12/24/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a highly metastatic cancer prevalent in Southern China and Southeast Asia. The current knowledge on the molecular pathogenesis of NPC is still inadequate to improve disease management. Using gene expression microarrays, we have identified the four-jointed box 1 (FJX1) gene to be upregulated in primary NPC tissues relative to nonmalignant tissues. An orthologue of human FJX1, the four-jointed (fj) gene in Drosophila and Fjx1 in mouse, has reported to be associated with cancer progression pathways. However, the exact function of FJX1 in human is not well characterized. The overexpression of FJX1 mRNA was validated in primary NPC tissue samples, and the level of FJX1 protein was significantly higher in a subset of NPC tissues (42%) compared to the normal epithelium, where no expression of FJX1 was observed (p = 0.01). FJX1 is also found to be overexpressed in microarray datasets and TCGA datasets of other cancers including head and neck cancer, colorectal, and ovarian cancer. Both siRNA knockdown and overexpression experiments in NPC cell lines showed that FJX1 promotes cell proliferation, anchorage-dependent growth, and cellular invasion. Cyclin D1 and E1 mRNA levels were increased following FJX1 expression indicating that FJX1 enhances proliferation by regulating key proteins governing the cell cycle. Our data suggest that the overexpression of FJX1 contributes to a more aggressive phenotype of NPC cells and further investigations into FJX1 as a potential therapeutic target for NPC are warranted. The evaluation of FJX1 as an immunotherapy target for NPC and other cancers is currently ongoing.
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8
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Huang JF, Jiang HY, Cai H, Liu Y, Zhu YQ, Lin SS, Hu TT, Wang TT, Yang WJ, Xiao B, Sun SH, Ma LY, Yin HR, Wang F. Genome-wide screening identifies oncofetal lncRNA Ptn-dt promoting the proliferation of hepatocellular carcinoma cells by regulating the Ptn receptor. Oncogene 2019; 38:3428-3445. [PMID: 30643194 DOI: 10.1038/s41388-018-0643-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/04/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023]
Abstract
Oncofetal genes are genes that express abundantly in both fetal and tumor tissues yet downregulated or undetected in adult tissues, and can be used as tumor markers for cancer diagnosis and treatment. Meanwhile, long noncoding RNAs (lncRNAs) are known to play crucial roles in the pathogenesis of hepatocellular carcinoma (HCC), including tumor growth, proliferation, metastasis, invasion, and recurrence. We performed a genome-wide screening using microarrays to detect the lncRNA expression profiles in fetal livers, adult livers, and liver cancer tissues from mice to identify oncofetal lncRNAs in HCC. From the microarray data analysis, we identified lncRNA Ptn-dt as a possible oncofetal gene. Both in vitro and in vivo experiments results confirmed that overexpression of Ptn-dt significantly promoted the proliferation of mouse HCC cells. RNA pulldown assay showed that Ptn-dt could interact with the HuR protein. Interestingly, miR-96 binds with HuR to maintain its stability as well. Overexpression of lncRNA Ptn-dt led to the downregulation of miR-96, which might be due to the interaction between Ptn-dt and HuR. Meanwhile, previous studies have reported that Ptn can promote tumor growth and vascular abnormalization via anaplastic lymphoma kinase (Alk) signaling. In our study, we found that overexpression of Ptn-dt could promote the expression of Alk through repressing miR-96 via interacting with HuR, thus enhancing the biologic function of Ptn. In summary, a new oncofetal lncRNA Ptn-dt is identified, and it can promote the proliferation of HCC cells by regulating the HuR/miR-96/Alk pathway and Ptn-Alk axis.
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Affiliation(s)
- Jin-Feng Huang
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China.,Department of Clinical Genetics, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China
| | - Hong-Yue Jiang
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
| | - Hui Cai
- Department of General Surgery, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China
| | - Yan Liu
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China
| | - Yi-Qing Zhu
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China
| | - Sha-Sha Lin
- Center of Reproductive Medicine, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China
| | - Ting-Ting Hu
- Center of Reproductive Medicine, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China
| | - Tian-Tian Wang
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China.,Department of Clinical Genetics, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China
| | - Wen-Jun Yang
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China
| | - Bang Xiao
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China
| | - Shu-Han Sun
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China.,Department of Clinical Genetics, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China
| | - Li-Ye Ma
- Department of General Surgery, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China.
| | - Hui-Rong Yin
- Center of Reproductive Medicine, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China.
| | - Fang Wang
- Department of Medical Genetics, Second Military Medical University, 200433, Shanghai, China. .,Department of Clinical Genetics, Changhai Hospital, Second Military Medical University, 200433, Shanghai, China.
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9
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Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas. Nat Commun 2018; 9:5330. [PMID: 30552315 PMCID: PMC6294258 DOI: 10.1038/s41467-018-07232-8] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
Understanding metabolic dysregulation in different disease settings is vital for the safe and effective incorporation of metabolism-targeted therapeutics in the clinic. Here, using transcriptomic data for 10,704 tumor and normal samples from The Cancer Genome Atlas, across 26 disease sites, we present a novel bioinformatics pipeline that distinguishes tumor from normal tissues, based on differential gene expression for 114 metabolic pathways. We confirm pathway dysregulation in separate patient populations, demonstrating the robustness of our approach. Bootstrapping simulations were then applied to assess the biological significance of these alterations. We provide distinct examples of the types of analysis that can be accomplished with this tool to understand cancer specific metabolic dysregulation, highlighting novel pathways of interest, and patterns of metabolic flux, in both common and rare disease sites. Further, we show that Master Metabolic Transcriptional Regulators explain why metabolic differences exist, can segregate patient populations, and predict responders to different metabolism-targeted therapeutics.
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10
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SKA1 overexpression is associated with poor prognosis in hepatocellular carcinoma. BMC Cancer 2018; 18:1240. [PMID: 30537941 PMCID: PMC6288885 DOI: 10.1186/s12885-018-5119-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SKA1, an important mitosis protein, has been indicated in the initiation and progression of several malignancies. However, its clinical significance in hepatocellular carcinoma (HCC) remain to be elucidated. METHODS mRNA expression of SKA1 was examined in 126 HCC and paired non-neoplastic tissues using real-time PCR and validated in The Cancer Genome Atlas (TCGA) database. SKA1 protein expression was detected using immunohistochemistry in the 126 HCC tissues and its associations with clinicopathological parameters and prognosis were analyzed. Hierarchical cluster analysis and gene set enrichment analysis (GSEA) were performed in selected Gene Expression Omnibus data sets. RESULTS SKA1 mRNA expression was significantly elevated in HCC tissues from both local hospital and TCGA database. Immunohistochemistry revealed that increased SKA1 expression was present in 65 of the 126 cases and was significantly associated with higher serum alpha-fetoprotein concentration, larger tumor size and higher TNM stage. Patients with positive SKA1 expression showed significantly worse overall and relapse-free survival. Multivariate Cox regression analysis revealed that SKA1 was an independent predictor of patient prognosis. Gene expression profiling analysis of public data showed that high-SKA1 expression HCC tissues had similar gene expression profiles with fetal liver tissues. Moreover, GSEA showed that genes up-regulated in high SKA1 HCC subgroup were significantly enriched in cell cycle pathway, while genes down-regulated were significantly enriched in apoptosis pathway. CONCLUSIONS Our findings indicate that the oncofetal gene SKA1 might be involved in the progression of the HCC and could serve as a prognostic marker for HCC.
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11
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Chai SJ, Fong SCY, Gan CP, Pua KC, Lim PVH, Lau SH, Zain RB, Abraham T, Ismail SM, Abdul Rahman ZA, Ponniah S, Patel V, Cheong SC, Lim KP. In vitro evaluation of dual-antigenic PV1 peptide vaccine in head and neck cancer patients. Hum Vaccin Immunother 2018; 15:167-178. [PMID: 30193086 DOI: 10.1080/21645515.2018.1520584] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Peptide vaccines derived from tumour-associated antigens have been used as an immunotherapeutic approach to induce specific cytotoxic immune response against tumour. We previously identified that MAGED4B and FJX1 proteins are overexpressed in HNSCC patients; and further demonstrated that two HLA-A2-restricted 9-11 amino acid peptides derived from these proteins were able to induce anti-tumour immune responses in vitro independently using PBMCs isolated from these patients. In this study, we evaluated the immunogenicity and efficacy of a dual-antigenic peptide vaccine (PV1), comprised of MAGED4B and FJX1 peptides in HNSCC patients. We first demonstrated that 94.8% of HNSCC patients expressed MAGED4B and/or FJX1 by immunohistochemistry, suggesting that PV1 could benefit the majority of HNSCC patients. The presence of pre-existing MAGED4B and FJX1-specific T-cells was detected using a HLA-A2 dimer assay and efficacy of PV1 to induce T-cell to secrete cytotoxic cytokine was evaluated using ELISPOT assay. Pre-existing PV1-specific T-cells were detected in all patients. Notably, we demonstrated that patients' T-cells were able to secrete cytotoxic cytokines upon exposure to target cells expressing the respective antigen post PV1 stimulation. Furthermore, patients with high expression of MAGED4B and FJX1 in their tumours were more responsive to PV1 stimulation, demonstrating the specificity of the PV1 peptide vaccine. Additionally, we also demonstrated the expression of MAGED4B and FJX1 in breast, lung, colon, prostate and rectal cancer suggesting the potential use of PV1 in these cancers. In summary, PV1 could be a good vaccine candidate for the treatment of HNSCC patients and other cancers expressing these antigens.
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Affiliation(s)
- San Jiun Chai
- a Cancer Research Malaysia , Subang Jaya , Selangor , Malaysia
| | | | - Chai Phei Gan
- a Cancer Research Malaysia , Subang Jaya , Selangor , Malaysia
| | - Kin Choo Pua
- b Department of Otorhinolaryngology , Hospital Pulau Pinang , Penang , Malaysia
| | - Paul Vey Hong Lim
- c Ear, Nose and Throat Department , Tung Shin Hospital , Kuala Lumpur , Malaysia
| | - Shin Hin Lau
- d Stomatology Unit , Cancer Research Centre, Institute for Medical Research , Kuala Lumpur , Malaysia
| | - Rosnah Binti Zain
- e Faculty of Dentistry , MAHSA University , Selangor , Malaysia.,f Oral Cancer Research and Coordinating Centre, Faculty of Dentistry , University of Malaya , Kuala Lumpur , Malaysia
| | - Thomas Abraham
- g Department of Oral & Maxillofacial Surgery , Tengku Ampuan Rahimah Hospital , Klang , Malaysia
| | - Siti Mazlipah Ismail
- h Department of Oro-Maxillofacial Surgery and Medical Sciences, Faculty of Dentistry , University of Malaya , Kuala Lumpur , Malaysia
| | - Zainal Ariff Abdul Rahman
- h Department of Oro-Maxillofacial Surgery and Medical Sciences, Faculty of Dentistry , University of Malaya , Kuala Lumpur , Malaysia
| | - Sathibalan Ponniah
- i Cancer Vaccine Development Program, Department of Surgery , Uniformed Services University of the Health Sciences , Bethesda , MD , USA
| | - Vyomesh Patel
- a Cancer Research Malaysia , Subang Jaya , Selangor , Malaysia
| | - Sok Ching Cheong
- a Cancer Research Malaysia , Subang Jaya , Selangor , Malaysia.,h Department of Oro-Maxillofacial Surgery and Medical Sciences, Faculty of Dentistry , University of Malaya , Kuala Lumpur , Malaysia
| | - Kue Peng Lim
- a Cancer Research Malaysia , Subang Jaya , Selangor , Malaysia
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12
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Chen J, Chen CY, Nguyen C, Chen L, Lee K, Stiles BL. Emerging signals regulating liver tumor initiating cells. LIVER RESEARCH 2018. [DOI: 10.1016/j.livres.2018.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Noncoding RNAs in liver cancer stem cells: The big impact of little things. Cancer Lett 2018; 418:51-63. [DOI: 10.1016/j.canlet.2018.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 12/21/2017] [Accepted: 01/03/2018] [Indexed: 12/12/2022]
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14
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Increased liver carcinogenesis and enrichment of stem cell properties in livers of Dickkopf 2 (Dkk2) deleted mice. Oncotarget 2018; 7:28903-13. [PMID: 25826080 PMCID: PMC5045365 DOI: 10.18632/oncotarget.3293] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 02/08/2015] [Indexed: 01/02/2023] Open
Abstract
Dkk2 a antagonist of the Wnt/β-catenin-signaling pathway was shown to be silenced in diverse cancers. More recent data indicate that Dkk family members may also possess functions independent of Wnt-signaling during carcinogenesis. The detailed biological function of Dkks and its relevance for liver cancer is unknown. We analyzed the effects of a genetic deletion of Dkk2 (Dkk2−/−) in a hepatocarcinogenesis model using DEN/Phenobarbital. Untreated Dkk2−/− animals, showed considerable atypia with variation of hepatocyte size and chromatin density. In livers of Dkk2−/− mice nodule formation was seen at 9 months of age with focal loss of trabecular architecture and atypical hepatocytes and after DEN induction Dkk2−/− mice developed significantly more liver tumors compared to controls. Whole transcriptome analysis of untreated Dkk2−/− liver tissue revealed a Dkk2-dependent genetic network involving Wnt/β-Catenin but also multiple additional oncogenic factors, such as e.g. Pdgf-b, Gdf-15 and Hnf4a. Dkk2−/− tumor cells showed a significant deregulation of stemness genes associated with enhanced colony forming properties. Integration of the Dkk2−/− signature into human data was strongly associated with patients survival. Dkk2 deletion results in alterations of liver morphology leading to an increased frequency of liver cancer. The associated genetic changes included factors not primarily related to Wnt/β-Catenin-signaling and correlated with the clinical outcome of HCC-patients.
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15
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Yuan JH, Liu XN, Wang TT, Pan W, Tao QF, Zhou WP, Wang F, Sun SH. The MBNL3 splicing factor promotes hepatocellular carcinoma by increasing PXN expression through the alternative splicing of lncRNA-PXN-AS1. Nat Cell Biol 2017; 19:820-832. [PMID: 28553938 DOI: 10.1038/ncb3538] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/25/2017] [Indexed: 02/07/2023]
Abstract
Understanding the roles of splicing factors and splicing events during tumorigenesis would open new avenues for targeted therapies. Here we identify an oncofetal splicing factor, MBNL3, which promotes tumorigenesis and indicates poor prognosis of hepatocellular carcinoma patients. MBNL3 knockdown almost completely abolishes hepatocellular carcinoma tumorigenesis. Transcriptomic analysis revealed that MBNL3 induces lncRNA-PXN-AS1 exon 4 inclusion. The transcript lacking exon 4 binds to coding sequences of PXN mRNA, causes dissociation of translation elongation factors from PXN mRNA, and thereby inhibits PXN mRNA translation. In contrast, the transcript containing exon 4 preferentially binds to the 3' untranslated region of PXN mRNA, protects PXN mRNA from microRNA-24-AGO2 complex-induced degradation, and thereby increases PXN expression. Through inducing exon 4 inclusion, MBNL3 upregulates PXN, which mediates the pro-tumorigenic roles of MBNL3. Collectively, these data demonstrate detailed mechanistic links between an oncofetal splicing factor, a splicing event and tumorigenesis, and establish splicing factors and splicing events as potential therapeutic targets.
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Affiliation(s)
- Ji-Hang Yuan
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Xiao-Ning Liu
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Tian-Tian Wang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Wei Pan
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Qi-Fei Tao
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China
| | - Wei-Ping Zhou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200433, China
| | - Fang Wang
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
| | - Shu-Han Sun
- Department of Medical Genetics, Second Military Medical University, Shanghai 200433, China
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16
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Gopal R, Selvarasu K, Pandian PP, Ganesan K. Integrative transcriptome analysis of liver cancer profiles identifies upstream regulators and clinical significance of ACSM3 gene expression. Cell Oncol (Dordr) 2017; 40:219-233. [PMID: 28390038 DOI: 10.1007/s13402-017-0321-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2017] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Hepatocellular carcinoma (HCC) is one of the most common human malignancies. It has frequently been associated with metabolic perturbations and liver damages. Various members of the family of acyl-CoA synthetases are known to be involved in the production of bioactive fatty acids, and altered expression of its encoding genes has been found to be involved in metabolic perturbations. For the development of novel diagnostic and therapeutic HCC options, a fundamental understanding of the mechanisms associated with the deregulation of candidate genes involved in metabolic perturbation is required. METHODS A meta-analysis of multiple HCC mRNA profiles was performed to identify consistently deregulated genes. Expression of the acyl-CoA synthetase medium chain family member 3 (ACSM3) gene was subsequently assessed in different HCC tumor stages and correlated with various clinicopathological features. Transcription regulation, survival and pathway-associated features of the ACSM3 gene were investigated using integrative functional genomic and molecular cell biological methods. RESULTS We found that expression of the ACSM3 gene was significantly reduced in HCC tissues and was frequently downregulated in patients exhibiting high alpha-fetoprotein (AFP) levels, high alanine aminotransferase (ALT) levels, multiple nodules and large tumors. Loss of ACSM3 expression was found to correlate with advanced HCC stages and a poor survival. In addition, HNF4α was found to positively regulate the expression of the ACSM3 gene, while PPARγ was found to transcriptionally repress it. Downregulation of ACSM3 expression was perceived upon activation of the TGFβ, WNT, AKT and MYC signalling pathways. In addition, we found that ACSM3 expression correlates with fatty acid oxidation in HCC. CONCLUSION Our data provide evidence for a differential expression and regulation of the ACSM3 gene in HCC, and may lay a foundation for therapeutically targeting fatty acid metabolism in these tumors.
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Affiliation(s)
- Ramani Gopal
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Karthikeyan Selvarasu
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Ponmathi Panneer Pandian
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, India.
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17
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Ittisoponpisan S, Alhuzimi E, Sternberg MJE, David A. Landscape of Pleiotropic Proteins Causing Human Disease: Structural and System Biology Insights. Hum Mutat 2017; 38:289-296. [PMID: 27957775 DOI: 10.1002/humu.23155] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 12/03/2016] [Indexed: 12/13/2022]
Abstract
Pleiotropy is the phenomenon by which the same gene can result in multiple phenotypes. Pleiotropic proteins are emerging as important contributors to rare and common disorders. Nevertheless, little is known on the mechanisms underlying pleiotropy and the characteristic of pleiotropic proteins. We analyzed disease-causing proteins reported in UniProt and observed that 12% are pleiotropic (variants in the same protein cause more than one disease). Pleiotropic proteins were enriched in deleterious and rare variants, but not in common variants. Pleiotropic proteins were more likely to be involved in the pathogenesis of neoplasms, neurological, and circulatory diseases and congenital malformations, whereas non-pleiotropic proteins in endocrine and metabolic disorders. Pleiotropic proteins were more essential and had a higher number of interacting partners compared with non-pleiotropic proteins. Significantly more pleiotropic than non-pleiotropic proteins contained at least one intrinsically long disordered region (P < 0.001). Deleterious variants occurring in structurally disordered regions were more commonly found in pleiotropic, rather than non-pleiotropic proteins. In conclusion, pleiotropic proteins are an important contributor to human disease. They represent a biologically different class of proteins compared with non-pleiotropic proteins and a better understanding of their characteristics and genetic variants can greatly aid in the interpretation of genetic studies and drug design.
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Affiliation(s)
- Sirawit Ittisoponpisan
- Structural Bioinformatics Group, Department of Life Sciences, Imperial College London, London, UK
| | - Eman Alhuzimi
- Structural Bioinformatics Group, Department of Life Sciences, Imperial College London, London, UK
| | - Michael J E Sternberg
- Structural Bioinformatics Group, Department of Life Sciences, Imperial College London, London, UK
| | - Alessia David
- Structural Bioinformatics Group, Department of Life Sciences, Imperial College London, London, UK
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18
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Sumazin P, Chen Y, Treviño LR, Sarabia SF, Hampton OA, Patel K, Mistretta TA, Zorman B, Thompson P, Heczey A, Comerford S, Wheeler DA, Chintagumpala M, Meyers R, Rakheja D, Finegold MJ, Tomlinson G, Parsons DW, López-Terrada D. Genomic analysis of hepatoblastoma identifies distinct molecular and prognostic subgroups. Hepatology 2017; 65:104-121. [PMID: 27775819 DOI: 10.1002/hep.28888] [Citation(s) in RCA: 272] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 08/16/2016] [Accepted: 09/28/2016] [Indexed: 12/13/2022]
Abstract
UNLABELLED Despite being the most common liver cancer in children, hepatoblastoma (HB) is a rare neoplasm. Consequently, few pretreatment tumors have been molecularly profiled, and there are no validated prognostic or therapeutic biomarkers for HB patients. We report on the first large-scale effort to profile pretreatment HBs at diagnosis. Our analysis of 88 clinically annotated HBs revealed three risk-stratifying molecular subtypes that are characterized by differential activation of hepatic progenitor cell markers and metabolic pathways: high-risk tumors were characterized by up-regulated nuclear factor, erythroid 2-like 2 activity; high lin-28 homolog B, high mobility group AT-hook 2, spalt-like transcription factor 4, and alpha-fetoprotein expression; and high coordinated expression of oncofetal proteins and stem-cell markers, while low-risk tumors had low lin-28 homolog B and lethal-7 expression and high hepatic nuclear factor 1 alpha activity. CONCLUSION Analysis of immunohistochemical assays using antibodies targeting these genes in a prospective study of 35 HBs suggested that these candidate biomarkers have the potential to improve risk stratification and guide treatment decisions for HB patients at diagnosis; our results pave the way for clinical collaborative studies to validate candidate biomarkers and test their potential to improve outcome for HB patients. (Hepatology 2017;65:104-121).
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Affiliation(s)
- Pavel Sumazin
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Yidong Chen
- Departments of Epidemiology and Biostatistics, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Lisa R Treviño
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | - Oliver A Hampton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Kayuri Patel
- Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | | | - Barry Zorman
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Patrick Thompson
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX
| | - Andras Heczey
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Sarah Comerford
- Departments of Molecular Genetics and Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX
| | - David A Wheeler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Murali Chintagumpala
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX
| | - Rebecka Meyers
- Department of Pediatric Surgery, University of Utah, Salt Lake City, UT
| | - Dinesh Rakheja
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Milton J Finegold
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX.,Pathology & Immunology, Baylor College of Medicine, Houston, TX
| | - Gail Tomlinson
- Departments of Pediatric Hematology and Oncology, School of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - D Williams Parsons
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Dolores López-Terrada
- Texas Children's Cancer Center, Baylor College of Medicine, Houston, TX.,Department of Pediatrics, Baylor College of Medicine, Houston, TX.,Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX.,Pathology & Immunology, Baylor College of Medicine, Houston, TX
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19
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Lee J, Kim YJ, Lee J, Kim BJ, Lee S, Park T. Gene-set association tests for next-generation sequencing data. Bioinformatics 2016; 32:i611-i619. [PMID: 27587681 PMCID: PMC5013913 DOI: 10.1093/bioinformatics/btw429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
MOTIVATION Recently, many methods have been developed for conducting rare-variant association studies for sequencing data. These methods have primarily been based on gene-level associations but have not been proven to be as effective as expected. Gene-set-level tests have shown great advantages over gene-level tests in terms of power and robustness, because complex diseases are often caused by multiple genes that comprise of biological gene sets. RESULTS Here, we propose several novel gene-set tests that employ rapid and efficient dimensionality reduction. The performance of these tests was investigated using extensive simulations and application to 1058 whole-exome sequences from a Korean population. We identified some known pathways and novel pathways whose rare or common variants are associated with elevated liver enzymes and replicated the results in an independent cohort. AVAILABILITY AND IMPLEMENTATION Source R code for our algorithm is freely available at http://statgen.snu.ac.kr/software/QTest CONTACT tspark@stats.snu.ac.kr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jaehoon Lee
- Department of Statistics, Seoul National University, Seoul 151-742, Korea
| | - Young Jin Kim
- Division of Structural and Functional Genomics, Korean National Institute of Health, Osong, Chungchungbuk-Do 363-951, Korea
| | - Juyoung Lee
- Division of Structural and Functional Genomics, Korean National Institute of Health, Osong, Chungchungbuk-Do 363-951, Korea
| | - Bong-Jo Kim
- Division of Structural and Functional Genomics, Korean National Institute of Health, Osong, Chungchungbuk-Do 363-951, Korea
| | - Seungyeoun Lee
- Department of Mathematics and Statistics, Sejong University, Seoul 143-747, Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul 151-742, Korea
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20
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Farooq M, Wadaan MAM. Epigenetic targets in hepatocellular carcinoma cells: identification of chaperone protein complexes with histone deacetylases. Epigenomics 2016; 5:501-12. [PMID: 24059797 DOI: 10.2217/epi.13.45] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIMS The study was designed to find out the protein complex(s) associated with HDAC3 in liver cancer using a modified form of affinity purification coupled with a mass spectrometry technique in HepG2 cells. The organ-specific requirement for HDAC1 and HDAC3 during liver formation in zebrafish and their altered expression in liver cancer tissues indicates they are indispensible for hepato-organogenesis and hepatocarcinogenesis. However, how they exert their function is unknown. MATERIAL & METHODS HepG2 cells were transfected with either mock or construct-containing HDAC3 using a C-terminal strepIII-HA tag as bait. The bait proteins were purified by double affinity columns and were analyzed on a Thermo LTQ Orbitrap™ (Thermo Scientific, MA, USA) chromatography system. RESULTS Affinity purification coupled with mass spectrometry resulted in the identification of 24 putative binders of HDAC3 in HepG2 cells. The majority (83%) of these are novel interactions are reported for the first time in this study. CONCLUSION This is the first study reporting the affinity purification and identification of protein complexes with two closely related proteins in one cell line. The novel HDAC1 and HDAC3 complexes identified in HepG2 cells could serve as a platform for the design of future therapeutic medicine for the treatment of liver cancer.
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Affiliation(s)
- Muhammad Farooq
- Bioproducts Research Chair, College of Science, Department of Zoology, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia
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21
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Li Y, Zong Y, Xiao Z, Zhu M, Xiao H, Qi J, Liu K, Wang H. Developmental Stage-Specific Embryonic Induction of HepG2 Cell Differentiation. Dig Dis Sci 2016; 61:1098-106. [PMID: 26668056 DOI: 10.1007/s10620-015-3966-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 11/07/2015] [Indexed: 01/15/2023]
Abstract
BACKGROUND Although hepatocellular carcinoma cells can sometimes undergo differentiation in an embryonic microenvironment, the mechanism is poorly understood. AIM The developmental stage-specific embryonic induction of tumor cell differentiation was investigated. METHODS Both chick and mouse liver extracts and hepatoblast-enriched cells at different developmental stages were used to treat human hepatoma HepG2 cells, and the effects on the induction of differentiation were evaluated. The nuclear factors controlling differentiation, hepatocyte nuclear factor (HNF)-4α, HNF-1α, HNF-6 and upstream stimulatory factor-1 (USF-1), and the oncogene Myc and alpha-fetoprotein (AFP) were measured. HNF-4α RNA interference was used to verify the role of HNF-4α. Embryonic induction effects were further tested in vivo by injecting HepG2 tumor cells into immunodeficient nude mice. RESULTS The 9-11-days chick liver extracts and 13.5-14.5-days mouse hepatoblast-enriched cells could inhibit proliferation and induce differentiation of HepG2 cells, leading to either death or maturation to hepatocytes. The maturation of surviving HepG2 cells was confirmed by increases in the expressions of HNF-4α, HNF-1α, HNF-6, and USF-1, and decreases in Myc and AFP. The embryonic induction of HepG2 cell maturation could be attenuated by HNF-4α RNA interference. Furthermore, the 13.5-days mouse hepatoblast culture completely eliminated HepG2 tumors with inhibited Myc and induced HNF-4α, confirming this embryonic induction effect in vivo. CONCLUSIONS This study demonstrated that developmental stage-specific embryonic induction of HepG2 cell differentiation might help in understanding embryonic differentiation and oncogenesis.
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Affiliation(s)
- Yanning Li
- Department of Molecular Biology, Hebei Key Lab of Laboratory Animal, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
| | - Yanhong Zong
- Department of Biochemistry, Hebei Key Laboratory of Medical Biotechnology, Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050017, Hebei, China
| | - Zhigang Xiao
- Department of Biochemistry, Hebei Key Laboratory of Medical Biotechnology, Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050017, Hebei, China
| | - Mengxuan Zhu
- Department of Biochemistry, Hebei Key Laboratory of Medical Biotechnology, Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050017, Hebei, China
| | - Hui Xiao
- Department of Biochemistry, Hebei Key Laboratory of Medical Biotechnology, Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050017, Hebei, China
| | - Jinsheng Qi
- Department of Biochemistry, Hebei Key Laboratory of Medical Biotechnology, Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050017, Hebei, China.
| | - Kun Liu
- Department of Biochemistry, Hebei Key Laboratory of Medical Biotechnology, Hebei Medical University, No. 361 East Zhongshan Road, Shijiazhuang, 050017, Hebei, China
| | - Hui Wang
- Department of Pathology, Hebei Medical University, Shijiazhuang, 050017, Hebei, China
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22
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Abstract
The cancer stem cell model in solid tumors has evolved significantly from the early paradigm shifting work highlighting parallels between the stem cell hierarchy in hematologic malignancies and solid tumors. Putative stem cells can dedifferentiated, be induced by context, and be the result of accumulated genetic mutations. The simple hypothesis that stem cell therapies will overcome the minority of cells that lead to recurrence has evolved with it. Nevertheless, the body of evidence that this field is clinically relevant in patients and patient care has grown with the complexity of the hypotheses, and numerous clinical strategies to target these cells have been identified. Herein we review this progress and highlight the work still outstanding.
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Affiliation(s)
- Wendy A Woodward
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
| | - Richard P Hill
- Princess Margaret Cancer Centre, Ontario Cancer Insitute, Toronto, ON, M5G 2M9, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
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23
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Berasain C, Avila MA. Regulation of hepatocyte identity and quiescence. Cell Mol Life Sci 2015; 72:3831-51. [PMID: 26089250 PMCID: PMC11114060 DOI: 10.1007/s00018-015-1970-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/23/2015] [Accepted: 06/12/2015] [Indexed: 12/11/2022]
Abstract
The liver is a highly differentiated organ with a central role in metabolism, detoxification and systemic homeostasis. To perform its multiple tasks, liver parenchymal cells, the hepatocytes, express a large complement of enabling genes defining their complex phenotype. This phenotype is progressively acquired during fetal development and needs to be maintained in adulthood to guarantee the individual's survival. Upon injury or loss of functional mass, the liver displays an extraordinary regenerative response, mainly based on the proliferation of hepatocytes which otherwise are long-lived quiescent cells. Increasing observations suggest that loss of hepatocellular differentiation and quiescence underlie liver malfunction in chronic liver disease and pave the way for hepatocellular carcinoma development. Here, we briefly review the essential mechanisms leading to the acquisition of liver maturity. We also identify the key molecular factors involved in the preservation of hepatocellular homeostasis and finally discuss potential strategies to preserve liver identity and function.
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Affiliation(s)
- Carmen Berasain
- Division of Hepatology, CIMA, University of Navarra, CIBEREHD, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Avda. Pio XII, n55, 31008, Pamplona, Spain.
| | - Matías A Avila
- Division of Hepatology, CIMA, University of Navarra, CIBEREHD, Instituto de Investigación Sanitaria de Navarra (IdiSNA), Avda. Pio XII, n55, 31008, Pamplona, Spain.
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24
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Wu J, Zhao X, Lin Z, Shao Z. A system level analysis of gastric cancer across tumor stages with RNA-seq data. MOLECULAR BIOSYSTEMS 2015; 11:1925-32. [DOI: 10.1039/c5mb00105f] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Gastric cancer is the third leading cause of cancer-related death in the world.
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Affiliation(s)
- Jun Wu
- Department of Automation
- Shanghai Jiao Tong University
- and Key Laboratory of System Control and Information Processing of Ministry of Education
- Shanghai
- China
| | - Xiaodong Zhao
- School of Biomedical Engineering
- Shanghai Jiao Tong University
- Shanghai
- China
| | - Zongli Lin
- Charles L. Brown Department of Electrical and Computer Engineering
- University of Virginia
- Charlottesville
- USA
| | - Zhifeng Shao
- School of Biomedical Engineering
- Shanghai Jiao Tong University
- Shanghai
- China
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25
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ECR-MAPK regulation in liver early development. BIOMED RESEARCH INTERNATIONAL 2014; 2014:850802. [PMID: 25580437 PMCID: PMC4281454 DOI: 10.1155/2014/850802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/27/2014] [Accepted: 09/16/2014] [Indexed: 02/06/2023]
Abstract
Early growth is connected to a key link between embryonic development and aging. In this paper, liver gene expression profiles were assayed at postnatal day 22 and week 16 of age. Meanwhile another independent animal experiment and cell culture were carried out for validation. Significance analysis of microarrays, qPCR verification, drug induction/inhibition assays, and metabonomics indicated that alpha-2u globulin (extracellular region)-socs2 (-SH2-containing signals/receptor tyrosine kinases)-ppp2r2a/pik3c3 (MAPK signaling)-hsd3b5/cav2 (metabolism/organization) plays a vital role in early development. Taken together, early development of male rats is ECR and MAPK-mediated coordination of cancer-like growth and negative regulations. Our data represent the first comprehensive description of early individual development, which could be a valuable basis for understanding the functioning of the gene interaction network of infant development.
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26
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Wang F, Yuan JH, Wang SB, Yang F, Yuan SX, Ye C, Yang N, Zhou WP, Li WL, Li W, Sun SH. Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2. Hepatology 2014; 60:1278-90. [PMID: 25043274 DOI: 10.1002/hep.27239] [Citation(s) in RCA: 352] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 05/21/2014] [Indexed: 12/14/2022]
Abstract
UNLABELLED Many protein-coding oncofetal genes are highly expressed in murine and human fetal liver and silenced in adult liver. The protein products of these hepatic oncofetal genes have been used as clinical markers for the recurrence of hepatocellular carcinoma (HCC) and as therapeutic targets for HCC. Herein we examined the expression profiles of long noncoding RNAs (lncRNAs) found in fetal and adult liver in mice. Many fetal hepatic lncRNAs were identified; one of these, lncRNA-mPvt1, is an oncofetal RNA that was found to promote cell proliferation, cell cycling, and the expression of stem cell-like properties of murine cells. Interestingly, we found that human lncRNA-hPVT1 was up-regulated in HCC tissues and that patients with higher lncRNA-hPVT1 expression had a poor clinical prognosis. The protumorigenic effects of lncRNA-hPVT1 on cell proliferation, cell cycling, and stem cell-like properties of HCC cells were confirmed both in vitro and in vivo by gain-of-function and loss-of-function experiments. Moreover, mRNA expression profile data showed that lncRNA-hPVT1 up-regulated a series of cell cycle genes in SMMC-7721 cells. By RNA pulldown and mass spectrum experiments, we identified NOP2 as an RNA-binding protein that binds to lncRNA-hPVT1. We confirmed that lncRNA-hPVT1 up-regulated NOP2 by enhancing the stability of NOP2 proteins and that lncRNA-hPVT1 function depends on the presence of NOP2. CONCLUSION Our study demonstrates that the expression of many lncRNAs is up-regulated in early liver development and that the fetal liver can be used to search for new diagnostic markers for HCC. LncRNA-hPVT1 promotes cell proliferation, cell cycling, and the acquisition of stem cell-like properties in HCC cells by stabilizing NOP2 protein. Regulation of the lncRNA-hPVT1/NOP2 pathway may have beneficial effects on the treatment of HCC.
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Affiliation(s)
- Fang Wang
- Department of Medical Genetics, Second Military Medical University, Shanghai, 200433, China; Center of Reproductive Medicine, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, 200003, China
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27
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Elizalde M, Urtasun R, Azkona M, Latasa MU, Goñi S, García-Irigoyen O, Uriarte I, Segura V, Collantes M, Di Scala M, Lujambio A, Prieto J, Ávila MA, Berasain C. Splicing regulator SLU7 is essential for maintaining liver homeostasis. J Clin Invest 2014; 124:2909-20. [PMID: 24865429 DOI: 10.1172/jci74382] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 03/28/2014] [Indexed: 12/13/2022] Open
Abstract
A precise equilibrium between cellular differentiation and proliferation is fundamental for tissue homeostasis. Maintaining this balance is particularly important for the liver, a highly differentiated organ with systemic metabolic functions that is endowed with unparalleled regenerative potential. Carcinogenesis in the liver develops as the result of hepatocellular de-differentiation and uncontrolled proliferation. Here, we identified SLU7, which encodes a pre-mRNA splicing regulator that is inhibited in hepatocarcinoma, as a pivotal gene for hepatocellular homeostasis. SLU7 knockdown in human liver cells and mouse liver resulted in profound changes in pre-mRNA splicing and gene expression, leading to impaired glucose and lipid metabolism, refractoriness to key metabolic hormones, and reversion to a fetal-like gene expression pattern. Additionally, loss of SLU7 also increased hepatocellular proliferation and induced a switch to a tumor-like glycolytic phenotype. Slu7 governed the splicing and/or expression of multiple genes essential for hepatocellular differentiation, including serine/arginine-rich splicing factor 3 (Srsf3) and hepatocyte nuclear factor 4α (Hnf4α), and was critical for cAMP-regulated gene transcription. Together, out data indicate that SLU7 is central regulator of hepatocyte identity and quiescence.
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28
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Staib F, Krupp M, Maass T, Itzel T, Weinmann A, Lee JS, Schmidt B, Müller M, Thorgeirsson SS, Galle PR, Teufel A. CellMinerHCC: a microarray-based expression database for hepatocellular carcinoma cell lines. Liver Int 2014; 34:621-31. [PMID: 24016071 PMCID: PMC6993137 DOI: 10.1111/liv.12292] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 07/24/2013] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Therapeutic options for hepatocellular carcinoma (HCC) still remain limited. Development of gene targeted therapies is a promising option. A better understanding of the underlying molecular biology is gained in in vitro experiments. However, even with targeted manipulation of gene expression varying treatment responses were observed in diverse HCC cell lines. Therefore, information on gene expression profiles of various HCC cell lines may be crucial to experimental designs. To generate a publicly available database containing microarray expression profiles of diverse HCC cell lines. METHODS Microarray data were analyzed using an individually scripted R program package. Data were stored in a PostgreSQL database with a PHP written web interface. Evaluation and comparison of individual cell line expression profiles are supported via public web interface. RESULTS This database allows evaluation of gene expression profiles of 18 HCC cell lines and comparison of differential gene expression between multiple cell lines. Analysis of commonly regulated genes for signaling pathway enrichment and interactions demonstrates a liver tumor phenotype with enrichment of major cancer related KEGG signatures like 'cancer' and 'inflammatory response'. Further molecular associations of strong scientific interest, e.g. 'lipid metabolism', were also identified. CONCLUSIONS We have generated CellMinerHCC (http://www.medicalgenomics.org/cellminerhcc), a publicly available database containing gene expression data of 18 HCC cell lines. This database will aid in the design of in vitro experiments in HCC research, because the genetic specificities of various HCC cell lines will be considered.
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Affiliation(s)
- Frank Staib
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Markus Krupp
- Institute of Computer Science, Johannes Gutenberg University, Mainz, Germany
| | - Thorsten Maass
- Department of Medicine I, University of Regensburg, Regensburg, Germany
| | - Timo Itzel
- Department of Medicine I, University of Regensburg, Regensburg, Germany
| | - Arndt Weinmann
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Ju-Seog Lee
- Kleberg Center for Molecular Markers, Department of Systems Biology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Bertil Schmidt
- Institute of Computer Science, Johannes Gutenberg University, Mainz, Germany
| | - Martina Müller
- Department of Medicine I, University of Regensburg, Regensburg, Germany
| | - Snorri S. Thorgeirsson
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Peter R. Galle
- Department of Medicine I, Johannes Gutenberg University, Mainz, Germany
| | - Andreas Teufel
- Department of Medicine I, University of Regensburg, Regensburg, Germany
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Cytomegalovirus-induced salivary gland pathology: AREG, FGF8, TNF-α, and IL-6 signal dysregulation and neoplasia. Exp Mol Pathol 2013; 94:386-97. [DOI: 10.1016/j.yexmp.2013.01.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/10/2013] [Accepted: 01/31/2013] [Indexed: 12/19/2022]
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