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Zhong W, Wang D, Yao B, Chen X, Wang Z, Qu H, Ma B, Ye L, Qiu J. Integrative analysis of prognostic long non-coding RNAs with copy number variation in bladder cancer. J Zhejiang Univ Sci B 2021; 22:664-681. [PMID: 34414701 DOI: 10.1631/jzus.b2000494] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Copy number variations (CNVs), which can affect the role of long non-coding RNAs (lncRNAs), are important genetic changes seen in some malignant tumors. We analyzed lncRNAs with CNV to explore the relationship between lncRNAs and prognosis in bladder cancer (BLCA). Messenger RNA (mRNA) expression levels, DNA methylation, and DNA copy number data of 408 BLCA patients were subjected to integrative bioinformatics analysis. Cluster analysis was performed to obtain different subtypes and differently expressed lncRNAs and coding genes. Weighted gene co-expression network analysis (WGCNA) was performed to identify the co-expression gene and lncRNA modules. CNV-associated lncRNA data and their influence on cancer prognosis were assessed with Kaplan-Meier survival curve. Multi-omics integration analysis revealed five prognostic lncRNAs with CNV, namely NR2F1-AS1, LINC01138, THUMPD3-AS1, LOC101928489,and TMEM147-AS1,and a risk-score signature related to overall survival in BLCA was identified. Moreover, validated results in another independent Gene Expression Omnibus (GEO) dataset, GSE31684, were consistent with these results. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the mitogen-activated protein kinase (MAPK) signaling pathway, focal adhesion pathway, and Janus kinase-signal transducers and activators of transcription (JAK-STAT) signaling pathway were enriched in a high-risk score pattern, suggesting that imbalance in these pathways is closely related to tumor development. We revealed the prognosis-related lncRNAs by analyzing the expression profiles of lncRNAs and CNVs, which can be used as prognostic biomarkers for BLCA.
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Affiliation(s)
- Wenwen Zhong
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Dejuan Wang
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Bing Yao
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Xiaoxia Chen
- Department of Medical Record Management Section, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Zhongyang Wang
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Hu Qu
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Bo Ma
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Lei Ye
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China
| | - Jianguang Qiu
- Department of Urology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510655, China.
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Tompkins SC, Sheldon RD, Rauckhorst AJ, Noterman MF, Solst SR, Buchanan JL, Mapuskar KA, Pewa AD, Gray LR, Oonthonpan L, Sharma A, Scerbo DA, Dupuy AJ, Spitz DR, Taylor EB. Disrupting Mitochondrial Pyruvate Uptake Directs Glutamine into the TCA Cycle away from Glutathione Synthesis and Impairs Hepatocellular Tumorigenesis. Cell Rep 2020; 28:2608-2619.e6. [PMID: 31484072 PMCID: PMC6746334 DOI: 10.1016/j.celrep.2019.07.098] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 06/14/2019] [Accepted: 07/26/2019] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a devastating cancer increasingly caused by non-alcoholic fatty liver disease (NAFLD). Disrupting the liver Mitochondrial Pyruvate Carrier (MPC) in mice attenuates NAFLD. Thus, we considered whether liver MPC disruption also prevents HCC. Here, we use the N-nitrosodiethylamine plus carbon tetrachloride model of HCC development to test how liver-specific MPC knock out affects hepatocellular tumorigenesis. Our data show that liver MPC ablation markedly decreases tumorigenesis and that MPC-deficient tumors transcriptomically downregulate glutathione metabolism. We observe that MPC disruption and glutathione depletion in cultured hepatomas are synthetically lethal. Stable isotope tracing shows that hepatocyte MPC disruption reroutes glutamine from glutathione synthesis into the tricarboxylic acid (TCA) cycle. These results support a model where inducing metabolic competition for glutamine by MPC disruption impairs hepatocellular tumorigenesis by limiting glutathione synthesis. These findings raise the possibility that combining MPC disruption and glutathione stress may be therapeutically useful in HCC and additional cancers. Tompkins et al. utilize stable glutamine isotope tracers in vivo and ex vivo to demonstrate hepatocyte MPC disruption increases TCA cycle glutamine utilization at the expense of glutathione synthesis and decreases hepatocellular tumorigenesis.
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Affiliation(s)
- Sean C Tompkins
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Ryan D Sheldon
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Adam J Rauckhorst
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Maria F Noterman
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Shane R Solst
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Jane L Buchanan
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Kranti A Mapuskar
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Alvin D Pewa
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; FOEDRC Metabolomics Core Research Facility, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Lawrence R Gray
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Lalita Oonthonpan
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Arpit Sharma
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Diego A Scerbo
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Douglas R Spitz
- Free Radical and Radiation Biology Program, Department of Radiation Oncology, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
| | - Eric B Taylor
- Department of Biochemistry, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Fraternal Order of Eagles Diabetes Research Center (FOEDRC), University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Abboud Cardiovascular Research Center, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; Pappajohn Biomedical Institute, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA; FOEDRC Metabolomics Core Research Facility, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA.
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Fu L, Yao T, Chen Q, Mo X, Hu Y, Guo J. Screening differential circular RNA expression profiles reveals hsa_circ_0004018 is associated with hepatocellular carcinoma. Oncotarget 2017; 8:58405-58416. [PMID: 28938566 PMCID: PMC5601662 DOI: 10.18632/oncotarget.16881] [Citation(s) in RCA: 148] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 03/14/2017] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) have been emerged as an indispensable part of endogenous RNA network. However, the expression significance of circRNAs in hepatocellular carcinoma (HCC) is rarely revealed. The aim of this study was to determine the circRNA expression profile in HCC, and to investigate their clinical significances and relevant mechanisms for cancer progression. The global circRNA expression profile in HCC was measured by circRNA microarray. Levels of one representative circRNAs, hsa_circ_0004018, were confirmed by real-time reverse transcription-polymerase chain reaction. The expression levels of hsa_circ_0004018 in HCC were significantly lower compared with para-tumorous tissue (P<0.001). Our data further showed that lower expression of hsa_circ_0004018 was correlated with serum alpha-fetoprotein (AFP) level, tumor diameters, differentiation, Barcelona Clinic Liver Cancer stage and Tumor-node-metastasis stage. More importantly, we detected liver tissues from chronic hepatitis, cirrhosis and HCC patients; and found that hsa_circ_0004018 harbored HCC-stage-specific expression features in diverse chronic liver diseases (P<0.001). The area under receiver operating characteristic curve was up to 0.848 (95% CI=0.803–0.894, P<0.001). The sensitivity and specificity were 0.716 and 0.815, respectively. Finally, hsa_circ_0004018 might be involved in cancer-related pathways via interactions with miRNAs.
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Affiliation(s)
- Liyun Fu
- Department of Hepatology, Ningbo No. 2 Hospital and The Affiliated Hospital, Medical School of Ningbo University, Ningbo 315010, China
| | - Ting Yao
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Qingqing Chen
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Xiaoyan Mo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
| | - Yaoren Hu
- Department of Hepatology, Ningbo No. 2 Hospital and The Affiliated Hospital, Medical School of Ningbo University, Ningbo 315010, China
| | - Junming Guo
- Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Medical School of Ningbo University, Ningbo 315211, China
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Hu MH, Ma CY, Wang XM, Ye CD, Zhang GX, Chen L, Wang JG. MicroRNA-126 inhibits tumor proliferation and angiogenesis of hepatocellular carcinoma by down-regulating EGFL7 expression. Oncotarget 2016; 7:66922-66934. [PMID: 27611944 PMCID: PMC5341847 DOI: 10.18632/oncotarget.11877] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 08/12/2016] [Indexed: 12/25/2022] Open
Abstract
This study aims to explore the effects of microRNA-126 (miR-126) on tumor proliferation and angiogenesis of hepatocellular carcinoma (HCC) by targeting EGFL7. HCC tissues and adjacent normal tissues were obtained from 71 HCC patients. Immunohistochemistry (IHC) was conducted to detect expressions of EGFL7 and VEGF and the micro-vessel density (MVD). HCC cell lines were collected and assigned into the blank, miR-126 mimics, miR-126 inhibitors, miR-126 mimics negative control (NC), miR-126 inhibitors NC, si-EGFL7, and miR-126 inhibitors + si-EGFL7 groups. Expressions of miR-126 and EGFL7 mRNA were detected by qRT-PCR assay. The protein expressions of EGFL7 and VEGF were measured by Western blotting. MTT assay was used to measure the proliferation of HCC cells. Tumor xenograft model in nude mice was utilized to evaluate the influence of miR-126 on tumor growth. HCC tissues had higher miR-126 expression and lower EGFL7 mRNA expression than adjacent normal tissues. Compared with the blank, miR-126 mimic NC, miR-126 inhibitor NC and miR-126 inhibitors + si-EGFL7 groups, the protein expressions of EGFL7 and VEGF and cell proliferation were reduced in the miR-126 mimics and si-EGFL7 groups, while the opposite trend was found in the miR-126 inhibitors group. Compared with the blank and miR-126 inhibitors + siRNA-EGFL7 groups, tumor size, tumor weight, and MVD of transplanted tumors in nude mice were significantly reduced in the miR-126 mimics and siRNA-EGFL7 groups, while the opposite trend was found in the miR-126 inhibitors group. In conclusion, miR-126 could inhibit tumor proliferation and angiogenesis of HCC by down-regulating EGFL7 expression.
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Affiliation(s)
- Ming-Hua Hu
- 1 Department of Surgery, Yijishan Hospital, Wannan Medical College, Wuhu 241001, P.R. China
| | - Chen-Yang Ma
- 1 Department of Surgery, Yijishan Hospital, Wannan Medical College, Wuhu 241001, P.R. China
| | - Xiao-Ming Wang
- 1 Department of Surgery, Yijishan Hospital, Wannan Medical College, Wuhu 241001, P.R. China
| | - Chen-Dong Ye
- 2 Department of Surgery, The Second Affiliated Hospital, Wannan Medical College, Wuhu 241001, P.R. China
| | - Guang-Xian Zhang
- 1 Department of Surgery, Yijishan Hospital, Wannan Medical College, Wuhu 241001, P.R. China
| | - Lin Chen
- 1 Department of Surgery, Yijishan Hospital, Wannan Medical College, Wuhu 241001, P.R. China
| | - Jin-Guo Wang
- 1 Department of Surgery, Yijishan Hospital, Wannan Medical College, Wuhu 241001, P.R. China
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Chappell G, Silva GO, Uehara T, Pogribny IP, Rusyn I. Characterization of copy number alterations in a mouse model of fibrosis-associated hepatocellular carcinoma reveals concordance with human disease. Cancer Med 2016; 5:574-85. [PMID: 26778414 PMCID: PMC4799957 DOI: 10.1002/cam4.606] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/22/2015] [Accepted: 11/16/2015] [Indexed: 12/16/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a prevalent human cancer with rising incidence worldwide. Human HCC is frequently associated with chronic liver inflammation and cirrhosis, pathophysiological processes that are a consequence of chronic viral infection, disturbances in metabolism, or exposure to chemical toxicants. To better characterize the pathogenesis of HCC, we used a human disease‐relevant mouse model of fibrosis‐associated hepatocarcinogenesis. In this model, marked liver tumor response caused by the promutagenic chemical N‐nitrosodiethylamine in the presence of liver fibrosis was associated with epigenetic events indicative of genomic instability. Therefore, we hypothesized that DNA copy number alterations (CNAs), a feature of genomic instability and a common characteristic of cancer, are concordant between human HCC and mouse models of fibrosis‐associated hepatocarcinogenesis. We evaluated DNA CNAs and changes in gene expression in the mouse liver (normal, tumor, and nontumor fibrotic tissues). Additionally, we compared our findings to DNA CNAs in human HCC cases (tumor and nontumor cirrhotic/fibrotic tissues) using publicly available data from The Cancer Genome Atlas (TCGA). We observed that while fibrotic liver tissue is largely devoid of DNA CNAs, highly frequently occurring DNA CNAs are found in mouse tumors, which is indicative of a profound increase in chromosomal instability in HCC. The cross‐species gene‐level comparison of CNAs identified shared regions of CNAs between human fibrosis‐ and cirrhosis‐associated liver tumors and mouse fibrosis‐associated HCC. Our results suggest that CNAs most commonly arise in neoplastic tissue rather than in fibrotic or cirrhotic liver, and demonstrate the utility of this mouse model in replicating the molecular features of human HCC.
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Affiliation(s)
- Grace Chappell
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, 77843.,Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Grace O Silva
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, 27599.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill, North Carolina, 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Takeki Uehara
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina, 27599
| | - Igor P Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, 72079
| | - Ivan Rusyn
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas, 77843
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