1
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Yang X, Lou C, Zhang Q, Liu G, Ding Y, Zhang Q, Ye C. Hypoxia-induced circRTN4IP1 promotes progression and glycolysis of hepatocellular carcinoma cells. Funct Integr Genomics 2023; 23:339. [PMID: 37982910 DOI: 10.1007/s10142-023-01256-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/21/2023]
Abstract
Hypoxia is one of the hallmarks of solid tumors, especially in hepatocellular carcinoma (HCC). CircRNAs are reported to be tightly connected to hypoxia and also have essential roles in cancer progression. However, many circRNAs implicated in hypoxia-mediated HCC progression are still unclear and require further exploration. In this study, a hypoxia cell model was structured by exposing cells to hypoxia conditions (1% O2) and normoxia conditions (21% O2) as a control. The effects of hypoxia and normoxia on cell viability, migration, invasion, and glycolysis were examined. The expressions of circRNARTN4IP1 under hypoxia were identified. Finally, molecular mechanisms and biological function of circRTN4IP1 were explored. We confirmed that hypoxia treatment facilitated capacities of proliferation, migration, invasion, and glycolysis in tumor cells. Hypoxia induced a significant increase expression of circRTN4IP1 in cells. Functionally, knockdown of circRTN4IP1 inhibited cell malignant progression and glycolysis under hypoxia HCC cells. Mechanistically, HIF1A targeted the promoter region of circRTN4IP1 and positively regulated the expression of circRTN4IP1. In addition, circRTN4IP1 targeted miR-532-5p/G6PC3 axis. In short, hypoxia induced activation of the HIF1A/circRTN4IP1/miR-532-5p/G6PC3 signaling axis, which promoted proliferation, migration, invasion, and glycolysis of HCC cells. This study may reveal a possible mechanism driving the progression of hypoxia HCC, so as to find potential effective candidates for targeting hypoxia microenvironment therapy.
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Affiliation(s)
- Xijing Yang
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China
| | - Cheng Lou
- Department of Oncology, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), Shanghai, 201805, China
| | - Qing Zhang
- Clinical Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200065, China
| | - Guofang Liu
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China
| | - Yongmei Ding
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China
| | - Qian Zhang
- Department of Biotherapy, Third Affiliated Hospital of Naval Medical University (Eastern Hepatobiliary Surgery Hospital), No. 700, North Moyu Road, Jiading District, Shanghai, 201805, China.
| | - Chun Ye
- Department of General Surgery, Tongji Hospital, Tongji University School of Medicine, No. 389, Xincun Road, Putuo District, Shanghai, 200065, China.
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2
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Lai Q, Li W, Wang H, Xu S, Deng Z. Emerging role of circRNAs in cancer under hypoxia (Review). Oncol Lett 2022; 24:372. [PMID: 36238836 PMCID: PMC9494632 DOI: 10.3892/ol.2022.13492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/12/2022] [Indexed: 11/17/2022] Open
Abstract
Circular RNA (circRNA), a recently identified type of non-coding RNAs (ncRNAs), forms a covalently closed loop with neither a 5′ cap structure nor a 3′ polyadenylated tail. Due to their lack of free ends, circRNAs are not easily cleaved by RNase R, thus avoiding degradation and being more stable than linear RNAs. Recent studies have suggested that circRNAs play a crucial role in regulating gene expression by acting as microRNAs sponges, RNA binding protein sponges and translational regulators. Currently, circRNAs are hot research topics due to their close association with the development of cancer and other diseases. Hypoxia is the most common microenvironment during tumor growth, and hypoxia-inducible factors have different effects on tumor growth and influence important cancer characteristics, including cell proliferation, apoptosis, differentiation, vascularization/angiogenesis, genetic instability, tumor metabolism, tumor immune response, invasion and metastasis. The present review aimed to study the biogenesis and mechanisms of gene regulation of circRNAs in hypoxia, to summarize the latest studies on circRNAs as potential diagnostic and prognostic biomarkers in hypoxia, and to understand the role of circRNAs in the process of tumor drug resistance under hypoxia.
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Affiliation(s)
- Qun Lai
- Department of Hematology and Oncology, The Second Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Wenqiang Li
- Department of Pulmonary and Critical Care Medicine, First People's Hospital of Zigong, Zigong, Sichuan 643000, P.R. China
| | - Hongping Wang
- Department of Neurosurgery, Tangshan Gongren Hospital of Hebei Medical University, Tangshan, Hebei 063000, P.R. China
| | - Siran Xu
- Department of Pulmonary and Critical Care Medicine, First People's Hospital of Zigong, Zigong, Sichuan 643000, P.R. China
| | - Zhiping Deng
- Department of Pulmonary and Critical Care Medicine, First People's Hospital of Zigong, Zigong, Sichuan 643000, P.R. China
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3
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Zhang F, Wang Y, Chen G, Li Z, Xing X, Putz-Bankuti C, Stauber RE, Liu X, Madl T. Growing Human Hepatocellular Tumors Undergo a Global Metabolic Reprogramming. Cancers (Basel) 2021; 13:1980. [PMID: 33924061 PMCID: PMC8074141 DOI: 10.3390/cancers13081980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy with poor prognosis, high morbidity and mortality concerning with lack of effective diagnosis and high postoperative recurrence. Similar with other cancers, HCC cancer cells have to alter their metabolism to adapt to the changing requirements imposed by the environment of the growing tumor. In less vascularized regions of tumor, cancer cells experience hypoxia and nutrient starvation. Here, we show that HCC undergoes a global metabolic reprogramming during tumor growth. A combined proteomics and metabolomics analysis of paired peritumoral and tumor tissues from 200 HCC patients revealed liver-specific metabolic reprogramming and metabolic alterations with increasing tumor sizes. Several proteins and metabolites associated with glycolysis, the tricarboxylic acid cycle and pyrimidine synthesis were found to be differentially regulated in serum, tumor and peritumoral tissue with increased tumor sizes. Several prognostic metabolite biomarkers involved in HCC metabolic reprogramming were identified and integrated with clinical and pathological data. We built and validated this combined model to discriminate against patients with different recurrence risks. An integrated and comprehensive metabolomic analysis of HCC is provided by our present work. Metabolomic alterations associated with the advanced stage of the disease and poor clinical outcomes, were revealed. Targeting cancer metabolism may deliver effective therapies for HCC.
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Affiliation(s)
- Fangrong Zhang
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria;
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Geng Chen
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Zhenli Li
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Xiaohua Xing
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
| | - Csilla Putz-Bankuti
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (C.P.-B.); (R.E.S.)
| | - Rudolf E. Stauber
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria; (C.P.-B.); (R.E.S.)
| | - Xiaolong Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China; (Y.W.); (G.C.); (Z.L.); (X.X.)
- Xiamen Institute of Rare Earth Materials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Xiamen 361024, China
| | - Tobias Madl
- Gottfried Schatz Research Center, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstraße 6/6, 8010 Graz, Austria;
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
- Xiamen Institute of Rare Earth Materials, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Xiamen 361024, China
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Xing X, Yuan H, Liu H, Tan X, Zhao B, Wang Y, Ouyang J, Lin M, Liu X, Huang A. Quantitative Secretome Analysis Reveals Clinical Values of Carbonic Anhydrase II in Hepatocellular Carcinoma. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:94-107. [PMID: 33662630 PMCID: PMC8498920 DOI: 10.1016/j.gpb.2020.09.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/15/2020] [Accepted: 11/03/2020] [Indexed: 12/24/2022]
Abstract
Early detection and intervention are key strategies to reduce mortality, increase long-term survival, and improve the therapeutic effects of hepatocellular carcinoma (HCC) patients. Herein, the isobaric tag for relative and absolute quantitation (iTRAQ)-based quantitative proteomic strategy was used to study the secretomes in conditioned media from HCC cancerous tissues, surrounding noncancerous tissues, and distal noncancerous tissues to identify diagnostic and prognostic biomarkers for HCC. In total, 22 and 49 dysregulated secretory proteins were identified in the cancerous and surrounding noncancerous tissues, respectively, compared with the distal noncancerous tissues. Among these proteins, carbonic anhydrase II (CA2) was identified to be significantly upregulated in the secretome of cancerous tissues; correspondingly, the serum concentrations of CA2 were remarkably increased in HCC patients compared with that in normal populations. Interestingly, a significant increase of serum CA2 in recurrent HCC patients after radical resection was also confirmed compared with HCC patients without recurrence, and the serum level of CA2 could act as an independent prognostic factor for time to recurrence and overall survival. Regarding the mechanism, the secreted CA2 enhances the migration and invasion of HCC cells by activating the epithelial mesenchymal transition pathway. Taken together, this study identified a novel biomarker for HCC diagnosis and prognosis, and provided a valuable resource of HCC secretome for investigating serological biomarkers.
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Affiliation(s)
- Xiaohua Xing
- Department of Pathology and Institute of Oncology, School of Basic Medical Sciences of Fujian Medical University, Fuzhou 350004, China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Hui Yuan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Hongzhi Liu
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xionghong Tan
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Bixing Zhao
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Yingchao Wang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Jiahe Ouyang
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Minjie Lin
- The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China
| | - Xiaolong Liu
- Department of Pathology and Institute of Oncology, School of Basic Medical Sciences of Fujian Medical University, Fuzhou 350004, China; The United Innovation of Mengchao Hepatobiliary Technology Key Laboratory of Fujian Province, Mengchao Hepatobiliary Hospital of Fujian Medical University, Fuzhou 350025, China.
| | - Aimin Huang
- Department of Pathology and Institute of Oncology, School of Basic Medical Sciences of Fujian Medical University, Fuzhou 350004, China.
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5
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Weng S, Wang M, Zhao Y, Ying W, Qian X. Optimised data-independent acquisition strategy recaptures the classification of early-stage hepatocellular carcinoma based on data-dependent acquisition. J Proteomics 2021; 238:104152. [PMID: 33609755 DOI: 10.1016/j.jprot.2021.104152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 01/21/2021] [Accepted: 02/08/2021] [Indexed: 12/27/2022]
Abstract
Proteomics is increasingly used for exploring disease biomarkers and therapeutic targets. The data-independent acquisition (DIA) method collects all peptide signals in a sample, and provides a convenient way to archive disease-related molecular features for further exploration. In this study, we first established a high-coverage human hepatocellular carcinoma (HCC) spectral library containing 9393 protein groups, 119,903 peptides. Furthermore, we optimised the DIA method with respect to four key parameters: settings for mass spectrometry acquisition, gradient length, amount of sample loading, and length of analytical column. More than 6000 proteins from HepG2 cells could be stably quantified using the optimised one-shot DIA approach with a 2 h gradient time. One-shot DIA identified a similar number of proteins as did multi-fraction data-dependent acquisition (DDA) from the same group of HCC samples, but at a quarter of the total acquisition time. DIA data could recapture the classification results obtained from DDA data, thus paving the way for large-scale, multi-centre proteomics analysis of clinical samples. SIGNIFICANCE: The organ-specific spectral library for HCC and the optimised 2 h DIA approach met the urgent demands for large-scale quantitative proteomics analysis of HCC clinical samples. Compared with multi-fraction-DDA, the optimised one-shot DIA could reach a similar identification while consuming shorter acquisition time, thus making it possible to analyse thousands of clinical samples.
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Affiliation(s)
- Shuang Weng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Mingchao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yingyi Zhao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wantao Ying
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
| | - Xiaohong Qian
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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6
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Qin S, Li B, Li R, Cai Y, Zheng K, Huang H, Xiao F, Zeng M, Xu X. Proteomic characteristics and identification of PM 2.5-induced differentially expressed proteins in hepatocytes and c-Myc silenced hepatocytes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 209:111838. [PMID: 33387776 DOI: 10.1016/j.ecoenv.2020.111838] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/16/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Proteomics and bioinformatics were applied to explore PM2.5-induced differentially expressed proteins (DEPs) in hepatocytes (L02 cells) and c-Myc-silenced hepatocytes. L02 cells and c-Myc-silenced hepatocytes were treated with PM2.5 for 24 h. Fifty-two DEPs were screened in L02 hepatocytes, of which 28 were upregulated and 24 were downregulated. Forty-one DEPs were screened in the c-Myc-silenced hepatocytes, of which 31 were upregulated and 10 were downregulated. GO analysis showed that DEPs in L02 cells were mainly concentrated in the cytosol and were involved in biological processes such as the response to metal ions. DEPs in c-Myc-silenced cells were mainly enriched in the extracellular space and were involved in lipoprotein metabolism. KEGG analysis showed that DEPs in L02 cells were mainly involved in arachidonic acid metabolism and mineral absorption. DEPs in c-Myc-silenced cells were mainly enriched in pathways involving nerve absorption, complement and coagulation cascades, and other pathways. Twenty key proteins, including Metallothionein-2A (MT2A), Metallothionein-1X (MT1X), zinc transporter ZIP10 (SLC39A10) and Serine protease 23 (PRSS23) were screened in two groups through analysis of protein-protein interactions. Based on the identification of the selected DEPs, PRSS23 and SLC39A10 might be the potential biomarker of PM2.5-induced carcinogenesis, which provide the scientific basis for further research into the carcinogenic mechanisms of PM2.5.
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Affiliation(s)
- Shuangjian Qin
- Xiangya School of Public Health, Central South University, Changsha, Hunan 410078, China; Institute of environment and health, Shenzhen center for disease control and prevention, Shenzhen, Guangdong 518055, China
| | - Boru Li
- Xiangya School of Public Health, Central South University, Changsha, Hunan 410078, China; Institute of environment and health, Shenzhen center for disease control and prevention, Shenzhen, Guangdong 518055, China
| | - Runbing Li
- Institute of environment and health, Shenzhen center for disease control and prevention, Shenzhen, Guangdong 518055, China; School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Ying Cai
- Institute of environment and health, Shenzhen center for disease control and prevention, Shenzhen, Guangdong 518055, China; School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Kai Zheng
- Institute of environment and health, Shenzhen center for disease control and prevention, Shenzhen, Guangdong 518055, China; School of public health, University of South China, Hengyang, Hunan 421001, China
| | - Haiyan Huang
- Institute of environment and health, Shenzhen center for disease control and prevention, Shenzhen, Guangdong 518055, China
| | - Fang Xiao
- Xiangya School of Public Health, Central South University, Changsha, Hunan 410078, China.
| | - Ming Zeng
- Xiangya School of Public Health, Central South University, Changsha, Hunan 410078, China.
| | - Xinyun Xu
- Institute of environment and health, Shenzhen center for disease control and prevention, Shenzhen, Guangdong 518055, China.
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7
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Shu J, Du J, Wang F, Cheng Y, Chen G, Xu B, Zhang D, Chen S. Circ_0091579 enhances the malignancy of hepatocellular carcinoma via miR-1287/PDK2 axis. Open Life Sci 2021; 16:69-83. [PMID: 33817300 PMCID: PMC7874672 DOI: 10.1515/biol-2021-0009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 01/03/2023] Open
Abstract
Several articles have indicated that circular RNAs are involved in pathogenesis of human cancers. Nevertheless, the role of circ_0091579 in hepatocellular carcinoma (HCC) progression remains to be revealed. Quantitative reverse transcriptase polymerase chain reaction was carried out to examine the expression of circ_0091579 and miR-1287. The proliferation of HCC cells was determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Flow cytometry was performed to analyze cell cycle progression and apoptosis. Western blot assay was conducted to detect the protein expression of CyclinD1, Cleaved caspase3, and pyruvate dehydrogenase kinase 2 (PDK2). Cell glycolysis was evaluated by measuring the uptake of glucose, the production of lactate, and extracellular acidification rate. The target relationship between miR-1287 and circ_0091579 or PDK2 was verified by dual-luciferase reporter assay, RNA immunoprecipitation assay, and RNA-pull down assay. The enrichment of circ_0091579 was enhanced in HCC tissues (n = 77) and four HCC cell lines (HB611, Huh-7, MHCC97, and SNU423) compared with adjacent non-tumor tissues (n = 77) and normal human liver cell line THLE-2. Circ_0091579 mediated the promotion of proliferation and glycolysis and the suppression of apoptosis of HCC cells. MiR-1287 was a direct target of circ_0091579 in HCC cells. MiR-1287 knockdown reversed the effects caused by circ_0091579 interference on the functions of HCC cells. PDK2 could bind to miR-1287 in HCC cells. Circ_0091579 upregulated the enrichment of PDK2 by acting as a sponge of miR-1287 in HCC cells. The influence caused by circ_0091579 intervention on HCC cells was attenuated by overexpression of PDK2. Circ_0091579 interference impeded the progression of HCC in vivo. Circ_0091579 deteriorated HCC by promoting the proliferation and glycolytic metabolism and suppressing the apoptosis of HCC cells via miR-1287/PDK2 axis.
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Affiliation(s)
- Junwei Shu
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
| | - Jiayuan Du
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
| | - Futao Wang
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
| | - Yong Cheng
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
| | - Gangxin Chen
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
| | - Bing Xu
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
| | - Dianpeng Zhang
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
| | - Shuangjiang Chen
- Department of General Surgery, Ankang People's Hospital of Shanxi Province, Ankang, 6-1-3302, Shifu Courtyard, High-Tech Zone, Ankang 725000, Shanxi Province, China
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8
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Lam S, Bayraktar A, Zhang C, Turkez H, Nielsen J, Boren J, Shoaie S, Uhlen M, Mardinoglu A. A systems biology approach for studying neurodegenerative diseases. Drug Discov Today 2020; 25:1146-1159. [PMID: 32442631 DOI: 10.1016/j.drudis.2020.05.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 04/13/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023]
Abstract
Neurodegenerative diseases (NDDs), such as Alzheimer's (AD) and Parkinson's (PD), are among the leading causes of lost years of healthy life and exert a great strain on public healthcare systems. Despite being first described more than a century ago, no effective cure exists for AD or PD. Although extensively characterised at the molecular level, traditional neurodegeneration research remains marred by narrow-sense approaches surrounding amyloid β (Aβ), tau, and α-synuclein (α-syn). A systems biology approach enables the integration of multi-omics data and informs discovery of biomarkers, drug targets, and treatment strategies. Here, we present a comprehensive timeline of high-throughput data collection, and associated biotechnological advancements and computational analysis related to AD and PD. We hereby propose that a philosophical change in the definitions of AD and PD is now needed.
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Affiliation(s)
- Simon Lam
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Abdulahad Bayraktar
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Cheng Zhang
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-17121, Sweden
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, 25240, Turkey
| | - Jens Nielsen
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Jan Boren
- Department of Molecular and Clinical Medicine, University of Gothenburg, The Wallenberg Laboratory, Sahlgrenska University Hospital, Gothenburg, SE-413 45, Sweden
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-17121, Sweden
| | - Mathias Uhlen
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-17121, Sweden
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK; Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, SE-17121, Sweden.
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9
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Tan Y, Du B, Zhan Y, Wang K, Wang X, Chen B, Wei X, Xiao J. Antitumor effects of circ-EPHB4 in hepatocellular carcinoma via inhibition of HIF-1α. Mol Carcinog 2019; 58:875-886. [PMID: 30644610 DOI: 10.1002/mc.22976] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 12/14/2022]
Abstract
The protein EPHB4 plays a vital role in various tumor types. However, few studies into the function of circ-EPHB4 (hsa_circ_0001730) in tumors have been conducted. This study aimed to investigate the functions of circ-EPHB4 and the underlying mechanism of circ-EPHB4 in regulating hepatocellular carcinoma (HCC). The expression of circ-EPHB4 was found to be downregulated in HCC tumor tissues, whereas circ-EPHB4 overexpression suppressed cell viability, induced apoptosis, and inhibited cell migration and invasion in Huh7 and HepG2 cells. circ-EPHB4 levels were negatively correlated with tumor weight, size, and metastasis foci in nude mouse models, suggesting circ-EPHB4 inhibits tumorigenesis, tumor development, and metastasis. In addition, HIF-1α and PI3K-AKT pathways were markedly affected by circ-EPHB4 overexpression. HIF-1α could potentially be the target of circ-EPHB4. By overexpressing both HIF-1α and circ-EPHB4, the antitumor effect of circ-EPHB4 should be most probably correlated with HIF-1α. In conclusion, circ-EPHB4 is a tumor inhibitor in HCC and functions by inhibiting HIF-1α expression.
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Affiliation(s)
- Yuhui Tan
- Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Biaoyan Du
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yujuan Zhan
- Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Kun Wang
- Department of Pathology, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xiaolan Wang
- Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Bonan Chen
- Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xianli Wei
- Department of Medical Instruments, Guangdong Food and Drug Vocational College, Guangzhou, Guangdong, China
| | - Jianyong Xiao
- Department of Biochemistry, Guangzhou University of Chinese Medicine, Guangzhou, China
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10
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Mato JM, Elortza F, Lu SC, Brun V, Paradela A, Corrales FJ. Liver cancer-associated changes to the proteome: what deserves clinical focus? Expert Rev Proteomics 2018; 15:749-756. [PMID: 30204005 DOI: 10.1080/14789450.2018.1521277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is recognized as the fifth most common neoplasm and currently represents the second leading form of cancer-related death worldwide. Despite great progress has been done in the understanding of its pathogenesis, HCC represents a heavy societal and economic burden as most patients are still diagnosed at advanced stages and the 5-year survival rate remain below 20%. Early detection and revolutionary therapies that rely on the discovery of new molecular biomarkers and therapeutic targets are therefore urgently needed to develop precision medicine strategies for a more efficient management of patients. Areas covered: This review intends to comprehensively analyse the proteomics-based research conducted in the last few years to address some of the principal still open riddles in HCC biology, based on the identification of molecular drivers of tumor progression and metastasis. Expert commentary: The technical advances in mass spectrometry experienced in the last decade have significantly improved the analytical capacity of proteome wide studies. Large-scale protein and protein variant (post-translational modifications) identification and quantification have allowed detailed dissections of molecular mechanisms underlying HCC progression and are already paving the way for the identification of clinically relevant proteins and the development of their use on patient care.
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Affiliation(s)
- José M Mato
- a CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park , Derio , Spain.,b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain
| | - Félix Elortza
- a CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park , Derio , Spain.,b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain
| | - Shelly C Lu
- c Division of Digestive and Liver Diseases , Cedars-Sinai Medical Center , LA , CA , USA
| | - Virginie Brun
- d Université Grenoble-Alpes, CEA, BIG, Biologie à Grande Echelle, Inserm , Grenoble , France
| | - Alberto Paradela
- e Functional Proteomics Laboratory , Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, CIBERehd , Madrid , Spain
| | - Fernando J Corrales
- b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain.,e Functional Proteomics Laboratory , Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, CIBERehd , Madrid , Spain
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11
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Promoting Collaborations Between Radiologists and Scientists. Acad Radiol 2018; 25:9-17. [PMID: 28844844 DOI: 10.1016/j.acra.2017.05.020] [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] [Received: 01/31/2017] [Revised: 04/30/2017] [Accepted: 05/02/2017] [Indexed: 12/17/2022]
Abstract
Radiology as a discipline thrives on the dynamic interplay between technological and clinical advances. Progress in almost all facets of the imaging sciences is highly dependent on complex tools sourced from physics, engineering, biology, and the clinical sciences to obtain, process, and view imaging studies. The application of these tools, however, requires broad and deep medical knowledge about disease pathophysiology and its relationship with medical imaging. This relationship between clinical medicine and imaging technology, nurtured and fostered over the past 75 years, has cultivated extraordinarily rich collaborative opportunities between basic scientists, engineers, and physicians. In this review, we attempt to provide a framework to identify both currently successful collaborative ventures and future opportunities for scientific partnership. This invited review is a product of a special working group within the Association of University Radiologists-Radiology Research Alliance.
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12
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Mora MI, Molina M, Odriozola L, Elortza F, Mato JM, Sitek B, Zhang P, He F, Latasa MU, Ávila MA, Corrales FJ. Prioritizing Popular Proteins in Liver Cancer: Remodelling One-Carbon Metabolism. J Proteome Res 2017; 16:4506-4514. [PMID: 28944671 DOI: 10.1021/acs.jproteome.7b00390] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Primary liver cancer (HCC) is recognized as the fifth most common neoplasm and the second leading cause of cancer death worldwide. Most risk factors are known, and the molecular pathogenesis has been widely studied in the past decade; however, the underlying molecular mechanisms remain to be unveiled, as they will facilitate the definition of novel biomarkers and clinical targets for more effective patient management. We utilize the B/D-HPP popular protein strategy. We report a list of popular proteins that have been highly cocited with the expression "liver cancer". Several enzymes highlight the known metabolic remodeling of liver cancer cells, four of which participate in one-carbon metabolism. This pathway is central to the maintenance of differentiated hepatocytes, as it is considered the connection between intermediate metabolism and epigenetic regulation. We designed a targeted selective reaction monitoring (SRM) method to follow up one-carbon metabolism adaptation in mouse HCC and in regenerating liver following exposure to CCl4. This method allows systematic monitoring of one-carbon metabolism and could prove useful in the follow-up of HCC and of chronically liver-diseased patients (cirrhosis) at risk of HCC. The SRM data are available via ProteomeXchange in PASSEL (PASS01060).
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Affiliation(s)
- María Isabel Mora
- Proteomics Laboratory, CIMA, University of Navarra , ProteoRed-ISCIII, 31008 Pamplona, Spain
| | - Manuela Molina
- Proteomics Laboratory, CIMA, University of Navarra , ProteoRed-ISCIII, 31008 Pamplona, Spain
| | - Leticia Odriozola
- Proteomics Laboratory, CIMA, University of Navarra , ProteoRed-ISCIII, 31008 Pamplona, Spain
| | - Félix Elortza
- Proteomics Platform, CIC bioGUNE , CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - José María Mato
- Proteomics Platform, CIC bioGUNE , CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park, 48160 Derio, Spain
| | - Barbara Sitek
- Medizinisches Proteom-Center, Ruhr-Universität Bochum , 44801 Bochum, Germany
| | - Pumin Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100039, China.,National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine , Beijing 100039, China.,National Center for Protein Sciences (The PHOENIX Center, Beijing) , Beijing 102206, China
| | - María Uxue Latasa
- Hepatology Laboratory, CIMA, University of Navarra , CIBERehd, 31008 Pamplona, Spain
| | - Matías Antonio Ávila
- Hepatology Laboratory, CIMA, University of Navarra , CIBERehd, 31008 Pamplona, Spain
| | - Fernando José Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología-CSIC , Proteored-ISCIII, CIBERehd. 28049 Madrid, Spain
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13
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Yang X, Xiong Q, Wu Y, Li S, Ge F. Quantitative Proteomics Reveals the Regulatory Networks of Circular RNA CDR1as in Hepatocellular Carcinoma Cells. J Proteome Res 2017; 16:3891-3902. [PMID: 28892615 DOI: 10.1021/acs.jproteome.7b00519] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Circular RNAs (circRNAs), a class of widespread endogenous RNAs, play crucial roles in diverse biological processes and are potential biomarkers in diverse human diseases and cancers. Cerebellar-degeneration-related protein 1 antisense RNA (CDR1as), an oncogenic circRNA, is involved in human tumorigenesis and is dysregulated in hepatocellular carcinoma (HCC). However, the molecular mechanisms underlying CDR1as functions in HCC remain unclear. Here we explored the functions of CDR1as and searched for CDR1as-regulated proteins in HCC cells. A quantitative proteomics strategy was employed to globally identify CDR1as-regulated proteins in HCC cells. In total, we identified 330 differentially expressed proteins (DEPs) upon enhanced CDR1as expression in HepG2 cells, indicating that they could be proteins regulated by CDR1as. Bioinformatic analysis revealed that many DEPs were involved in cell proliferation and the cell cycle. Further functional studies of epidermal growth factor receptor (EGFR) found that CDR1as exerts its effects on cell proliferation at least in part through the regulation of EGFR expression. We further confirmed that CDR1as could inhibit the expression of microRNA-7 (miR-7). EGFR is a validated target of miR-7; therefore, CDR1as may exert its function by regulating EGFR expression via targeting miR-7 in HCC cells. Taken together, we revealed novel functions and underlying mechanisms of CDR1as in HCC cells. This study serves as the first proteome-wide analysis of a circRNA-regulated protein in cells and provides a reliable and highly efficient method for globally identifying circRNA-regulated proteins.
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Affiliation(s)
- Xue Yang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Qian Xiong
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China
| | - Ying Wu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Siting Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China.,University of Chinese Academy of Sciences , Beijing 100049, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences , Wuhan 430072, China
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14
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Qin G, Dang M, Gao H, Wang H, Luo F, Chen R. Deciphering the protein–protein interaction network regulating hepatocellular carcinoma metastasis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [DOI: 10.1016/j.bbapap.2017.06.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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