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Angata K, Sawaki H, Tsujikawa S, Ocho M, Togayachi A, Narimatsu H. Glycogene Expression Profiling of Hepatic Cells by RNA-Seq Analysis for Glyco-Biomarker Identification. Front Oncol 2020; 10:1224. [PMID: 32850363 PMCID: PMC7402167 DOI: 10.3389/fonc.2020.01224] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/15/2020] [Indexed: 01/01/2023] Open
Abstract
Glycans are primarily generated by “glycogenes,” which consist of more than 200 genes for glycosynthesis, including sugar-nucleotide synthases, sugar-nucleotide transporters, and glycosyltransferases. Measuring the expression level of glycogenes is one of the approaches to analyze the glycomes of particular biological and clinical samples. To develop an effective strategy for identifying the glycosylated biomarkers, we performed transcriptome analyses using quantitative real-time polymerase chain reaction (qRT-PCR) arrays and RNA sequencing (RNA-Seq). First, we measured and analyzed the transcriptome from the primary culture of human liver cells and hepatocarcinoma cells using RNA-Seq. This analysis revealed similar but distinctive expression profiles of glycogenes among hepatic cells as indicated by the qRT-PCR arrays, which determined a copy number of 186 glycogenes. Both data sets indicated that altered expression of glycosyltransferases affect the glycosylation of particular glycoproteins, which is consistent with the mass analysis data. Moreover, RNA-Seq analysis can uncover mutations in glycogenes and search differently expressed genes out of more than 50,000 distinct human gene transcripts including candidate biomarkers that were previously reported for hepatocarcinoma cells. Identification of candidate glyco-biomarkers from the expression profile of the glycogenes and proteins from liver cancer tissues available from public database emphasized the possibility that even though the expression level of biomarkers might not be altered, the expression of the glycogenes modifying biomarkers, generating glyco-biomarkers, might be different. Pathway analysis revealed that ~20% of the glycogenes exhibited different expression levels in normal and cancer cells. Thus, transcriptome analyses using both qRT-PCR array and RNA-Seq in combination with glycome and glycoproteome analyses can be advantageous to identify “glyco-biomarkers” by reinforcing information at the expression levels of both glycogenes and proteins.
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Affiliation(s)
- Kiyohiko Angata
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hiromichi Sawaki
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Shigeko Tsujikawa
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Makoto Ocho
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Akira Togayachi
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Hisashi Narimatsu
- Molecular and Cellular Glycoproteomics Research Group, Department of Life Science and Biotechnology, Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
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Pan Q, Long X, Song L, Zhao D, Li X, Li D, Li M, Zhou J, Tang X, Ren H, Ding K. Transcriptome sequencing identified hub genes for hepatocellular carcinoma by weighted-gene co-expression analysis. Oncotarget 2018; 7:38487-38499. [PMID: 27220887 PMCID: PMC5122405 DOI: 10.18632/oncotarget.9555] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/05/2016] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common malignancies worldwide, and it remains a challenge to understand the genetic mechanisms underlying hepatocarcinogenesis. A global gene network of differential expression profiles in HCC has yet to be fully characterized. In the present study, we performed transcriptome sequencing (mRNA and lncRNA) in liver cancer and cirrhotic tissues of nine HCC patients. We identified differentially expressed genes (DEGs) and constructed a weighted gene co-expression network for the DEGs. In total, 755 DEGs (747 mRNA and eight lncRNA) were identified, and several co-expression modules were significantly associated with HCC clinical traits, including tumor location, tumor grade, and the α-fetoprotein (AFP) level. Of note, we identified 15 hub genes in the module associated with AFP level, and three (SPX, AFP and ADGRE1) of four hub genes were validated in an independent HCC cohort (n=78). Identification of hub genes for HCC clinical traits has implications for further understanding of the molecular genetic basis of HCC.
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Affiliation(s)
- Qi Pan
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Xianli Long
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Liting Song
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Dachun Zhao
- Department of Pathology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xiaoyuan Li
- Department of Medical Oncology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Dewei Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Min Li
- Department of Hepatobiliary Surgery, Suining Central Hospital, Suining, Sichuan Province, P. R. China
| | - Jiahua Zhou
- Department of Hepatobiliary Surgery, Henan Tumor Hospital, Zhenzhou, Henan Province, P.R. China
| | - Xia Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Hong Ren
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
| | - Keyue Ding
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, P.R. China
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Mao J, Wang D, Wang Z, Tian W, Li X, Duan J, Wang Y, Yang H, You L, Cheng Y, Bian J, Chen Z, Yang Y. Combretastatin A-1 phosphate, a microtubule inhibitor, acts on both hepatocellular carcinoma cells and tumor-associated macrophages by inhibiting the Wnt/β-catenin pathway. Cancer Lett 2016; 380:134-43. [PMID: 27349166 DOI: 10.1016/j.canlet.2016.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 02/07/2023]
Abstract
Combretastatin A-1 phosphate (CA1P) is a microtubule polymerization inhibitor that binds to the colchicine-binding site of tubulin. We demonstrated that CA1P has outstanding anti-cancer activity against hepatocellular carcinoma (HCC) in vitro and in vivo. As determined by fluorescence staining and western blots (WBs), CA1P induced reactive oxygen species (ROS) accumulation and apoptosis in HepG2 cells with a down-regulation of Mcl-1. Additional studies indicated that CA1P induced microtubule depolymerization-mediated AKT inactivation, which resulted in GSK-3β activation, Wnt/β-Catenin pathway inhibition, and Mcl-1 down-regulation. The induction of HepG2 cell apoptosis by CA1P was prevented by a GSK-3β-specific inhibitor. Furthermore, immunohistochemistry studies on hepatocellular carcinoma mouse models showed that CA1P had activity against tumor-associated macrophages (TAMs). CA1P induced TAM apoptosis in vitro through the same mechanism observed with HepG2 cells, and it eliminated TAMs in the tumor microenvironment (TME) in vivo. In TME, the expression of TGF-β and TNF-α was also altered. The adoptive transfer of macrophages partly rescued the growth of tumor inhibited by CA1P. These findings indicate that CA1P has great potential to impact both cancer cells and the microenvironment, and our results should accelerate the application of CA1P for HCC therapy in clinic.
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Affiliation(s)
- Jie Mao
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Duowei Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Zhuo Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China; School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Wei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Xianjing Li
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Jingjing Duan
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Yun Wang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Hongbao Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Linjun You
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Yan Cheng
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China
| | - Jinsong Bian
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Zhen Chen
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China.
| | - Yong Yang
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Center for New Drug Safety Evaluation and Research, China Pharmaceutical University, Nanjing 211198, China.
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Kekeeva T, Tanas A, Kanygina A, Alexeev D, Shikeeva A, Zavalishina L, Andreeva Y, Frank GA, Zaletaev D. Novel fusion transcripts in bladder cancer identified by RNA-seq. Cancer Lett 2016; 374:224-8. [PMID: 26898937 DOI: 10.1016/j.canlet.2016.02.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 10/25/2022]
Abstract
Urothelial carcinoma (UC) is the most common type of bladder cancer and is the second most frequently diagnosed genitourinary tumor. The identification of fusion genes in bladder cancer might provide new perspectives for its classification and significance. In this study, we present a thorough search on three UC samples for novel fusion transcripts in bladder cancer using high-throughput RNA sequencing. We used stringent requirements for 819 fusion candidates and nominated 10 candidate fusion transcripts. Among them four novel fusion genes SEPT9/CYHR, IGF1R/TTC23, SYT8/TNNI2 and CASZ1/DFFA were validated and characterized in 48 formalin-fixed paraffin-embedded (FFPE) specimens of bladder cancer. Chromosomal rearrangements of regions 17q25, 15q26.3 and 1p36.22 resulting in the fusion transcripts SEPT9/CYHR, IGF1R/TTC23 and CASZ1/DFFA, appeared to be rare or unique events because they were not detected in the 48 UC samples. In contrast, the SYT8/TNNI2 fusion transcript resulting from transcription-induced chimerism by read-through mechanisms was a rather common and tumor-specific event occurring in 37.5% (18/48) of the UC specimens. Further investigation of functional and clinical relevance of novel fusion genes remains to be elucidated to reveal their role in bladder carcinogenesis.
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Affiliation(s)
- T Kekeeva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation.
| | - A Tanas
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation
| | - A Kanygina
- Department of Molecular Biophysics, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny, 141700, Russian Federation
| | - D Alexeev
- Medical and Rehabilitation Center of Ministry of Healthcare of Russian Federation, Ivankovskoye, 3, Moscow, 125367, Russian Federation; Department of Molecular Biophysics, Moscow Institute of Physics and Technology, Institutskii Per. 9, Moscow Region, Dolgoprudny, 141700, Russian Federation
| | - A Shikeeva
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - L Zavalishina
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - Y Andreeva
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - G A Frank
- Pathology Department, Russian Medical Academy of Postgraduate Education, Polikarpov st., 12, Moscow, 125284, Russian Federation
| | - D Zaletaev
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moskvorechie st., 1, Moscow, 115478, Russian Federation; Laboratory of Human Molecular Genetics, I. M. Sechenov First Moscow State Medical University, Trubetskaya Str., 8, Moscow 119991, Russian Federation
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