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The Expression and Function of Circadian Rhythm Genes in Hepatocellular Carcinoma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:4044606. [PMID: 34697563 PMCID: PMC8541861 DOI: 10.1155/2021/4044606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 09/07/2021] [Accepted: 09/25/2021] [Indexed: 12/25/2022]
Abstract
Hepatocellular carcinoma (HCC) is among the most common and lethal form of cancer worldwide. However, its diagnosis and treatment are still dissatisfactory, due to limitations in the understanding of its pathogenic mechanism. Therefore, it is important to elucidate the molecular mechanisms and identify novel therapeutic targets for HCC. Circadian rhythm-related genes control a variety of biological processes. These genes play pivotal roles in the initiation and progression of HCC and are potential diagnostic markers and therapeutic targets. This review gives an update on the research progress of circadian rhythms, their effects on the initiation, progression, and prognosis of HCC, in a bid to provide new insights for the research and treatment of HCC.
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Sharma A, Colonna G. System-Wide Pollution of Biomedical Data: Consequence of the Search for Hub Genes of Hepatocellular Carcinoma Without Spatiotemporal Consideration. Mol Diagn Ther 2021; 25:9-27. [PMID: 33475988 PMCID: PMC7847983 DOI: 10.1007/s40291-020-00505-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 12/17/2022]
Abstract
Biomedical institutions rely on data evaluation and are turning into data factories. Big-data storage centers, supercomputing systems, and increased algorithmic efficiency allow us to analyze the ever-increasing amount of data generated every day in biomedical research centers. In network science, the principal intrinsic problem is how to integrate the data and information from different experiments on genes or proteins. Data curation is an essential process in annotating new functional data to known genes or proteins, undertaken by a biobank curator, which is then reflected in the calculated networks. We provide an example of how protein-protein networks today have space-time limits. The next step is the integration of data and information from different biobanks. Omics data and networks are essential parts of this step but also have flawed protocols and errors. Consider data from patients with cancer: from biopsy procedures to experimental tests, to archiving methods and computational algorithms, these are continuously handled so require critical and continuous "updates" to obtain reproducible, reliable, and correct results. We show, as a second example, how all this distorts studies in cellular hepatocellular carcinoma. It is not unlikely that these flawed data have been polluting biobanks for some time before stringent conditions for the veracity of data were implemented in Big data. Therefore, all this could contribute to errors in future medical decisions.
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Affiliation(s)
- Ankush Sharma
- Department of Biosciences, University of Oslo, Oslo, Norway.
- Department of Informatics, University of Oslo, Oslo, Norway.
- Institute of Cancer Research, Institute of Clinical medicine, University of Oslo, Oslo, Norway.
| | - Giovanni Colonna
- Medical Informatics, AOU-Vanvitelli, Università della Campania, Naples, Italy
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Yuan W, Liu L, Wei C, Li X, Sun D, Dai C, Li S, Peng S, Jiang L. Identification and meta-analysis of copy number variation-driven circadian clock genes for colorectal cancer. Oncol Lett 2019; 18:4816-4824. [PMID: 31611992 PMCID: PMC6781691 DOI: 10.3892/ol.2019.10830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/26/2019] [Indexed: 12/24/2022] Open
Abstract
Both copy number variation (CNV) and circadian clock genes play a critical role in the etiology and pathogenesis of colorectal cancer (CRC); however, a comprehensive analysis of CNV-driven circadian clock genes is urgently required. The present study aimed to investigate the systematic associations between somatic cell CNVs and circadian clock gene expression in patients with CRC. Using somatic CNV, legacy clinical information and gene expression data from The Cancer Genome Atlas, 295 genes that were significantly differentially expressed and with significantly different CNV were obtained, and the expression of the genes, among which 15 were circadian clock genes, was significantly associated with CNV. Further analysis revealed that aryl hydrocarbon receptor nuclear translocator-like 2 (ARNTL2) expression and CNV in these circadian clock genes were significantly associated with survival time in patients with CRC, and the expression of ARNTL2 was also significantly associated with the pathological stage of CRC. Gene set enrichment analysis found that ARNTL2 is enriched for gene sets associated with CRC pathogenesis such as the p53 signaling pathway. These results suggest that ARNTL2 may be a promising prognostic biomarker for patients with CRC, and that circadian clock genes play an important role in CRC through CNV.
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Affiliation(s)
- Wenliang Yuan
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, P.R. China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China.,College of Mathematics and Computer Science, Chizhou University, Chizhou, Anhui 247000, P.R. China
| | - Li Liu
- College of Mathematics and Computer Science, Chizhou University, Chizhou, Anhui 247000, P.R. China
| | - Cai Wei
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Xiaobo Li
- Institute of Biomedical Informatics, Lishui University, Lishui, Zhejiang 323000, P.R. China.,College of Engineering, Lishui University, Lishui, Zhejiang 323000, P.R. China
| | - Dan Sun
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Chaoxu Dai
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Sicong Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Sihua Peng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, P.R. China.,National Pathogen Collection Center for Aquatic Animals, Ministry of Agriculture, Shanghai 201306, P.R. China.,International Research Center for Marine Biosciences at Shanghai Ocean University, Ministry of Science and Technology, Shanghai 201306, P.R. China
| | - Linhua Jiang
- School of Optical-Electric and Computer Engineering, University of Shanghai for Science and Technology, Shanghai 200093, P.R. China
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Xie Y, Tang Q, Chen G, Xie M, Yu S, Zhao J, Chen L. New Insights Into the Circadian Rhythm and Its Related Diseases. Front Physiol 2019; 10:682. [PMID: 31293431 PMCID: PMC6603140 DOI: 10.3389/fphys.2019.00682] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/13/2019] [Indexed: 12/18/2022] Open
Abstract
Circadian rhythms (CR) are a series of endogenous autonomous oscillators generated by the molecular circadian clock which acting on coordinating internal time with the external environment in a 24-h daily cycle. The circadian clock system is a major regulatory factor for nearly all physiological activities and its disorder has severe consequences on human health. CR disruption is a common issue in modern society, and researches about people with jet lag or shift works have revealed that CR disruption can cause cognitive impairment, psychiatric illness, metabolic syndrome, dysplasia, and cancer. In this review, we summarized the synchronizers and the synchronization methods used in experimental research, and introduced CR monitoring and detection methods. Moreover, we evaluated conventional CR databases, and analyzed experiments that characterized the underlying causes of CR disorder. Finally, we further discussed the latest developments in understanding of CR disruption, and how it may be relevant to health and disease. Briefly, this review aimed to synthesize previous studies to aid in future studies of CR and CR-related diseases.
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Affiliation(s)
- Yanling Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingming Tang
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guangjin Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Mengru Xie
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shaoling Yu
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiajia Zhao
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Chen
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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