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Liu P, Zhang M, Gao H, Han S, Liu J, Sun X, Zhao L. Regulation of whole-transcriptome sequencing expression in COPD after personalized precise exercise training: a pilot study. Respir Res 2023; 24:156. [PMID: 37312153 DOI: 10.1186/s12931-023-02461-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/23/2023] [Indexed: 06/15/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is one of the world's leading causes of death and a major chronic respiratory disease. Aerobic exercise, the cornerstone of pulmonary rehabilitation, improves prognosis of COPD patients; however, few studies have comprehensively examined the changes in RNA transcript levels and the crosstalk between various transcripts in this context. This study identified the expression of RNA transcripts in COPD patients who engaged in aerobic exercise training for 12 weeks, and further constructions of the possible RNAs networks were made. METHODS Peripheral blood samples for all four COPD patients who benefited from 12 weeks of PR were collected pre- and post-aerobic exercises and evaluated for the expression of mRNA, miRNA, lncRNA, and circRNA with high-throughput RNA sequencing followed by GEO date validation. In addition, enrichment analyses were conducted on different expressed mRNAs. LncRNA-mRNA and circRNA-mRNA coexpression networks, as well as lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA competing expression networks (ceRNAs) in COPD were constructed. RESULTS We identified and analyzed the differentially expressed mRNAs and noncoding RNAs in the peripheral blood of COPD patients' post-exercise. Eighty-six mRNAs, 570 lncRNAs, 8 miRNAs, and 2087 circRNAs were differentially expressed. Direct function enrichment analysis and Gene Set Variation Analysis showed that differentially expressed RNAs(DE-RNAs) correlated with several critical biological processes such as chemotaxis, DNA replication, anti-infection humoral response, oxidative phosphorylation, and immunometabolism, which might affect the progression of COPD. Some DE-RNAs were validated by Geo databases and RT-PCR, and the results were highly correlated with RNA sequencing. We constructed ceRNA networks of DE-RNAs in COPD. CONCLUSIONS The systematic understanding of the impact of aerobic exercise on COPD was achieved using transcriptomic profiling. This research offers a number of potential candidates for clarifying the regulatory mechanisms that exercise has on COPD, which could ultimately help in understanding the pathophysiology of COPD.
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Affiliation(s)
- Panpan Liu
- Department of Pulmonary and Critical Care Medicine, Shanghai Pudong New Area Gongli Hospital, 219 MiaoPu Road, Shanghai, 200315, People's Republic of China
| | - Meilan Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Pudong New Area Gongli Hospital, 219 MiaoPu Road, Shanghai, 200315, People's Republic of China
| | - Hongchang Gao
- Department of Pulmonary and Critical Care Medicine, Shanghai Pudong New Area Gongli Hospital, 219 MiaoPu Road, Shanghai, 200315, People's Republic of China
| | - Shaojun Han
- Department of Pulmonary and Critical Care Medicine, Shanghai Pudong New Area Gongli Hospital, 219 MiaoPu Road, Shanghai, 200315, People's Republic of China
| | - Jinming Liu
- Department of Pulmonary and Critical Care Medicine, Shanghai Pulmonary Hospital Affiliated to TongJi University, Shanghai, China
| | - Xingguo Sun
- Department of Physiology and Medicine, Fuwai Hospital, Chinese Academy of Medical Sciences National Center of Cardiovascular Diseases, Beijing, People's Republic of China.
| | - Lei Zhao
- Department of Pulmonary and Critical Care Medicine, Shanghai Pudong New Area Gongli Hospital, 219 MiaoPu Road, Shanghai, 200315, People's Republic of China.
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Zhang K, Zhou J, Wu T, Tian Q, Liu T, Wang W, Zhong H, Chen Z, Xiao X, Wu G. Combined analysis of expression, prognosis and immune infiltration of GINS family genes in human sarcoma. Aging (Albany NY) 2022; 14:5895-5907. [PMID: 35896011 PMCID: PMC9365567 DOI: 10.18632/aging.204191] [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: 04/16/2022] [Accepted: 07/05/2022] [Indexed: 11/30/2022]
Abstract
Objective: This study was undertaken to explore the expression and prognostic value of GINS family in human sarcoma, as well as the association between the expression levels of the GINS family and sarcoma immune infiltration. Results: We discovered that the mRNA expression levels of GINS1, GINS2, GINS3, and GINS4 were all higher in the majority of tumor tissues than in normal samples, of course, including sarcoma. Through the CCLE, all the four members expression were observed in high levels in sarcoma cell lines. In Gene Expression Profiling Analysis (GEPIA) and Kaplan-Meier Plotter, our results indicated that the poor overall survival (OS), disease-free survival (DFS) and relapse free survival (RFS) were tightly associated with the increased expression of GINS genes. In TIMER database, we found that highly expressed GINS was significantly correlated with the low infiltration level of CD4+ T cell and macrophage. Conclusions: The four GINS family members were all the prognostic biomarkers for the prognosis of human sarcoma and can reduce the level of immune cell infiltration in the sarcoma microenvironment. Methods: In terms of the expression levels of mRNA for GINS family members, a particular contrast in various cancers, especially human sarcoma, was conducted through ONCOMINE and GEPIA and CCLE databases. Kaplan-Meier Plotter was used to identify the prognostic value of GINS family in sarcoma. The relationship between the expression level of GINS and the infiltration of immune cells was analyzed in TIMER database.
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Affiliation(s)
- Kexin Zhang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China.,Department of Psychology, School of Public Health, Southern Medical University, Guangzhou 510515, China
| | - Jian Zhou
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Tong Wu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Qunyan Tian
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Tang Liu
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Wanchun Wang
- Department of Orthopedics, The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China
| | - Hua Zhong
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou 510900, Guangdong, China
| | - Ziyuan Chen
- Department of Orthopedics, The First People's Hospital of Changde City, Changde 415003, Hunan, China
| | - Xungang Xiao
- Department of Orthopedics, Chenzhou No.1 People's Hospital, Chenzhou 423000, Hunan, China
| | - Gen Wu
- Department of Orthopedics, The Fifth Affiliated Hospital, Southern Medical University, Guangzhou 510900, Guangdong, China
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Gözen D, Kahraman DC, Narci K, Shehwana H, Konu Ö, Çetin-Atalay R. Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells. ACTA ACUST UNITED AC 2021; 45:149-161. [PMID: 33907497 PMCID: PMC8068766 DOI: 10.3906/biy-2009-56] [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: 10/06/2020] [Accepted: 02/01/2021] [Indexed: 12/09/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common cancer types with high mortality rates and displays increased resistance to various stress conditions such as oxidative stress. Conventional therapies have low efficacies due to resistance and off-target effects in HCC. Here we aimed to analyze oxidative stress-related gene expression profiles of HCC cells and identify genes that could be crucial for novel diagnostic and therapeutic strategies. To identify important genes that cause resistance to reactive oxygen species (ROS), a model of oxidative stress upon selenium (Se) deficiency was utilized. The results of transcriptome-wide gene expression data were analyzed in which the differentially expressed genes (DEGs) were identified between HCC cell lines that are either resistant or sensitive to Se-deficiency-dependent oxidative stress. These DEGs were further investigated for their importance in oxidative stress resistance by network analysis methods, and 27 genes were defined to have key roles; 16 of which were previously shown to have impact on liver cancer patient survival. These genes might have Se-deficiency-dependent roles in hepatocarcinogenesis and could be further exploited for their potentials as novel targets for diagnostic and therapeutic approaches.
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Affiliation(s)
- Damla Gözen
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
| | - Deniz Cansen Kahraman
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
| | - Kübra Narci
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
| | - Huma Shehwana
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi Pakistan
| | - Özlen Konu
- Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University, Ankara Turkey
| | - Rengül Çetin-Atalay
- Cancer Systems Biology Laboratory, Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara Turkey
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He S, Zhang M, Ye Y, Song Y, Ma X, Wang G, Zhuang J, Xia W, Zhao B. GINS2 affects cell proliferation, apoptosis, migration and invasion in thyroid cancer via regulating MAPK signaling pathway. Mol Med Rep 2021; 23:246. [PMID: 33537829 PMCID: PMC7893785 DOI: 10.3892/mmr.2021.11885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/30/2020] [Indexed: 01/04/2023] Open
Abstract
Globally, thyroid cancer (TC) is considered to be the commonest endocrine malignancy. GINS complex subunit 2 (GINS2) belongs to the GINS complex family and is associated with cellular migration, invasion and growth. The present study aimed to investigate the underlying mechanisms of GINS2 on cell viability, migration and invasion in TC cells. By using MTT, wound healing and Transwell assays, the cell viability, migration and invasion were determined. Apoptosis was examined by immunofluorescence. Western blotting was used to detect protein expression levels. In the present study, biological function analysis demonstrated that GINS2 interference attenuated cell viability, migration and invasion in TC cell lines (K1 and SW579). It was discovered that, compared with the control group, GINS2 silencing induced apoptosis in TC cells. Additionally, GINS2 interference inhibited key proteins in the MAPK signaling pathway, including JNK, ERK and p38. According to these comparative experiments, GINS2 was considered to act a pivotal part in cell viability, migration and invasion of TC by regulating the MAPK signaling pathway and might be a potential therapeutic target for treating TC.
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Affiliation(s)
- Saifei He
- Central Laboratory, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Miao Zhang
- Central Laboratory, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Ying Ye
- Central Laboratory, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Yanan Song
- Central Laboratory, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Xing Ma
- Department of Nuclear Medicine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Guoyu Wang
- Department of Nuclear Medicine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Juhua Zhuang
- Department of Nuclear Medicine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Wei Xia
- Department of Nuclear Medicine, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
| | - Bin Zhao
- Department of General Surgery, Seventh People's Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai 200137, P.R. China
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Hao YQ, Liu KW, Zhang X, Kang SX, Zhang K, Han W, Li L, Li ZH. GINS2 was regulated by lncRNA XIST/miR-23a-3p to mediate proliferation and apoptosis in A375 cells. Mol Cell Biochem 2021; 476:1455-1465. [PMID: 33389496 DOI: 10.1007/s11010-020-04007-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/26/2020] [Indexed: 10/22/2022]
Abstract
Melanoma ranks second in aggressive tumors, and the occurrence of metastasis in melanoma results in a persistent drop in the survival rate of patients. Therefore, it is very necessary to find a novel therapeutic method for treating melanoma. It has been reported that lncRNA XIST could promote the tumorigenesis of melanoma. However, the mechanism by which lncRNA XIST regulates the progression of melanoma remains unclear. The proliferation of A375 cells was measured by clonal formation. Cell viability was detected by MTT assay. Flow cytometry was performed to detect cell apoptosis and cycle. The level of GINS2, miR-23a-3p, and lncRNA XIST was investigated by qRT-PCR. Protein level was detected by Western blot, and the correctness of prediction results was confirmed by Dual luciferase. In present study, GINS2 and lncRNA XIST were overexpressed in melanoma, while miR-23a-3p was downregulated. Silencing of GINS2 or overexpression of miR-23a-3p reversed cell growth and promoted apoptosis in A375 cells. Mechanically, miR-23a-3p directly targeted GINS2, and XIST regulated GINS2 level though mediated miR-23a-3p. Moreover, XIST exerted its function on cell proliferation, cell viability, and promoted the cell apoptosis of A375 cells though miR-23a-3p/GINS2 axis. LncRNA XIST significantly promoted the tumorigenesis of melanoma via sponging miR-23a-3p and indirectly targeting GINS2, which can be a potential new target for treating melanoma.
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Affiliation(s)
- Yu-Qin Hao
- Department of Dermatology, Peking University Third Hospital, Beijing, 100191, People's Republic of China.,Department of Dermatology, Third Affiliated Hospital of Inner Mongolia Medical University, Baotou, 014010, People's Republic of China
| | - Ke-Wei Liu
- Department of Dermatology, Mental Health Center of Inner Mongolia Autonomous Region, Hohhot, 010000, People's Republic of China
| | - Xin Zhang
- Department of Dermatology, Halison International Peace Hospital, Hengshui, 053000, People's Republic of China
| | - Shu-Xia Kang
- Department of Dermatology, People's Hospital Affiliated to Inner Mongolia Medical University, Hohhot, 010000, People's Republic of China
| | - Kun Zhang
- Department of Hematology, The Second Affiliated Hospital of Baotou Medical College, Baotou, 014010, People's Republic of China
| | - Wurihan Han
- Inner Mongolia Medical University, Hohhot, 010000, People's Republic of China
| | - Li Li
- Inner Mongolia Medical University, Hohhot, 010000, People's Republic of China
| | - Zhe-Hai Li
- Department of Orthopedics, Peking University Third Hospital, Beijing, 100191, People's Republic of China.
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Zhang Z, Sui Y, Luan L, Li B, Qin C. Retracted: A Novel CircRNA Circ_0095424 Regulates Proliferation, Metastasis, and Apoptosis of Osteosarcoma Cells Via the PI3K/AKT Signaling Pathway Through Targeting the miR-1238/ HMGB1 Axis. Cancer Biother Radiopharm 2020; 35:e802-e813. [PMID: 32822247 DOI: 10.1089/cbr.2020.3563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cancer Biotherapy and Radiopharmaceuticals is officially retracting the article entitled, A Novel CircRNA Circ_0095424 Regulates Proliferation, Metastasis, and Apoptosis of Osteosarcoma Cells Via the PI3K/AKT Signaling Pathway Through Targeting the miR-1238/HMGB1 Axis by Zhang et al., (Cancer Biother Radiopharm epub 19 Aug 2020; DOI: 10.1089/cbr.2020.3563), due to manipulated images appearing in the published paper. The Editor of the journal received an email on August 31, 2020 from the corresponding author of the article, Dr. Chuan Qin, indicating that, ''due to our negligence in organizing the pictures, the protein pictures are repeatedly placed in Figure 7G PI3K. For this, we express our sincerest apologies. We need to [issue] an [erratum] on this issue. We have replaced the protein picture of Figure 7G with the correct picture.'' However, one of the attachments submitted with the request appeared to be the original version of Figure 7 from the accepted manuscript. A second attachment appeared to be the data from three replicates to be used (by the journal) to construct a revised version of Figure 7. The Editor, in turn, informed the authors that it was not at the journal's discretion to create a new image for them, and asked the authors to create the revised figure and supply it to the publisher. Below is the response from Dr. Qin, dated September 2, 2020. "In fact, our team's Western blot experiment commissioned a third-party company for testing. At present, some peers have found that the company has forged experimental reports. We believe that the authenticity of the data provided by the company is problematic. After contacting the company, they were unable to provide the original images. In view of the problems in this manuscript, all the authors discussed and agreed to withdraw the manuscript." As the entirety of the situation is unacceptable, the Editor officially retracts the article based on the "forged experimental reports" and the questionable validity of the data provided. The Editor and Publisher of Cancer Biotherapy and Radiopharmaceuticals is dedicated to preserving the integrity of the scientific literature and the community it serves.
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Affiliation(s)
- Zhiguo Zhang
- Department of Orthopedics, Rizhao City Traditional Chinese Medicine Hospital, Rizhao, China
| | - Yutong Sui
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Liyi Luan
- Department of Orthopedic, The People's Hospital of Gaotang, Liaocheng, China
| | - Bo Li
- Department of Joint Surgery, No. 1 Hospital of Jilin University, Changchun, China
| | - Chuan Qin
- Department of Orthopedics, The No. 4 Hospital of Jinan, Jinan, China
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Fan X, Hou T, Guan Y, Li X, Zhang S, Wang Z. Genomic responses of DNA methylation and transcript profiles in zebrafish cells upon nutrient deprivation stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 722:137980. [PMID: 32208287 DOI: 10.1016/j.scitotenv.2020.137980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/14/2020] [Accepted: 03/15/2020] [Indexed: 06/10/2023]
Abstract
Environmental stress such as nutrient deprivation across multiple fields in nature causes physiological and biochemical changes in organism. Understanding the potential epigenetic modulations to phenotypic variation upon nutrient deprivation stress is crucial for environmental assessments. Here, the methyl-cytosine at single-base resolution was mapped across the whole genome and the methylation patterns and methylation levels coordinated with transcript analysis were systemically elaborated in zebrafish embryonic fibroblast cells under serum starvation stress. The down-regulated genes mainly annotated to the pathways of DNA replication and cell cycle that were consistent with cell physiological changes. Vast differentially methylated regions were identified in genomic chromosome and showed enrichment in the intron and intergenic regions. In an integrated transcriptome and DNA methylation analyses, 135 negatively correlated genes were determined, wherein the hub genes of gins2, cdca5, fbxo5, slc29a2, suv39h1b, and zgc:174160 were predominant responsive to the nutrient condition changes. Besides, nutrient recovery and DNA methyltransferases inhibitor supplements partly rescued cell proliferation with decrease of DNA methylation and reactivation of several depressed genes, implying the possible intrinsic relationships among cell physiological state, mRNA expression, and DNA methylation. Collectively, current study proved the broad role of DNA methylation in governing cellular responses to nutrient deprivation and revealed the epigenetic risk of starvation stress in zebrafish.
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Affiliation(s)
- Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongjing Guan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiangju Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuai Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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