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Pokorná M, Černá M, Boussios S, Ovsepian SV, O’Leary VB. lncRNA Biomarkers of Glioblastoma Multiforme. Biomedicines 2024; 12:932. [PMID: 38790894 PMCID: PMC11117901 DOI: 10.3390/biomedicines12050932] [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: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules of 200 nucleotides or more in length that are not translated into proteins. Their expression is tissue-specific, with the vast majority involved in the regulation of cellular processes and functions. Many human diseases, including cancer, have been shown to be associated with deregulated lncRNAs, rendering them potential therapeutic targets and biomarkers for differential diagnosis. The expression of lncRNAs in the nervous system varies in different cell types, implicated in mechanisms of neurons and glia, with effects on the development and functioning of the brain. Reports have also shown a link between changes in lncRNA molecules and the etiopathogenesis of brain neoplasia, including glioblastoma multiforme (GBM). GBM is an aggressive variant of brain cancer with an unfavourable prognosis and a median survival of 14-16 months. It is considered a brain-specific disease with the highly invasive malignant cells spreading throughout the neural tissue, impeding the complete resection, and leading to post-surgery recurrences, which are the prime cause of mortality. The early diagnosis of GBM could improve the treatment and extend survival, with the lncRNA profiling of biological fluids promising the detection of neoplastic changes at their initial stages and more effective therapeutic interventions. This review presents a systematic overview of GBM-associated deregulation of lncRNAs with a focus on lncRNA fingerprints in patients' blood.
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Affiliation(s)
- Markéta Pokorná
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK;
- Faculty of Medicine, Health, and Social Care, Canterbury Christ Church University, Canterbury CT2 7PB, UK
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
- Kent Medway Medical School, University of Kent, Canterbury CT2 7LX, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
| | - Saak V. Ovsepian
- Faculty of Engineering and Science, University of Greenwich London, Chatham Maritime, Kent ME4 4TB, UK;
- Faculty of Medicine, Tbilisi State University, Tbilisi 0177, Georgia
| | - Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
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Mu L, Hu S, Li G, Wu P, Zheng K, Zhang S. Comprehensive analysis of DNA methylation gene expression profiles in GEO dataset reveals biomarkers related to malignant transformation of sinonasal inverted papilloma. Discov Oncol 2024; 15:53. [PMID: 38427106 PMCID: PMC10907326 DOI: 10.1007/s12672-024-00903-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 02/21/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND DNA methylation may be involved in the regulation of malignant transformation from sinonasal inverted papilloma (SNIP) to squamous cell carcinoma (SCC). The study of gene methylation changes and screening of differentially methylated loci (DMLs) are helpful to predict the possible key genes in the malignant transformation of SNIP-SCC. MATERIALS AND METHODS Microarray dataset GSE125399 was downloaded from the Gene Expression Omnibus (GEO) database and differentially methylated loci (DMLs) were analyzed using R language (Limma package). ClusterProfiler R package was used to perform Gene Ontology (GO) analysis on up-methylated genes and draw bubble maps. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and its visualization analysis were analyzed to speculate the possible key Genes in SNIP-SCC malignant transformation. Subsequently, SNIP cases archived in our department were collected, tissue microarray was made, and immunohistochemical staining was performed to analyze the expression levels of UCKL1, GSTT1, HLA-G, MAML2 and NRGN in different grades of sinonasal papilloma tissues. RESULTS Analysis of dataset GSE125399 identified 56 DMLs, including 49 upregulated DMLs and 7 downregulated DMLs. Thirty-one genes containing upregulated DNA methylation loci and three genes containing downregulated DNA methylation loci were obtained by methylation microarray annotation analysis. In addition, KEGG pathway visualization analysis of 31 up-methylated genes showed that there were four significantly up-methylated genes including UCKL1, GSTT1, HLA-G and MAML2, and one significantly down-methylated gene NRGN. Subsequently, compared with non-neoplasia nasal epithelial tissues, the expression of HLA-G and NRGN was upregulated in grade I, II, III and IV tissues, while the expression of MAML2 was lost. The protein expression changes of MAML2 and NRGN were significantly negatively correlated with their gene methylation levels. CONCLUSIONS By analyzing the methylation dataset, we obtained four up-regulated methylation genes UCKL1, GSTT1, HLA-G and MAML2 and one down-regulated gene NRGN. MAML2, a tumor suppressor gene with high methylation modification but loss of protein expression, and NRGN, a tumor gene with low methylation modification but upregulated protein expression, can be used as biological indicators to judge the malignant transformation of SNIP-SCC.
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Affiliation(s)
- Li Mu
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, Fujian, China
- Department of Pathology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 999 Huashan Road, Fuzhou, 350212, China
| | - Shun Hu
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, Fujian, China
- Department of Pathology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 999 Huashan Road, Fuzhou, 350212, China
| | - Guoping Li
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, Fujian, China
- Department of Pathology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 999 Huashan Road, Fuzhou, 350212, China
| | - Ping Wu
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, Fujian, China
- Department of Pathology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 999 Huashan Road, Fuzhou, 350212, China
| | - Ke Zheng
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, Fujian, China.
- Department of Pathology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 999 Huashan Road, Fuzhou, 350212, China.
| | - Sheng Zhang
- Department of Pathology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, Fujian, China.
- Department of Pathology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, 999 Huashan Road, Fuzhou, 350212, China.
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Chen D, Li Q, Xu Y, Wei Y, Li J, Zhu X, Li H, Lu Y, Liu X, Yan D. Leveraging a disulfidptosis‑related lncRNAs signature for predicting the prognosis and immunotherapy of glioma. Cancer Cell Int 2023; 23:316. [PMID: 38066643 PMCID: PMC10709922 DOI: 10.1186/s12935-023-03147-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 11/14/2023] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Gliomas, a prevalent form of primary brain tumors, are linked with a high mortality rate and unfavorable prognoses. Disulfidptosis, an innovative form of programmed cell death, has received scant attention concerning disulfidptosis-related lncRNAs (DRLs). The objective of this investigation was to ascertain a prognostic signature utilizing DRLs to forecast the prognosis and treatment targets of glioma patients. METHODS RNA-seq data were procured from The Cancer Genome Atlas database. Disulfidptosis-related genes were compiled from prior research. An analysis of multivariate Cox regression and the least absolute selection operator was used to construct a risk model using six DRLs. The risk signature's performance was evaluated via Kaplan-Meier survival curves and receiver operating characteristic curves. Additionally, functional analysis was carried out using GO, KEGG, and single-sample GSEA to investigate the biological functions and immune infiltration. The research also evaluated tumor mutational burden, therapeutic drug sensitivity, and consensus cluster analysis. Reverse transcription quantitative PCR was conducted to validate the expression level of DRLs. RESULTS A prognostic signature comprising six DRLs was developed to predict the prognosis of glioma patients. High-risk patients had significantly shorter overall survival than low-risk patients. The robustness of the risk model was validated by receiver operating characteristic curves and subgroup survival analysis. Risk model was used independently as a prognostic indicator for the glioma patients. Notably, the low-risk patients displayed a substantial decrease in the immune checkpoints, the proportion of immune cells, ESTIMATE and immune score. IC50 values from the different risk groups allowed us to discern three drugs for the treatment of glioma patients. Lastly, the potential clinical significance of six DRLs was determined. CONCLUSIONS A novel six DRLs signature was developed to predict prognosis and may provide valuable insights for patients with glioma seeking novel immunotherapy and targeted therapy.
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Affiliation(s)
- Di Chen
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Qiaoqiao Li
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, No. 76 Linjiang Road, 400010, Chongqing, China
| | - Yuan Xu
- The First Clinical Medical College, Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Yanfei Wei
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Jianguo Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xuqiang Zhu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Hongjiang Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Yan Lu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
| | - Dongming Yan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, Henan, China.
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Chen GR, Zhang YB, Zheng SF, Xu YW, Lin P, Shang-Guan HC, Lin YX, Kang DZ, Yao PS. Decreased SPTBN2 expression regulated by the ceRNA network is associated with poor prognosis and immune infiltration in low‑grade glioma. Exp Ther Med 2023; 25:253. [PMID: 37153896 PMCID: PMC10161196 DOI: 10.3892/etm.2023.11952] [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: 08/16/2022] [Accepted: 02/24/2023] [Indexed: 05/10/2023] Open
Abstract
The majority of low-grade gliomas (LGGs) in adults invariably progress to glioblastoma over time. Spectrin β non-erythrocytic 2 (SPTBN2) is detected in numerous tumors and is involved in tumor occurrence and metastasis. However, the specific roles and detailed mechanisms of SPTBN2 in LGG are largely unknown. The present study performed pan-cancer analysis for the expression and prognosis of SPTBN2 in LGG using The Cancer Genome Atlas and The Genotype-Tissue Expression. Western blotting was used to detect the amount of SPTBN2 between glioma tissues and normal brain tissues. Subsequently, based on expression, prognosis, correlation and immune infiltration, non-coding RNAs (ncRNAs) were identified that regulated SPTBN2 expression. Finally, tumor immune infiltrates associated with SPTBN2 and prognosis were performed. Lower expression of SPTBN2 was correlated with an unfavorable outcome in LGG. A significant correlation between the low SPTBN2 mRNA expression and poor clinicopathological features was observed, including wild-type isocitrate dehydrogenase status (P<0.001), 1p/19q non-codeletion (P<0.001) and elders (P=0.019). The western blotting results revealed that, compared with normal brain tissues, the amount of SPTBN2 was significantly lower in LGG tissues (P=0.0266). Higher expression of five microRNAs (miRs/miRNAs), including hsa-miR-15a-5p, hsa-miR-15b-5p, hsa-miR-16-5p, hsa-miR-34c-5p and hsa-miR-424-5p, correlated with poor prognosis by targeting SPTBN2 in LGG. Subsequently, four long ncRNAs (lncRNAs) [ARMCX5-GPRASP2, BASP1-antisense RNA 1 (AS1), EPB41L4A-AS1 and LINC00641] were observed in the regulation of SPTBN2 via five miRNAs. Moreover, the expression of SPTBN2 was significantly correlated with tumor immune infiltration, immune checkpoint expression and biomarkers of immune cells. In conclusion, SPTBN2 was lowly expressed and correlated with an unfavorable prognosis in LGG. A total of six miRNAs and four lncRNAs were identified as being able to modulate SPTBN2 in a lncRNA-miRNA-mRNA network of LGG. Furthermore, the current findings also indicated that SPTBN2 possessed anti-tumor roles by regulating tumor immune infiltration and immune checkpoint expression.
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Affiliation(s)
- Guo-Rong Chen
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Yi-Bin Zhang
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Shu-Fa Zheng
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Ya-Wen Xu
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Peng Lin
- Department of Pain, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - Huang-Cheng Shang-Guan
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
| | - Yuan-Xiang Lin
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
| | - De-Zhi Kang
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Fujian Provincial Institutes of Brain Disorders and Brain Sciences, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Correspondence to: Professor De-Zhi Kang or Dr Pei-Sen Yao, Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Taijiang, Fuzhou, Fujian 350005, P.R. China
| | - Pei-Sen Yao
- Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350005, P.R. China
- Department of Neurosurgery, National Regional Medical Center, Binhai Campus of The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian 350212, P.R. China
- Correspondence to: Professor De-Zhi Kang or Dr Pei-Sen Yao, Department of Neurosurgery, Neurosurgical Research Institute, The First Affiliated Hospital, Fujian Medical University, 20 Chazhong Road, Taijiang, Fuzhou, Fujian 350005, P.R. China
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Bader JM, Deigendesch N, Misch M, Mann M, Koch A, Meissner F. Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status. Cell Rep Med 2022; 4:100877. [PMID: 36584682 PMCID: PMC9873829 DOI: 10.1016/j.xcrm.2022.100877] [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: 08/25/2021] [Revised: 07/15/2022] [Accepted: 12/07/2022] [Indexed: 12/30/2022]
Abstract
High-grade adult-type diffuse gliomas are malignant neuroepithelial tumors with poor survival rates in combined chemoradiotherapy. The current WHO classification is based on IDH1/2 mutational and 1p/19q codeletion status. Glioma proteome alterations remain undercharacterized despite their promise for a better molecular patient stratification and therapeutic target identification. Here, we use mass spectrometry to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wild-type (IDHwt) gliomas, IDH-mutant (IDHmut) gliomas with and without 1p/19q codeletion, and non-neoplastic controls. Based on more than 5,500 quantified proteins and 5,000 phosphosites, gliomas separate by IDH1/2 mutational status but not by 1p/19q status. Instead, IDHmut gliomas split into two proteomic subtypes with widespread perturbations, including aerobic/anaerobic energy metabolism. Validations with three independent glioma proteome datasets confirm these subgroups and link the IDHmut subtypes to the established proneural and classic/mesenchymal subtypes in IDHwt glioma. This demonstrates common phenotypic subtypes across the IDH status with potential therapeutic implications for patients with IDHmut gliomas.
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Affiliation(s)
- Jakob Maximilian Bader
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Nikolaus Deigendesch
- Pathology, Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, 4031 Basel, Switzerland
| | - Martin Misch
- Department of Neurosurgery, Charité, Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany,Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Arend Koch
- Department of Neuropathology, Charité, Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, and Humboldt-Universität zu Berlin, Berlin Institute of Health, 13353 Berlin, Germany.
| | - Felix Meissner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Department of Systems Immunology and Proteomics, Institute of Innate Immunity, University Hospital Bonn, 53127 Bonn, Germany.
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Jin W, Liu J, Yang J, Feng Z, Feng Z, Huang N, Yang T, Yu L. Identification of a key ceRNA network associated with ferroptosis in gastric cancer. Sci Rep 2022; 12:20088. [PMID: 36418919 PMCID: PMC9684404 DOI: 10.1038/s41598-022-24402-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/15/2022] [Indexed: 11/24/2022] Open
Abstract
Ferroptosis, a newly discovered irondependent form of regulated cell death caused by excessive accumulation of lipid peroxides, is linked to the development and treatment response of various types of cancer, including gastric cancer (GC). Noncoding RNAs (ncRNAs), as key regulators in cancer, have both oncogenic and tumor suppressive roles. However, studies on ferroptosis-related ncRNA networks in GC are still lacking. Here, we first identified 61 differentially expressed genes associated with ferroptosis in GC by computing and analyzing gene expression profile of tumor and normal tissues for GC. Then, upstream lncRNAs and miRNAs interacting with them were found through miRNet and miRBase databases, and hub lncRNAs and miRNAs were obtained through topological analysis. Finally, the ceRNA regulatory network linked to ferroptosis in GC was established, which includes two ferroptosis marker genes (TXNIP and TSC22D3), one driver gene (GABARAPL1), and one suppressor gene (CAV1). Kaplan-Meier survival analysis showed that changes in the expression of these genes were associated with the survival of GC patients. Furthermore, our study revealed that this ceRNA network may influence the progression of GC by regulating ferroptosis process. These results will help experimental researchers to design an experiment study to further explore the roles of this regulatory network in GC ferroptosis.
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Affiliation(s)
- Wen Jin
- grid.440229.90000 0004 1757 7789Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People’s Hospital, Hohhot, 010010 China
| | - Jianli Liu
- grid.162107.30000 0001 2156 409XSchool of Water Resource and Environment Engineering, China University of Geosciences, Beijing, 100083 China
| | - Jie Yang
- grid.440229.90000 0004 1757 7789Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People’s Hospital, Hohhot, 010010 China
| | - Zongqi Feng
- grid.440229.90000 0004 1757 7789Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People’s Hospital, Hohhot, 010010 China
| | - Zhenxing Feng
- grid.411648.e0000 0004 1797 7993College of Sciences, Inner Mongolia University of Technology, Hohhot, 010051 China
| | - Na Huang
- grid.440229.90000 0004 1757 7789Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People’s Hospital, Hohhot, 010010 China
| | - Tingyu Yang
- grid.440229.90000 0004 1757 7789Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People’s Hospital, Hohhot, 010010 China
| | - Lan Yu
- grid.440229.90000 0004 1757 7789Clinical Medical Research Center/Inner Mongolia Key Laboratory of Gene Regulation of the Metabolic Disease, Inner Mongolia People’s Hospital, Hohhot, 010010 China
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Guo X, Jiao H, Cao L, Meng F. Biological implications and clinical potential of invasion and migration related miRNAs in glioma. Front Integr Neurosci 2022; 16:989029. [DOI: 10.3389/fnint.2022.989029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/07/2022] [Indexed: 11/22/2022] Open
Abstract
Gliomas are the most common primary malignant brain tumors and are highly aggressive. Invasion and migration are the main causes of poor prognosis and treatment resistance in gliomas. As migration and invasion occur, patient survival and prognosis decline dramatically. MicroRNAs (miRNAs) are small, non-coding 21–23 nucleotides involved in regulating the malignant phenotype of gliomas, including migration and invasion. Numerous studies have demonstrated the mechanism and function of some miRNAs in glioma migration and invasion. However, the biological and clinical significance (including diagnosis, prognosis, and targeted therapy) of glioma migration and invasion-related miRNAs have not been systematically discussed. This paper reviews the progress of miRNAs-mediated migration and invasion studies in glioma and discusses the clinical value of migration and invasion-related miRNAs as potential biomarkers or targeted therapies for glioma. In addition, these findings are expected to translate into future directions and challenges for clinical applications. Although many biomarkers and their biological roles in glioma invasion and migration have been identified, none have been specific so far, and further exploration of clinical treatment is still in progress; therefore, we aimed to further identify specific markers that may guide clinical treatment and improve the quality of patient survival.
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8
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LincRNAs and snoRNAs in Breast Cancer Cell Metastasis: The Unknown Players. Cancers (Basel) 2022; 14:cancers14184528. [PMID: 36139687 PMCID: PMC9496948 DOI: 10.3390/cancers14184528] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/10/2022] [Accepted: 09/16/2022] [Indexed: 11/17/2022] Open
Abstract
Recent advances in research have led to earlier diagnosis and targeted therapies against breast cancer, which has resulted in reduced breast cancer-related mortality. However, the majority of breast cancer-related deaths are due to metastasis of cancer cells to other organs, a process that has not been fully elucidated. Among the factors and genes implicated in the metastatic process regulation, non-coding RNAs have emerged as crucial players. This review focuses on the role of long intergenic noncoding RNAs (lincRNAs) and small nucleolar RNAs (snoRNAs) in breast cancer cell metastasis. LincRNAs are transcribed between two protein-coding genes and are longer than 200 nucleotides, they do not code for a specific protein but function as regulatory molecules in processes such as cell proliferation, apoptosis, epithelial-to-mesenchymal transition, migration, and invasion while most of them are highly elevated in breast cancer tissues and seem to function as competing endogenous RNAs (ceRNAs) inhibiting relevant miRNAs that specifically target vital metastasis-related genes. Similarly, snoRNAs are 60-300 nucleotides long and are found in the nucleolus being responsible for the post-transcriptional modification of ribosomal and spliceosomal RNAs. Most snoRNAs are hosted inside intron sequences of protein-coding and non-protein-coding genes, and they also regulate metastasis-related genes affecting related cellular properties.
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Xia P, Huang Y, Chen G. A novel signature based on necroptosis-related long non-coding RNAs for predicting prognosis of patients with glioma. Front Oncol 2022; 12:940220. [PMID: 36033510 PMCID: PMC9399791 DOI: 10.3389/fonc.2022.940220] [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: 05/10/2022] [Accepted: 07/19/2022] [Indexed: 11/21/2022] Open
Abstract
Necroptosis is closely related to the occurrence and development of tumors, including glioma. A growing number of studies indicate that targeting necroptosis could be an effective treatment strategy against cancer. Long non-coding RNA (lncRNA) is also believed to play a pivotal role in tumor epigenetics. Therefore, it is necessary to identify the functions of necroptosis-related lncRNAs in glioma. In this study, the transcriptome and clinical characteristic data of glioma patients from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases were collected, and the differentially expressed necroptosis-related lncRNAs in TCGA that have an impact on overall survival (OS) were screened out to construct risk score (RS) formula, which was verified in CGGA. A nomogram was constructed to predict the prognosis of glioma patients based on clinical characteristics and RS. In addition, Gene Set Enrichment Analysis (GSEA) was used to analyze the main enrichment functions of these necroptosis-related lncRNAs and the immune microenvironment. A total of nine necroptosis-related lncRNAs have been identified to construct the RS formula, and the Kaplan–Meier (K-M) survival analysis showed significantly poorer outcomes in the high RS group in both TCGA and CGGA databases. Moreover, the receiver operating characteristic (ROC) curve shows that our prediction RS model has good predictability. Regarding the analysis of the immune microenvironment, significant differences were observed in immune function and immune checkpoint between the high RS group and the low RS group. In conclusion, we constructed a necroptosis-related lncRNA RS model that can effectively predict the prognosis of glioma patients and provided the theoretical basis and the potential therapeutic targets for immunotherapy against gliomas.
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Affiliation(s)
- Pengfei Xia
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yimin Huang
- Department of Neurosurgery, Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology, Wuhan, China
| | - Gang Chen
- Department of Neurosurgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Gang Chen,
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Long Intergenic Noncoding RNA 00641 Promotes Growth and Invasion of Colorectal Cancer through Regulating miR-450b-5p/GOLPH3 Axis. JOURNAL OF ONCOLOGY 2022; 2022:8259135. [PMID: 35756081 PMCID: PMC9217543 DOI: 10.1155/2022/8259135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/26/2022] [Accepted: 05/24/2022] [Indexed: 11/18/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) have a vital function in tumor onset and progress. For instance, long intergenic noncoding RNA 00641 (LINC00641) has been linked to cancer modulation. Nonetheless, the precise biological roles of LINC00641 in colorectal cancer (CRC) remain elusive. Methods The expression levels of LINC00641 as well as the docking sites for LINC00641 and miR-450b-5p were analyzed using public data resources and web-based analytic tools. The putative downstream targets of miR-450b-5p were also predicted. Next, we evaluated the biological functions and the contents of LINC00641 in CRC both in vivo and in vitro. We next explored the influence of LINC00641 on the growth, migration, and infiltration of CRC cells via cell proliferation, migration, and invasion experiments. Besides, qRT-PCR, western blotting, flow cytometry, luciferase enzyme reporter assay, and in vivo tumorigenicity assays were conducted. Results Our results confirmed that LINC00641 was markedly upmodulated in CRC tissues and CRC cell lines, and the upmodulation was linked to poor survival. Notably, the proliferative and migratory abilities of HCT-116 and SW480 cells were significantly inhibited by the knockdown of LINC00641 both in vitro and in vivo, illustrating that LINC00641 exerted a tumor-promotion role in CRC. Mechanistically, LINC00641 could competitively bind miR-450b-5p, thereby expunging its inhibitory effect on GOLPH3 expression. Moreover, miR-450-5p and GOLPH3 were able to reverse LINC00641-mediated cellular processes. Conclusions Overall, the findings of this study suggest that LINC00641 promotes the proliferative and migratory abilities of CRC through sponging the miR-450b-5p/GOLPH3 axis.
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Integrative analysis of expression profile indicates the ECM receptor and LTP dysfunction in the glioma-related epilepsy. BMC Genomics 2022; 23:430. [PMID: 35676651 PMCID: PMC9175475 DOI: 10.1186/s12864-022-08665-8] [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: 03/24/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022] Open
Abstract
Background Seizures are a common symptom in glioma patients, and they can cause brain dysfunction. However, the mechanism by which glioma-related epilepsy (GRE) causes alterations in brain networks remains elusive. Objective To investigate the potential pathogenic mechanism of GRE by analyzing the dynamic expression profiles of microRNA/ mRNA/ lncRNA in brain tissues of glioma patients. Methods Brain tissues of 16 patients with GRE and 9 patients with glioma without epilepsy (GNE) were collected. The total RNA was dephosphorylated, labeled, and hybridized to the Agilent Human miRNA Microarray, Release 19.0, 8 × 60 K. The cDNA was labeled and hybridized to the Agilent LncRNA + mRNA Human Gene Expression Microarray V3.0, 4 × 180 K. The raw data was extracted from hybridized images using Agilent Feature Extraction, and quantile normalization was performed using the Agilent GeneSpring. P-value < 0.05 and absolute fold change > 2 were considered the threshold of differential expression data. Data analyses were performed using R and Bioconductor. Results We found that 3 differentially expressed miRNAs (miR-10a-5p, miR-10b-5p, miR-629-3p), 6 differentially expressed lncRNAs (TTN-AS1, LINC00641, SNHG14, LINC00894, SNHG1, OIP5-AS1), and 49 differentially expressed mRNAs play a vitally critical role in developing GRE. The expression of GABARAPL1, GRAMD1B, and IQSEC3 were validated more than twofold higher in the GRE group than in the GNE group in the validation cohort. Pathways including ECM receptor interaction and long-term potentiation (LTP) may contribute to the disease’s progression. Meanwhile, We built a lncRNA-microRNA-Gene regulatory network with structural and functional significance. Conclusion These findings can offer a fresh perspective on GRE-induced brain network changes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08665-8.
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Ma S, Wang F, Wang N, Jin J, Yan X, Wang L, Zheng X, Hu S, Du J. Extended Application of Genomic Selection to Screen Multi-Omics Data for the Development of Novel Pyroptosis-Immune Signatures and Predicting Immunotherapy of Glioma. Front Pharmacol 2022; 13:893160. [PMID: 35620284 PMCID: PMC9127445 DOI: 10.3389/fphar.2022.893160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/12/2022] [Indexed: 11/13/2022] Open
Abstract
Glioma is one of the most human malignant diseases and the leading cause of cancer-related deaths worldwide. Nevertheless, the present stratification systems do not accurately predict the prognosis and treatment benefit of glioma patients. Currently, no comprehensive analyses of multi-omics data have been performed to better understand the complex link between pyroptosis and immune. In this study, we constructed four pyroptosis immune subgroups by pyroptosis regulators and obtained nine pyroptosis immune signatures by analyzing the differentially expressed genes between the four pyroptosis immune subgroups. Nine novel pyroptosis immune signatures were provided for assessing the complex heterogeneity of glioma by the analyses of multi-omics data. The pyroptosis immune prognostic model (PIPM) was constructed by pyroptosis immune signatures, and the PIPM risk score was established for glioma cohorts with a total of 1716 samples. Then, analyses of the tumor microenvironment revealed an unanticipated correlation of the PIPM risk score with stemness, immune checkpoint expression, infiltrating the immune system, and therapy response in glioma. The low PIPM risk score patients had a better response to immunotherapy and showed sensitivity to radio-chemotherapy. The results of the pan-cancer analyses revealed the significant correlation between the PIPM risk score and clinical outcome, immune infiltration, and stemness. Taken together, we conclude that pyroptosis immune signatures may be a helpful tool for overall survival prediction and treatment guidance for glioma and other tumors patients.
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Affiliation(s)
- Shuai Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China,Emergency Medicine Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital Affiliated to Hangzhou Medical College, Hangzhou, China
| | - Fang Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Nan Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaqi Jin
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiuwei Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lili Wang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiangrong Zheng
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shaoshan Hu
- Emergency Medicine Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital Affiliated to Hangzhou Medical College, Hangzhou, China,*Correspondence: Shaoshan Hu, , ; Jianyang Du,
| | - Jianyang Du
- Emergency Medicine Center, Department of Neurosurgery, Zhejiang Provincial People’s Hospital Affiliated to Hangzhou Medical College, Hangzhou, China,Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China,*Correspondence: Shaoshan Hu, , ; Jianyang Du,
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Chen Y, Guo Y, Li S, Xu J, Wang X, Ning W, Ma L, Qu Y, Zhang M, Zhang H. Identification of N6-Methyladenosine-Related lncRNAs as a Prognostic Signature in Glioma. Front Oncol 2022; 12:789283. [PMID: 35311131 PMCID: PMC8927984 DOI: 10.3389/fonc.2022.789283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most abundant modification in long noncoding RNAs (lncRNAs). Current studies have shown that the abnormal expression of m6A-related genes is closely associated with the tumorigenesis and progression of glioma. However, the role of m6A-related lncRNAs in glioma development is still unclear. Herein, we screened 566 m6A-related lncRNAs in glioma from The Cancer Genome Atlas (TCGA) database. The expression pattern of these lncRNAs could cluster samples into two groups, in which various classical tumor-related functions and the tumor immune microenvironment were significantly different. Subsequently, a nine-factor m6A-related lncRNA prognostic signature (MLPS) was constructed by using a LASSO regression analysis in the training set and was validated in the test set and independent datasets. The AUC values of the MLPS were 0.881, 0.918 and 0.887 for 1-, 3- and 5-year survival in the training set, respectively, and 0.856, 0.916 and 0.909 for 1-, 3-, and 5-year survival in the test set, respectively. Stratification analyses of the MLPS illustrated its prognostic performance in gliomas with different characteristics. Correlation analyses showed that the infiltrations of monocytes and tumor-associated macrophages (TAMs) were significantly relevant to the risk score in the MLPS. Moreover, we detected the expression of four MLPS factors with defined sequences in glioma and normal cells by using RT-PCR. Afterwards, we investigated the functions of LNCTAM34A (one of the MLPS factors) in glioma cells, which have rarely been reported. Via in vitro experiments, LNCTAM34A was demonstrated to promote the proliferation, migration and epithelial-mesenchymal transition (EMT) of glioma cells. Overall, our study revealed the critical role of m6A-related lncRNAs in glioma and elucidated that LNCTAM34A could promote glioma proliferation, migration and EMT.
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Affiliation(s)
- Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shenglun Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jiacheng Xu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xiang Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yanming Qu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Mingshan Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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Han X, Zhang S. Role of Long Non-Coding RNA LINC00641 in Cancer. Front Oncol 2022; 11:829137. [PMID: 35155216 PMCID: PMC8828736 DOI: 10.3389/fonc.2021.829137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding RNAs with more than 200 nucleic acids in length. When lncRNAs are located in the nucleus, they regulate chromosome structure, participate in chromatin remodeling, and act as transcription regulators. When lncRNAs are exported to the cytoplasm, they regulate mRNA stability, regulate translation, and interfere with post-translational modification. In recent years, more and more evidences have shown that lncRNA can regulate the biological processes of tumor proliferation, apoptosis, invasion and metastasis, and can participate in a variety of tumor signaling pathways. Long-gene non-protein coding RNA641 (LINC00641), located on human chromosome 14q11.2, is differentially expressed in a variety of tumors and is related to overall survival and prognosis, etc. Interfering the expression of LINC00641 can lead to changes in tumor cell proliferation, invasion, metastasis, apoptosis and other biological behaviors. Therefore, LINC00641 is a promising new biomarker and potential clinical therapeutic target. In this review, the biological functions, related mechanisms and clinical significance of LINC00641 in many human cancers are described in detail.
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Affiliation(s)
- Xue Han
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shitai Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
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Li W, Cui Y, Ma W, Wang M, Cai Y, Jiang Y. LncRNA RBPMS-AS1 promotes NRGN transcription to enhance the radiosensitivity of glioblastoma through the microRNA-301a-3p/CAMTA1 axis. Transl Oncol 2021; 15:101282. [PMID: 34800915 PMCID: PMC8605343 DOI: 10.1016/j.tranon.2021.101282] [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: 08/04/2021] [Revised: 11/04/2021] [Accepted: 11/05/2021] [Indexed: 02/07/2023] Open
Abstract
RBPMS-AS1 and CAMTA1 are lowly expressed in GBM patients. RBPMS-AS1 and CAMTA1 enhance the radiosensitivity of GBM. miR-301a-3p diminishes the radiosensitivity of GBM. RBPMS-AS1 enhances CAMTA1 expression in GBM cells through sponging miR-301a-3p. CAMTA1 promotes NRGN transcription.
Objective Glioblastoma (GBM) is the most frequent brain malignancy with high incidence, and long noncoding RNAs (lncRNAs) exerts functions in GBM. In this research, we focused on the capabilities of lncRNA RBPMS-AS1 in radiosensitivity of GBM. Methods RBPMS-AS1 and CAMTA1 expression levels were determined in GBM tissues and cells. StarBase v3.0 database was searched for predicting miRNAs that simultaneously bound to RBPMS-AS1 and CAMTA1. pcDNA3.1-RBPMS-AS1, pcDNA3.1-CAMTA1, miR-301a-3p mimic, or pcDNA3.1-RBPMS-AS1/pcDNA3.1-CAMTA1 and miR-301a-3p mimic were transfected into GBM cells to test radiosensitivity, cell proliferation and apoptosis. The interactions of miR-301a-3p with RBPMS-AS1 and CAMTA1, as well as CAMTA1 and NRGN, were confirmed. In vivo imaging technology was utilized to detect tumor growth in orthotopic xenograft tumors, and Ki67 expression was tested in intracranial tumors. Results RBPMS-AS1 and CAMTA1 levels were reduced in GBM tissues and cells. miR-301a-3p had a binding site with both RBPMS-AS1 and CAMTA1 and it was the most significantly-upregulated one. Upregulation of RBPMS-AS1 or CAMTA1 enhanced the radiosensitivity and cell apoptosis while suppressing proliferation of GBM cells. Conversely, miR-301a-3p overexpression diminished the radiosensitivity and cell apoptosis while inducing proliferation of GBM cells. Overexpression of RBPMS-AS1 or CAMTA1 reversed the effects of overexpressed miR-301a-3p in GBM cells. Mechanistically, RBPMS-AS1 enhanced CAMTA1 expression in GBM cells through sponging miR-301a-3p, and CAMTA1 promoted NRGN expression. In animal experiments, overexpressed RBPMS-AS1 inhibited tumor growth and the positive expression of Ki67 both before and after radiation therapy. Conclusion RBPMS-AS1 promotes NRGN transcription through the miR-301a-3p/CAMTA1 axis and enhances the radiosensitivity of GBM.
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Affiliation(s)
- Wenyang Li
- Department of Neurosurgery, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, PR China
| | - Yan Cui
- Department of Neurosurgery, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, PR China
| | - Wenjia Ma
- Department of Neurosurgery, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, PR China
| | - Ming Wang
- Department of Neurosurgery, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, PR China
| | - Yang Cai
- Department of Neurosurgery, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, PR China
| | - Yugang Jiang
- Department of Neurosurgery, Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, PR China.
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Li Y, Lv M, Wang J, Gao C, Wu Y. LINC00641 inhibits the proliferation and invasion of ovarian cancer cells by targeting miR-320a. Transl Cancer Res 2021; 10:4894-4904. [PMID: 35116341 PMCID: PMC8798150 DOI: 10.21037/tcr-21-2314] [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: 09/16/2021] [Accepted: 11/17/2021] [Indexed: 11/15/2022]
Abstract
BACKGROUND Ovarian cancer is a common malignancy of the female reproductive system, with one of the highest mortality rates among all malignant tumors. However, the pathogenesis of ovarian cancer has not been fully elucidated. This study investigated the role and molecular mechanism of LINC00641 in the development and progression of ovarian cancer. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was used to detect the expression level of LINC00641 in ovarian cancer tissue and adjacent normal tissue. Cell Counting Kit-8 (CCK-8), colony formation, and Transwell assays were used to detect the effects of LINC00641 overexpression on the proliferation and migration of ovarian cancer cells. Bioinformatics analysis and luciferase reporter gene assay were employed to detect the binding of LINC00641 to the downstream target molecule, microRNA-320a (miR-320a). Western blotting was used to determine the effect of miR-320a overexpression on the expression of proliferation-related proteins [Ki-67 and proliferating cell nuclear antigen (PCNA)] and invasion-related proteins (E-cadherin, N-cadherin, and vimentin) in overexpressed LINC00641 cells. RESULTS qRT-PCR results showed that LINC00641 was under-expressed in ovarian cancer tissue compared to adjacent tissue. Cell function experiments showed that the overexpression of LINC00641 could significantly inhibit the proliferation and migration of ovarian cancer cells. The luciferase reporter gene assay showed that LINC00641 could bind to miR-320a, and the overexpression of LINC00641 could markedly inhibit the expression of miR-320a in ovarian cancer cells. Overexpression of miR-320a could significantly block the inhibitory effect of LINC00641 on the proliferation and migration of ovarian cancer cells. CONCLUSIONS As a tumor suppressor gene, LINC00641 can inhibit the proliferation and invasion of ovarian cancer cells by targeting miR-320a. The LINC00641/miR-320a axis may be a new target for the early diagnosis, treatment, or prognosis of ovarian cancer patients.
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Affiliation(s)
- Yan Li
- Department of Obstetrics and Gynecology, The Yancheng Clinical College of Xuzhou Medical University & The First People’s Hospital of Yancheng, Yancheng, China
| | - Mengmeng Lv
- Department of Gynecologic Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianhua Wang
- Department of Gastroenterology, The Yancheng Clinical College of Xuzhou Medical University & The First People’s Hospital of Yancheng, Yancheng, China
| | - Chengzhen Gao
- Department of Obstetrics and Gynecology, The Yancheng Clinical College of Xuzhou Medical University & The First People’s Hospital of Yancheng, Yancheng, China
| | - Yuzhong Wu
- Department of Gynecologic Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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Qiu Y, Pan M, Chen X. A Liquid-Liquid Phase Separation-Related Gene Signature as Prognostic Biomarker for Epithelial Ovarian Cancer. Front Oncol 2021; 11:671892. [PMID: 34168991 PMCID: PMC8217755 DOI: 10.3389/fonc.2021.671892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Objective The aim of the present study was to construct and test a liquid-liquid phase separation (LLPS)-related gene signature as a prognostic tool for epithelial ovarian cancer (EOC). Materials and Methods The data set GSE26712 was used to screen the differentially expressed LLPS-related genes. Functional enrichment analysis was performed to reveal the potential biological functions. GSE17260 and GSE32062 were combined as the discovery to construct an LLPS-related gene signature through a three-step analysis (univariate Cox, least absolute shrinkage and selection operator, and multivariate Cox analyses). The EOC data set from The Cancer Genome Atlas as the test set was used to test the LLPS-related gene signature. Results The differentially expressed LLPS-related genes involved in several cancer-related pathways, such as MAPK signaling pathway, cell cycle, and DNA replication. Eleven genes were selected to construct the LLPS-related gene signature risk index as prognostic biomarker for EOC. The risk index could successfully divide patients with EOC into high- and low-risk groups. The patients in high-risk group had significantly shorter overall survival than those with in low-risk group. The LLPS-related gene signature was validated in the test set and may be an independent prognostic factor compared to routine clinical features. Conclusion We constructed and validated an LLPS-related gene signature as a prognosis tool in EOC through integrated analysis of multiple data sets.
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Affiliation(s)
- Yan Qiu
- Department of Gynecology, Maoming People's Hospital, Maoming, China
| | - Min Pan
- Department of Gynecology, Maoming People's Hospital, Maoming, China
| | - Xuemei Chen
- Department of Gynecology, Maoming People's Hospital, Maoming, China
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Liu W, Liu X. LINC00641 Inhibits the Development of Cutaneous Squamous Cell Carcinoma By Downregulating miR-424 in A431 Cells. Cancer Biother Radiopharm 2021:cbr.2020.4325. [PMID: 33885353 DOI: 10.1089/cbr.2020.4325] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background: Cutaneous squamous cell carcinoma (CSCC) is the most deadly disease among nonmelanoma skin cancers. LINC00641 plays a role in various cancers, but its role in CSCC has not been reported so far. Methods and Materials: The expression of LINC00641 and miR-424 in cells was detected by RT-qPCR. CCK-8 and colony formation assay were used to detect the proliferation of cells. Western blot was used to detect the expression levels of proliferation-, invasion-, and migration-related proteins. Wound Healing and Transwell experiments detected the ability of cell invasion and migration. In animal experiments, a tumor-bearing model was established in nude mice, and tumor volume was measured and photographed. The expression levels of proliferation-, invasion-, and migration-related proteins were detected by western blot. Results: The expression of LINC00641 was significantly decreased in CSCC cell lines. The overexpression of LINC00641 at the cellular level inhibited the proliferation and migration of CSCC cell line A431 by downregulating the expression of miR-424. The overexpression of LINC00641 in animals inhibited the tumor volume of nude mice by downregulating the expression of miR-424 to inhibit the expression of proliferation- and migration-related proteins. Conclusion: LINC00641 inhibits the development of CSCC by downregulating miR-424.
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Affiliation(s)
- Wenmin Liu
- Department of Dermatology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan City, China
| | - Xinxin Liu
- Department of Cardiology, The Second Hospital of Shandong University, Jinan City, China
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Li Z, Yang H, Ye L, Quan R, Chen M. Role of exosomal miRNAs in brain metastasis affected by radiotherapy. Transl Neurosci 2021; 12:127-137. [PMID: 33821195 PMCID: PMC8012736 DOI: 10.1515/tnsci-2020-0163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 12/26/2022] Open
Abstract
In oncogenesis and development of malignant tumor, microRNAs (miRNAs) regulate the complex gene expression associated with the tumor pathogenesis. Currently, only few studies have been conducted to identify miRNAs and the potential pathways involved in the pathogenesis of brain metastasis in patients who underwent radiotherapy, especially miRNAs in the plasma exosomes. Therefore, this study is aimed to use small RNA analysis to identify miRNAs and their potential target genes in plasma exosomes during the initiation and development of brain metastasis in patients who underwent radiotherapy. Using high-throughput sequencing technologies, we identified 35 differentially expressed miRNAs in patients with brain metastasis who had undergone radiotherapy. In annotation of miRNA targets, gene ontology enrichment analysis revealed that the targets of the differentially expressed miRNAs were significantly enriched in the regulation of cellular processes. Kyoto Encyclopedia of Genes and Genomes revealed that most of the miRNA targets were cancer-related, including genes involved in the mitogen-activated protein kinase signaling pathway, cancer-related pathways, phosphatidylinositol 3-kinase-protein kinase B signaling pathway, microtubule-associated protein kinase signaling pathway, Ras signaling pathway, regulation of the actin cytoskeleton, and axon guidance. In conclusion, this study provides a new perspective to understand the possible function of these miRNAs in the pathogenesis of brain metastasis. This was the first time that a pilot study identified plasma exosomal miRNAs in five patients with brain metastasis before and after radiotherapy. This study is the beginning; more specimen and further research are needed to explore the functional role of specific miRNAs and their potential as therapeutic targets for brain metastasis.
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Affiliation(s)
- Zihuang Li
- Department of Radiation Oncology, The Second Clinical Medical College of Jinan University, Shenzhen Municipal People's Hospital, 1017 Dongmen North Road, Shenzhen, Guangdong, 518020, China
| | - Hongli Yang
- Department of Radiation Oncology, The Second Clinical Medical College of Jinan University, Shenzhen Municipal People's Hospital, 1017 Dongmen North Road, Shenzhen, Guangdong, 518020, China
| | - Ling Ye
- Department of oncology, The First Affiliated Hospital of Ji Nan University, Guangzhou, Guangdong, China
| | - Rencui Quan
- Department of Radiation Oncology, The Second Clinical Medical College of Jinan University, Shenzhen Municipal People's Hospital, 1017 Dongmen North Road, Shenzhen, Guangdong, 518020, China
| | - Meili Chen
- Department of Radiation Oncology, The Second Clinical Medical College of Jinan University, Shenzhen Municipal People's Hospital, 1017 Dongmen North Road, Shenzhen, Guangdong, 518020, China
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Hang Q, Lu J, Zuo L, Liu M. Linc00641 promotes the progression of gastric carcinoma by modulating the miR-429/Notch-1 axis. Aging (Albany NY) 2021; 13:8497-8509. [PMID: 33714199 PMCID: PMC8034904 DOI: 10.18632/aging.202661] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 01/04/2021] [Indexed: 12/23/2022]
Abstract
Linc00641 plays different roles in various types of human cancers. However, the function of linc00641 and its underlying mechanism of action in gastric cancer have not been fully elucidated. Therefore, the aim of our current study was to explore the molecular mechanism of linc00641 in gastric cancer. MTT assays, flow cytometry, wound healing assays, and Transwell invasion assays were utilized to measure cell viability, apoptosis, migration and invasion, respectively. Western blotting and RT-PCR assays were carried out to explore the mechanism of linc00641 in gastric cancer cells. We found that silencing linc00641 suppressed the viability and stimulated the apoptosis of gastric cancer cells, while linc00641 overexpression had the opposite effects. Moreover, linc00641 sponged the expression of miR-429 and subsequently upregulated Notch-1 expression in gastric cancer cells. We concluded that linc00641 promoted the malignant progression of gastric cancer by modulating the miR-429/Notch-1 axis.
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Affiliation(s)
- Qun Hang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Jie Lu
- Department of Operating Theatre, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Lugen Zuo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
| | - Mulin Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, PR China
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Zhang C, Liu H, Xu P, Tan Y, Xu Y, Wang L, Liu B, Chen Q, Tian D. Identification and validation of a five-lncRNA prognostic signature related to Glioma using bioinformatics analysis. BMC Cancer 2021; 21:251. [PMID: 33750353 PMCID: PMC7941710 DOI: 10.1186/s12885-021-07972-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 02/25/2021] [Indexed: 12/03/2022] Open
Abstract
Background To accurately predict the prognosis of glioma patients. Methods A total of 541 samples from the TCGA cohort, 181 observations from the CGGA database and 91 samples from our cohort were included in our study. Long non-coding RNAs (LncRNAs) associated with glioma WHO grade were evaluated by weighted gene co-expression network analysis (WGCNA). Five lncRNA features were selected out to construct prognostic signatures based on the Cox regression model. Results By weighted gene co-expression network analysis (WGCNA), 14 lncRNAs related to glioma grade were identified. Using univariate and multivariate Cox analysis, five lncRNAs (CYTOR, MIR155HG, LINC00641, AC120036.4 and PWAR6) were selected to develop the prognostic signature. The Kaplan-Meier curve depicted that the patients in high risk group had poor prognosis in all cohorts. The areas under the receiver operating characteristic curve of the signature in predicting the survival of glioma patients at 1, 3, and 5 years were 0.84, 0.92, 0.90 in the CGGA cohort; 0.8, 0.85 and 0.77 in the TCGA set and 0.72, 0.90 and 0.86 in our own cohort. Multivariate Cox analysis demonstrated that the five-lncRNA signature was an independent prognostic indicator in the three sets (CGGA set: HR = 2.002, p < 0.001; TCGA set: HR = 1.243, p = 0.007; Our cohort: HR = 4.457, p = 0.008, respectively). A nomogram including the lncRNAs signature and clinical covariates was constructed and demonstrated high predictive accuracy in predicting 1-, 3- and 5-year survival probability of glioma patients. Conclusion We established a five-lncRNA signature as a potentially reliable tool for survival prediction of glioma patients. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-07972-9.
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Affiliation(s)
- Chunyu Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Haitao Liu
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Jiaxing University, Jiaxing, 314001, Zhejiang Province, People's Republic of China
| | - Pengfei Xu
- Sun Yat-sen University, The Seventh Affiliated Hospital, Shenzhen, 518000, Guangdong Province, People's Republic of China
| | - Yinqiu Tan
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Yang Xu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Long Wang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Baohui Liu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China
| | - Daofeng Tian
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, 430060, Hubei Province, People's Republic of China.
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