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Azimi P, Yazdanian T, Ahmadiani A. mRNA markers for survival prediction in glioblastoma multiforme patients: a systematic review with bioinformatic analyses. BMC Cancer 2024; 24:612. [PMID: 38773447 PMCID: PMC11106946 DOI: 10.1186/s12885-024-12345-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is a type of fast-growing brain glioma associated with a very poor prognosis. This study aims to identify key genes whose expression is associated with the overall survival (OS) in patients with GBM. METHODS A systematic review was performed using PubMed, Scopus, Cochrane, and Web of Science up to Journey 2024. Two researchers independently extracted the data and assessed the study quality according to the New Castle Ottawa scale (NOS). The genes whose expression was found to be associated with survival were identified and considered in a subsequent bioinformatic study. The products of these genes were also analyzed considering protein-protein interaction (PPI) relationship analysis using STRING. Additionally, the most important genes associated with GBM patients' survival were also identified using the Cytoscape 3.9.0 software. For final validation, GEPIA and CGGA (mRNAseq_325 and mRNAseq_693) databases were used to conduct OS analyses. Gene set enrichment analysis was performed with GO Biological Process 2023. RESULTS From an initial search of 4104 articles, 255 studies were included from 24 countries. Studies described 613 unique genes whose mRNAs were significantly associated with OS in GBM patients, of which 107 were described in 2 or more studies. Based on the NOS, 131 studies were of high quality, while 124 were considered as low-quality studies. According to the PPI network, 31 key target genes were identified. Pathway analysis revealed five hub genes (IL6, NOTCH1, TGFB1, EGFR, and KDR). However, in the validation study, only, the FN1 gene was significant in three cohorts. CONCLUSION We successfully identified the most important 31 genes whose products may be considered as potential prognosis biomarkers as well as candidate target genes for innovative therapy of GBM tumors.
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Affiliation(s)
- Parisa Azimi
- Neurosurgeon, Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Arabi Ave, Daneshjoo Blvd, Velenjak, Tehran, 19839- 63113, Iran.
| | | | - Abolhassan Ahmadiani
- Neurosurgeon, Neuroscience Research Center, Shahid Beheshti University of Medical Sciences, Arabi Ave, Daneshjoo Blvd, Velenjak, Tehran, 19839- 63113, Iran.
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Karami Fath M, Karimfar N, Fazlollahpour Naghibi A, Shafa S, Ghasemi Shiran M, Ataei M, Dehghanzadeh H, Nabi Afjadi M, Ghadiri T, Payandeh Z, Tarhriz V. Revisiting characteristics of oncogenic extrachromosomal DNA as mobile enhancers on neuroblastoma and glioma cancers. Cancer Cell Int 2022; 22:200. [PMID: 35614494 PMCID: PMC9131661 DOI: 10.1186/s12935-022-02617-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/18/2022] [Indexed: 12/21/2022] Open
Abstract
Cancer can be induced by a variety of possible causes, including tumor suppressor gene failure and proto-oncogene hyperactivation. Tumor-associated extrachromosomal circular DNA has been proposed to endanger human health and speed up the progression of cancer. The amplification of ecDNA has raised the oncogene copy number in numerous malignancies according to whole-genome sequencing on distinct cancer types. The unusual structure and function of ecDNA, and its potential role in understanding current cancer genome maps, make it a hotspot to study tumor pathogenesis and evolution. The discovery of the basic mechanisms of ecDNA in the emergence and growth of malignancies could lead researchers to develop new cancer therapies. Despite recent progress, different aspects of ecDNA require more investigation. We focused on the features, and analyzed the bio-genesis, and origin of ecDNA in this review, as well as its functions in neuroblastoma and glioma cancers.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Nastaran Karimfar
- Faculty of Veterinary Medicine, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | | | - Shahriyar Shafa
- School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Melika Ghasemi Shiran
- Department of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mehran Ataei
- Department of Biology, Faculty of Sciences, Shahid Chamran University, Ahvaz, Iran
| | | | - Mohsen Nabi Afjadi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
| | - Tahereh Ghadiri
- Department of Neuroscience and Cognition, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran. .,Shefa Neuroscience Research Center, Khatam Alanbia Hospital, Tehran, Iran. .,Neurosiences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Zahra Payandeh
- Department Medical Biochemistry and Biophysics, Division Medical Inflammation Research, Karolinska Institute, Stockholm, Sweden.
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran.
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Integrative analysis of DNA methylation and gene expression profiles to identify biomarkers of glioblastoma. Cancer Genet 2021; 258-259:135-150. [PMID: 34773808 DOI: 10.1016/j.cancergen.2021.10.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/21/2021] [Accepted: 10/31/2021] [Indexed: 12/26/2022]
Abstract
Glioblastoma multiforme (GBM) is the most common, most invasive, and malignant type of primary brain tumor with poor prognosis and poor survival rate. Using GSE22891 the expression and methylation status of same GBM patients was evaluated to identify key epigenetic genes in GBM. Using |log2FC| > 1 and FDR 〈 0.05 as the threshold, DEGs including 4910 downregulated and 2478 upregulated were screened and by |log2FC| 〉 0.2 and p-value < 0.05, 3223 DMCs were detected. By merging the results of DEGs and DMCs, 643 genes were selected for network analysis by WGCNA, and based on expression values three modules and by methylation values, one module was selected. Using STRING and Cytoscape databases, PPI network of genes of all modules were constructed separately. According to the PPI network, core genes were picked out. The expression status of core genes was evaluated using GSE77043, GSE42656, GSE30563, GSE22891, GSE15824, and GSE122498, and 50 genes were validated. The methylation status of 50 genes was explored using GSE50923, GSE22891, and GSE36245, and finally, 12 hub genes including ARHGEF7, RAB11FIP4, PPP1R16B, OLFM1, CLDN10, BCAT1, C1QB, C1QC, IFI16, NUP37, PARP9, and PCLAF were selected. Using GEPIA database, the expression and by cBioportal the survival plot and also scatterplot of methylation versus expression of 12 hub genes were extracted based on TCGA. To determine the diagnostic values of the hub genes, the receiver operating characteristic (ROC) curve and the area under the curve (AUC) were extracted based on GSE22891 and GSE122498. Finally, we evaluated the expression level of the genes in tissue of 83 GBM patients and also non-tumoral adjacent (as control) tissues.
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Tessarollo NG, Domingues ACM, Antunes F, da Luz JCDS, Rodrigues OA, Cerqueira OLD, Strauss BE. Nonreplicating Adenoviral Vectors: Improving Tropism and Delivery of Cancer Gene Therapy. Cancers (Basel) 2021; 13:cancers13081863. [PMID: 33919679 PMCID: PMC8069790 DOI: 10.3390/cancers13081863] [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: 02/26/2021] [Revised: 04/05/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Recent preclinical and clinical studies have used viral vectors in gene therapy research, especially nonreplicating adenovirus encoding strategic therapeutic genes for cancer treatment. Adenoviruses were the first DNA viruses to go into therapeutic development, mainly due to well-known biological features: stability in vivo, ease of manufacture, and efficient gene delivery to dividing and nondividing cells. However, there are some limitations for gene therapy using adenoviral vectors, such as nonspecific transduction of normal cells and liver sequestration and neutralization by antibodies, especially when administered systemically. On the other hand, adenoviral vectors are amenable to strategies for the modification of their biological structures, including genetic manipulation of viral proteins, pseudotyping, and conjugation with polymers or biological membranes. Such modifications provide greater specificity to the target cell and better safety in systemic administration; thus, a reduction of antiviral host responses would favor the use of adenoviral vectors in cancer immunotherapy. In this review, we describe the structural and molecular features of nonreplicating adenoviral vectors, the current limitations to their use, and strategies to modify adenoviral tropism, highlighting the approaches that may allow for the systemic administration of gene therapy.
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Li Q, Zhang L, Jiang J, Zhang Y, Wang X, Zhang Q, Wang Y, Liu C, Li F. CDK1 and CCNB1 as potential diagnostic markers of rhabdomyosarcoma: validation following bioinformatics analysis. BMC Med Genomics 2019; 12:198. [PMID: 31870357 PMCID: PMC6929508 DOI: 10.1186/s12920-019-0645-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 12/12/2019] [Indexed: 12/27/2022] Open
Abstract
Background Rhabdomyosarcoma (RMS), a common soft-tissue malignancy in pediatrics, presents high invasiveness and mortality. However, besides known changes in the PAX3/7-FOXO1 fusion gene in alveolar RMS, the molecular mechanisms of the disease remain incompletely understood. The purpose of the study is to recognize potential biomarkers related with RMS and analyse their molecular mechanism, diagnosis and prognostic significance. Methods The Gene Expression Omnibus was used to search the RMS and normal striated muscle data sets. Differentially expressed genes (DEGs) were filtered using R software. The DAVID has become accustomed to performing functional annotations and pathway analysis on DEGs. The protein interaction was constructed and further processed by the STRING tool and Cytoscape software. Kaplan–Meier was used to estimate the effect of hub genes on the ending of sarcoma sufferers, and the expression of these genes in RMS was proved by real-time polymerase chain reaction (RT-PCR). Finally, the expression of CDK1 and CCNB1 in RMS was validated by immunohistochemistry (IHC). Results A total of 1932 DEGs were obtained, amongst which 1505 were up-regulated and 427were down-regulated. Up-regulated genes were largely enriched in the cell cycle, ECM-receptor interaction, PI3K/Akt and p53 pathways, whilst down-regulated genes were primarily enriched in the muscle contraction process. CDK1, CCNB1, CDC20, CCNB2, AURKB, MAD2L1, HIST2H2BE, CENPE, KIF2C and PCNA were identified as hub genes by Cytoscape analyses. Survival analysis showed that, except for HIST2H2BE, the other hub genes were highly expressed and related to poor prognosis in sarcoma. RT-PCR validation showed that CDK1, CCNB1, CDC20, CENPE and HIST2H2BE were significantly differential expression in RMS compared to the normal control. IHC revealed that the expression of CDK1 (28/32, 87.5%) and CCNB1 (26/32, 81.25%) were notably higher in RMS than normal controls (1/9, 11.1%; 0/9, 0%). Moreover, the CCNB1 was associated with the age and location of the patient’s onset. Conclusions These results show that these hub genes, especially CDK1 and CCNB1, may be potential diagnostic biomarkers for RMS and provide a new perspective for the pathogenesis of RMS.
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Affiliation(s)
- Qianru Li
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China
| | - Liang Zhang
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China.,Department of Anesthesiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Jinfang Jiang
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China
| | - Yangyang Zhang
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China
| | - Xiaomeng Wang
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China
| | - Qiaochu Zhang
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China
| | - Yang Wang
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China
| | - Chunxia Liu
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China.
| | - Feng Li
- Department of Pathology, Shihezi University School of Medicine and The Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Chinese Ministry of Education, Shihezi, Xinjiang, 832002, China. .,Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, People's Republic of China.
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Luo S, Zhang P, Ma X, Wang Q, Lu J, Liu B, Zhao W, Allain JP, Li C, Li T. A rapid strategy for constructing novel simian adenovirus vectors with high viral titer and expressing highly antigenic proteins applicable for vaccine development. Virus Res 2019; 268:1-10. [DOI: 10.1016/j.virusres.2019.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 05/15/2019] [Accepted: 05/16/2019] [Indexed: 12/25/2022]
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