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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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Lam MS, Aw JJ, Tan D, Vijayakumar R, Lim HYG, Yada S, Pang QY, Barker N, Tang C, Ang BT, Sobota RM, Pavesi A. Unveiling the Influence of Tumor Microenvironment and Spatial Heterogeneity on Temozolomide Resistance in Glioblastoma Using an Advanced Human In Vitro Model of the Blood-Brain Barrier and Glioblastoma. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2302280. [PMID: 37649234 DOI: 10.1002/smll.202302280] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/26/2023] [Indexed: 09/01/2023]
Abstract
Glioblastoma (GBM) is the most common primary malignant brain cancer in adults with a dismal prognosis. Temozolomide (TMZ) is the first-in-line chemotherapeutic; however, resistance is frequent and multifactorial. While many molecular and genetic factors have been linked to TMZ resistance, the role of the solid tumor morphology and the tumor microenvironment, particularly the blood-brain barrier (BBB), is unknown. Here, the authors investigate these using a complex in vitro model for GBM and its surrounding BBB. The model recapitulates important clinical features such as a dense tumor core with tumor cells that invade along the perivascular space; and a perfusable BBB with a physiological permeability and morphology that is altered in the presence of a tumor spheroid. It is demonstrated that TMZ sensitivity decreases with increasing cancer cell spatial organization, and that the BBB can contribute to TMZ resistance. Proteomic analysis with next-generation low volume sample workflows of these cultured microtissues revealed potential clinically relevant proteins involved in tumor aggressiveness and TMZ resistance, demonstrating the utility of complex in vitro models for interrogating the tumor microenvironment and therapy validation.
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Affiliation(s)
- Maxine Sy Lam
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Joey Jy Aw
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Damien Tan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Ragavi Vijayakumar
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Hui Yi Grace Lim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Swathi Yada
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Qing You Pang
- Neuro-Oncology Research Laboratory, Department of Research, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Nick Barker
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Carol Tang
- Neuro-Oncology Research Laboratory, Department of Research, National Neuroscience Institute, Singapore, 308433, Singapore
- Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Beng Ti Ang
- Duke-National University of Singapore Medical School, Singapore, 169857, Singapore
- Department of Neurosurgery, National Neuroscience Institute, Singapore, 308433, Singapore
| | - Radoslaw M Sobota
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Functional Proteomics Laboratory, SingMass National Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Andrea Pavesi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
- Mechanobiology Institute, National University of Singapore, Singapore, 117411, Singapore
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Huang X, Shi S, Wang H, Zhao T, Wang Y, Huang S, Su Y, Zhao C, Yang M. Advances in antibody-based drugs and their delivery through the blood-brain barrier for targeted therapy and immunotherapy of gliomas. Int Immunopharmacol 2023; 117:109990. [PMID: 37012874 DOI: 10.1016/j.intimp.2023.109990] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/12/2023]
Abstract
Gliomas are highly invasive and are the most common type of primary malignant brain tumor. The routine treatments for glioma include surgical resection, radiotherapy, and chemotherapy. However, glioma recurrence and patient survival remain unsatisfactory after employing these traditional treatment approaches. With the rapid development of molecular immunology, significant breakthroughs have been made in targeted glioma therapy and immunotherapy. Antibody-based therapy has excellent advantages in treating gliomas due to its high specificity and sensitivity. This article reviewed various targeted antibody drugs for gliomas, including anti-glioma surface marker antibodies, anti-angiogenesis antibodies, and anti-immunosuppressive signal antibodies. Notably, many antibodies have been validated clinically, such as bevacizumab, cetuximab, panitumumab, and anti-PD-1 antibodies. These antibodies can improve the targeting of glioma therapy, enhance anti-tumor immunity, reduce the proliferation and invasion of glioma, and thus prolong the survival time of patients. However, the existence of the blood-brain barrier (BBB) has caused significant difficulties in drug delivery for gliomas. Therefore, this paper also summarized drug delivery methods through the BBB, including receptor-mediated transportation, nano-based carriers, and some physical and chemical methods for drug delivery. With these exciting advancements, more antibody-based therapies will likely enter clinical practice and allow more successful control of malignant gliomas.
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Affiliation(s)
- Xin Huang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Shuyou Shi
- College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Hongrui Wang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Tiesuo Zhao
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan, China
| | - Yibo Wang
- The College of Clinical College, Jilin University, Changchun, China
| | - Sihua Huang
- The College of Clinical College, Jilin University, Changchun, China
| | - Yingying Su
- College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China
| | - Chunyan Zhao
- College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China.
| | - Ming Yang
- College of Basic Medical Sciences, Jilin University, Changchun 130021, Jilin Province, China.
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Dome A, Dymova M, Richter V, Stepanov G. Post-Transcriptional Modifications of RNA as Regulators of Apoptosis in Glioblastoma. Int J Mol Sci 2022; 23:9272. [PMID: 36012529 PMCID: PMC9408889 DOI: 10.3390/ijms23169272] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/17/2022] Open
Abstract
This review is devoted to changes in the post-transcriptional maturation of RNA in human glioblastoma cells, which leads to disruption of the normal course of apoptosis in them. The review thoroughly highlights the latest information on both post-transcriptional modifications of certain regulatory RNAs, associated with the process of apoptosis, presents data on the features of apoptosis in glioblastoma cells, and shows the relationship between regulatory RNAs and the apoptosis in tumor cells. In conclusion, potential target candidates are presented that are necessary for the development of new drugs for the treatment of glioblastoma.
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Affiliation(s)
| | - Maya Dymova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Lu CH, Wei ST, Liu JJ, Chang YJ, Lin YF, Yu CS, Chang SLY. Recognition of a Novel Gene Signature for Human Glioblastoma. Int J Mol Sci 2022; 23:ijms23084157. [PMID: 35456975 PMCID: PMC9029857 DOI: 10.3390/ijms23084157] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 12/10/2022] Open
Abstract
Glioblastoma (GBM) is one of the most common malignant and incurable brain tumors. The identification of a gene signature for GBM may be helpful for its diagnosis, treatment, prediction of prognosis and even the development of treatments. In this study, we used the GSE108474 database to perform GSEA and machine learning analysis, and identified a 33-gene signature of GBM by examining astrocytoma or non-GBM glioma differential gene expression. The 33 identified signature genes included the overexpressed genes COL6A2, ABCC3, COL8A1, FAM20A, ADM, CTHRC1, PDPN, IBSP, MIR210HG, GPX8, MYL9 and PDLIM4, as well as the underexpressed genes CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C, SHANK2 and VIPR2. Protein functional analysis by CELLO2GO implied that these signature genes might be involved in regulating various aspects of biological function, including anatomical structure development, cell proliferation and adhesion, signaling transduction and many of the genes were annotated in response to stress. Of these 33 signature genes, 23 have previously been reported to be functionally correlated with GBM; the roles of the remaining 10 genes in glioma development remain unknown. Our results were the first to reveal that GBM exhibited the overexpressed GPX8 gene and underexpressed signature genes including CHST9, CSDC2, ENHO, FERMT1, IGFN1, LINC00836, MGAT4C and SHANK2, which might play crucial roles in the tumorigenesis of different gliomas.
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Affiliation(s)
- Chih-Hao Lu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 404333, Taiwan; (C.-H.L.); (J.-J.L.); (Y.-J.C.)
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404333, Taiwan
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan
| | - Sung-Tai Wei
- Department of Neurosurgery, China Medical University Hospital, Taichung 404332, Taiwan;
| | - Jia-Jun Liu
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 404333, Taiwan; (C.-H.L.); (J.-J.L.); (Y.-J.C.)
| | - Yu-Jen Chang
- The Ph.D. Program of Biotechnology and Biomedical Industry, China Medical University, Taichung 404333, Taiwan; (C.-H.L.); (J.-J.L.); (Y.-J.C.)
| | - Yu-Feng Lin
- Department of Medical Laboratory Science and Biotechnology, Asia University, Taichung 413305, Taiwan;
| | - Chin-Sheng Yu
- Department of Information Engineering and Computer Science, Feng Chia University, Taichung 407102, Taiwan;
| | - Sunny Li-Yun Chang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 404333, Taiwan
- Correspondence:
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DLL3 expression and methylation are associated with lower-grade glioma immune microenvironment and prognosis. Genomics 2022; 114:110289. [DOI: 10.1016/j.ygeno.2022.110289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 01/31/2022] [Indexed: 11/20/2022]
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Luo N, Wen Y, Zou Q, Ouyang D, Chen Q, Zeng L, He H, Anwar M, Qu L, Ji J, Yi W. Construction and validation of a risk prediction model for clinical axillary lymph node metastasis in T1-2 breast cancer. Sci Rep 2022; 12:687. [PMID: 35027588 PMCID: PMC8758717 DOI: 10.1038/s41598-021-04495-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/21/2021] [Indexed: 12/22/2022] Open
Abstract
The current diagnostic technologies for assessing the axillary lymph node metastasis (ALNM) status accurately in breast cancer (BC) remain unsatisfactory. Here, we developed a diagnostic model for evaluating the ALNM status using a combination of mRNAs and the T stage of the primary tumor as a novel biomarker. We collected relevant information on T1-2 BC from public databases. An ALNM prediction model was developed by logistic regression based on the screened signatures and then internally and externally validated. Calibration curves and the area under the curve (AUC) were employed as performance metrics. The prognostic value and tumor immune infiltration of the model were also determined. An optimal diagnostic model was created using a combination of 11 mRNAs and T stage of the primary tumor and showed high discrimination, with AUCs of 0.828 and 0.746 in the training sets. AUCs of 0.671 and 0.783 were achieved in the internal validation cohorts. The mean external AUC value was 0.686 and ranged between 0.644 and 0.742. Moreover, the new model has good specificity in T1 and hormone receptor-negative/human epidermal growth factor receptor 2- negative (HR-/HER2-) BC and good sensitivity in T2 BC. In addition, the risk of ALNM and 11 mRNAs were correlated with the infiltration of M2 macrophages, as well as the prognosis of BC. This novel prediction model is a useful tool to identify the risk of ALNM in T1-2 BC patients, particularly given that it can be used to adjust surgical options in the future.
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Affiliation(s)
- Na Luo
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
- Department of General Surgery, The First People's Hospital of Changde City, Changde, China
| | - Ying Wen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Qiongyan Zou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Dengjie Ouyang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Qitong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Liyun Zeng
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Hongye He
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Munawar Anwar
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Limeng Qu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Jingfen Ji
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.
| | - Wenjun Yi
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, China.
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