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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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Lakis NS, Brodsky AS, Karashchuk G, Audesse AJ, Yang D, Sturtevant A, Lombardo K, Wong IY, Webb AE, Anthony DC. Stem cell phenotype predicts therapeutic response in glioblastomas with MGMT promoter methylation. Acta Neuropathol Commun 2022; 10:159. [PMID: 36333778 PMCID: PMC9636755 DOI: 10.1186/s40478-022-01459-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
A growing body of evidence supports the presence of a population of cells in glioblastoma (GBM) with a stem cell-like phenotype which shares certain biological markers with adult neural stem cells, including expression of SOX2, CD133 (PROM1), and NES (nestin). This study was designed to determine the relationship between the expression of these stem cell markers and the clinical outcome in GBM patients. We quantified the intensity of expression of the proteins CD133 and SOX2 by immunohistochemistry (IHC) in a cohort of 86 patients with IDH-wildtype GBM, and evaluated patient outcomes using Kaplan-Meier and Cox proportional hazards analysis. In our patients, MGMT promoter methylation status and age were predictors of overall survival and progression free survival. The levels of SOX2 and CD133 were not associated with outcome in univariate analysis; however, stratification of tumors based on low or high levels of CD133 or SOX2 expression revealed that MGMT methylation was a predictor of progression-free survival and overall survival only for tumors with high levels of expression of CD133 or SOX2. Tumors with low levels of expression of CD133 or SOX2 did not show any relationship between MGMT methylation and survival. This relationship between MGMT and stem cell markers was confirmed in a second patient cohort, the TCGA dataset. Our results show that stratification of GBM by the level of expression of CD133 and SOX2 improved the prognostic power of MGMT promoter methylation status, identifying a low-expressing group in which the clinical outcome is not associated with MGMT promoter methylation status, and a high-expressing group in which the outcome was strongly associated with MGMT promoter methylation status. These findings support the concept that the presence of a high stem cell phenotype in GBM, as marked by expression of SOX2 or CD133, may be associated with the clinical response to treatment.
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Affiliation(s)
- Nelli S. Lakis
- Department of Pathology, Kansas University Medical Center, Kansas City, KS USA
- Department of Pathology and Laboratory Medicine, Lifespan Academic Medical Center, Providence, Rhode Island USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island USA
| | - Alexander S. Brodsky
- Department of Pathology and Laboratory Medicine, Lifespan Academic Medical Center, Providence, Rhode Island USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island USA
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island USA
| | - Galina Karashchuk
- Department of Pathology and Laboratory Medicine, Lifespan Academic Medical Center, Providence, Rhode Island USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island USA
| | - Amanda J. Audesse
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island USA
| | - Dongfang Yang
- Department of Pathology and Laboratory Medicine, Lifespan Academic Medical Center, Providence, Rhode Island USA
| | - Ashlee Sturtevant
- Department of Pathology and Laboratory Medicine, Lifespan Academic Medical Center, Providence, Rhode Island USA
| | - Kara Lombardo
- Department of Pathology and Laboratory Medicine, Lifespan Academic Medical Center, Providence, Rhode Island USA
| | - Ian Y. Wong
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island USA
- School of Engineering, Brown University, Providence, Rhode Island USA
| | - Ashley E. Webb
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island USA
- Center on Biology of Aging, Brown University, Providence, Rhode Island USA
- Carney Institute for Brain Science, Brown University, Providence, Rhode Island USA
| | - Douglas C. Anthony
- Department of Pathology and Laboratory Medicine, Lifespan Academic Medical Center, Providence, Rhode Island USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, Rhode Island USA
- Carney Institute for Brain Science, Brown University, Providence, Rhode Island USA
- Department of Neurology, Warren Alpert Medical School of Brown University, Providence, Rhode Island USA
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Reddy RG, Bhat UA, Chakravarty S, Kumar A. Advances in histone deacetylase inhibitors in targeting glioblastoma stem cells. Cancer Chemother Pharmacol 2020; 86:165-179. [PMID: 32638092 DOI: 10.1007/s00280-020-04109-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/26/2020] [Indexed: 12/17/2022]
Abstract
Glioblastoma multiforme (GBM) is a lethal grade IV glioma (WHO classification) and widely prevalent primary brain tumor in adults. GBM tumors harbor cellular heterogeneity with the presence of a small subpopulation of tumor cells, described as GBM cancer stem cells (CSCs) that pose resistance to standard anticancer regimens and eventually mediate aggressive relapse or intractable progressive GBM. Existing conventional anticancer therapies for GBM do not target GBM stem cells and are mostly palliative; therefore, exploration of new strategies to target stem cells of GBM has to be prioritized for the development of effective GBM therapy. Recent developments in the understanding of GBM pathophysiology demonstrated dysregulation of epigenetic mechanisms along with the genetic changes in GBM CSCs. Altered expression/activity of key epigenetic regulators, especially histone deacetylases (HDACs) in GBM stem cells has been associated with poor prognosis; inhibiting the activity of HDACs using histone deacetylase inhibitors (HDACi) has been promising as mono-therapeutic in targeting GBM and in sensitizing GBM stem cells to an existing anticancer regimen. Here, we review the development of pan/selective HDACi as potential anticancer agents in targeting the stem cells of glioblastoma as a mono or combination therapy.
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Affiliation(s)
- R Gajendra Reddy
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Unis Ahmad Bhat
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad, 500007, Telangana, India
| | - Sumana Chakravarty
- Applied Biology Division, CSIR-Indian Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad, 500007, Telangana, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India
| | - Arvind Kumar
- CSIR-Centre for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad, 500007, Telangana, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India.
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Haque MM, Kowtal P, Sarin R. Identification and characterization of TP53 gene Allele Dropout in Li-Fraumeni syndrome and Oral cancer cohorts. Sci Rep 2018; 8:11705. [PMID: 30076369 PMCID: PMC6076284 DOI: 10.1038/s41598-018-30238-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/21/2018] [Indexed: 12/20/2022] Open
Abstract
Allele Drop out (ADO) arising from non-amplification of one allele may produce false negative result and impact clinical management. In cancer, germline and somatic genetic analysis is being increasingly used but the prevalence, nature and implications of ADO has not been studied in any cohort. In a cohort of 290 Li Fraumeni/Li Fraumeni Like Syndrome cases undergoing TP53 genetic testing, of the 69 pathogenic mutations identified so far, 5 were initially missed and 4 were misgenotyped as homozygous mutation due to germline ADO. Of the 9 germline ADOs, 8 were sequence dependent, arising from a polymorphism (rs12951053) in the primer annealing region of exon 7. Of 35 somatic TP53 variants identified by exome sequencing in 50 oral cancer tissues registered under International Cancer Genome Consortium (ICGC), as a result of ADO, 4 were not detectable and 6 were not called as variant on Sanger Sequencing due to low peak height. High prevalence of germline and somatic ADO in the most frequently mutated cancer gene TP53, highlights the need for systematic evaluation of ADO prevalence and causes in clinically important cancer genes. False negative result for high penetrance germline mutations or actionable somatic mutations in oncogenes could have major clinical implications.
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Affiliation(s)
- Mohammed Moquitul Haque
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India
| | - Pradnya Kowtal
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India
| | - Rajiv Sarin
- Sarin Lab, Advanced Centre for Treatment Research and Education in Cancer-Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India. .,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400085, Maharashtra, India. .,Cancer Genetics Clinic, Tata Memorial Hospital, Tata Memorial Centre, Parel, Mumbai, 400012, Maharashtra, India.
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Su YK, Shih PH, Lee WH, Bamodu OA, Wu ATH, Huang CC, Tzeng YM, Hsiao M, Yeh CT, Lin CM. Antrodia cinnamomea sensitizes radio-/chemo-therapy of cancer stem-like cells by modulating microRNA expression. JOURNAL OF ETHNOPHARMACOLOGY 2017; 207:47-56. [PMID: 28602756 DOI: 10.1016/j.jep.2017.06.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 06/02/2017] [Accepted: 06/03/2017] [Indexed: 06/07/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The discovery of many tissue-specific cancer stem cells (CSCs) continues to attract scientific attention. These CSCs are considered to be associated with chemo- and radio-resistance, and consequently, failure of conventional anticancer therapies. The recent demonstration of several microRNAs as enhancers of tumorigenicity via modulation of epithelial-mesenchymal transition and cancer stemness, makes them putative novel therapeutic target in oncology. Antrodia cinnamomea is a Chinese traditional medicine with several biological functions including anti-inflammation, antioxidant, and cancer prevention. However, the anti-CSC capability of A. Cinnamomea is not clear yet. AIM OF THE STUDY To investigate the inhibitory effect of A. cinnamomea mycelium and extract on CSCs derived from various human cancer cell lines using our in-house therapeutics and human genome-wide miRNA screening panels. MATERIALS AND METHODS A broad range of human cancer cell lines, including the acute monocytic leukemia (THP-1), glioblastoma multiforme (GBM 8401), lung carcinoma (A549), breast adenocarcinoma (MDA-MB-231), hepatoblastoma (HepG2), colorectal adenocarcinoma (SW620), and foreskin fibroblast (HS68), were exposed to A. cinnamomea in this study. CD133+ CSCs generated from the cell lines were characterized and isolated by flow cytometry, effect of chemo- and radiotherapy was assessed using the MTT assay, while the RT-PCR and human genome wide qRT-PCR determined the differential gene expression patterns. A comparative analysis of the anticancer effect of A. cinnamomea and Cisplatin, Taxol, or irradiation was also performed. RESULTS Our results indicated that A. cinnamomea mycelium and its ethyl acetate extracts showed anti-proliferation effects against all types of CSCs, especially the lung, breast, and head and neck squamous cell carcinoma CSCs. Furthermore, CSCs treatment with A. cinnamomea combined with irradiation or chemotherapeutics demonstrated significant anti-cancer effect. We also established an association between the CSC-inhibitory effect of A. cinnamomea and significant downregulation of several microRNAs and cancer stemness expression levels in brain and breast CSCs. More importantly, higher CD133 expression is associated with poor prognosis in glioblastoma and breast cancer patients. CONCLUSION Herein, we demonstrate the putative role of A. cinnamomea as an effective ethnopharmacologic therapeutic agent for cancer treatment.
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Affiliation(s)
- Yu-Kai Su
- Department of Neurology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Neurosurgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan
| | - Ping-Hsiao Shih
- Department of Pediatrics, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan; Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Wei-Hwa Lee
- Department of Pathology, Taipei Medical University-Shuang Ho Hospital, Taipei, Taiwan
| | - Oluwaseun Adebayo Bamodu
- Cancer Center, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan; Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan
| | - Alexander T H Wu
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Chun-Chih Huang
- Department of Life Science, National Taitung University, Taitung, Taiwan
| | - Yew-Min Tzeng
- Department of Life Science, National Taitung University, Taitung, Taiwan
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Tai Yeh
- Cancer Center, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan; Department of Medical Research & Education, Taipei Medical University-Shuang Ho Hospital, New Taipei City, Taiwan.
| | - Chien-Min Lin
- Department of Neurology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Neurosurgery, Department of Surgery, Shuang Ho Hospital, Taipei Medical University, Taipei, Taiwan.
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