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Zhao L, He S, Liu Z, Song Z, Hou X, Gai L. Bioinformatics analysis of the prognostic role of alternative splicing data in lung adenocarcinoma. J Thorac Dis 2024; 16:1463-1472. [PMID: 38505068 PMCID: PMC10944774 DOI: 10.21037/jtd-24-6] [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: 01/02/2024] [Accepted: 02/04/2024] [Indexed: 03/21/2024]
Abstract
Background As a post-transcriptional regulatory mechanism, alternative splicing (AS) is engaged in a variety of pathophysiological processes, and it has been widely reported in connection with the occurrence, progression, metastasis, and drug resistance of cancer. However, the research on AS in lung adenocarcinoma (LUAD) is very limited. In addition, the prognostic effect of AS event (ASE) on LUAD and its related mechanism are not clear. This study aimed to explore the role and potential prognostic value of ASE in LUAD. Methods Relevant data and ASE datasets of the sample were acquired from The Cancer Genome Atlas (TCGA) and TCGASpliceSeq databases. We constructed a new prognostic criterion based on ASEs. Then, Cox regression and least absolute shrinkage and selection operator (LASSO) regression analysis were used to construct the model. Based on this model, the risk score of each ASE was calculated, and the reliability of this model was evaluated by Kaplan-Meier survival and receiver operating characteristic (ROC) curve analyses. Finally, these results were verified on different network platforms. Results We identified seven types of ASEs related to survival. The prognostic risk model for ASEs was established. The Kaplan-Meier curve showed that compared to the low-risk group, the overall survival (OS) rate of LUAD patients in the high-risk group was lower. ROC curve analysis showed that the prognostic risk model of LUAD patients was well predicted, and the area under the curve (AUC) also confirmed this. Conclusions This study screened the ASE related to the prognosis of LUAD patients, and provided a theoretical basis for further study of the correlation between ASE and the prognosis of LUAD patients. It has provided new ideas for developing new biomarkers and therapeutic targets for LUAD patients.
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Affiliation(s)
- Lingling Zhao
- Department of Ultrasound, The Second Affiliated Hospital of Nantong University, The First People’s Hospital of Nantong, Nantong, China
| | - Shuting He
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, China
- Department of Oncology, Medical School of Nantong University, Nantong, China
| | - Ziwei Liu
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, China
- Department of Oncology, Medical School of Nantong University, Nantong, China
| | - Zhibin Song
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, China
- Department of Oncology, Medical School of Nantong University, Nantong, China
| | - Xiaochun Hou
- Department of Oncology, The Second People’s Hospital of Nantong, Nantong, China
| | - Ling Gai
- Department of Chemotherapy, Affiliated Hospital of Nantong University, Nantong, China
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Huang Y, Chen F, Sun H, Zhong C. Exploring gene-patient association to identify personalized cancer driver genes by linear neighborhood propagation. BMC Bioinformatics 2024; 25:34. [PMID: 38254011 PMCID: PMC10804660 DOI: 10.1186/s12859-024-05662-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Driver genes play a vital role in the development of cancer. Identifying driver genes is critical for diagnosing and understanding cancer. However, challenges remain in identifying personalized driver genes due to tumor heterogeneity of cancer. Although many computational methods have been developed to solve this problem, few efforts have been undertaken to explore gene-patient associations to identify personalized driver genes. RESULTS Here we propose a method called LPDriver to identify personalized cancer driver genes by employing linear neighborhood propagation model on individual genetic data. LPDriver builds personalized gene network based on the genetic data of individual patients, extracts the gene-patient associations from the bipartite graph of the personalized gene network and utilizes a linear neighborhood propagation model to mine gene-patient associations to detect personalized driver genes. The experimental results demonstrate that as compared to the existing methods, our method shows competitive performance and can predict cancer driver genes in a more accurate way. Furthermore, these results also show that besides revealing novel driver genes that have been reported to be related with cancer, LPDriver is also able to identify personalized cancer driver genes for individual patients by their network characteristics even if the mutation data of genes are hidden. CONCLUSIONS LPDriver can provide an effective approach to predict personalized cancer driver genes, which could promote the diagnosis and treatment of cancer. The source code and data are freely available at https://github.com/hyr0771/LPDriver .
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Affiliation(s)
- Yiran Huang
- School of Computer, Electronics and Information, Guangxi University, Nanning, 530004, China
- Key Laboratory of Parallel, Distributed and Intelligent Computing in Guangxi Universities and Colleges, Guangxi University, Nanning, 530004, China
- Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, 530004, China
| | - Fuhao Chen
- School of Computer, Electronics and Information, Guangxi University, Nanning, 530004, China
| | - Hongtao Sun
- School of Computer, Electronics and Information, Guangxi University, Nanning, 530004, China
| | - Cheng Zhong
- School of Computer, Electronics and Information, Guangxi University, Nanning, 530004, China.
- Key Laboratory of Parallel, Distributed and Intelligent Computing in Guangxi Universities and Colleges, Guangxi University, Nanning, 530004, China.
- Guangxi Key Laboratory of Multimedia Communications and Network Technology, Guangxi University, Nanning, 530004, China.
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Development and Validation of a Liquid-Liquid Phase Separation-Related Gene Signature as Prognostic Biomarker for Low-Grade Gliomas. DISEASE MARKERS 2022; 2022:1487165. [PMID: 36193491 PMCID: PMC9525737 DOI: 10.1155/2022/1487165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/29/2022] [Accepted: 09/13/2022] [Indexed: 11/25/2022]
Abstract
Aim To explore whether the liquid-liquid phase separation- (LLPS-) related genes were potential prognostic markers that could contribute to the further classification of low-grade gliomas (LGGs). Methods The LLPS-related genes were subjected to functional enrichment analysis. The univariable, least absolute shrinkage and selection operator, and multivariable stepwise Cox regression analyses were performed to develop an LLPS-related gene signature (GS) in the discovery data set. The biological characteristics of the high-risk LGG were explored using gene set enrichment analysis. Two independent external data sets were used to validate the LLPS-related GS. Results LLPS-related genes are involved in multiple important cancer-related biological processes and pathways in LGG. Nine LLPS-related genes were identified to construct the LLPS-related GS, which was significantly associated with the prognosis of LGG patients. The LLPS-related GS could successfully divide patients with LGG into high- and low-risk groups, and the high-risk group showed a poorer prognosis than the low-risk group. Furthermore, the LLPS-related GS was independent of IDH and 1p19q status. Several cancer-related pathways may be more active in high-risk LGGs, such as IL6 JAK STAT3 signaling pathway. The LLPS-related GS was successfully validated with two independent external data sets. Conclusion We developed and validated a novel LLPS-related GS for risk stratification of LGG. Our findings may provide more precise management for LGGs and a useful reference for LLPS mechanism to link LGG studies.
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Rodriguez SMB, Staicu GA, Sevastre AS, Baloi C, Ciubotaru V, Dricu A, Tataranu LG. Glioblastoma Stem Cells-Useful Tools in the Battle against Cancer. Int J Mol Sci 2022; 23:ijms23094602. [PMID: 35562993 PMCID: PMC9100635 DOI: 10.3390/ijms23094602] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 02/01/2023] Open
Abstract
Glioblastoma stem cells (GSCs) are cells with a self-renewal ability and capacity to initiate tumors upon serial transplantation that have been linked to tumor cell heterogeneity. Most standard treatments fail to completely eradicate GSCs, causing the recurrence of the disease. GSCs could represent one reason for the low efficacy of cancer therapy and for the short relapse time. Nonetheless, experimental data suggest that the presence of therapy-resistant GSCs could explain tumor recurrence. Therefore, to effectively target GSCs, a comprehensive understanding of their biology and the survival and developing mechanisms during treatment is mandatory. This review provides an overview of the molecular features, microenvironment, detection, and targeting strategies of GSCs, an essential information required for an efficient therapy. Despite the outstanding results in oncology, researchers are still developing novel strategies, of which one could be targeting the GSCs present in the hypoxic regions and invasive edge of the glioblastoma.
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Affiliation(s)
- Silvia Mara Baez Rodriguez
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
| | - Georgiana-Adeline Staicu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
| | - Ani-Simona Sevastre
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Medicine and Pharmacy, 200349 Craiova, Romania;
| | - Carina Baloi
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
| | - Vasile Ciubotaru
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
| | - Anica Dricu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania; (G.-A.S.); (C.B.)
- Correspondence:
| | - Ligia Gabriela Tataranu
- Neurosurgical Department, Clinical Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania; (S.M.B.R.); (V.C.); (L.G.T.)
- Department 6—Clinical Neurosciences, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
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Tang X, Zuo C, Fang P, Liu G, Qiu Y, Huang Y, Tang R. Targeting Glioblastoma Stem Cells: A Review on Biomarkers, Signal Pathways and Targeted Therapy. Front Oncol 2021; 11:701291. [PMID: 34307170 PMCID: PMC8297686 DOI: 10.3389/fonc.2021.701291] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 06/25/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) remains the most lethal and common primary brain tumor, even after treatment with multiple therapies, such as surgical resection, chemotherapy, and radiation. Although great advances in medical development and improvements in therapeutic methods of GBM have led to a certain extension of the median survival time of patients, prognosis remains poor. The primary cause of its dismal outcomes is the high rate of tumor recurrence, which is closely related to its resistance to standard therapies. During the last decade, glioblastoma stem cells (GSCs) have been successfully isolated from GBM, and it has been demonstrated that these cells are likely to play an indispensable role in the formation, maintenance, and recurrence of GBM tumors, indicating that GSCs are a crucial target for treatment. Herein, we summarize the current knowledge regarding GSCs, their related signaling pathways, resistance mechanisms, crosstalk linking mechanisms, and microenvironment or niche. Subsequently, we present a framework of targeted therapy for GSCs based on direct strategies, including blockade of the pathways necessary to overcome resistance or prevent their function, promotion of GSC differentiation, virotherapy, and indirect strategies, including targeting the perivascular, hypoxic, and immune niches of the GSCs. In summary, targeting GSCs provides a tremendous opportunity for revolutionary approaches to improve the prognosis and therapy of GBM, despite a variety of challenges.
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Affiliation(s)
- Xuejia Tang
- Department of Neurosurgery, University-Town Hospital of Chongqing Medical University, Chongqing, China.,Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Chenghai Zuo
- Department of Neurosurgery and Key Laboratory of Neurotrauma, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, China
| | - Pengchao Fang
- Department of Pharmacy, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, China
| | - Guojing Liu
- Department of Neurosurgery, University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Yongyi Qiu
- Department of Neurosurgery, University-Town Hospital of Chongqing Medical University, Chongqing, China
| | - Yi Huang
- Department of Neurosurgery, The Ninth People's Hospital of Chongqing, Chongqing, China
| | - Rongrui Tang
- Department of Neurosurgery, University-Town Hospital of Chongqing Medical University, Chongqing, China
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SH3BGRL3, transcribed by STAT3, facilitates glioblastoma tumorigenesis by activating STAT3 signaling. Biochem Biophys Res Commun 2021; 556:114-120. [PMID: 33839406 DOI: 10.1016/j.bbrc.2021.03.165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/19/2022]
Abstract
Glioblastoma (GBM) is the most aggressive tumors of the central nervous system. Here, we report that SH3 binding glutamic acid-rich protein like 3 (SH3BGRL3) was extremely highly expressed in GBM and glioma stem cells. SH3BGRL3 high expression associates with worse survival of GBM patients. Functionally, Targeting SH3BGRL3 obviously impairs GSCs self-renewal in vitro. Most importantly, we first report that SH3BGRL3 is a direct transcriptional target gene of signal transducer and activator of transcription 3 (STAT3) and thereby activating STAT3 signaling in turn. Additionally, forced expression of the constitutively activated STAT3 (STAT3-C) rescued GSCs self-renewal inhibited by SH3BGRL3 silencing. Collectively, we first identified a critical positive feedback loop between SH3BGRL3 and STAT3, which facilitates the tumorigenic potential of GBM.
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