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Vieira FG, Bispo R, Lopes MB. Integration of Multi-Omics Data for the Classification of Glioma Types and Identification of Novel Biomarkers. Bioinform Biol Insights 2024; 18:11779322241249563. [PMID: 38812741 PMCID: PMC11135104 DOI: 10.1177/11779322241249563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 04/09/2024] [Indexed: 05/31/2024] Open
Abstract
Glioma is currently one of the most prevalent types of primary brain cancer. Given its high level of heterogeneity along with the complex biological molecular markers, many efforts have been made to accurately classify the type of glioma in each patient, which, in turn, is critical to improve early diagnosis and increase survival. Nonetheless, as a result of the fast-growing technological advances in high-throughput sequencing and evolving molecular understanding of glioma biology, its classification has been recently subject to significant alterations. In this study, we integrate multiple glioma omics modalities (including mRNA, DNA methylation, and miRNA) from The Cancer Genome Atlas (TCGA), while using the revised glioma reclassified labels, with a supervised method based on sparse canonical correlation analysis (DIABLO) to discriminate between glioma types. We were able to find a set of highly correlated features distinguishing glioblastoma from lower-grade gliomas (LGGs) that were mainly associated with the disruption of receptor tyrosine kinases signaling pathways and extracellular matrix organization and remodeling. Concurrently, the discrimination of the LGG types was characterized primarily by features involved in ubiquitination and DNA transcription processes. Furthermore, we could identify several novel glioma biomarkers likely helpful in both diagnosis and prognosis of the patients, including the genes PPP1R8, GPBP1L1, KIAA1614, C14orf23, CCDC77, BVES, EXD3, CD300A, and HEPN1. Collectively, this comprehensive approach not only allowed a highly accurate discrimination of the different TCGA glioma patients but also presented a step forward in advancing our comprehension of the underlying molecular mechanisms driving glioma heterogeneity. Ultimately, our study also revealed novel candidate biomarkers that might constitute potential therapeutic targets, marking a significant stride toward personalized and more effective treatment strategies for patients with glioma.
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Affiliation(s)
- Francisca G Vieira
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
| | - Regina Bispo
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Department of Mathematics, NOVA School of Science and Technology, Caparica, Portugal
| | - Marta B Lopes
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Department of Mathematics, NOVA School of Science and Technology, Caparica, Portugal
- UNIDEMI, Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, Portugal
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2
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Lv S, Chen Z, Mi H, Yu X. Cofilin Acts as a Booster for Progression of Malignant Tumors Represented by Glioma. Cancer Manag Res 2022; 14:3245-3269. [PMID: 36452435 PMCID: PMC9703913 DOI: 10.2147/cmar.s389825] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/10/2022] [Indexed: 07/20/2023] Open
Abstract
Cofilin, as a depolymerization factor of actin filaments, has been widely studied. Evidences show that cofilin has a role in actin structural reorganization and dynamic regulation. In recent years, several studies have demonstrated a regulatory role for cofilin in the migration and invasion mediated by cell dynamics and epithelial to mesenchymal transition (EMT)/EMT-like process, apoptosis, radiotherapy resistance, immune escape, and transcriptional dysregulation of malignant tumor cells, particularly glioma cells. On this basis, it is practical to evaluate cofilin as a biomarker for predicting tumor metastasis and prognosis. Targeting cofilin regulating kinases, Lin11, Isl-1 and Mec-3 kinases (LIM kinases/LIMKs) and their major upstream molecules inhibits tumor cell migration and invasion and targeting cofilin-mediated mitochondrial pathway induces apoptosis of tumor cells represent effective options for the development of novel anti-malignant tumor drug, especially anti-glioma drugs. This review explores the structure, general biological function, and regulation of cofilin, with an emphasis on the critical functions and prospects for clinical therapeutic applications of cofilin in malignant tumors represented by glioma.
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Affiliation(s)
- Shihong Lv
- Department of Gastroenterology, The Second Affiliated Hospital of Mudanjiang Medical College, Mudanjiang Medical College, Mudanjiang, 157011, People’s Republic of China
| | - Zhiye Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Hailong Mi
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
| | - Xingjiang Yu
- Department of Histology and Embryology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People’s Republic of China
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3
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Rioseras B, Moro-García MA, García-Torre A, Bueno-García E, López-Martínez R, Iglesias-Escudero M, Diaz-Peña R, Castro-Santos P, Arias-Guillén M, Alonso-Arias R. Acquisition of New Migratory Properties by Highly Differentiated CD4+CD28 null T Lymphocytes in Rheumatoid Arthritis Disease. J Pers Med 2021; 11:jpm11070594. [PMID: 34202487 PMCID: PMC8306508 DOI: 10.3390/jpm11070594] [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: 06/07/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 02/07/2023] Open
Abstract
Expanded CD4+CD28null T lymphocytes are found in the tissues and peripheral blood of patients with many autoimmune diseases, such as rheumatoid arthritis (RA). These highly differentiated cells present potent inflammatory activity and capability to induce tissue destruction, which has been suggested to predispose to the development of more aggressive disease. In fact, preferential migration to inflammatory sites has been proposed to be a contributing factor in the progression of autoimmune and cardiovascular diseases frequently found in these patients. The functional activity of CD4+CD28null T lymphocytes is largely dependent on interleukin 15 (IL-15), and this cytokine may also act as a selective attractor of these cells to local inflammatory infiltrates in damaged tissues. We have analysed, in RA patients, the migratory properties and transcriptional motility profile of CD4+CD28null T lymphocytes compared to their counterparts CD28+ T lymphocytes and the enhancing role of IL-15. Identification of the pathways involved in this process will allow us to design strategies directed to block effector functions that CD4+CD28null T lymphocytes have in the target tissue, which may represent therapeutic approaches in this immune disorder.
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Affiliation(s)
- Beatriz Rioseras
- Immunology Department, Medicine Laboratory, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (B.R.); (A.G.-T.); (E.B.-G.); rociolopez-@hotmail.com (R.L.-M.)
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain;
| | - Marco Antonio Moro-García
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain;
- Medicine Laboratory, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain
| | - Alejandra García-Torre
- Immunology Department, Medicine Laboratory, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (B.R.); (A.G.-T.); (E.B.-G.); rociolopez-@hotmail.com (R.L.-M.)
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain;
| | - Eva Bueno-García
- Immunology Department, Medicine Laboratory, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (B.R.); (A.G.-T.); (E.B.-G.); rociolopez-@hotmail.com (R.L.-M.)
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain;
| | - Rocio López-Martínez
- Immunology Department, Medicine Laboratory, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (B.R.); (A.G.-T.); (E.B.-G.); rociolopez-@hotmail.com (R.L.-M.)
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain;
| | | | - Roberto Diaz-Peña
- Faculty of Health Sciences, Universidad Autónoma de Chile, Talca 3460000, Chile;
| | - Patricia Castro-Santos
- Inmunologia, Centro de Investigaciones Biomédicas (CINBIO), Universidad de Vigo, 36310 Vigo, Spain;
| | - Miguel Arias-Guillén
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain;
- Servicio de Neumología, Hospital Universitario Central Asturias, 33011 Oviedo, Spain;
- CIBER—Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rebeca Alonso-Arias
- Immunology Department, Medicine Laboratory, Hospital Universitario Central de Asturias, 33011 Oviedo, Spain; (B.R.); (A.G.-T.); (E.B.-G.); rociolopez-@hotmail.com (R.L.-M.)
- Health Research Institute of the Principality of Asturias—ISPA, 33011 Oviedo, Spain;
- Correspondence:
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Liang J, Oyang L, Rao S, Han Y, Luo X, Yi P, Lin J, Xia L, Hu J, Tan S, Tang L, Pan Q, Tang Y, Zhou Y, Liao Q. Rac1, A Potential Target for Tumor Therapy. Front Oncol 2021; 11:674426. [PMID: 34079763 PMCID: PMC8165220 DOI: 10.3389/fonc.2021.674426] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/29/2021] [Indexed: 12/20/2022] Open
Abstract
RAS-related C3 botulinum toxin substrate 1 (Rac.1) is one of the important members of Rho GTPases. It is well known that Rac1 is a cytoskeleton regulation protein that regulates cell adhesion, morphology, and movement. Rac1 is highly expressed in different types of tumors, which is related to poor prognosis. Studies have shown that Rac1 not only participates in the tumor cell cycle, apoptosis, proliferation, invasion, migration and angiogenesis, but also participates in the regulation of tumor stem cell, thus promoting the occurrence of tumors. Rac1 also plays a key role in anti-tumor therapy and participates in immune escape mediated by the tumor microenvironment. In addition, the good prospects of Rac1 inhibitors in cancer prevention and treatment are exciting. Therefore, Rac1 is considered as a potential target for the prevention and treatment of cancer. The necessity and importance of Rac1 are obvious, but it still needs further study.
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Affiliation(s)
- Jiaxin Liang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Shan Rao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Yaqian Han
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Pin Yi
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jinguan Lin
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Longzheng Xia
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Jiaqi Hu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Shiming Tan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Lu Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,University of South China, Hengyang, China
| | - Qing Pan
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,University of South China, Hengyang, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Clinical Research Center for Wound Healing in Hunan Province, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,Clinical Research Center for Wound Healing in Hunan Province, Changsha, China
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5
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Ren B, Wang L, Nan Y, Liu T, Zhao L, Ma H, Li J, Zhang Y, Ren X. RAB1A regulates glioma cellular proliferation and invasion via the mTOR signaling pathway and epithelial-mesenchymal transition. Future Oncol 2021; 17:3203-3216. [PMID: 33947216 DOI: 10.2217/fon-2021-0116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Aim: We aimed at investigating the mechanism of RAB1A proliferation and invasion in gliomas. Materials & methods: Genome-wide expression profile data and immunohistochemistry were analyzed to assess RAB1A expression in gliomas. The Transwell assay, wound healing assay, brain slice coculture model, cellular fluorescence and intracranial xenograft model of nude mice were used to determine the proliferation and invasion of glioma cells. Results & conclusion: RAB1A was highly expressed in gliomas compared with normal brain tissue. The overall survival time of glioma patients with high RAB1A expression was significantly shortened. RAB1A regulated the activity of RAC1 by inhibiting the mTOR signaling pathway, affecting actin polymerization, cell morphology and cell polarity. RAB1A downregulation inhibited the epithelial-mesenchymal transition, proliferation and invasion of glioma cells.
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Affiliation(s)
- Bingcheng Ren
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, 300308, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, 300052, China
| | - Le Wang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, 300308, China
| | - Yang Nan
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, 300308, China
| | - Tong Liu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, 300308, China
| | - Liwen Zhao
- Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, 300308, China
| | - Haiwen Ma
- Department of Neurosurgery, Tianjin Medical University General Hospital Airport Site, Tianjin, 300308, China
| | - Jiabo Li
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, 300052, China
| | - Yiming Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, 300052, China
| | - Xiao Ren
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China.,Laboratory of Neuro-Oncology, Tianjin Neurological Institute, Tianjin, 300052, China
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6
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The Expressions and Mechanisms of Sarcomeric Proteins in Cancers. DISEASE MARKERS 2020; 2020:8885286. [PMID: 32670437 PMCID: PMC7346232 DOI: 10.1155/2020/8885286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/07/2020] [Accepted: 06/13/2020] [Indexed: 02/07/2023]
Abstract
The sarcomeric proteins control the movement of cells in diverse species, whereas the deregulation can induce tumours in model organisms and occurs in human carcinomas. Sarcomeric proteins are recognized as oncogene and related to tumor cell metastasis. Recent insights into their expressions and functions have led to new cancer therapeutic opportunities. In this review, we appraise the evidence for the sarcomeric proteins as cancer genes and discuss cancer-relevant biological functions, potential mechanisms by which sarcomeric proteins activity is altered in cancer.
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