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Larriba E, de Juan Romero C, García-Martínez A, Quintanar T, Rodríguez-Lescure Á, Soto JL, Saceda M, Martín-Nieto J, Barberá VM. Identification of new targets for glioblastoma therapy based on a DNA expression microarray. Comput Biol Med 2024; 179:108833. [PMID: 38981212 DOI: 10.1016/j.compbiomed.2024.108833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/11/2024]
Abstract
This study provides a comprehensive perspective on the deregulated pathways and impaired biological functions prevalent in human glioblastoma (GBM). In order to characterize differences in gene expression between individuals diagnosed with GBM and healthy brain tissue, we have designed and manufactured a specific, custom DNA microarray. The results obtained from differential gene expression analysis were validated by RT-qPCR. The datasets obtained from the analysis of common differential expressed genes in our cohort of patients were used to generate protein-protein interaction networks of functionally enriched genes and their biological functions. This network analysis, let us to identify 16 genes that exhibited either up-regulation (CDK4, MYC, FOXM1, FN1, E2F7, HDAC1, TNC, LAMC1, EIF4EBP1 and ITGB3) or down-regulation (PRKACB, MEF2C, CAMK2B, MAPK3, MAP2K1 and PENK) in all GBM patients. Further investigation of these genes and enriched pathways uncovered in this investigation promises to serve as a foundational step in advancing our comprehension of the molecular mechanisms underpinning GBM pathogenesis. Consequently, the present work emphasizes the critical role that the unveiled molecular pathways likely play in shaping innovative therapeutic approaches for GBM management. We finally proposed in this study a list of compounds that target hub of GBM-related genes, some of which are already in clinical use, underscoring the potential of those genes as targets for GBM treatment.
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Affiliation(s)
- Eduardo Larriba
- Human and Mammalian Genetics Group, Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Camino de Juan Romero
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Avda, Universidad s/n, Ed. Torregaitán, Elche, Spain.
| | - Araceli García-Martínez
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Unidad de Genética Molecular, Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain
| | - Teresa Quintanar
- Servicio de Oncología Médica. Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain
| | - Álvaro Rodríguez-Lescure
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Servicio de Oncología Médica. Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; School of Medicine. Universidad Miguel Hernández de Elche. Investigator, Spanish Breast Cancer Research Group (GEICAM), Spain
| | - José Luis Soto
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Unidad de Genética Molecular, Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain
| | - Miguel Saceda
- Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Instituto de Investigación, Desarrollo e Innovación en Biotecnología Sanitaria de Elche (IDiBE), Universidad Miguel Hernández, Avda, Universidad s/n, Ed. Torregaitán, Elche, Spain
| | - José Martín-Nieto
- Human and Mammalian Genetics Group, Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain.
| | - Víctor M Barberá
- Human and Mammalian Genetics Group, Departamento de Fisiología, Genética y Microbiología, Facultad de Ciencias, Universidad de Alicante, Alicante, Spain; Unidad de Investigación, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain; Unidad de Genética Molecular, Hospital General Universitario de Elche, Camí de l'Almazara 11, Elche, 03203, Alicante, Spain.
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Verma A, Patel R, Mahale A, Thorat RV, Rath SL, Sridhar E, Moiyadi A, Srivastava S. Multitarget Potential Drug Candidates for High-Grade Gliomas Identified by Multiple Reaction Monitoring Coupled with In Silico Drug Repurposing. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:59-75. [PMID: 38320249 DOI: 10.1089/omi.2023.0256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
High-grade gliomas (HGGs) are extremely aggressive primary brain tumors with high mortality rates. Despite notable progress achieved by clinical research and biomarkers emerging from proteomics studies, efficacious drugs and therapeutic targets are limited. This study used targeted proteomics, in silico molecular docking, and simulation-based drug repurposing to identify potential drug candidates for HGGs. Importantly, we performed multiple reaction monitoring (MRM) on differentially expressed proteins with putative roles in the development and progression of HGGs based on our previous work and the published literature. Furthermore, in silico molecular docking-based drug repurposing was performed with a customized library of FDA-approved drugs to identify multitarget-directed ligands. The top drug candidates such as Pazopanib, Icotinib, Entrectinib, Regorafenib, and Cabozantinib were explored for their drug-likeness properties using the SwissADME. Pazopanib exhibited binding affinities with a maximum number of proteins and was considered for molecular dynamic simulations and cell toxicity assays. HGG cell lines showed enhanced cytotoxicity and cell proliferation inhibition with Pazopanib and Temozolomide combinatorial treatment compared to Temozolomide alone. To the best of our knowledge, this is the first study combining MRM with molecular docking and simulation-based drug repurposing to identify potential drug candidates for HGG. While the present study identified five multitarget-directed potential drug candidates, future clinical studies in larger cohorts are crucial to evaluate the efficacy of these molecular candidates. The research strategy and methodology used in the present study offer new avenues for innovation in drug discovery and development which may prove useful, particularly for cancers with low cure rates.
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Affiliation(s)
- Ayushi Verma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Rushda Patel
- Sinhgad College of Pharmacy, Savitribai Phule Pune University, Pune, India
| | - Atharva Mahale
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal, India
| | - Rujuta Vijay Thorat
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Soumya Lipsa Rath
- Department of Biotechnology, National Institute of Technology, Warangal, India
| | - Epari Sridhar
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Aliasgar Moiyadi
- Advanced Centre for Treatment Research and Education in Cancer, Tata Memorial Centre, Navi Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Dai L, Li Z, Liang W, Hu W, Zhou S, Yang Z, Tao Y, Hou X, Xing Z, Mao J, Shi Z, Wang X. SOCS proteins and their roles in the development of glioblastoma. Oncol Lett 2021; 23:5. [PMID: 34820004 PMCID: PMC8607235 DOI: 10.3892/ol.2021.13123] [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: 07/29/2021] [Accepted: 10/11/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most common type of primary brain tumor in adults. GBM is characterized by a high degree of malignancy and aggressiveness, as well as high morbidity and mortality rates. GBM is currently treatable via surgical resection, chemotherapy and radiotherapy, but the prognosis of patients with GBM is poor. The suppressor of cytokine signaling (SOCS) protein family comprises eight members, including SOCS1-SOCS7 and cytokine-inducible SH2-containing protein. SOCS proteins regulate the biogenesis of GBM via the JAK/STAT and NF-κB signaling pathways. Driven by NF-κB, the expression of SOCS proteins can serve as a negative regulator of the JAK/STAT signaling pathway and exerts a potential inhibitory effect on GBM. In GBM, E3 ubiquitin ligase is involved in the regulation of cellular functions, such as the receptor tyrosine kinase (RTK) survival signal, in which SOCS proteins negatively regulate RTK signaling, and kinase overexpression or mutation can lead to the development of malignancies. Moreover, SOCS proteins affect the proliferation and differentiation of GBM cells by regulating the tumor microenvironment. SOCS proteins also serve specific roles in GBM of different grades and different isocitrate dehydrogenase mutation status. The aim of the present review was to describe the biogenesis and function of the SOCS protein family, the roles of SOCS proteins in the microenvironment of GBM, as well as the role of this protein family and E3 ubiquitin ligases in GBM. Furthermore, the role of SOCS proteins as diagnostic and prognostic markers in GBM and their potential role as GBM therapeutics were explored.
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Affiliation(s)
- Lirui Dai
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zian Li
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Wulong Liang
- Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Weihua Hu
- Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Shaolong Zhou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zhuo Yang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Yiran Tao
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Xuelei Hou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Jianchao Mao
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Zimin Shi
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
| | - Xinjun Wang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Science and Technology of Henan Province, Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, Henan 450052, P.R. China
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Yekula A, Taylor A, Beecroft A, Kang KM, Small JL, Muralidharan K, Rosh Z, Carter BS, Balaj L. The role of extracellular vesicles in acquisition of resistance to therapy in glioblastomas. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2021; 4:1-16. [PMID: 35582008 PMCID: PMC9019190 DOI: 10.20517/cdr.2020.61] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/05/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022]
Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumor with a median survival of 15 months despite standard care therapy consisting of maximal surgical debulking, followed by radiation therapy with concurrent and adjuvant temozolomide treatment. The natural history of GBM is characterized by inevitable recurrence with patients dying from increasingly resistant tumor regrowth after therapy. Several mechanisms including inter- and intratumoral heterogeneity, the evolution of therapy-resistant clonal subpopulations, reacquisition of stemness in glioblastoma stem cells, multiple drug efflux mechanisms, the tumor-promoting microenvironment, metabolic adaptations, and enhanced repair of drug-induced DNA damage have been implicated in therapy failure. Extracellular vesicles (EVs) have emerged as crucial mediators in the maintenance and establishment of GBM. Multiple seminal studies have uncovered the multi-dynamic role of EVs in the acquisition of drug resistance. Mechanisms include EV-mediated cargo transfer and EVs functioning as drug efflux channels and decoys for antibody-based therapies. In this review, we discuss the various mechanisms of therapy resistance in GBM, highlighting the emerging role of EV-orchestrated drug resistance. Understanding the landscape of GBM resistance is critical in devising novel therapeutic approaches to fight this deadly disease.
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Affiliation(s)
- Anudeep Yekula
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | | | - Keiko M. Kang
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Julia L. Small
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Koushik Muralidharan
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Zachary Rosh
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Bob S. Carter
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Leonora Balaj
- Department of Neurosurgery, Massachusetts General Hospital, Boston, MA 02114, USA
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