AccScience Publishing / EJMO / Online First / DOI: 10.36922/EJMO025200193
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ORIGINAL RESEARCH ARTICLE

Integrative bioinformatics analysis of the correlation between CDKN2A homozygous deletion, RB1 loss, and PDGFRA amplification in glioma

Xiaoyan Pan1† ,  Rong Chen1† ,  Yingyu Yang1 ,  Pengpeng Tang1 ,  Yijuan Fan1*
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1 Department of Pathology, Affiliated Renhe Hospital, Shanghai University, Shanghai, China
†These authors contributed equally to this work.
EJMO, 025200193 https://doi.org/10.36922/EJMO025200193
Received: 14 May 2025 | Revised: 28 July 2025 | Accepted: 15 August 2025 | Published online: 9 September 2025
© 2025 by the Author(s). This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution -Noncommercial 4.0 International License (CC-by the license) ( https://creativecommons.org/licenses/by-nc/4.0/ )
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Abstract

Introduction: Malignant gliomas constitute a heterogeneous group of primary central nervous system tumors originating from glial cells or their precursors. They display aggressive characteristics and unfavorable clinical outcomes. The 2021 World Health Organization classification emphasizes molecular markers as essential elements for glioma categorization, therapeutic planning, and prognostic assessment. Specific genetic alterations, including CDKN2A homozygous deletion, RB1 loss, and PDGFRA amplification, emerge as potentially crucial determinants of tumor behavior and patient outcomes.

Objectives: This investigation examines the relationship between these genetic modifications and survival outcomes while evaluating their influence on the tumor immune landscape.

Methods: We utilized the cBioPortal database to analyze the mutation status of CDKN2A homozygous deletion, RB1 loss, and PDGFRA amplification in gliomas, and further investigated the correlation between these mutations and glioma prognosis. Next, we evaluated the expression levels of these genes in gliomas by analyzing data from the Cancer Genome Atlas (TCGA) database. In addition, we explored the potential prognostic value of these genes in gliomas using information from the Chinese Glioma Genome Atlas and TCGA databases. Finally, immunohistochemistry was performed to detect the protein expression of cyclin-dependent kinase inhibitor 2A (CDKN2A), retinoblastoma 1 (RB1), and platelet-derived growth factor receptor alpha (PDGFRA) in gliomas.

Results: Our analysis revealed that the homozygous deletion of CDKN2A and the amplification of PDGFRA are significantly correlated with poor overall survival and reduced progression-free survival in glioma patients (p<0.05), while the loss of RB1 showed no significant association with prognosis. Additionally, the expression levels of PDGFRA and RB1 were closely related to immune cell infiltration.

Conclusion: High expression of CDKN2A and RB1 generally indicated poorer survival outcomes, whereas elevated expression of PDGFRA exhibited an opposite trend, potentially influencing glioma immune response and therapeutic efficacy by modulating the tumor microenvironment. Immunohistochemical analysis further confirmed the high expression of CDKN2A, RB1, and PDGFRA in gliomas.

Keywords
Glioma
Mutation
Tumor immune microenvironment
Immunohistochemistry
Funding
This study was funded by the Key Specialties in Baoshan District of Shanghai, China (BSZK-2023-BZ10).
Conflict of interest
The authors declare that they have no conflict of interest.
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Eurasian Journal of Medicine and Oncology, Electronic ISSN: 2587-196X Print ISSN: 2587-2400, Published by AccScience Publishing
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