Analysing Differential Alternative Splicing Events and Their Impact on Retinoblastoma Progression Using RNA-seq Metadata

Assane Rachidou, Mohamed Hameed Aslam; Vanniarajan, Ayyasamy; Kim, Usha; Devarajan, Bharanidharan

doi:10.31557/APJCP.2025.26.5.1781

Analysing Differential Alternative Splicing Events and Their Impact on Retinoblastoma Progression Using RNA-seq Metadata

Document Type : Research Articles

Authors

Mohamed Hameed Aslam Assane Rachidou ¹^{, 2}
Ayyasamy Vanniarajan ³
Usha Kim ⁴
Bharanidharan Devarajan ¹

¹ Department of Bioinformatics, Aravind Medical Research Foundation, Madurai, India.

² Department of Bioinformatics, Alagappa University, karaikudi, India.

³ Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, India.

⁴ Department of Orbit, Oculoplasty and Oncology, Aravind Eye Hospital, Madurai, India.

10.31557/APJCP.2025.26.5.1781

Abstract

Objective: Identify differential alternative splicing (DAS) events and their role in retinoblastoma (RB) progression. Methods: We conducted a meta-analysis of RNA sequencing data from 50 RB tumours and 17 normal retinal tissues to identify DAS events and differential expressed genes (DEGs) in RB progression. We performed functional and pathway enrichment analyses, Weighted Gene Co-expression Network Analysis (WGCNA), and protein-protein interaction analysis. Results: We identified 6136 DAS events involving 1262 genes and 1787 DEGs. Exon skipping and mutually exclusive exons were the most prevalent DAS events. Functional analyses of DAS events containing genes highlighted involvement in E2F targets, cell cycle, G2M checkpoint, MYC targets and fatty acid metabolism pathways. Notably, numerous DAS events were detected in ENO2. WGCNA identified TFDP1, PCNA, and CCNB1, potentially contributing to RB progression through alternative splicing. Splicing factors ILF2 and HNRNPA1 were highly co-expressed with DAS events containing genes, suggesting their regulatory role in splicing changes during RB progression. Conclusions: Our study reveals significant differential alternative splicing events that play a crucial role in the progression of retinoblastoma. Numerous DAS events, DEGs, and functional analyses underscore the complexity of gene regulation in RB. Importantly, DAS events in TFDP1, PCNA, and CCNB1 may play a crucial role, indicating that alternative splicing is a potential avenue for therapeutic intervention in RB.

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