Gene enrichment analysis and protein–protein interaction network topology delineates S-Phase kinase-associated protein 1 and catenin beta-1 as potential signature genes linked to glioblastoma prognosis

K Ashwini; Pavan Gollapalli; Shilpa S Shetty; Ananthan Raghotham; Praveenkumar Shetty; Jayaprakash Shetty; N Suchetha Kumari

doi:10.4103/bbrj.bbrj_344_22

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ORIGINAL ARTICLE

Year : 2023 \| Volume : 7 \| Issue : 1 \| Page : 37-47

Gene enrichment analysis and protein–protein interaction network topology delineates S-Phase kinase-associated protein 1 and catenin beta-1 as potential signature genes linked to glioblastoma prognosis K Ashwini¹, Pavan Gollapalli², Shilpa S Shetty¹, Ananthan Raghotham³, Praveenkumar Shetty⁴, Jayaprakash Shetty⁵, N Suchetha Kumari⁴ ¹ Central Research Laboratory, KS Hegde Medical Academy (KSHEMA), Nitte (Deemed to be University), Mangalore, Karnataka, India ² Division of Bioinformatics and Computational Genomics, Nitte University Center for Science Education and Research (NUCSER), Nitte (Deemed to be University), Deralakatte, Mangalore, Karnataka, India ³ Department of Neurosurgery, KS Hegde Medical Academy (KSHEMA), Nitte (Deemed to be University), Mangalore, Karnataka, India ⁴ Central Research Laboratory; Department of Biochemistry, KS Hegde Medical Academy (KSHEMA), Nitte (Deemed to be University), Mangalore, Karnataka, India ⁵ Department of Pathology, KS Hegde Medical Academy (KSHEMA), Nitte (Deemed to be University), Mangalore, Karnataka, India Correspondence Address: N Suchetha Kumari Department of Biochemistry, KS Hegde Medical Academy, Nitte (Deemed to be University), Deralakatte, Mangaluru - 575 018, Karnataka India Source of Support: None, Conflict of Interest: None DOI: 10.4103/bbrj.bbrj_344_22

Background: Glioblastoma (GBM) is the most malignant and accounts for 60% of brain tumors in adults. Current therapy for GBM involves surgical removal of the tumor followed by radiotherapy with concomitant adjuvant therapy temozolomide. Despite improvements in therapy, patient survival remains low. The exact etiology of a brain tumor is uncertain, and numerous unknown genes are involved in the progression of GBM. The aim of the present study was to evaluate various genes involved in GBM through bioinformatic approach. Methods: In the present study, gene expression profile of GSE68424 was retrieved from the GEO database to explore the genes in GBM. Results: Analysis of expression profile data revealed that 33 genes were upregulated and 1189 genes were downregulated based on the log2 fold change cut-off criteria. The genes S-Phase kinase-associated protein 1 (SKP1) and Catenin beta-1 (CTNNB1) have been linked to GBM prognosis. Conclusion: SKP1 and CTNNB1 were identified as a candidate gene for GBM study as a result of these findings. Catenin beta-1 was the protein with the highest closeness centrality value and is the key component of canonical Wnt signaling downstream pathway. More study is needed to establish the molecular function of SKP1 and CTNNB1 in GBM development, as well as the biomarker's specificity and sensitivity.



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