Gene Ontology-based Functional Enrichment and PPI Network Mapping of APOE4-associated Genes in Alzheimer’s Disease: A Method to Identify Potential Therapeutic Targets

Introduction: Apolipoprotein E (APOE) is a protein involved in cholesterol circulation and has been reported to play a role in neurodegenerative conditions such as Alzheimer’s Disease (AD). Improper lipidation of APOE leads to aggregation of transmembrane amyloid-β (Aβ) proteins and hyperphosphorylation of tau proteins in AD. APOE4, a variant of the apolipoprotein E gene, affects lipid transport, amyloid-β clearance, and neuroinflammation, thereby increasing the risk of neurodegenerative diseases. It also exhibits distinct DNA methylation patterns and post-translational modifications that alter its stability and function compared to other isoforms. Aim: To identify and evaluate APOE4-interacting proteins as potential therapeutic targets using functional enrichment tools. Materials and Methods: This computational bioinformatics study was carried out using open-source, web-based databases between January and September 2024. APOE protein–protein interaction (PPI) networks were constructed using STRING database (v11.5), GeneMANIA (v3.6.0), and BioGRID (v4.4.212) with a confidence cut-off score of 0.5. Interacting proteins were ranked based on interaction scores, and the top 10 candidates were selected for further functional analysis. Results were summarised in tabular and graphical formats. Results: A total of 32 genes were found to be associated with lipoprotein receptor activity, carbohydrate metabolism, cholesterol metabolism, and ribosome biogenesis, involving glucagon signalling and HIF-1 signalling pathways. Amyloid Precursor Protein (APP), Microtubule-Associated Protein Tau (MAPT), and Triggering Receptor Expressed on Myeloid cells 2 (TREM2) were repeatedly identified across multiple tools, with the highest confidence scores of 0.998, 0.997, and 0.995, respectively, in STRING database, and scores of 0.586 and 0.474 for APP and MAPT, in GeneMANIA. These three genes were present among other genes involved in apolipoprotein binding, with an enrichment score of 216.5 provided by the DAVID database. Conclusion: APP and MAPT were identified as promising druggable targets, highlighting their importance in AD. In the present study, APOE4-interacting, drug-targetable, functionally enriched ADrelated genes were shortlisted from hundreds of proteins reported across different Gene Ontology (GO) databases.