Computational Analysis of CRISPR-Cas9 Mediated Therapeutic Targeting in Alzheimer’s Disease

Objectives: The neurodegenerative disease Alzheimer’s disease (AD) causes progressive brain deterioration through amyloid-beta accumulation, tau hyperphosphorylation, and neuroinflammatory responses. Scientists have studied Alzheimer’s disease for multiple decades, yet they have not developed any treatment that can cure the condition. The genome-editing tool Clustered regularly interspaced short palindromic repeats associated protein 9 (CRISPR-Cas9) is a powerful technology that scientists use to make precise modifications to disease-related genes. The current research lacks a complete computational assessment of CRISPR targets and their therapeutic potential for treating Alzheimer’s disease. In the current study, we investigate computational CRISPR-Cas9 genome-editing methods targeting vital Alzheimer’s disease-related genes to evaluate their guide RNA sequences, biological pathway effects, and gene network responses. Material and Methods: In the current study, data on AD-related genes were retrieved from OMIM, DisseNET, and AlzGene, and differential expression analysis was conducted on the bulk RNA-seq dataset GSE33000. We used CHOPCHOP and CRISPOR to design guide RNAs (gRNAs) targeting APP, PSEN1, APOE, and TNF, and Cas-OFFinder to predict potential off-target effects. The researchers performed pathway enrichment through Enrichr and DAVID. The researchers constructed a fundamental gene regulatory network in Cytoscape and then ran Boolean simulations to predict gene-editing outcomes. Results: The study of differential expression showed that APP, PSEN1, PSEN2, TNF, and CLU genes exhibited increased expression in Alzheimer’s disease brain tissue. The designed gRNAs exhibited high on-target performance, with scores exceeding 85, and minimal predicted off-target effects. The pathway enrichment analysis identified amyloid processing, tau phosphorylation, cholesterol metabolism, and inflammation as critical biological processes. The Boolean simulations showed that APP knockout blocked the Aβ and Tau pathways, TNF knockout reduced neuroinflammation, and APOE4→3 correction restored cholesterol homeostasis and reduced inflammation to some extent. Conclusion: The computational study demonstrates that CRISPR-Cas9 technology enables researchers to manage vital disease mechanisms in Alzheimer’s disease. The combination of multiple editing strategies yields better therapeutic outcomes. The research findings create a foundation for experimental validation and logical development of CRISPR-based treatments for neurodegenerative diseases.