Re-Analysis of GSE294290 Human iPSC-Derived Induced Neurons Comparing Sporadic Alzheimers Disease and Wild Type Under Untreated Conditions

Abstract

The original investigation focused on the molecular basis of tau aggregation in neurodegenerative disorders, particularly Alzheimers disease, and highlighted the role of the deubiquitinase OTULIN in controlling linear ubiquitination that influences tau clearance. Motivated by a need to uncover additional regulatory networks underlying sporadic Alzheimers disease, we reanalysed the RNAseq dataset GSE294290, which contains iP- SCderived neuronal samples from patients and controls. Our workflow began by retrieving raw counts and metadata from ARCHS4, constructing an AnnData object, and performing differential expression analysis with limmavoom to generate a gene signature. The resulting upand downregulated gene sets were submit- ted to Enrichr for GO, KEGG, ChEA, and KOMP2 enrichment, and to PerturbSeqr to identify smallmolecule and gene perturbations that mimic or reverse the signature. The analysis revealed a pronounced immune and developmental signature in the upregulated genes, with enrichment for CD4 Tcell differentiation and organmorphogenesis pathways, while the downregulated genes were dominated by neurodevelopmental, epithelial differentiation, and metabolic rhythms, and were enriched for chromatinmodifying factors such as EZH2 and RNF2. PerturbSeqr highlighted chromatin remodelers Eed, Pax5, and Ezh2 as key mimics, suggesting a shift toward a lymphoidlike chromatin state in sporadic Alzheimers iPSCderived neurons. These findings underscore the interplay between neuroinflammation and overall disease context.