Single-cell gene networks nominate IKZF1 as an Alzheimer's microglial regulator

Authors

Ozkurt, C.

Abstract

Background: Microglia drive neuroinflammation in Alzheimer's disease (AD), yet no approved therapy targets this compartment. Human genome-wide association studies consistently implicate innate immune loci in AD risk, establishing microglial transcriptional programs as therapeutically relevant but pharmacologically underexploited targets. Objective: We sought to identify transcription factors (TFs) governing microglial state transitions computationally and to nominate structurally tractable drug repurposing candidates. Methods: We applied trajectory inference (PAGA), pseudobulk DESeq2, pySCENIC gene regulatory network (GRN) inference, CellChat, and virtual screening of 1,962 approved compounds to 236,002 microglial nuclei from 84 donors (SEA-AD atlas). Results: IKZF1 was the sole target TF retained under cisTarget v10 motif constraints, with peak regulon activity in LateAD-DAM (pseudotime {rho} = +0.309) and replication in an independent bulk cohort (GSE95587; adjusted P value = .004). CellChat identified SLIT2[->]ROBO2 from multiple neuron subtypes (predominantly inhibitory interneurons) as the top predicted pathway to microglia. Tafamidis ([->]IRF8) and diflunisal ([->]PPARG) were top virtual screening hits; all evaluated compounds failed the pre-specified selectivity threshold. Conclusions: IKZF1 is prioritised as a candidate late-disease microglial TF, supported by six convergent evidence dimensions including independent bulk replication. Tafamidis and diflunisal are low-confidence repurposing hypotheses requiring experimental validation.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 16 Jul 2026.

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