Transcriptomic Insights of Enrupatinib Administration in Alzheimer's Disease Mouse Models

Alzheimer's disease pathology is accompanied by a robust innate immune response featuring chronic microglial activation and elevated inflammatory cytokines. This neuroinflammatory environment is a critical mediator of synaptic dysfunction, neuronal loss, and the progression of cognitive deficits. Consequently, strategies to therapeutically modulate microglial activity are of significant interest. Enrupatinib, a brain-penetrant inhibitor of the Colony Stimulating Factor 1 Receptor (CSF1R), represents a clinical candidate for such an approach. Here, we examine the impact of enrupatinib treatment on microglial function in two transgenic models of amyloidosis: the 5xFAD and the J20.

Methods:

Mice were treated with enrupatinib (150 or 300 mg/kg) for 4 weeks, followed by behavioral assessment and cortical RNA-seq. Analysis used custom Python scripts. Gene expression matrices (raw counts, TPM, FPKM) were built with pandas. Differential expression was determined via PyDESeq2, applying a 10-read filter, a sex-adjusted negative binomial model, and an FDR < 0.05. Pathway enrichment (GSEApy) included GSEA (FDR < 0.25) on all genes and Over-Representation Analysis (ORA) on filtered gene sets (p<0.05, |log2FC|>0.1) against hallmark databases. Visualization (Plotly) featured Z-scored TPM heatmaps and FPKM bar plots with overlaid replicates; statistical comparisons used the Mann-Whitney U test (p < 0.05).

Results:

RNA-seq analysis demonstrated that enrupatinib therapy significantly reduced neuroinflammatory markers, suppressed disease-associated microglia (DAM) gene expression, and downregulated inflammatory pathways in the 5xFAD and J20 mouse models.

Conclusions:

Collectively, RNA-seq analysis shows enrupatinib exerts its therapeutic effect by suppressing neuroinflammatory pathways, offering a promising pharmacological strategy for Alzheimer’s disease.

Keywords: Alzheimer’s disease, CSF1R inhibitor, enrupatinib, microglia, neuroinflammation

KEY Take away: Transcriptomic analysis reveals that enrupatinib treatment dampens neuroinflammation in both 5xFAD and J20 modelS