Integrated Multi-Omics Analysis Reveals the Neuroprotective Mechanism of the Inflammation Repressor TNIP1/ABIN1 in Microglia following Ischemic Stroke

Abstract Cerebral ischemia-reperfusion injury (CIRI) acts as a core pathological driver of ischemic stroke. Microglia derived neuroinflammation, regulated by subpopulation heterogeneity, plays a bidirectional and opposite regulatory role in neuronal injury and post-stroke tissue repair. However, the precise molecular mechanisms regulating heterogeneous activation and functional modulation of microglia remain incompletely clarified. Here, we integrated bulk RNA-seq, single-cell RNA-seq (scRNA-seq), spatial transcriptomics, and in vivo experimental validation to systematically elucidate the central role of the TNIP1 gene in neuroinflammation after ischemic stroke. We found that TNIP1 was specifically upregulated in microglia post-ischemia and defined a functionally distinct TNIP1 + microglial subpopulation. This subpopulation underwent marked expansion after stroke, selectively accumulated in the ischemic penumbra, and engaged in robust crosstalk with injured neurons via the App-Trem2 signaling pathway. Functionally, TNIP1 , encoding the A20-binding inhibitor 1 (ABIN1) protein, served as a key endogenous negative regulator of the NF-κB signaling pathway to suppress the expression and release of proinflammatory cytokines such as tumor necrosis factor-α (TNF-α), thereby exerting a prominent neuroprotective effect. Furthermore, in vivo validation demonstrated that Genistein-3′-sodium sulfonate (GSS), a phytoestrogen, could upregulate ABIN1 expression and effectively attenuate ischemic brain injury. Our study is the first to characterize the spatiotemporal and functional specificity of the TNIP1 + microglial subpopulation, and to confirm that TNIP1 /ABIN1 constitutes a critical molecular node regulating post-stroke neuroinflammation. These findings provide a novel therapeutic target and theoretical basis for the development of precision immunomodulation-based strategies for ischemic stroke treatment.