Spatial multi-omics unveils sphingolipid metabolic reprogramming within the retinal pathological niche.

Retinal ischemia-reperfusion (RIR) injury is a central mechanism underlying irreversible vision loss in glaucoma and other retinal diseases, yet the spatial organization of the pathogenic microenvironment remains poorly understood. Here, we constructed a high-resolution, whole-eye spatial multi-omics atlas integrating Stereo-seq transcriptomics and MALDI-MSI-based metabolomics to capture the early molecular events in the RIR mouse model. Spatially, retinal ganglion cell (RGC) interactions with surrounding cells were markedly reduced after injury, whereas immune-glial interactions were enhanced, revealing a shift from a neuron-centered to an immunometabolic state. Within the ganglion cell layer (GCL), the primary pathological locus, we identified Trem2 + microglia that expand in situ, establish close proximity to degenerating RGCs, and exhibit strong spatial association with dysregulated sphingolipid metabolism. Mechanistically, using Trem2 knockout mice and microglia-specific Trem2 siRNA knockdown, we demonstrate that TREM2 directly binds to SPTLC2, the rate-limiting enzyme of de novo sphingolipid biosynthesis, driving ceramide-centric metabolic reprogramming that modulates the AKT-mTOR signaling axis and amplifies inflammatory activation. Pharmacological inhibition of serine palmitoyl transferase (SPT) with myriocin reverses this cascade, protecting RGCs. Multi-omics integration of human glaucoma aqueous humor datasets further reveals conserved upregulation of sphingolipid biosynthetic enzymes, sphingolipid metabolites, and lipid-sensing immune effectors, offering preliminary translational clues. Collectively, our findings reveal that spatially defined immunometabolic remodeling-in which Trem2 + microglia are central-converges on sphingolipid metabolism as a druggable regulatory axis, with the TREM2-SPTLC2 interface thus emerging as a new therapeutic opportunity for retinal neurodegenerative diseases.