AbstractBackgroundMicroglia mediate key functions in inflammation and phagocytic clearance central to Alzheimer’s disease (AD). Semaphorins and their receptors, plexins and neuropilins, are best known for their role in axon guidance, but emerging roles include the regulation of innate immunity. Semaphorin receptors are highly expressed in microglia, including those encoded by AD risk genes discovered through genome‐wide association studies (e.g. PLXNA4 and PLCγ2). We investigate the function of semaphorin 6D (Sema6D) and interacting receptors in human iPSC‐derived microglia (iMG).MethodWe generated TREM2 knockout (KO) human iPSCs using CRISPR/Cas9. Following differentiation to iMG, we used a proximity labeling approach to demonstrate the interaction of known Sema6D receptors (Plexin‐A1 or Plexin‐A4) with TREM2. WT and KO cells were treated with Sema6D to assay (i) phagocytosis activity via live‐cell imaging and (ii) secretion of inflammatory cytokines via multiplex immunoassays (iii) downstream signaling events.ResultWe demonstrated that Sema6D promotes phagocytic uptake of oligomeric Aβ, and human synaptosomes, as well as significantly increases secretion of several inflammatory cytokines including IL‐1β, IL‐6, TNF‐α and IL‐8. TREM2 KO abrogates Sema6D‐induced cellular changes in iMG. Plexin‐A1 and Plexin‐A4 interact with TREM2 in the intact cell.ConclusionSema6D is a novel ligand for microglial Plexin‐A1and Plexin‐A4 and likely mediates signaling via a co‐receptor complex harboring TREM2. Sema6D is a regulator of microglial phagocytosis and cytokine release in a TREM2‐dependent manner, suggesting a Sema6D‐Plexin/TREM2 pathway as a novel therapeutic target for AD.