Cell-cell interactions control the physiology and pathology of the central nervous system (CNS). To study astrocyte cell interactions in vivo, we developed rabies barcode interaction detection followed by sequencing (RABID-seq), which combines barcoded viral tracing and single-cell RNA sequencing (scRNA-seq). Using RABID-seq, we identified axon guidance molecules as candidate mediators of microglia-astrocyte interactions that promote CNS pathology in experimental autoimmune encephalomyelitis (EAE) and, potentially, multiple sclerosis (MS). In vivo cell-specific genetic perturbation EAE studies, in vitro systems, and the analysis of MS scRNA-seq datasets and CNS tissue established that Sema4D and Ephrin-B3 expressed in microglia control astrocyte responses via PlexinB2 and EphB3, respectively. Furthermore, a CNS-penetrant EphB3 inhibitor suppressed astrocyte and microglia proinflammatory responses and ameliorated EAE. In summary, RABID-seq identified microglia-astrocyte interactions and candidate therapeutic targets.

细胞-细胞相互作用控制中枢神经系统 (CNS) 的生理学和病理学。为了研究体内星形胶质细胞的相互作用，我们开发了狂犬病条形码相互作用检测和测序 (RABID-seq)，它结合了条形码病毒追踪和单细胞 RNA 测序 (scRNA-seq)。使用 RABID-seq，我们将轴突引导分子鉴定为小胶质细胞-星形胶质细胞相互作用的候选介质，可促进实验性自身免疫性脑脊髓炎 (EAE) 和多发性硬化症 (MS) 中的 CNS 病理学。体内细胞特异性遗传扰动 EAE 研究、体外系统以及对 MS scRNA-seq 数据集和 CNS 组织的分析确定，在小胶质细胞中表达的 Sema4D 和 Ephrin-B3 分别通过 PlexinB2 和 EphB3 控制星形胶质细胞的反应。此外，一种 CNS 渗透性 EphB3 抑制剂抑制星形胶质细胞和小胶质细胞促炎反应并改善 EAE。总之，RABID-seq 确定了小胶质细胞-星形胶质细胞的相互作用和候选治疗靶点。