Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain. Conserved and cell type-specific transcriptional responses to IFN-γ in the ventral midbrain

Dysregulated inflammation within the central nervous system (CNS) contributes to neuropathology in infectious, autoimmune, and neurodegenerative disease. With the exception of microglia, major histocompatibility complex (MHC) proteins are virtually undetectable in the mature, healthy central nervous system (CNS). Neurons have generally been considered incapable of antigen presentation, and although interferon gamma (IFN-γ) can elicit neuronal MHC class I (MHC-I) expression and antigen presentation in vitro, it remains unclear whether similar responses occur in vivo. Here we directly injected IFN-γ into the ventral midbrain of mature mice and analyzed gene expression profiles of specific CNS cell types. We find that IFN-γ induces cellular proliferation and expression of MHC-II and associated genes only in microglia. However, IFN-γ upregulated MHC-I and associated mRNAs in ventral midbrain microglia, astrocytes, oligodendrocytes, and GABAergic, glutamatergic, and dopaminergic neurons. The core set of IFN-γ-induced genes and their response kinetics were conserved across neurons and glia, with a lower amplitude of expression in neurons. A diverse repertoire of genes was upregulated in glia, particularly microglia, while no neuron-specific responses to IFN-γ were observed. Using mutant mice to selectively delete the IFN-γ-binding domain of IFNGR1 in dopaminergic neurons, we demonstrate that dopaminergic neurons respond directly to IFN-γ. Our results suggest that most neurons are capable of responding directly to IFN-γ and upregulating MHC-I and related genes in vivo, but their expression amplitude and repertoire is limited compared to oligodendrocytes, astrocytes, and microglia. Overall design: Bulk and single-nucleus RNA-seq comparing murine midbrain samples that are treated with IFNG or vehicle control.

中枢神经系统（central nervous system, CNS）内的炎症失调可参与感染性、自身免疫性及神经退行性疾病的神经病理进程。除小胶质细胞（microglia）外，成熟健康的中枢神经系统（CNS）中几乎无法检测到主要组织相容性复合体（major histocompatibility complex, MHC）蛋白。长期以来，神经元被认为不具备抗原呈递能力；尽管体外实验中γ干扰素（interferon gamma, IFN-γ）可诱导神经元表达MHC I类（MHC-I）蛋白并行使抗原呈递功能，但体内是否存在此类应答仍不明确。本研究直接向成熟小鼠的腹侧中脑注射IFN-γ，并分析了特定中枢神经系统细胞类型的基因表达谱。研究发现，IFN-γ仅在小胶质细胞中诱导细胞增殖以及MHC II类（MHC-II）与相关基因的表达。但IFN-γ可在腹侧中脑的小胶质细胞、星形胶质细胞（astrocytes）、少突胶质细胞（oligodendrocytes），以及γ-氨基丁酸能（GABAergic）、谷氨酸能（glutamatergic）与多巴胺能（dopaminergic）神经元中上调MHC-I与相关mRNA的表达。IFN-γ诱导的核心基因集及其应答动力学在神经元与胶质细胞（glia）中保守存在，但神经元中的表达幅度更低。胶质细胞（尤其是小胶质细胞）中存在丰富多样的上调基因集，且未观察到神经元特异性的IFN-γ应答。通过构建在多巴胺能神经元中选择性敲除γ干扰素受体1（interferon gamma receptor 1, IFNGR1）的IFN-γ结合结构域的突变小鼠，我们证实多巴胺能神经元可直接应答IFN-γ。本研究结果表明，大多数神经元可在体内直接应答IFN-γ并上调MHC-I与相关基因，但与少突胶质细胞、星形胶质细胞和小胶质细胞相比，神经元的基因表达幅度与应答谱均存在局限。总体实验设计：采用批量RNA测序与单细胞核RNA测序（bulk and single-nucleus RNA-seq），对比经IFNG（干扰素γ）或载体对照处理的小鼠中脑样本。