snRNAseq- Neuroectodermal IL-12R signaling in neuroinflammation/EAE

We performed single-nucleus RNA sequencing (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 protocol, 10X Genomics) of FANS-isolated Hoechst+ nuclei from the cerebellum, brainstem and cervical spinal cord of NestinCre/+Il12rb2fl/fl mice and their Il12rb2fl/fl littermates at the onset of clinical EAE symptoms (10 dpi) .
We performed two independent sequencing experiments and successfully sequenced 8 samples. The first experiment included two samples: Il12rb2fl, NestinCre_Il12rb2fl. The second experiment included six samples: three Il12rb2fl mice and three NestinCre_Il12rb2fl mice. After quality control and doublet exclusion, snRNA-seq yielded a total of 133,151 single-nucleus transcriptomic profiles, among which 21,552 distinct genes were detected. Batches were integrated using SCVI. Unsupervised clustering of these data identified clusters that were assigned to diverse neuronal, glial and other cell types on the basis of known lineage marker genes. This allowed us to assess how the transcriptional profile of the neuroectoderm differed in the presence or absence of IL-12 receptor signaling by interrogating differentially expressed genes (DEGs). This revealed pronounced alterations particularly in excitatory neurons, granule cells, mature oligodendrocytes (MOLs) and myelin forming oligodendrocytes (MOLs1) suggesting a specific/concentrated action of IL-12 on these populations in the inflamed CNS.
Our data suggest IL-12 to be critically involved in neuroprotection and shaping the trophic factor milieu within the inflamed CNS. Conversely, dysregulation or loss of trophic factor release by neurons in the absence of IL-12 may further propagate the degeneration of neurons, oligodendrocytes and possibly other cell types.

Sequencing raw data and processed gene expression data will be deposited into the GEO repository upon publication. Code for analyses will be available upon contacting the corresponding authors: [e-mail] and [e-mail]