Augmentation of a neuroprotective myeloid state by hematopoietic cell transplantation: Control Cohort

Multiple sclerosis (MS) is an autoimmune disease associated with inflammatory demyelination in the central nervous system (CNS). Autologous hematopoietic cell transplantation (HCT) is under investigation as a promising therapy for treatment-refractory MS. Here we identify a reactive myeloid state in chronic experimental autoimmune encephalitis (EAE) that is surprisingly associated with neuroprotection and immune suppression. HCT in EAE mice leads to an enhancement of this myeloid state, as well as clinical improvement, reduction of demyelinated lesions, decrease in effector T cells, and amelioration of reactive astrogliosis reflected in reduced expression of EAE-associated gene signatures in oligodendrocytes and astrocytes. Further enhancement of myeloid cell incorporation into the CNS following a modified HCT protocol results in an even more consistent therapeutic effect corroborated by additional amplification of HCT-induced transcriptional changes, hence underlining myeloid-derived beneficial effects in the chronic phase of EAE. Replacement or manipulation of CNS myeloid cells thus represents an intriguing therapeutic direction for inflammatory demyelinating disease. Overall design: Single-nuclei RNA transcriptomes of spinal cords obtained from C57BL/6JN mice injected either with phosphate-buffered saline (PBS) or Complete Freund's Adjuvant (CFA) using 10x Genomics Drop-seq (v3.1). Per library (PBS and CFA), 4 biological samples were pooled and each sample was hashtagged with oligos. The gex library has the RNAseq information, hto the oligo sequence information (needed for demultiplexing). Thus, the *.tar.gz processed data files are generated from both GEX and HTO raw files, and are linked to the corresponding GEX sample records.