Integrative single-cell analysis of neural stem/progenitor cells reveals epigenetically dysregulated interferon response in progressive multiple sclerosis

Abstract

SUMMARYProgressive multiple sclerosis (PMS) is characterized by a primary smouldering pathological disease process associated with a superimposed inflammatory activity. Cellular and molecular processes sustaining the pathobiology of PMS remain to be identified.We previously discovered senescence signatures in neural stem/progenitor cells (NSCs) from people with PMS. Applying direct reprogramming to generate directly induced NSCs (iNSCs) from somatic fibroblasts, we retain epigenetic information and observe hypomethylation of genes associated with lipid metabolic processes and IFN signalling only in PMS lines. Single-cell/nucleus transcriptomic and epigenetic profiling reveal an inflammatory, senescent-like, IFN-responsive radial glia (RG)-like cell subcluster mainly in PMS iNSCs that is driven by IFN-associated transcription factors. Lastly, we identify a population of senescent, IFN-responsive, disease-associated RG-like cells (DARGs) in the PMS brain that share pseudotime trajectories with iNSCsin vitro.We describe the existence of a non-neurogenic, dysfunctional DARG population that has the potential to fuel smouldering inflammation in PMS.

Increased Cholesterol Synthesis Drives Neurotoxicity in Patient Stem Cell-Derived Model of Multiple Sclerosis

“…1A ). 28 RT-PCR of NESTIN , SOX2 , and PAX6 confirmed comparable expression levels via band density across all iNSC lines, while the pluripotency marker gene OCT4 was absent ( Fig. S1E ).…”

“…1B ). 28 We observed no difference in senescence gene expression when comparing the parental PMS and Ctrl fibroblasts ( Fig. 1B ).…”

“…As iPSC reprogramming has been demonstrated to rejuvenate the epigenome 29 , we next utilized direct reprogramming technology to generate cell lines that retain aging-related markers. 28 We reprogrammed skin fibroblasts from 3 non-diseased individuals (Ctrl) and 4 people with PMS between 25 to 63 years of age into iNSCs ( Table 1 ). 27,30 Quality control analysis by immunocytochemistry showed superimposable expression of the established NSC/radial glial markers NESTIN, SOX2, and ETNPPL in both Ctrl and PMS iNSC lines ( Fig.…”

“…As the SASP is transcriptionally controlled 38,42,43 , we then performed a transcription factor (TF) enrichment analysis on differentially expressed mRNA species 28 , intracellular proteins, and secreted factors. We identified 6 significantly enriched TF candidates (E2F1, Egr1, WT1, Sp1, c-JUN, and JunB), which could account for the expression signatures observed in PMS iNSCs, across all three profiled expression modalities ( Fig.…”

“…27 We chose to use the direct induction of fibroblasts into NSCs as this method has improved fidelity in maintaining the aging signature of the donor. 28 This affords the capability to more faithfully model disease- and age-associated metabolic alterations in PMS iNSCs and their functional implications. Using this model, we performed a multi-omics phenotypical characterization of cells, including intra and extracellular proteomics, metabolomics, and lipidomics.…”