To examine differential DNA methylation in Neurological Post Acute Sequelae of SARS-CoV2 Infection (Neuro-PASC), Multiple Sclerosis (MS), and Neuromyelitis Optica (NMO).

PASC (also known as long COVID) is associated with neurological signs and symptoms in a subset of patients, but its pathogenesis and possible associations with autoimmune processes are poorly understood. MS and NMO are neurological autoimmune conditions with well-established effects on the central nervous system.

Following informed consent, peripheral blood samples were collected from MS (n=70), Neuro-PASC (n=24), NMO (n=10), and control donors with non-inflammatory neurological conditions (n=42) at the University of Illinois Chicago Neurology Clinic. Genomic DNA was isolated from whole blood samples and characterized using Infinium MethylationEPIC bead arrays. Data analysis was performed in R software using the Minfi, MissMethyl, and DMRcate packages, as done in previous DNA methylation analysis pipelines in our research group.

The top 20,000 most significant differentially methylated probe loci (DMPs) from MS (p<1.3e-13, ANOVA), Neuro-PASC (p<4.1e-9), and NMO (p<2.0e-4) were analyzed. A total of 47,919 unique DMPs were identified. Approximately 22% (n=10,560) of the DMPs were common between MS and Neuro-PASC but only about 2% between Neuro-PASC and NMO (n=908). The number of DMPs unique to each disease state was 18% (n=8,827) for MS, 19% (n=9,178) for Neuro-PASC, and 39% (n=18,479) for NMO.  Analysis of differentially methylated regions (DMRs) demonstrated CTSZ and ARID5B as common markers between MS and Neuro-PASC. Unique associations included CLU, SPI1, and TNF superfamily members for MS, CD19 and IER3 for NMO, and NLRC4 for Neuro-PASC. KEGG pathway analysis showed associations of T cell receptor and chemokine signaling in MS and Neuro-PASC, and unexpected associations of methylation signatures of solid tumors with NMO.

Shared DNA methylation signatures between Neuro-PASC and MS, but not NMO, suggest involvement of common inflammatory pathways in the pathogenesis of the two conditions.