Dysregulated Antiviral Mechanisms in Multiple Sclerosis Through CSF Expression Profiling

Multiple sclerosis (MS), a complex immine-mediated neurodegenerative disease, has long posed a scientific puzzle regarding its underlying immune dysregulation. Despite significant strides, there remains a gap in understanding the specific mechanisms that drive this debilitating disease. A recent study published in Brain by Ban et al. addresses this gap, offering new insights into the antiviral responses associated with MS by profiling cerebrospinal fluid (CSF) cells at single-cell resolution.

CSF as a Window into MS Pathogenesis
MS is characterized by inflammatory demyelination and neurodegeneration within the central nervous system (CNS). Traditionally, most studies focused on circulating immune cells, providing limited insights due to the CNS's unique immune environment. The researchers hypothesized that analyzing CSF—given its proximity to CNS pathology—could reveal more disease-relevant immune responses.

By employing single-cell RNA sequencing (scRNA-seq) on CSF cells from 33 MS patients and 48 individuals with other neurological conditions, they identified distinct immune cell populations and pathway dysregulations that differentiate MS from other neurological diseases. This approach enabled a high-resolution view of 96,732 CSF cells and the identification of rare but potentially critical immune cell populations.

A Rare Population of CD8+ T Cells Linked to MS
One of the most striking findings of the study was the identification of a rare subset of CD8+ T cells that were notably increased in MS patients. These cells were marked by upregulation of inhibitory receptors, including HAVCR2 (also known as TIM-3) and TIGIT, suggesting that they might represent exhausted T cells—a population known to arise in chronic viral infections and autoimmune conditions. These cells could provide clues to the chronic immune activation seen in MS, potentially triggered by viral antigens.

Antiviral Mechanisms Under Scrutiny: ZC3HAV1 and IFITM2
The study also highlighted the role of genetic variants in antiviral defense mechanisms in MS. Two key MS susceptibility variants—rs10271373 and rs1059091—were found to influence the expression of antiviral genes ZC3HAV1 and IFITM2, respectively, in CD8+ T cells.

ZC3HAV1 encodes an antiviral protein that targets viral RNAs for degradation, playing a pivotal role in controlling viral infections. Interestingly, the rs10271373 variant was linked to altered splicing of ZC3HAV1, leading to increased production of the ZAP-L isoform, which has enhanced antiviral activity due to its ability to localize to endocytic and lysosomal compartments where viral replication occurs. This variant could potentially impair the ability of MS patients to control viral infections, thereby contributing to disease pathogenesis.

Similarly, IFITM2, which is part of the interferon-induced transmembrane protein family, inhibits viral entry into host cells. The rs1059091 variant was associated with reduced expression of IFITM2 in CD8+ T cells, further weakening the antiviral response in MS patients. The authors speculate that this dysregulation in viral control mechanisms might be a critical factor in MS development, aligning with previous research that implicates viruses, especially Epstein-Barr virus (EBV), in MS pathogenesis.

MOFA Reveals Altered Inflammatory and Antiviral Responses
o gain further insights into the cellular programs altered in MS, the researchers applied multi-omics factor analysis (MOFA), which integrates gene expression data across cell types to identify co-regulated gene sets. This analysis revealed several MS-associated gene expression programs, particularly within T cells and macrophages.

One key finding was the reduced activity of genes involved in type I interferon (IFN) responses—crucial for antiviral immunity—in T cells from MS patients. The dysregulation of these genes points to an impaired antiviral defense, potentially contributing to the chronic immune activation observed in MS.

Macrophages in MS: Polarization and Antigen Presentation
In addition to T cells, macrophages also exhibited disease-specific changes. MS patients showed reduced polarization towards the anti-inflammatory M2 macrophage phenotype, alongside increased antigen presentation machinery, suggesting a pro-inflammatory shift in the macrophage population. This altered macrophage activity could exacerbate CNS inflammation, further driving MS progression.

No Viral Enrichment in CSF, but the Question Remains
Given the long-standing association between viruses and MS, the researchers also explored the presence of viral genomes in CSF samples. While they detected viral transcripts, including human endogenous retroviruses (HERVs), there was no significant enrichment of any particular virus in MS patients. However, the study's identification of exhausted-like CD8+ T cells raises the possibility that chronic viral exposure, possibly from EBV or other viruses, could still play a role in driving the immune dysregulation seen in MS.

Conclusions and Future Directions
This study sheds new light on the antiviral mechanisms that may be disrupted in MS, highlighting the importance of the immune response to viral infections in disease development. The identification of MS-associated genetic variants that affect antiviral gene expression in CSF cells emphasizes the need for further research into the role of viral infections in MS. Understanding how these antiviral pathways are dysregulated could pave the way for new therapeutic strategies aimed at restoring immune balance and potentially preventing disease progression.

As the authors suggest, further research into the phenotypes and functions of the identified CD8+ T cell subsets and macrophage populations will be crucial to fully unraveling their roles in MS pathogenesis.

Reference:
Ban, M., Bredikhin, D., Huang, Y., Bonder, M. J., Katarzyna, K., Oliver, A. J., Wilson, N. K., Coupland, P., Hadfield, J., Göttgens, B., Madissoon, E., Stegle, O., & Sawcer, S. (2024). Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis. Brain : a journal of neurology, 147(2), 554–565.