Comparing Single-Cell Transcriptomes of Blood and Cerebrospinal Fluid Leukocytes in Multiple Sclerosis

Abstract

Background. Multiple sclerosis (MS) is a chronic autoimmune disorder of the central nervous system, marked by inflammation, demyelination, and neurodegeneration. Diagnosis is complex due to overlapping symptoms with other neurological conditions, typically relying on clinical evaluation, neurological exams, and tests like magnetic resonance imaging (MRI) and cerebrospinal fluid (CSF) analysis. Recent advances in technology, particularly single-cell analysis of blood and CSF leukocytes, hold promise for enhancing MS diagnosis by providing insights into immune cell involvement at a molecular level, potentially enabling more precise diagnostics and personalized treatments. Method. We acquired single-cell RNA Sequence (RNA-Seq) data (GSE138266) from the website of the National Institutes of Health of the United States (NIH), comprising blood and CSF samples from patients diagnosed with idiopathic intracranial hypertension (IIH) and MS. Our analysis focused on identifying genes, pathways and gene ontology terms with distinct expression patterns in MS compared to IIH. Results. We identified clear differences in gene expression profiles between blood and CSF samples in MS, contrasting with single-cell leukocyte samples from IIH. The increased expression of genes in MS suggests a boost in immune activity and regulation of cellular proliferation, while decreased expression points to disruptions across various functional categories. Gene ontology analysis identifies upregulated terms associated with cellular differentiation, apoptotic regulation, and immune responses in MS, while downregulated terms suggest disruptions in cellular signaling cascades and myelination processes. Similarly, Reactome pathway analysis unveils upregulated pathways in MS related to cell cycle regulation and immune mechanisms, contrasting with downregulated pathways indicative of disruptions in oxygen transport and cellular metabolism. Conclusion. Our study offers a thorough examination of single-cell transcriptomic data, unveiling unique gene expression patterns, gene ontology terms, and Reactome pathways linked to MS pathophysiology. Notably, our findings identify CD69 and HNRNPK as potential key genes driving MS progression. By clarifying molecular differences between MS and IIH, our findings enhances our grasp of MS pathogenesis and unveils promising targets for diagnostic and therapeutic interventions.