Single-cell Cerebrospinal Fluid Transcriptome Profiling Suggests Dysfunctional Boarder Associated Macrophages Underlying Progression Independent of Relapse Activity in Multiple Sclerosis
Damiano Marastoni1, Ermanna Turano1, Francesco Patanè4, Federica Virla1, Daniela Anni1, Stefano Ziccardi1, Monica Castellucci2, Elena Zenaro3, Massimiliano Calabrese1
1Dept. of Neurosciences, Biomedicine and Movement, 2Centro Piattaforme Tecnologiche, 3Pathology Section, Department of Medicine, University of Verona, 4Biology Department, University of Padua
Objective:
To characterize the cellular compartment of cerebrospinal fluid (CSF) in patients with relapsing multiple sclerosis (MS) with and without progression independent from relapse activity (PIRA) and infer differential cell-cell communication between groups.
Background:
Occurrence of PIRA is common and associates with future disability. Evaluation of its molecular correlates, through single cell transcriptomics (scRNAseq) and bioinformatic approaches, is still lacking.
Design/Methods:
Eight patients with PIRA, 8 without PIRA, 1 control with NMOSD were enrolled. All patients were clinically stable, free from MRI activity and not on disease-modifying therapy in the last 6 months. ScRNA-seq libraries were prepared using the 10x Chromium Single Cell 3′ Solution (10x Genomics). An uniform pipeline of pre-processing with quality control was employed on all samples. Seurat and scDblFinder were employed for the preprocessing step. Azimuth was used for cell type assignment, myeloid cells were manually determined. Cells were annotated and visualized in a UMAP. Differential expressed genes (DEGs) and enrichment analysis were assessed using DESeq2 and SCPA. Cell-cell communication among groups was analyzed with CellChat.
Results:
Within subclusters of myeloid cells, we identified upregulation of SCL7A5, RASGRP2, CBX6, C1orf56, AC130324.2 and down-regulation of GPNMB, FABP5, ATP1B1 in Boarder Associated Macrophages (BAM) in PIRA group. Gene ontology analysis of upregulated genes yelded terms as B-cell mediated immunity, antigen processing and presentation, T-cell activation, leukocyte cell-cell adhesion. Communication strenght analysis between cells revealed a relative enrichment of CD30 and osteopontin pathways in patients with PIRA. Communication probabilities between cells showed a major involvement of BAM in both CD30 and SPP1 signaling.
Conclusions:
Patients with PIRA show a specific CSF trascriptome signature in BAM, that emerged from both DEGs, enrichment and cell-cell interaction analysis. These findings confirm intrathecal compartmentalized inflammation at the CNS boarders as a niche that contributes to MS disease progression.
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