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Multiple Sclerosis Single-Cell Transcriptome Study Highlights Affected Cell Types, Brain Regions

NEW YORK – A team of researchers from the US, the UK, and Germany has characterized the gene expression changes that occur across distinct cell types in brain samples from individuals with multiple sclerosis (MS), uncovering projection neuron damage that appeared to be prompted by aberrant immune cell activity.

"We found that antibody-producing immune cells are related to the damage of the important projection neurons in MS brains," co-senior and co-corresponding author David Rowitch, a researcher affiliated with the University of California, San Francisco and the University of Cambridge, said in a statement. "This suggests that cell therapies targeting these immune cells could protect projection neurons and provide a novel treatment for progressive MS."

For a study published online today in Nature, Rowitch and colleagues performed single-nucleus RNA sequencing (snRNA-seq) to tally heterogeneous cell types from cortical and subcortical brain regions in 21 postmortem brain samples from individuals with or without MS. From there, they incorporated data from multiplex small-molecule fluorescence in situ hybridization (smFISH) experiments and mouse or human cell culture assays to confirm MS-related shifts in the grey and white matter cells.

In particular, the team's results pointed to the loss in an upper cortical layer of excitatory projection neurons that express a gene called CUX2, along with enhanced expression of stress-related pathways and long, non-coding RNAs in these neurons. At the borders of the MS lesions, meanwhile, the group saw signs of stress in oligodendrocytes, reactive astrocytes, and activated microglial macrophage immune cells.

"Our results indicate that genes that are most dysregulated in MS map to vulnerable upper-cortical-layer neurons and reactive glia at the borders of subcortical MS lesions associated with progression in MS," the authors explained.

The team decided to assess brain samples from both the cortical grey matter and nearby subcortical white matter lesions in individuals with MS based on past studies of the progressive neuroinflammatory disease, which hinted that MS lesions affect the brain's grey and white matter differently.

After successfully processing a dozen postmortem brain sections from grey and white matter areas of the brain with or without lesions in 17 MS patients, the researchers conducted snRNA-seq on 48,919 individual cells that passed their subsequent quality controls steps, comparing the transcripts in these nuclei with those in cells from nine postmortem brain samples for MS-free control individuals.

Based on the expression of some 2,400 transcripts for each nucleus, on average, the team placed these cells into 22 distinct clusters, which were subsequently annotated with the help of lineage marker gene profiles. With the cell type data and other differential expression profiles in the nuclei, they were then able to tease apart MS-related changes in the brain samples being considered.

With a series of validation and follow-up analyses in human and mouse cell lines, the authors teased out the MS-related effects on CUX2-expressing excitatory projection neurons and other cells.

"Our findings indicate lineage- and region-specific transcriptomic changes associated with selective cortical neuron damage and glial activation contributing to the progression of MS lesions," they reported.

More broadly, the approaches used in the MS study "have wide applicability in the understanding of human neurodevelopmental and neurological disorders and are providing new insight into not only MS, but also autism spectrum disorder," said co-senior and co-corresponding author Arnold Kriegstein, a researcher at UCSF, in a statement.