Single-Cell Gene Expression Patterns Provide New MS Insights

148
Nerve cells, illustration
3d illustration of nerve cells.

The mechanisms that underlie the progression of MS are not well understood. Now, an international, multi-institutional team of researchers has studied pathological events at a higher resolution than has been done in the past, describing the gene expression, at the single cell level, of the major cell types found in lesions of MS. They combined the gene expression data with spatial transcriptomics to validate the MS-specific gene expression changes in tissue. The team found that differentially regulated genes in the different cell types are consistent with the main pathomechanisms that had already been identified before, albeit a much lower resolution.

By studying the patterns of gene expression in single cells taken from the brains of 12 deceased individuals who had MS, and comparing them with 9 control samples, the team identified cell-type-specific changes that are linked to the progression of MS and found evidence for the upregulation of various stress pathways in cortical neurons and non-neuronal cells of the nervous system.

The work, which used single-nucleus RNA sequencing (snRNA-seq) to profile cortical grey matter and adjacent subcortical white matter MS lesions, is published in Nature in a paper titled, “Neuronal vulnerability and multilineage diversity in multiple sclerosis.”

“An exciting point made by this work,” notes David Rowitch MD, PhD, professor at the University of California, San Francisco, and senior author on the paper, “is that we can apply single cell transcriptomic approaches directly to the human brain in a complex neuroinflammatory disease to gain insights.” Being able to confirm gene expression in situ, Rowitch tells GEN, “is a technical advance that helps prioritize gene targets/pathways for therapy.”

“The findings are novel,” notes Roland Martin, MD, professor for neurology and neuroimmunology at the University Zürich, “in that they discover a host of differentially expressed genes in several cell types including neuronal subtypes, macroglia, and microglia, which are identified by signature molecules.” The altered pathways, Martin adds, indicate that “the different cell types respond to inflammatory cues and stress, which underlie the pathogenesis of MS brain lesions in different areas such as grey and white matter.”

“These authors have meticulously examined at the single cell level the differential gene expression by neurons of different subtypes and localization within the human cortex,” notes Anne Cross, MD, and professor of neurology at the Washington University School of Medicine in St. Louis.

In doing so, the authors discovered that one type of neuron, known as a “projection neuron” is vulnerable to damage in the brains of MS patients indicating that these cells may play a central role in MS.

Although they expected many changes in glia (particularly oligodendrocytes), Rowitch notes that it was a surprise to find that a subtype of neuron, [the cortical projection neuron] was lost. This, he adds, “advances our understanding of how the cortex atrophies in MS.”

“There is a differential vulnerability of neurons in the human cortex,” notes Cross, adding that the neurons close to the surface of the brain are more vulnerable and show more loss. At the gene expression level, these neurons show signs of cellular stress, including upregulation of genes of oxidative stress, mitochondrial dysfunction, and cell death pathways. The team found that these neurons are more affected, and they also found certain types of neurons (the excitatory neurons in layers II and III of the cortex) to be more vulnerable to signs of stress than the inhibitory neurons in those same levels.

MS lesions are heterogenous, with distinct patterns of inflammatory demyelination. Grey matter cortical lesions, notes Cross, “have only been fully recognized in recent years, but their sequelae including cortical volume loss is very much associated with disability and cognitive impairment.” Therefore, she stresses that these lesions are important to better understand.

Martin explains that this study differs from a recent study of Alzheimer’s disease brains, which employed similar techniques and led to the unexpected observations of a myelination signature and clear gender effects because “the observations of the Schirmer et al., study are consistent with what was known about MS tissue damage in the brain” but, he adds, “take the existing knowledge much further.”

Q. Richard Lu, PhD, chair in cancer epigenetics at the Cincinnati Children’s Hospital Medical Center agrees, noting that “the findings of spatial diversity will offer a comprehensive picture of regional and cell type-specific dysregulation during MS pathogenesis, pointing to a potentially important contribution of neuronal degeneration to the failure of myelin repair in MS patients.”

The team’s discovery of genes expressed by B cells (specifically plasma cells) commonly found in the meninges adjacent to cortical demyelinated lesions is “not surprising,” according to Cross, as it has been shown previously through other methods. But, the ongoing support for an association between the two “further invokes a role for plasma cells in MS and particularly cortical demyelinating lesions,” notes Cross.

The authors note that this particular finding “highlights the importance of B cells in progressive MS and that damaged cortical neuron populations may potentially benefit from B-cell-depleting therapies.” Indeed, Arnold Kriegstein, MD, PhD, professor of neurology at UCSF and author on the paper tells GEN that “treatments that modulate the immune response might rescue these vulnerable nerve cells” opening up a novel area of treatment development for MS.

According to Rowitch, “this work opens up MS research to direct exploration of cell damage pathways based on high-resolution single cell data.” He adds that, with regard to the neurons that are lost, “we believe we can trace the cell death pathways shown by our data to develop new cell type specific neuroprotective therapies to work in conjunction with conventional therapies for MS.”

This site uses Akismet to reduce spam. Learn how your comment data is processed.