• Gary Birnbaum, MD

Important Progress in Progressive MS

Identification of early neurodegenerative pathways

in progressive multiple sclerosis

M. Kaufmann, A. L. Schaupp, R. Sun, F. Coscia, C. A. Dendrou, A. Cortes, et al.

Nat Neurosci 2022 Vol. 25 Issue 7 Pages 944-955


Bottom Line:

Most persons with MS present with a relapsing form of disease, the relapses resulting from bouts of acute central nervous system inflammation. At the same time another disease process is occurring, one not related to acute inflammation but one of tissue degeneration. As bouts of acute inflammation subside over time, the degenerative changes increase and eventually becomes the dominant disease pattern. We don’t know what triggers this disease pattern nor the underlying sequences of disease-related events. Unlike treatments for relapsing MS, there are no robustly effective therapies for this progressive, degenerative phase that is present from onset of the illness.

The above noted paper, using a multitude of cutting-edge molecular techniques (described below) describes for the first time the sequence of molecular events leading to tissue degeneration in persons with progressive MS. The results are complex, with multiple counteracting reactions occurring at the same time. While the results are relatively preliminary, they provide an important insight into disease processes that may allow the development of therapies for a phase of the disease resistant to current treatments. While controlling inflammation will continue to be an important part of therapy, to fully control tissue destruction from onset, other therapeutic approaches will be needed to truly cure MS.

Key Points:

1. As noted above, multiple disease processes occur at the same time in the brains of persons with MS. These are present from onset of the illness and little is known about how and why they start. Tissue degeneration is one of these processes, a process that eventually becomes dominant and resistant to substantive treatment.

2. Using a relatively new molecular technique called “spatial transcriptomics” the authors of the above paper were able to study gene activity at the cellular level using central nervous system tissues from persons with secondary progressive MS.

3. “Transcriptomics” is a technique that measures all genes that are active or “turned on” in a cell. It does so by measuring the products of the activated genes, namely messenger RNAs (mRNAs). mRNAs provide the necessary information for the cell to produce proteins. These proteins are then released from the cell, allowing them to interact with “receptor” proteins on the surfaces of adjacent cells.

4. The generic term for proteins binding to receptors is “ligands.” Binding of a ligand to a receptor leads to a cascade of reactions in the receptor-bearing cell, varying with the nature of the ligand:receptor binding. The authors of the above paper were able to determine how cells responded to these reactions.

5. Previous transcriptomic technologies required cells to be separated from one another in order to measure their mRNAs. Using “spatial transcriptomics” the authors of this paper were able to measure mRNAs in intact tissue samples. This allowed them to identify cells with activated genes in the context of their neighboring cells. Most importantly, it allowed the researchers to identify how the activation of one cell’s genes, and the interactions of the resulting proteins, affected the receptors and genes of adjacent cells.

6. Central nervous system tissues from thirteen persons with progressive MS and five controls were studied using spatial transcriptomics. Light microcopy was used to correlate the transcriptomic data with MS lesions.

7. Lesions were separated as to whether they occurred in gray matter (areas with nerve cells or neurons) and white matter (areas with axons or nerve fibers). They were also distinguished based on their degree of disease activity (normal appearing tissue, actively inflamed tissue, degenerating tissue, and quiescent or scarred tissue).

8. Activated genes, producing proteins with similar functions, were grouped into “modules.” Multiple module functions were identified, ranging from control of remyelination (forming new myelin) to regulating communication between cells (forming new synapses) to either stimulating or suppressing immune responses.

9. Some gene modules were limited to particular cell types (e.g., genes associated with remyelination were limited to myelin-producing cells or oligodendrocytes). In other cells there was considerable overlap with different cell modules expressed in the same cell.

10.As expected, gene modules associated with nerve cell function were decreased in areas of neuronal loss, but loss was also noted in areas that looked normal, indicating that nerve cell degeneration was a very early feature of degeneration, occurring in the absence of any inflammation.

11.The authors then asked, “what was the effect of the proteins produced by the activated genes on nearby cells?” Results were, as expected, complex.

12.To determine the very earliest phases of degeneration they compared normal appearing MS gray matter to normal control gray matter. 61 protein interactions were studied. Fifteen were decreased in normal appearing MS gray matter, 46 were increased in intact MS gray matter, while another 30 were at or below levels noted in control gray matter.

13.Some of the protein interactions between cells in MS gray matter were already known to participate in the disease, but multiple new cell-cell interactions were also noted.

14.Of particular interest was the observation that opposing­ functions were present at the same time and were variably expressed in intact MS gray matter. For example, interactions associated with immune suppression and with immune activation (proinflammatory), were noted, with an overall decrease, even in normal appearing MS gray matter, of reactions that encouraged cell growth and repair (“trophic functions”). Thus, changes related to decreased tissue survival were present even before such effects could be detected visually in MS tissue.

15. Signals for survival of cells were found to originate mainly from nerve cells with effects on other nearby nerve cells as well as other brain cells such as astrocytes, oligodendrocytes, and cells lining blood vessels (endothelial cells).

16. Non-brain cells entering the brain from blood, such as macrophages and microglial cells, also participated in the complex collaboration of brain and non-brain cells, again providing competing signals for cell survival and inflammatory and anti-inflammatory signaling. In degenerating MS gray matter, as expected, signals related to cell survival were markedly decreased, with increased pro-inflammatory signaling.

17. The authors summarize their finding by stating: “when taken together, seemingly intact gray matter areas in patients with progressive MS appear to exhibit competing protective and pathogenic features where the outcome of cell survival may depend on specific anti-inflammatory and trophic cues in addition to inflammation itself.” In other words, there is a continual battle between healing and destructive factors even in “normal” appearing tissues, suggesting that tipping the balance in favor of healing factors could prevent subsequent tissue loss.

18. To support their studies with human tissues the authors looked at animal models of central nervous system diseases where the genes involved in MS pathology had been altered or deleted, resulting in altered expression of gene-related proteins. The effects of such gene alterations and deletions in the animal diseases were similar to those seen in human tissues, with some protein-protein interactions being protective and others destructive. To add to the complexity, the effects varied depending on the stage of disease in the animal model. For example, early in a disease process pro-inflammatory signals were destructive whereas later in the disease course inflammation was protective. Such dual outcomes of immune system activity have been well described in the past.

19. The authors again note that “chronic, inflammatory stress alone does not habitually lead to the full extent of multicomponent neurodegeneration in the cortical brain tissue of patients with MS, but that association with a local failure of trophic and anti-inflammatory intercellular communication appears to be required.” In other words, treating inflammation alone would not be sufficient to prevent tissue loss. These observations support the observations of others that treatments aimed at protecting and restoring cells early in progressive MS need to be part of the “therapeutic cocktail.”

20. Finally, the researchers looked for gene activation and protein interactions in tissues other than the central nervous system that were similar to those found in MS brain. Some were found, suggesting that modulating effects of these interactions with the intent of benefitting the central nervous system could have broader effects outside of the brain.


Insights into the pathogenesis of MS have changed greatly in the past decade. It was long known that chronic progression of disability was a potential late outcome in persons with relapsing forms of multiple sclerosis. How this related to the acute relapsing phase of the disease was, and still is, not clear. Most initial concepts of disability progression were felt to be the direct result of acute relapses, but that may not be the case.

The explosion of knowledge on immune system functions led to the development of highly effective disease-modifying therapies that controlled the acute inflammatory phases of the disease and most research was devoted to understanding the immune changes that led to acute relapses.

However, in the past decade scientists noted there were many non-immunologic changes in MS brains that either preceded or contributed to inflammatory mediated tissue destruction. These included changes to myelin-producing cells (oligodendrocytes), changes to energy-producing cell components (mitochondria) , and to brain cells such as astrocytes. A concept long noted by clinical neurologists, but previously not well defined, was PIRA (progression independent of relapse activity. PIRA was noted even very early in the disease and the conclusion from multiple observations was that a great deal of tissue destruction in MS was not caused by acute inflammation but by non-inflammatory processes. The above paper is one of the first to provide insights into the complex mechanisms of the tissue destruction in progressive MS.

The authors studied the products of activated genes in tissue slices from brains of persons with progressive MS and non-MS individuals. In particular they studied messenger RNA (mRNA) and the proteins that resulted from that process. They grouped the identified genes and proteins into “modules” based on function, e.g. trophic functions that supported cell health, proteins that supported myelin regeneration, proteins that were involved in reducing inflammation and proteins that increased local inflammation.

As expected, in areas of tissue damage there were reduced myelin proteins and nerve cells proteins, along with evidence of scar formation. What was unexpected and most important was that in areas that appeared normal under the microscope there were changes showing early degeneration in the absence of inflammation. Loss of modules related to trophic or brain-health functions were reduced as were modules related to cell-cell communication (synaptic health). In addition, there was a complex mix of proteins related to increasing and suppressing inflammation. The authors were also able to identify which cells were involved in the production of the protein modules, as well as identifying the responses of cells adjacent to them, providing for the first time an insight into the complex interactions of both primary cells of the central nervous system and non-brain cells such as microglia.

These observations, as well as ones made previously, support the concept that the first features of tissue damage in MS are not related to inflammation but may result from cell death due to loss of essential trophic and restorative proteins. That does not reduce the need to control active inflammation in persons during the relapsing phase of their illness. It does mean that, to fully control tissue destruction from onset of disease, other therapeutic approaches are needed to truly cure MS.

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