The Neuroinflammatory Puzzle of the Autoimmune Disease Multiple Sclerosis

What is Multiple Sclerosis?

In 1868, a German physician Leopold Ordenstein and his mentor Jean-Martin Charcot, published a work that fundamentally changed our understanding of the disease Multiple Sclerosis1. For the first time in history, based on pathological findings, Ordentstein reported that Multiple Sclerosis (MS) and Parkinson’s disease (PD) were two different clinical conditions1.  Previously, these diseases were thought to be the same as the symptoms presented are often alike.

MS symptoms are variable and unpredictable and include dysesthesia, vision problems, walking difficulties, pain, spasticity, numbness, and fatigue. Today, MS is categorized as a chronic inflammatory disease of the central nervous system (CNS) that leads to demyelination and neurodegeneration.

MS disorder is a heterogeneous, multifactorial, immune-mediated disease that is influenced by both genetic and environmental factors.  The pathologic hallmark of MS is multiple focal areas of myelin loss (demyelination) called plaques or lesions and damage to nerve fibers (axonal degeneration/neurodegeneration) within the CNS.

The classic multiple sclerosis plaques are thought to result from a cascade of inflammatory events triggered by activated T cells trafficking to the CNS and encountering their cognate antigen to begin a cascade of lymphocyte, macrophage, and microglial responses that cause damage to oligodendrocytes, myelin, neurons, and axons.

Finally, demyelination and neurodegeneration are accomplished by oxidative injury and mitochondrial damage which leads to a state of “virtual hypoxia”, essentially an energy deficit caused by impaired mitochondrial that cannot synthesize ATP fast enough to meet increased energy demand. Among genetic factors, alleles of the interleukin-2 receptor α gene and human leukocyte antigen (HLA) gene cluster have been identified as heritable risk factors for MS. Environmental variables such as smoking, levels of vitamin D, and Epstein–Barr infection are some established risk factors for MS. 

Drug Development in Multiple Sclerosis Research: Is There a Cure?

MS symptoms vary according to the location and severity of lesions occurring within the CNS. Further, the course of MS is also highly variable. Nevertheless, in most patients, MS is characterized by the onset of recurring clinical symptoms lasting several days or weeks followed by total or partial recovery, namely, the classic relapsing-remitting form of multiple sclerosis (RRMS).

After 10–15 years of disease, this pattern becomes progressive in up to 50% of untreated patients, during which time clinical symptoms slowly cause progressive deterioration over many years, a disease stage defined as secondary progressive multiple sclerosis (SPMS). However, in about 15% of MS patients, disease progression is relentless from the onset, a condition called primary progressive multiple sclerosis (PPMS).

Most of the MS drugs available currently are either immunomodulators or immunosuppressants and patients are treated based on the presentation of RRMS, SPMS, and PPMS2. About 75-85% of patients with MS are suffering from RRMS. Remarkable advances in treatment for RRMS have favorably changed the long-term outlook for many patients.

Some of the current drugs approved for RRMS in the United States include Diroximel fumarate (ALKS 8700, VUMERITY), an immunomodulator thought to activate Nrf2 (Nuclear factor-erythroid factor 2-related factor 2) that is a regulator of cellular resistance to oxidants, and Ofatumumab (ARZERRA), a subcutaneous anti-CD20 (B-lymphocyte antigen CD20) monoclonal antibody that selectively depletes B cells.

For SPMS stage of MS there are several drugs in Phase 2 and Phase 3, and only one has achieved approval in the United States, namely, Siponimod (MAYZENT). This drug is a selective sphingosine 1-phosphate1,5 receptor modulator that has neuroprotective effects in the CNS.

Therapeutic options for PPMS remain comparatively disappointing and challenging as the diagnosis is usually retrospective and, biomarkers, as well as imaging methods, are not well established. Several trials during the last 20 years have investigated the potential of medications approved for RRMS to also positively attenuate progressive disease.

Many therapeutics, such as azathioprine, glatiramer acetate, fingolimod, or natalizumab have failed. However, positive trials during the last few years have led to the approval of ocrelizumab, a monoclonal antibody against CD20, and was shown to lower rates of clinical and MRI-evidenced progression in patients with PPMS3. Currently, there are only three drugs in Phase 2 and two drugs in Phase 3 for PPMS.

Ibudilast, a repurposed drug which is in Phase 2, holds promise and is being investigated for patients with PPMS and SPMS. Ibudilast inhibits an enzyme phosphodiesterase and modifies the invasion of macrophages into the CNS and is neuroprotective in function4.

Spatial Biology and the Hunt for New Multiple Sclerosis Biomarkers

Today most therapeutic targets for MS are discovered by using animal models, imaging, and histology. These methods limit insights into multiple sclerosis research by restricting characterization to a few biomarkers at once.  

Microarray technologies and traditional or single-cell RNA sequencing have expanded the number of biomarkers that can be investigated at a time but suffer from low resolution and lose out on the ability to gain deep mechanistic insight into multiple sclerosis research that can be achieved by maintaining the spatial architecture of CNS tissue and the immune infiltrate.

Today, the evolution of spatial biology with the GeoMx® Digital Spatial Profiler  (DSP) allows for expression profiling of many transcripts or proteins within a given immune cell population or CNS tissue architecture across many samples and can be a key tool in the fight against MS.

The GeoMx DSP combines spatial and molecular barcoding technology to generate a tissue image and expression profiling data for tens to thousands of RNA or protein analytes on FFPE or fixed/fresh frozen tissue slides per day. The GeoMx Whole Transcriptome Atlas can be used to spatially profile the entire human or mouse transcriptome, expanding the number of biomarkers that can be discovered on MS samples.  

The expression levels of transcripts and proteins can be quantified on the GeoMx DSP using either the nCounter® Analysis System or via an Illumina sequencer. In addition to being used as the readout for GeoMx DSP, the nCounter system can be used with an ecosystem of targeted gene expression panels based on the topic of research, biologic pathway/process, or particular gene(s) of interest.

Direct, Digital Expression Analysis for Translational Multiple Sclerosis Research

Once novel biomarkers for MS have been discovered using spatial biology, more routine analysis of clinical samples can be accomplished with the 770-plex nCounter Neuroinflammation and Autoimmune Profiling Gene Expression  Panels, providing valuable insights into immune dysfunction and evaluation of inflammatory processes that can help with drug mechanism of action (MOA) studies. Cerebrospinal fluid, blood, peripheral blood mononuclear cells (PBMCs) or even plasma can be used with these nCounter Panels in addition to FFPE or fixed/frozen tissue to find MS biomarkers from a non-invasive liquid biopsy.

Apart from routine analysis in clinical trials, the nCounter® Neuroinflammation Panel can be used for basic research to study factors that change in the microenvironment of an MS lesion.  Understanding this process and the molecular mechanisms of remyelination is crucial to developing treatments for MS as remyelination is promising one therapeutic approach being investigated.

Remyelination occurs spontaneously but is less pronounced in the aging brain. One of the major factors inhibiting remyelination is the inflammatory microenvironment within MS lesions. Factors such as chondroitin sulfate proteoglycans (CSPGs), an extracellular matrix component, and fibrinogen, a blood clotting factor have been identified as inhibitors of remyelination5. Investigational studies show that many drugs in clinical trials increased myelin repair in a normal environment but were not effective when factors such as fibrinogen were present.

The failure of immune cells to distinguish self from non-self that causes MS could be studied in greater depth using the nCounter Autoimmune Profiling Panel.

Immune self-tolerance is developed through an interplay between two inter-dependent clusters of immune activity: immune stimulation and immune regulation. The mechanisms of immune regulation, for example by immune checkpoints, can be exploited as therapeutic targets for the treatment of MS by and the content in the Autoimmune Profiling Panel, as well as other nCounter panels is well suited for exploring immunotherapy as a treatment for MS. 

What Lies Ahead for Multiple Sclerosis Research?

There is much more to be learned about the pathogenesis and progression of MS, including why the disease is more prevalent in women, which is currently unknown.  Certainly, some of the benefits of precision medicine and immunotherapy that have been gained in immuno-oncology research could be applied to develop treatments for MS.

Whether it’s by studying proteomic or transcriptome expression changes spatially at the level of different brain structures with GeoMx DSP, or by studying gene expression changes from liquid biopsy with the nCounter Analysis System, researchers are beginning to map disease-related changes in gene expression to the course of MS progression to improve the quality of life for countless sufferers of MS.


Lehmann HC, Hartung HP, Kieseier BC. Leopold Ordenstein: on paralysis agitans and multiple sclerosis. Mult Scler. 2007 Nov;13(9):1195-9.

Hauser SL, Cree BAC. Treatment of Multiple Sclerosis: A Review. Am J Med. 2020 Dec;133(12):1380-1390.

Mulero P, Midaglia L, Montalban X. Ocrelizumab: a new milestone in multiple sclerosis therapy. Ther Adv Neurol Disord. 2018;11:1756286418773025.

Faissner S, Gold R. Progressive multiple sclerosis: latest therapeutic developments and future directions. Ther Adv Neurol Disord. 2019;12:1756286419878323.

Petersen MA, Tognatta R, Meyer-Franke A, et al. BMP receptor blockade overcomes extrinsic inhibition of remyelination and restores neurovascular homeostasis. Brain. 2021

For Research Use Only. Not for use in diagnostic procedures.

By Nirupama Deshpande
For research use only. Not for use in diagnostic procedures.