High-dimensional immune profiling identifies a biomarker to monitor dimethyl fumarate response in multiple sclerosis

Abstract

Dimethyl fumarate (DMF) is an immunomodulatory treatment for multiple sclerosis (MS). Despite its wide clinical use, the mechanisms underlying clinical response are not understood. This study aimed to reveal immune markers of therapeutic response to DMF treatment in MS. For this purpose, we prospectively collected peripheral blood mononuclear cells (PBMCs) from a highly characterized cohort of 44 individuals with MS before and at 12 and 48 wk of DMF treatment. Single cells were profiled using high-dimensional mass cytometry. To capture the heterogeneity of different immune subsets, we adopted a bioinformatic multipanel approach that allowed cell population–cluster assignment of more than 50 different parameters, including lineage and activation markers as well as chemokine receptors and cytokines. Data were further analyzed in a semiunbiased fashion implementing a supervised representation learning approach to capture subtle longitudinal immune changes characteristic for therapy response. With this approach, we identified a population of memory T helper cells expressing high levels of neuroinflammatory cytokines (granulocyte–macrophage colony-stimulating factor [GM-CSF], interferon γ [IFNγ]) as well as CXCR3, whose abundance correlated with treatment response. Using spectral flow cytometry, we confirmed these findings in a second cohort of patients. Serum neurofilament light-chain levels confirmed the correlation of this immune cell signature with axonal damage. The identified cell population is expanded in peripheral blood under natalizumab treatment, substantiating a specific role in treatment response. We propose that depletion of GM-CSF–, IFNγ-, and CXCR3-expressing T helper cells is the main mechanism of action of DMF and allows monitoring of treatment response.

Single-Cell Analysis to Better Understand the Mechanisms Involved in MS

“…A population of CD4+ T cells with a cytotoxic phenotype (expression of GZMB, PRF1, CCL5) was found to be expanded in the CSF of MS patients, but not in the blood. It would appear that this population does not encompass those that were previously described as targeted by DMF treatment (CD4+ helper cells expressing GM-CSF and CXCR4 or CXCR3) [ 39 , 40 ], as in this study the CD4+ T cells did not express genes coding for CXCR4 or GM-CSF. In addition to this population, T follicular helper (TFH) cells were also enriched in the CSF of MS patients.…”

“…Dimethyl fumarate (DMF), which is frequently used to suppress relapses in MS patients, was shown to reduce this population, noting its relevance as a therapeutic target [ 40 ]. In a later study, Diebold et al used single-cell profiling in order to elucidate the mode of action of DMF [ 39 ]. PBMCs were collected from MS patients before and after DMF treatment and single cells were profiled using the CyTOF method.…”

Full spectrum flow cytometry in the clinical laboratory

“…While there are far too many to list, we refer the reader to several examples of non-clinical assays with human specimens. [20][21][22][23][24][25][26] The above method-comparison studies provide strong preliminary evidence that spectral flow cytometers are likely functionally equivalent to conventional flow cytometers but are superior in the sense that they can perform high-dimensional assays in a single-tube format that otherwise requires 4 separate tubes on current 10-to-12-color conventional flow cytometers. It is critical that comprehensive validation studies be published in reputable peer-reviewed journals with comparisons against regulatory agency-approved predicate conventional flow cytometers.…”

Gut microbiota composition as a candidate risk factor for dimethyl fumarate-induced lymphopenia in multiple sclerosis

“…Namely, A. muciniphilia and B. dorei 1 , 19 – both overrepresented in lymphopenia patients – and P. copri were shown to be reduced in MS patients 12 but increase upon DMT. 11 While we cannot exclude that this small exploratory pilot study may have been affected by unrecorded dietary effects or under-powered to identify associations for rare events – including an association of gut microbiota with disease activity 20 – observations from this first longitudinal microbiome analysis under DMF provide pivotal evidence for a role of microbiota in the development of lymphopenia. We therefore believe that larger studies are warranted to evaluate the feasibility of microbiome testing for the prediction of DMF-associated lymphopenia in MS patients with implications for the assessment of microbiota in mediating clinically relevant side-effects under other DMTs.…”