Deciphering SNPs involved in oligodendroglia functional resilience in multiple sclerosis

Project Information

ResilMS

Grant agreement ID: 101150016

DOI

10.3030/101150016

Project closed

EC signature date 6 March 2024

Start date 1 June 2024

End date 31 May 2026

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 206 887,68

Coordinated by

KAROLINSKA INSTITUTET
Sweden

Periodic Reporting for period 1 - ResilMS (Deciphering SNPs involved in oligodendroglia functional resilience in multiple sclerosis)

Reporting period: 2024-06-01 to 2026-05-31

Summary of the context and overall objectives of the project

Multiple sclerosis (MS) is a challenging chronic neurological disease in which the immune system repeatedly attacks the myelin sheath in the central nervous system (CNS), resulting in episodic cognitive and motor symptoms that worsen over decades. This lengthy disease period, combined with repetitive symptoms that typically begin in young adulthood, has raised high concern from multiple perspectives — including physical and mental health as well as broader societal impact.
To date, the main line of treatment for MS is centred around the peripheral immune system, whereas the damaged cell population in charge of (re-)generating myelin — namely oligodendroglia (OL) — has had difficulty receiving efficient treatment that facilitates its repairing mechanisms when MS occurs. Interestingly, recent research has made it clear that even under adverse inflammation such as in MS pathology, not all oligodendrocytes succumb: some survive repeated attacks and continue to support neural function. The survivors' identity, however, remains unclear. Therefore, understanding what signatures make which OLs resilient is central to developing better treatments, because if their protective mechanisms could be harnessed, it might be possible to slow or even halt disease progression.
ResilMS (Deciphering SNPs involved in oligodendroglia functional resilience in multiple sclerosis) set out to answer this question by combining advanced genomic technologies with animal models that mimic the relapsing–remitting disease course seen in most patients. The project pursued three main objectives. First, it aimed to generate high-resolution spatial and single-cell transcriptomic maps of oligodendrocytes in MS mouse models, capturing which genes are active in surviving versus damaged cells and in which tissue locations. Second, it sought to link human MS-associated genetic variants — identified through large genome-wide association studies — to the gene-regulatory programmes of oligodendrocytes, thereby connecting population-level genetic risk to cellular-level function. Third, it planned to validate the most promising genetic targets through single-cell CRISPR screens in human oligodendrocytes, testing whether specific variants functionally alter cell behaviour.
By bridging spatial tissue biology, human genetics and functional genomics, ResilMS aimed to produce an integrated picture of oligodendrocyte resilience that could ultimately inform diagnostic and therapeutic strategies for MS.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The project began by establishing a reproducible relapsing–remitting experimental autoimmune encephalomyelitis (EAE) model with a longer symptom-observation window and more distinct disease peaks than in previous reference studies, better reflecting the clinical disease course seen in patients. A chronic EAE model with additional disease-severity levels and time points was developed in parallel as a complementary paradigm. Alongside model development, single-cell viral barcode tracing was set up for tracking oligodendrocyte lineage and survival across disease episodes, and is now at the final stage of characterisation and sequencing.
A flagship single-cell spatial transcriptomic dataset was then generated using the Xenium 5k platform augmented with over 100 disease-relevant genes — the most advanced panel available at the time of data generation. The dataset spans four disease trajectories and 18 disease stages, encompassing 158 tissue sections and nearly 1.4 million cells passing quality control. An integrative analysis framework combining reference single-cell RNA-sequencing data with the new spatial data was built and tested, and the KaroSpace rapid-access exploration tool was developed as a direct spin-off to handle the dataset's scale.
On the genetic-variant side, MS risk variants — both prevalence- and severity-associated — were integrated with oligodendrocyte-specific chromatin-accessibility data from healthy and diseased cells, producing an initial catalogue of resilient oligodendrocyte gene signatures connected to human genetic risk. For functional validation, single-cell CRISPR analysis training was completed and applied in two collaborative studies examining gene-regulatory regions and transcription factors in human oligodendrocyte precursor cells.
The project's main scientific achievements to date include two peer-reviewed publications in leading journals, two preprints, and a main manuscript in preparation targeting a top-tier journal. A novel tissue-grid layout was developed that maximised use of mounting space, reducing reagent costs and enabling near-zero waste of collected samples. The datasets, analysis pipelines and experimental protocols generated by the project have already become cross-project resources supporting multiple collaborative outputs within and beyond the host group.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

ResilMS made good progress across and beyond its objectives, generating experimental models and protocols, new methods and software, as well as critical datasets that extend the current knowledge base.
The centrepiece dataset — a single-cell spatial transcriptomic atlas covering 18 disease stages with nearly 1.4 million cells — provides an unprecedented view of how different cell types are distributed, interact and change across the course of the disease. This resource has no comparable precedent in its disease-stage coverage and cellular resolution for MS mouse models.
The integrative analysis linking MS risk variants to oligodendrocyte-specific gene-regulatory regions produced the first catalogue connecting resilient oligodendrocyte gene signatures to human genetic risk, advancing the field beyond correlative GWAS findings toward cell-type-specific mechanistic understanding. The two collaborative single-cell CRISPR studies further extended the functional validation toolkit for oligodendrocyte biology.
Additional outputs beyond the original scope include the KaroSpace spatial-omics exploration framework, contributions to a study linking an Epstein–Barr virus protein to MS-relevant immune responses, and a study on the developmental origins of specific brain cell types. Translational discussion during the funding period also identified concrete therapeutic angles — in particular strategies aimed at modulating CNS-resident immune cells that communicate closely with OLs — which open new preclinical research directions.