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Defining the Oligodendrocyte Lineage in Multiple Sclerosis Lesions by Single Cell RNA-Sequencing

Periodic Reporting for period 1 - MuSeq (Defining the Oligodendrocyte Lineage in Multiple Sclerosis Lesions by Single Cell RNA-Sequencing)

Reporting period: 2018-05-01 to 2020-04-30

MS is a chronic inflammatory demyelinating neurological disorder with about 2.5M affected people worldwide and is the major cause of disability in young adults not related to accidents. It is characterized by the damage to a particular cell type in our brain, oligodendrocytes, and the loss of the fatty substance myelin they produce – which we call demyelination. This myelin is tightly wrapped around the long fibers (called axons) that connect our nerve cells in the brain and has two functions; it provides nutrients to the axons and also speeds up the conduction of nerve impulses along them. As a result, its loss leads to reduced function and then degeneration of the axon. This in turn causes the disability that characterizes progressive MS, for which there are currently no treatments.
Repair mechanisms within human brains initially cope with the damage caused by MS and replace the lost myelin– a process that we call remyelination. However as the years go by, the remyelination capacity of the brain decreases and persistent areas of myelin loss – called demyelinated lesions – remain. A key question for those trying to develop new treatments for progressive MS is therefore: What is the balance between damage and repair in the brain of each person affected with MS? Only by knowing this can treatments be targeted at the right process in the patient. However, up to now, we know little about how oligodendrocytes change with damage and repair in MS and between different people.
In order address this gap of knowledge, in this project, I used a powerful technology called single-nuclei RNA-sequencing allowing me to analyse the pattern of gene expression in thousands of individual brain cells within a frozen tissue sample from human brains post mortem. With this, I discovered which cells were present and how they function first in the healthy human brain, and then whether these were different in normal and damaged areas MS brain. This helped me discover clues about how oligodendrocyte changes link with damage and repair.
By gaining a better knowledge about oligodendrocytes in our brain, the work of this project was a key step towards understanding the cellular changes that are happening in MS. The results are important for two reasons. First, this understanding will enable rational approaches to drug discovery based on targeting both the damage-causing mechanisms that are responsible for the selective loss of some oligodendrocytes and the repair mechanisms required to restore an optimal balance of them. Second, the innovative technology that I have established in our lab will enable far greater accuracy in the pathological analysis of MS brain that is possible by current microscopy-based methods. This has now led to a far bigger current study that will in turn lead to greatly improved knowledge as to the variation in MS between different patients.
I have used single nuclear RNA-sequencing on 20 human brain samples, including 4 non-pathological control donors and 4 donors that were diagnosed with MS. The results from this were bioinformatically analysed and further validated on a different cohort of tissue donors using immunohistochemistry and in-situ hybridisation.
I found (as we expected from previous studies in animal brains) that the human brain contains distinct oligodendrocyte states distinguished by the levels of expression of different genes. Most surprisingly, although I could identify the same states in MS lesions, the balance between them was substantially altered, with some being over- and some underrepresented. Additionally, we found that – in terms of oligodendrocyte composition – the normal appearing white matter in MS patients is more similar to lesions, suggesting that MS is actually a more global disease as previously thought. While I do not know yet whether each oligodendrocyte type has a distinct role in the brain, the fact that examples of each being located in distinct regions of the brain strongly suggests this to be the case. I conclude therefore that the changing balance of oligodendrocyte types in MS may influence the disease course.
I have published this work in the journal Nature and presented this to the scientific community on several occasions. Moreover, the preliminary work has further attracted the interest of the pharma company Roche, which has now invested in a current much larger study addressing lesion differences with the aim to exploit this for the search of new drug targets enhancing remyelination.
Until this point, MS research has mostly focussed on animal models, which never reflect the entirety of the disease, especially when it comes to remyelination. Human pathology has previously focused on describing the pattern of MS damage and the morphology of cells . However, with this new technology, we can focus more on cellular function in damaged and repairing areas of MS brain. This understanding will improve the translatability to human patients by being human-specific.
For the first time , this project gave insights into the changes in cellular composition and function in MS lesions at an unprecedented resolution using an unbiased approach, and providing us with many new markers for cellular subtypes. My findings together with some other recent studies using different approaches have contributed to a shift away from the idea that all oligodendrocytes are equally affected by MS pathology and that remyelination is purely driven by oligodendrocyte progenitor cells. Moreover, this approach revealed new markers for human oligodendrocytes and their progenitor cells that now can be used by the entire research community.
Although this is not the only study using single nuclei transcriptomics to study the human brain, it was one of the first published addressing human pathology, thus being an exemplar study proving that this is a suitable method to address pathology at a new level.
Summary of the skewed oligodendrocyte heterogenity in MS