Dynamics of transcriptomic and epigenomic states in mouse and human central nervous system cells in multiple sclerosis

Multiple sclerosis (MS) is a chronic autoimmune disorder characterized by immunologically mediated demyelination in the central nervous system (CNS). Oligodendrocytes, a type of glial cell in the CNS, are responsible for the synthesis and maintenance of myelin. In our previous study, we identified a subset of disease-specific oligodendroglia (OLG) expressing genes associated with antigen presentation and immune response in MS and its animal model, experimental autoimmune encephalomyelitis (EAE). These findings suggest the potential of OLGs as immunomodulators in MS but also raise questions about their temporal and spatial characteristics in the disease. Therefore, this thesis aims to investigate the dynamics of OLGs and other glial cells in MS and EAE.

In Paper I, by focusing on the peak stage of EAE, interferon gamma treated OPCs, as well as human MS samples, we found that chromatin accessibility, transcription factor regulations, histone modifications, and chromatin architecture remodeling are involved in regulating immune gene expression. However, the chromatin of several immune genes also exhibits a primed state in mouse and human OLGs even under non-disease conditions. Additionally, a group of MS susceptibility single nucleotide polymorphisms (SNPs) was found to overlap with accessible chromatin regions in OLGs in human and mice.

In Paper II, by applying single-cell multi-omics sequencing to OLGs from various time points of EAE, we observed immune gene expression in OLGs from the initial stages of the disease, with high chromatin accessibility retained until the late stage. Furthermore, we classified mature oligodendrocytes (MOLs) into several subtypes (MOL1, MOL2, and MOL5/6), and revealed a heightened immune profile in MOL2, as well as a greater nervous system repair and remyelination potential in MOL5/6 when compared to each other.

In Paper III, we applied single-cell resolution in situ sequencing to CNS tissue sections and identified distinct lesion compartments in MS and EAE. We characterized the dynamics of disease-associated glia throughout the disease course, and observed a progressive decrease in immune infiltration towards cranial regions. Cellular interactions were inferred based on their spatial positions, and distinct hubs of interaction among glial cells were identified across different stages of EAE.

In our preliminary data, we investigated the role of embryonic ectoderm development (EED), a subunit of the polycomb repressive complex 2 crucial for H3K27me3-mediated gene silencing, under physiological and demyelination conditions. We found that knocking down Eed expression in OLGs increased their expression of immune genes. Additionally, when induced EAE in mice with Eed knockdown in OLGs, male mice exhibited earlier onset of the disease compared to female mice.

In summary, the studies included in this thesis investigate the dynamics of OLGs and other glial cells across a transcriptomic, epigenomic, and spatial axis throughout the disease course. By exploring these molecular and spatial characteristics, our studies aim to enhance the understanding of MS pathogenesis and identify specific cell types or genes that could reveal novel therapeutic targets for the disease.

List of scientific papers

I. Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility. Mandy Meijer*, Eneritz Agirre*, Mukund Kabbe, Cassandra A van Tuijn, Abeer Heskol, Chao Zheng, Ana Mendanha Falc‹o, Marek Bartosovic, Leslie Kirby, Daniela Calini, Michael R Johnson, M Ryan Corces, Thomas J Montine, Xingqi Chen, Howard Y Chang, Dheeraj Malhotra, and GonŤalo Castelo-Branco. Neuron. 2022.
https://doi.org/10.1016/j.neuron.2021.12.034

II. Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis. Chao Zheng*, Bastien HervŽ*, Mandy Meijer, Leslie Ann Rubio Rodr’guezKirby, AndrŽ Ortlieb Guerreiro Cacais, Petra Kukanja, Mukund Kabbe, Tomas Olsson, Eneritz Agirre, GonŤalo Castelo-Branco. bioRxiv. 2023. Preprint. [Manuscript]
https://doi.org/10.1101/2023.12.18.572120

III. Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology. Petra Kukanja*, Christoffer M. Langseth*, Leslie A. Rubio Rodr’guez-Kirby, Eneritz Agirre, Chao Zheng, Amitha Raman, Chika Yokota, Christophe Avenel, Katarina Tiklov‡, AndrŽ O. Guerreiro Cacais, Tomas Olsson, Markus M. Hilscher, Mats Nilsson, GonŤalo Castelo-Branco. Cell. 2024.
https://doi.org/10.1016/j.cell.2024.02.030