Gene regulatory mechanisms in the oligodendrocyte lineage in development and disease

Oligodendrocytes are the myelinating cells of the central nervous system (CNS). They contribute to the neuronal network through the insulation of neuronal axons, facilitating communication between neurons and providing metabolic support. In multiple sclerosis (MS), oligodendrocytes are attacked by the immune system leading to a wide variety of symptoms. Remyelination is necessary for functional recovery, which can occur through the recruitment and differentiation of oligodendrocyte precursor cells (OPCs) that reside in the adult CNS. During development and in disease, oligodendrocytes and OPCs (oligodendroglia) undergo significant changes at the transcriptional level. However, the genomes remain the same within these cells, so how do these transcriptional changes occur? In this thesis, we investigate gene regulatory mechanisms in the oligodendrocyte lineage in development and disease.

In Paper I we investigate the role of citrullination in the differentiation of oligodendrocytes. We identify peptidylarginine deiminase 2 (PAD2) as the major citrullinating enzyme in oligodendrocytes, promoting oligodendrocyte differentiation through the upregulation of myelin genes. Interestingly, the main targets of PAD2 are proteins involved in transcriptional and posttranscriptional regulation. Other PAD2 targets are myelin proteins, which might explain the motor and cognitive deficits and the decrease in myelinated axons we observe upon loss of PAD2.

In Paper II we characterize how the oligodendrocyte lineage is affected in disease, using single-cell transcriptomics in the MS mouse model experimental autoimmune encephalomyelitis (EAE). Oligodendroglia in EAE mice show an increase in immune pathway genes including major histocompatibility complex (MHC) class-I and -II genes involved in antigen processing and presentation. Furthermore, OPCs stimulated with interferon-gamma interact with and activate CD4 positive T cells. Thus, oligodendroglia might have a more active role in mediating the inflammatory response in MS than previously thought.

In Paper III we investigate how oligodendroglia transition to the immune state, using single- cell ATAC-seq in EAE mice. We find that immune genes are primed and increase their expression in an inflammatory environment through changes in the histone modification landscape, in chromatin interactions, and in transcription factor binding. Overall, we identify gene regulatory mechanisms of the immune program in oligodendroglia that could be possible therapeutic targets for MS.

In Paper IV we develop an extension of the method genome architecture mapping (immunoGAM), which we apply to study genome-wide chromatin interactions in intact brain tissue. We find interactions and mechanisms that are specific for different brain cell types. Long neuronal genes that are active, often show decondensation or ‘melting’. Furthermore, topologically associating domains and A/B compartments reorganize extensively upon differentiation, and cell type-specific interactions form mediated by specific transcription factor pairs.

To conclude, this thesis examines different layers of gene regulation including chromatin accessibility, histone modifications, genome interactions, and transcription factor binding. More specifically, we investigate how these different layers are involved in the transitioning of oligodendroglia during differentiation or to disease states. The findings in this thesis will hopefully contribute to the development of improved treatment strategies for MS.

List of scientific papers

I. PAD2-mediated citrullination contributes to efficient oligodendrocyte differentiation and myelination. Ana Mendanha Falcão, Mandy Meijer, Antonella Scaglione, Puneet Rinwa, Eneritz Agirre, Jialiang Liang, Sara C Larsen, Abeer Heskol, Rebecca Frawley, Michael Klingener, Manuel Varas-Godoy, Alexandre ASF Raposo, Patrik Ernfors, Diogo S Castro, Michael L Nielsen, Patrizia Casaccia, and Gonçalo Castelo-Branco. Cell Reports. 2019, Vol. 27, Page 1090-1102.
https://doi.org/10.1016/j.celrep.2019.03.108

II. Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis. Ana Mendanha Falcão*, David van Bruggen*, Sueli Marques, Mandy Meijer, Sarah Jäkel, Eneritz Agirre, Elisa M Floriddia, Darya P Vanichkina, Anna Williams, André Ortlieb Guerreiro-Cacais, and Gonçalo Castelo-Branco. Nature Medicine. 2018, Vol. 24, Page 1837-1844. *Equal contribution.
https://doi.org/10.1038/s41591-018-0236-y

III. 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 Falcão, Marek Bartosovic, Leslie Kirby, Daniela Calini, Michael R Johnson, M Ryan Corces, Thomas J Montine, Xingqi Chen, Howard Y Chang, Dheeraj Malhotra, and Gonçalo Castelo-Branco. Neuron. 2022, Vol. 110, Page 1193-1210. *Equal contribution.
https://doi.org/10.1016/j.neuron.2021.12.034

IV. Cell-type specialization is encoded by specific chromatin topologies. Warren Winick-Ng*, Alexander Kukalev*, Izabela Harabula*, Luna Zea-Redondo*, Dominik Szabó*, Mandy Meijer, Leonid Serebreni, Yingnan Zhang, Simona Bianco, Andrea M Chiariello, Ibai Irastorza-Azcarate, Christoph J Thieme, Thomas M Sparks, Sílvia Carvalho, Luca Fiorillo, Francesco Musella, Ehsan Irani, Elena Torlai Triglia, Aleksandra A Kolodziejczyk, Andreas Abentung, Galina Apostolova, Eleanor J Paul, Vedran Franke, Rieke Kempfer, Altuna Akalin, Sarah A Teichmann, Georg Dechant, Mark A Ungless, Mario Nicodemi, Lonnie Welch, Gonçalo Castelo-Branco, and Ana Pombo. Nature. 2021, Vol. 599, Page 684-691. *Equal contribution.
https://doi.org/10.1038/s41586-021-04081-2