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dc.contributor.authorKular, Lara
dc.contributor.authorNeedhamsen, Maria
dc.contributor.authorAdzemovic, Milena Z.
dc.contributor.authorKramarova, Tatiana
dc.contributor.authorGomez-Cabrero, David
dc.contributor.authorEwing, Ewoud
dc.contributor.authorPiket, Eliane
dc.contributor.authorTegner, Jesper
dc.contributor.authorBeck, Stephan
dc.contributor.authorPiehl, Fredrik
dc.contributor.authorBrundin, Lou
dc.contributor.authorJagodic, Maja
dc.date.accessioned2019-08-04T07:43:11Z
dc.date.available2019-08-04T07:43:11Z
dc.date.issued2019-05-30
dc.identifier.citationKular, L., Needhamsen, M., Adzemovic, M. Z., Kramarova, T., Gomez-Cabrero, D., Ewing, E., … Jagodic, M. (2019). Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis. Clinical Epigenetics, 11(1). doi:10.1186/s13148-019-0678-1
dc.identifier.doi10.1186/s13148-019-0678-1
dc.identifier.urihttp://hdl.handle.net/10754/656314
dc.description.abstractBackground: Due to limited access to brain tissue, the precise mechanisms underlying neuro-axonal dysfunction in neurological disorders such as multiple sclerosis (MS) are largely unknown. In that context, profiling DNA methylation, which is a stable and cell type-specific regulatory epigenetic mark of genome activity, offers a unique opportunity to characterize the molecular mechanisms underpinning brain pathology in situ. We examined DNA methylation patterns of neuronal nuclei isolated from post-mortem brain tissue to infer processes that occur in neurons of MS patients. Results: We isolated subcortical neuronal nuclei from post-mortem white matter tissue of MS patients and non-neurological controls using flow cytometry. We examined bulk DNA methylation changes (total n = 29) and further disentangled true DNA methylation (5mC) from neuron-specific DNA hydroxymethylation (5hmC) (n = 17), using Illumina Infinium 450K arrays. We performed neuronal sub-type deconvolution using glutamate and GABA methylation profiles to further reduce neuronal sample heterogeneity. In total, we identified 2811 and 1534 significant (genome-wide adjusted P value < 0.05) differentially methylated and hydroxymethylated positions between MS patients and controls. We found striking hypo-5mC and hyper-5hmC changes occurring mainly within gene bodies, which correlated with reduced transcriptional activity, assessed using published RNAseq data from bulk brain tissue of MS patients and controls. Pathway analyses of the two cohorts implicated dysregulation of genes involved in axonal guidance and synaptic plasticity, with meta-analysis confirming CREB signalling as the most highly enriched pathway underlying these processes. We functionally investigated DNA methylation changes of CREB signalling-related genes by immunohistofluoresence of phosphorylated CREB in neurons from brain sections of a subcohort of MS patients and controls (n = 15). Notably, DNA methylation changes associated with a reduction of CREB activity in white matter neurons of MS patients compared to controls. Conclusions: Our data demonstrate that investigating 5mC and 5hmC modifications separately allows the discovery of a substantial fraction of changes occurring in neurons, which can escape traditional bisulfite-based DNA methylation analysis. Collectively, our findings indicate that neurons of MS patients acquire sustained hypo-5mC and hyper-5hmC, which may impair CREB-mediated neuro-axonal integrity, in turn relating to clinical symptoms.
dc.description.sponsorshipWe are grateful to A. van Vollenhoven for flow cytometry processing (Center for Molecular Medicine and Karolinska Institutet core facility), D. Fauvin for assistance with TrueMethyl and T. Morris for support in the BS/oxBS data pipeline. We thank R. Covacu for helpful feedback on data interpretation. We acknowledge GenomeScan/ServiceXS (Leiden, The Netherlands) for processing Illumina 450K array BS and oxBS data (cohort 2) and BEA core facility (Karolinska Institutet) for processing Illumina 450K array BS data (pilot samples and cohort 1). We thank the Multiple Sclerosis and Parkinson’s Tissue Bank (Imperial College London) for provision of brain tissue samples. Computations were performed on resources provided by SNIC through Uppsala Multidisciplinary Center for Advanced Computational Science (UPPMAX).
dc.description.sponsorshipFunding This work was supported by grants from the Swedish Research Council, the Swedish Association for Persons with Neurological Disabilities, the Swedish Brain Foundation, the Swedish MS Foundation, Åsa Vilhelmsson Foundation, Petrus and Augusta Hedlunds Foundation, the Stockholm County Council (ALF project) and Karolinska Institutet. L. Kular was supported by fellowship from the Margaretha af Ugglas Foundation. D. Gomez-Cabrero and J. Tegner were supported by EU FP7 306000 STATegra.
dc.publisherSpringer Nature
dc.relation.urlhttps://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-019-0678-1
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectMultiple sclerosis
dc.subjectNeurons
dc.subjectDNA methylation
dc.subjectDNA hydroxymethylation
dc.subjectAxonal guidance
dc.subjectSynaptic
dc.subjectplasticity
dc.subjectCREB
dc.subjectNeurodegeneration
dc.titleNeuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis
dc.typeArticle
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.identifier.journalClinical Epigenetics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionDepartment of Medicine, Unit of Computational Medicine, Center for Molecular Medicine, Karolinska Institutet Solna Sweden
dc.contributor.institutionDepartment of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet Stockholm Sweden
dc.contributor.institutionMucosal and Salivary Biology Division, King's College London Dental Institute London SE1 9RT UK
dc.contributor.institutionTranslational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA Pamplona Spain
dc.contributor.institutionMedical Genomics, UCL Cancer Institute, University College London London UK
dc.contributor.institutionDepartment of Neurology, Karolinska University Hospital Stockholm Sweden
kaust.personTegner, Jesper
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.c.4524122.v1
refterms.dateFOA2019-08-04T07:46:33Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Dataset]</i> <br/> Kular, L., Needhamsen, M., Adzemovic, M., Kramarova, T., Gomez-Cabrero, D., Ewing, E., Piket, E., Tegnér, J., Beck, S., Piehl, F., Brundin, L., &amp; Jagodic, M. (2019). <i>Neuronal methylome reveals CREB-associated neuro-axonal impairment in multiple sclerosis</i>. Figshare. https://doi.org/10.6084/M9.FIGSHARE.C.4524122.V1. DOI: <a href="https://doi.org/10.6084/m9.figshare.c.4524122.v1" >10.6084/m9.figshare.c.4524122.v1</a> Handle: <a href="http://hdl.handle.net/10754/664737" >10754/664737</a></a></li></ul>
dc.date.published-online2019-05-30
dc.date.published-print2019-12


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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.