Implication of DNA methylation changes at chromosome 1q21.1 in the brain pathology of primary progressive multiple sclerosis

Multiple Sclerosis (MS) is a heterogeneous inflammatory and neurodegenerative disease of the central nervous system with an unpredictable course toward progressive disability. Understanding and treating progressive MS remains extremely challenging due to the limited knowledge of the underlying mechanisms. We examined the molecular changes associated with primary progressive MS (PPMS) using a cross-tissue (blood and post-mortem brain) and multilayered data (genetic, epigenetic, transcriptomic) from independent cohorts. We identified and replicated hypermethylation of an intergenic region within the chromosome 1q21.1 locus in the blood of PPMS patients compared to other MS patients and healthy individuals. We next revealed that methylation is under genetic control both in the blood and brain. Genetic analysis in the largest to date PPMS dataset yielded evidence of association of genetic variations in the 1q21.1 locus with PPMS risk. Several variants affected both 1q21.1 methylation and the expression of proximal genes (CHD1L, PRKAB2, FMO5) in the brain, suggesting a genetic-epigenetic-transcriptional interplay in PPMS pathogenesis. We addressed the causal link between methylation and expression using reporter systems and dCas9-TET1-induced CpG demethylation in the 1q21.1 region, which resulted in upregulation of CHD1L and PRKAB2 genes in SH-SY5Y neuron-like cells. Independent exploration using unbiased correlation network analysis confirmed the putative implication of CHD1L and PRKAB2 in brain processes in PPMS patients. Thus, several lines of evidence suggest that distinct molecular changes in 1q21.1 locus, known to be important for brain development and disorders, associate with genetic predisposition to high methylation in PPMS patients that regulates the expression of proximal genes. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study 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, the Stockholm County Council - ALF project, the European Unions Horizon 2020 research, innovation programme (grant agreement No 733161) and the European Research Council (ERC, grant agreement No 818170), the Knut and Alice Wallenberg Foundation, Hedlund Foundation, Ake Wiberg Foundation and Karolinska Institutes funds. LK is supported by a fellowship from the Margaretha af Ugglas Foundation. MPK is supported by McDonald Fellowship from Multiple Sclerosis International Federation (MSIF) and the EU/EFPIA/OICR/McGill/KTH/Diamond Innovative Medicines Initiative 2 Joint Undertaking (EUbOPEN grant agreement No 875510). CSC is supported by the Blanceflor Boncompagni Ludovisi, nee Bildt Foundation. PC is supported by NIH R35-NS111604. The funders of the study had no role in study design, sample acquisition, data collection, data analysis, data interpretation or writing of the manuscript. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Swedish Ethical Review Authority of Stockholm gave ethical approval for The importance of environment and living habits for aetiology and progress of multiple sclerosis a case-control study (EIMS) Swedish Ethical Review Authority of Stockholm gave ethical approval for Genes and Environment in Multiple Sclerosis (GEMS) Swedish Ethical Review Authority of Stockholm gave ethical approval for Genetics and biomarker analysis in Natalizumab-treated Multiple Sclerosis (IMSE I) Swedish Ethical Review Authority of Stockholm gave ethical approval for Genetic and epidemiological studies of newly launched immunomodulatory drugs for individuals with Multiple Sclerosis (MS) (IMSE II) Ethical Review Board at Karolinska Institutet of Stockholm gave ethical approval for Prospective Assessment of Multiple Sclerosis (SPASM) Swedish Ethical Review Authority of Stockholm gave ethical approval for Stockholm Prospective Assessment of Multiple Sclerosis a prospective study of people with newly diagnosed MS or possible MS, as well as biomarker studies of treatment effects (STOPMS II) I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The 450K array methylome data generated from whole blood (cohort 1) are available in the Gene Expression Omnibus (GEO) database under accession number GSE106648. The RNA-sequencing data used for correlation network analysis in MS brain are accessible under the accession numbers GSE174647, GSE118257, GSE179427, PRJNA544731 with details presented in Supplementary Table S11. Results from the genetic association analysis (cohort 3) are available in SI Appendix Tables. Due to the GDPR regulations, we cannot deposit any personal information including genetic data, which can be shared upon request and under a Data Access Agreement.