Epigenetic clock indicates accelerated aging in glial cells of progressive multiple sclerosis patients

Background: Multiple sclerosis (MS) is a chronic inflammatory neurodegenerative disease of the central nervous system (CNS) characterized by irreversible disability at later progressive stages. A growing body of evidence suggests that disease progression depends on age and inflammation within the CNS. We aimed to investigate epigenetic aging in bulk brain tissue and sorted nuclei from MS patients using DNA methylation-based epigenetic clocks. Methods: We applied Horvath’s multi-tissue and Shireby’s brain-specific Cortical clock on bulk brain tissue (n = 46), sorted neuronal (n = 54), and glial nuclei (n = 66) from post-mortem brain tissue of progressive MS patients and controls. Results: We found a significant increase in age acceleration residuals, corresponding to 3.6 years, in glial cells of MS patients compared to controls (P = 0.0024) using the Cortical clock, which held after adjustment for covariates (Padj = 0.0263). The 4.8-year age acceleration found in MS neurons (P = 0.0054) did not withstand adjustment for covariates and no significant difference in age acceleration residuals was observed in bulk brain tissue between MS patients and controls. Conclusion: While the findings warrant replication in larger cohorts, our study suggests that glial cells of progressive MS patients exhibit accelerated biological aging.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 Union’s Horizon 2020 research, innovation program (grant agreement No. 733161) and the European Research Council (ERC, grant agreement No. 818170), the Knut and Alice Wallenberg Foundation grant, Åke Wilberg Foundation, and Karolinska Institute’s funds. LK was supported by a fellowship from the Margaretha af Ugglas Foundation. DK was supported by an Erasmus fellowship. The funders of the study had no role in study design, sample acquisition, data collection, data analysis, data interpretation, or writing of the manuscript. AU-C was supported by “Doctorados industriales 2018–2020” and “Contrato predoctoral en investigación en ciencias y tecnologías de la salud en el periodo 2019–2022” fellowships, both funded by the Government of Navarra and by an Erasmus fellowship. The computations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX, partially funded by the Swedish Research Council through grant agreement No. 2018-05973

Contribution of Heritability and Epigenetic Factors to Skeletal Muscle Mass Variation in United Kingdom Twins

Context: Skeletal muscle mass (SMM) is one of the major components of human body composition, with deviations from normal values often leading to sarcopenia.Objective: Our major aim was to conduct a genome-wide DNA methylation study in an attempt to identify potential genomic regions associated with SMM.Design: This was a mixed cross-sectional and longitudinal study.Setting: Community-based study.Participants: A total of 1550 middle-aged UK twin (monozygotic and dizygotic) twins, 297 of which were repeatedly measured participated in the study.Main Outcome Measure: Appendicular lean mass assessed using DXA technology, and MeDIP-seq DNA methylation profiling genome-wide were obtained from each individual.Results: Heritability estimate of SMM, with simultaneous adjustment for covariates obtained using variance decomposition analysis was h2=0.809±0.050. After quality control and analysis of longitudinal stability, the DNA methylation data comprised of 723,029 genomic sites, with positive correlations between repeated measurements (Rrepeated =0.114–0.905). Correlations between MZ and DZ twins were 0.51 and 0.38 at a genome-wide average, respectively and clearly increased with Rrepeated. Testing for DNA methylation association with SMM in 50 discordant MZ twins revealed 36,081 nominally significant results, of which the top-ranked 134 signals (P&lt;0.01 and Rrepeated&gt;0.40) were subjected to replication in the sample of 1,196 individuals. Seven SMM-methylation association signals replicated at a false discovery rate &lt;0.1, and these were located in or near genes DNAH12, CAND1, CYP4F29P, ZFP64 which have previously been highlighted in muscle-related studies. Adjusting for age, smoking and blood cell heterogeneity did not alter significance of these associations.Conclusion: This epigenome-wide study, testing longitudinally stable methylation sites discovered and replicated a number of associations between DNA methylation at CpG loci and skeletal muscle mass. Four replicated signals were related to genes with potential muscle functions, suggesting that the methylome of whole blood may be informative of SMM variation<br/

Small non-coding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology

To improve our understanding of MS pathology and heterogeneity and provide new strategies for biomarkers and treatments development we carried out a genome-wide small non-coding RNA analysis. The analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. We aimed to detect differentially expressed small non-coding RNAs between MS and controls. The data contains unique molecular identifier (UMI) count information for each transcript. The small non-coding RNA analysis was performed in paired peripheral blood mononuclear cells, plasma, cerebrospinal fluid (CSF) cells and cell-free CSF from 29 MS patients and 16 controls using next-generation sequencing. One INDC control was missing a CSF cell and cell-free CSF sample and one NINDC control was missing a PBMC and plasma sample. Small non-coding RNAs were isolated from 300 ul of plasma or CSF using the miRCURY RNA isolation kit for biofluids (Exiqon, Denmark) or from CSF cells and peripheral blood mononuclear cells precipitate using the miRNAeasy micro kit (Qiagen, Germany). Small non-coding RNA libraries were prepared as previously described at PMID: 27798564. The libraries were sequenced on eight lanes of HiSeq2500. Preprocessing and alignment were done according to PMID: 30250291. The "Unique molecular identifier_sncRNAs_analysis_MS" file contains unique molecular identifier count information for each small non-coding RNA transcript as well as other types of transcripts identified in the sequencing libraries from 44 individuals and 4 compartments (PBMCs, CSF cells, plasma, cell-free CSF). Altogether 176 samples. The metafile contains information about the disease status, sex, age for all MS patients and controls. The "readme" explains the contents of the data files and contains the variables list.Små icke-kodade RNA (sncRNA) spelar en viktig roll i regleringen av olika processer i kroppen, särskilt i immunsystemet och kan lätt detekteras i kroppsvätskor. Projektets specifika syfte är att genomföra screening av små-icke-kodande RNA från perifert blod och cerebrospinalvätska hos MS-patienter i syfte att avslöja deras biologiska roll i MS och testa deras potential som nya MS-biomarkörer. Vi analyserade förändringarna i nivån av sncRNA i blod och cerebrospinalvätska hos patienter med MS (29) och kontroller (16). Patienter med olika former av MS inkluderades i analysen för att klargöra mekanismerna genom vilka sncRNA kan bidra till utvecklingen av en viss form av sjukdomen. Uppgifterna innehåller råinformation om molekyler för varje transkript. För mer information se den engelska katalogsidan https://snd.gu.se/en/catalogue/study/SND115

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies

Abstract Background The advent of array-based genome-wide DNA methylation methods has enabled quantitative measurement of single CpG methylation status at relatively low cost and sample input. Whereas the use of Infinium Human Methylation BeadChips has shown great utility in clinical studies, no equivalent tool is available for rodent animal samples. We examined the feasibility of using the new Infinium MethylationEPIC BeadChip for studying DNA methylation in mouse. Results In silico, we identified 19,420 EPIC probes (referred as mEPIC probes), which align with a unique best alignment score to the bisulfite converted reference mouse genome mm10. Further annotation revealed that 85% of mEPIC probes overlapped with mm10.refSeq genes at different genomic features including promoters (TSS1500 and TSS200), 1st exons, 5′UTRs, 3′UTRs, CpG islands, shores, shelves, open seas and FANTOM5 enhancers. Hybridization of mouse samples to Infinium Human MethylationEPIC BeadChips showed successful measurement of mEPIC probes and reproducibility between inter-array biological replicates. Finally, we demonstrated the utility of mEPIC probes for data exploration such as hierarchical clustering. Conclusions Given the absence of cost and labor convenient genome-wide technologies in the murine system, our findings show that the Infinium MethylationEPIC BeadChip platform is suitable for investigation of the mouse methylome. Furthermore, we provide the “mEPICmanifest” with genomic features, available to users of Infinium Human MethylationEPIC arrays for mouse samples

Comparison of EM-seq and PBAT methylome library methods for low-input DNA

DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples

DNA methylation changes in glial cells of the normal-appearing white matter in Multiple Sclerosis patients

Multiple Sclerosis (MS), the leading cause of non-traumatic neurological disability in young adults, is a chronic inflammatory and neurodegenerative disease of the central nervous system (CNS). Due to the poor accessibility to the target organ, CNS-confined processes underpinning the later progressive form of MS remain elusive thereby limiting treatment options. We aimed to examine DNA methylation, a stable epigenetic mark of genome activity, in glial cells to capture relevant molecular changes underlying MS neuropathology. We profiled DNA methylation in nuclei of non-neuronal cells, isolated from 38 post-mortem normal-appearing white matter (NAWM) specimens of MS patients (n = 8) in comparison to white matter of control individuals (n = 14), using Infinium MethylationEPIC BeadChip. We identified 1,226 significant (genome-wide adjusted P-value < 0.05) differentially methylated positions (DMPs) between MS patients and controls. Functional annotation of the altered DMP-genes uncovered alterations of processes related to cellular motility, cytoskeleton dynamics, metabolic processes, synaptic support, neuroinflammation and signaling, such as Wnt and TGF-β pathways. A fraction of the affected genes displayed transcriptional differences in the brain of MS patients, as reported by publically available transcriptomic data. Cell type-restricted annotation of DMP-genes attributed alterations of cytoskeleton rearrangement and extracellular matrix remodelling to all glial cell types, while some processes, including ion transport, Wnt/TGF-β signaling and immune processes were more specifically linked to oligodendrocytes, astrocytes and microglial cells, respectively. Our findings strongly suggest that NAWM glial cells are highly altered, even in the absence of lesional insult, collectively exhibiting a multicellular reaction in response to diffuse inflammation

TET2 mutations are associated with hypermethylation at key regulatory enhancers in normal and malignant hematopoiesis

TET2 mutations are frequent in myeloid malignancies and in elderly individuals with or without cytopenia. Here, the authors analyse the association between TET2 mutations and methylation changes in healthy elderly twins and patients with cytopenia and compare them to those from leukemia

La Charente

15 mai 18811881/05/15 (A10,N4342)-1881/05/15.Appartient à l’ensemble documentaire : PoitouCh

Competitive repopulation of an empty microglial niche yields functionally distinct subsets of microglia-like cells

Circulating monocytes can compete for virtually any tissue macrophage niche and become long-lived replacements that are phenotypically indistinguishable from their embryonic counterparts. As the factors regulating this process are incompletely understood, we studied niche competition in the brain by depleting microglia with &gt;95% efficiency using Cx3cr1CreER/+R26DTA/+ mice and monitored long-term repopulation. Here we show that the microglial niche is repopulated within weeks by a combination of local proliferation of CX3CR1+F4/80lowClec12a– microglia and infiltration of CX3CR1+F4/80hiClec12a+ macrophages that arise directly from Ly6Chi monocytes. This colonization is independent of blood brain barrier breakdown, paralleled by vascular activation, and regulated by type I interferon. Ly6Chi monocytes upregulate microglia gene expression and adopt microglia DNA methylation signatures, but retain a distinct gene signature from proliferating microglia, displaying altered surface marker expression, phagocytic capacity and cytokine production. Our results demonstrate that monocytes are imprinted by the CNS microenvironment but remain transcriptionally, epigenetically and functionally distinct