AbstractBackgroundFrontotemporal lobar degeneration (FTLD) is an umbrella term describing the neuropathology of a clinically, genetically and pathologically heterogeneous group of diseases, which includes frontotemporal dementia and progressive supranuclear palsy. About 90% of the FTLD cases show either TDP‐43 or tau pathology (FTLD‐TDP or FTLD‐tau, respectively). Though aberrant brain DNA methylation has consistently been associated with Alzheimer’s disease and other neurodegenerative diseases, studies on FTLD are scarce. The main goal of this study was to investigate DNA methylation variation in FTLD bulk brain tissue and brain‐derived nuclei.MethodsWe used bulk frontal cortex genome‐wide DNA methylation profiles (Illumina 450K or EPIC microarrays) from three FTLD cohorts (N = 228). To identify unique and shared differentially methylated loci across FTLD subgroups/subtypes, we performed cohort‐specific epigenome‐wide association studies (EWAS) followed by a meta‐analysis. Additionally, we used weighted gene correlation network analysis to identify co‐methylation signatures associated with FTLD, FTLD pathological subtypes, and other disease‐related traits. To identify disturbed cell‐types and biological processes within disease associated signatures, we then carried out cell‐type and functional enrichment analyses. We also generated and have ongoing analysis of DNA methylation profiles (EPIC microarrays) of neuronal (NeuN+) and glial nuclei (NeuN‐) from FTLD‐TDP cases and controls (N = 40). Wherever possible, we also integrated additional DNA methylation, and gene and protein expression datasets.ResultsIn bulk tissue, the EWAS meta‐analysis identified four shared differentially methylated loci in FTLD, including hypomethylation in OTUD4, a gene we found to be upregulated (mRNA and protein) in FTLD. Two of the four meta‐analysis hits (mapping to OTUD4 and CEBPZ), were found to be co‐methylated within signatures strongly associated with FTLD. Disease‐associated signatures implicate transcription regulation, the ubiquitin system, RNA/stress granule formation and glutamatergic synaptic signalling, and specific brain cell‐types, including pyramidal neurons and oligodendrocytes, in FTLD. Preliminary analysis of the neuronal and glial datasets also revealed FTLD‐associated DNA methylation signatures, which will further inform on cell‐type‐specific changes in FTLD.ConclusionsOur findings identified novel FTLD‐associated loci, including OTUD4, and point to DNA methylation as an important mechanism in the dysregulation of biological processes relevant to the FTLD pathogenesis, such as RNA/stress granule formation.
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