Exploring the Genetic Predisposition to Epigenetic Changes in Alzheimer's Disease

Abnormal epigenetic modification of lysosome and lipid regulating genes in Alzheimer's disease

BackgroundAbnormal lipid metabolism has been identified as a potential pathogenic mechanism of Alzheimer's disease (AD), which might be epigenetically regulated. Lysosomes are critical organelles for lipid metabolism. However, the epigenetic modifications of lysosome and lipid regulating genes remain unclear in AD patients.ObjectiveExplore the role of abnormal epigenetic modifications, especially methylation of lysosome and lipid metabolism-related genes in AD.MethodsMethylation beadchip and MALDI-TOF mass spectrometry were used to detect genome-wide DNA methylation levels and validate key gene methylation, respectively. Clinical data were collected from all participants. Associations between clinical biochemical characteristics and altered DNA methylation in AD patients were analyzed, and a risk factor model of AD was established.Results41 differentially methylated positions (DMPs) corresponding to 33 genes were identified in AD patients, with 18 hypermethylated and 23 hypomethylated positions. Significant alterations were observed in lipid regulating genes (CTNNB1, DGKQ, SLC27A1) and lysosomal transmembrane gene (TMEM175). Clinical analysis revealed that TP, ALB, IB, ADA, ALP, HCY, GLU, TC, BUN, HDL-C, LDL-C, and APOA1 levels were significantly higher in AD patients, whereas A/G and DB levels were lower. TMEM175 hypermethylation was further verified and found to correlate with TC, HDL-C, LDL-C, APOA1, IB, and HCY. The AUC of the AD risk model, which integrated clinical lipid markers and TMEM175 methylation, reached 0.9519 (p < 0.0001).ConclusionsAbnormal epigenetic regulation of lysosomal gene and lipid dyshomeostasis were high-risk factors in AD. Methylation modifications of lysosome and lipid regulating genes might be key processes in AD pathogenesis.

Proximity labeling of the Tau repeat domain enriches RNA-binding proteins that are altered in Alzheimer's disease and related tauopathies

In Alzheimer's disease (AD) and other tauopathies, tau dissociates from microtubules and forms toxic aggregates that contribute to neurodegeneration. Although some of the pathological interactions of tau have been identified from postmortem brain tissue, these studies are limited by their inability to capture transient interactions. To investigate the interactome of aggregate-prone fragments of tau, we applied an in vitro proximity labeling technique using split TurboID biotin ligase (sTurbo) fused with the tau microtubule repeat domain (TauRD), a core region implicated in tau aggregation. We characterized sTurbo TauRD co-expression, robust enzyme activity and nuclear and cytoplasmic localization in a human cell line. Following enrichment of biotinylated proteins and mass spectrometry, we identified over 700 TauRD interactors. Gene ontology analysis of enriched TauRD interactors highlighted processes often dysregulated in tauopathies, including spliceosome complexes, RNA-binding proteins (RBPs), and nuclear speckles. The disease relevance of these interactors was supported by integrating recombinant TauRD interactome data with human AD tau interactome datasets and protein co-expression networks from individuals with AD and related tauopathies. This revealed an overlap with the TauRD interactome and several modules enriched with RBPs and increased in AD and Progressive Supranuclear Palsy (PSP). These findings emphasize the importance of nuclear pathways in tau pathology, such as RNA splicing and nuclear-cytoplasmic transport and establish the sTurbo TauRD system as a valuable tool for exploring the tau interactome.

Evolutionary feedback from the environment shapes mechanisms that generate genome variation

Darwin recognized that 'a grand and almost untrodden field of inquiry will be opened, on the causes and laws of variation.' However, because the Modern Synthesis assumes that the intrinsic probability of any individual mutation is unrelated to that mutation's potential adaptive value, attention has been focused on selection rather than on the intrinsic generation of variation. Yet many examples illustrate that the term 'random' mutation, as widely understood, is inaccurate. The probabilities of distinct classes of variation are neither evenly distributed across a genome nor invariant over time, nor unrelated to their potential adaptive value. Because selection acts upon variation, multiple biochemical mechanisms can and have evolved that increase the relative probability of adaptive mutations. In effect, the generation of heritable variation is in a feedback loop with selection, such that those mechanisms that tend to generate variants that survive recurring challenges in the environment would be captured by this survival and thus inherited and accumulated within lineages of genomes. Moreover, because genome variation is affected by a wide range of biochemical processes, genome variation can be regulated. Biochemical mechanisms that sense stress, from lack of nutrients to DNA damage, can increase the probability of specific classes of variation. A deeper understanding of evolution involves attention to the evolution of, and environmental influences upon, the intrinsic variation generated in gametes, in other words upon the biochemical mechanisms that generate variation across generations. These concepts have profound implications for the types of questions that can and should be asked, as omics databases become more comprehensive, detection methods more sensitive, and computation and experimental analyses even more high throughput and thus capable of revealing the intrinsic generation of variation in individual gametes. These concepts also have profound implications for evolutionary theory, which, upon reflection it will be argued, predicts that selection would increase the probability of generating adaptive mutations, in other words, predicts that the ability to evolve itself evolves.

The Role of microRNAs in Epigenetic Regulation of Signaling Pathways in Neurological Pathologies

In recent times, there has been a significant increase in researchers' interest in the functions of microRNAs and the role of these molecules in the pathogenesis of many multifactorial diseases. This is related to the diagnostic and prognostic potential of microRNA expression levels as well as the prospects of using it in personalized targeted therapy. This review of the literature analyzes existing scientific data on the involvement of microRNAs in the molecular and cellular mechanisms underlying the development of pathologies such as Alzheimer's disease, cerebral ischemia and reperfusion injury, and dysfunction of the blood-brain barrier.