Three 2022 papers on methylation epigenetic modifiers, starting with a human study focused on mitochondrial DNA non-CpG methylation involving nucleobases other than guanine (arginine, cytosine, or thymine): “We collected brain tissue in the nucleus accumbens and prefrontal cortex from deceased individuals without (n = 39) and with (n = 14) drug use, and used whole-genome bisulfite sequencing to cover … Continue reading Non-CpG methylation
This 2017 Korean review compared and contrasted CpG and non-CpG DNA methylation: “Non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells. Accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Non-CpG methylation is established during … Continue reading Non-CpG DNA methylation
This 2022 human cell study investigated DNA methylation and aging: “Models based on DNA methylation can be used to predict the age of biological samples, but their interpretability is limited due to the lack of causal inferences. Neither existing epigenetic clocks nor DNA methylation changes are enriched in causal CpG sites. Causal CpGs include similar … Continue reading Measuring epigenetic DNA causes
Two epigenetic clock papers, starting with a 2022 rodent study: “We tested performance of new pan-tissue and liver-specific epigenetic mouse clocks, evaluating how these related to metabolic states, genotype-dependent life expectancy, and methylome entropy. Entropy, a measure of noise and information loss, increases as a function of time and age. In context of the methylome, … Continue reading Epigenetic clocks and entropy
Here are three papers that cited last year’s Part 1. First is a 2021 rodent study investigating a microRNA’s pro-depressive effects: “Depressive rat models were established via chronic unpredicted mild stress (CUMS) treatment. Cognitive function of rats was assessed by a series of behavioral tests. Nrf2 was weakly expressed in CUMS-treated rats, whereas Nrf2 upregulation … Continue reading Eat broccoli sprouts for depression, Part 2
This 2022 study developed new epigenetic clocks: “Maximum lifespan is deemed to be a stable trait in species. The rate of biological function decline (i.e., aging) would be expected to correlate inversely with maximum species lifespan. Although aging and maximum lifespan are intimately intertwined, they nevertheless appear in some investigations to be distinct processes. Some … Continue reading Lifespan Uber Correlation
Two 2021 papers of Nrf2 activation effects on lung diseases, with the first a McGill University review: “Oxidative stress and subsequent activation of Nrf2 have been demonstrated in many human respiratory diseases. The purpose of this review is to summarize involvement of Nrf2 and its inducers in acute respiratory distress syndrome, chronic obstructive pulmonary disease … Continue reading Your lungs and Nrf2 activity
This 2021 rodent study measured sequential liver changes caused by a high-fat diet: “Using a longitudinal mouse study of diet-induced obesity in male mice, we investigated kinetics of hepatic DNA methylation and gene expression compared to those of obesity-induction to assess if they could be causal for development of insulin resistance. We aimed to find … Continue reading Is liver damage reversible?
This 2021 human study used epigenetic clock technology to assess chronic inflammation as a driver of cognitive decline through its effects on brain structure: “An epigenetic measure of C-reactive protein (DNAm CRP) was assembled for each participant. We found that higher inflammatory burden, indexed by DNAm CRP scores, associated with poor cognitive and neuroimaging brain … Continue reading Human agency vs. brain dysfunction
This 2021 review subject was the follow-on condition of chicken pox: “Varicella-zoster virus (VZV) is a pathogenic human alpha herpes virus which is a significant cause of morbidity. VZV causes a primary infection, usually in children, called varicella (chicken pox), following which it establishes ganglionic latency in neurons. Latency is established in ganglia throughout the … Continue reading Endless shingles
This 2021 rodent study developed epigenetic clocks for deer mice: “We have undertaken a genome-wide analysis of DNA methylation in Peromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Analysis involved tails, whole brain, … Continue reading Do genes determine monogamy / polygamy?
Another excellent blog post by Josh Mitteldorf, A New Approach to Methylation Clocks, that curated the same study: “The Levine/Horvath PhenoAge epigenetic clock was calibrated using a combination of metabolic factors that correlate with health, including inflammation, DNA transcription, DNA repair, and mitochondrial activity. Evolution is not an engineer. Living things are not constructed out … Continue reading Part 2 of Improving epigenetic clocks’ signal-to-noise ratio
This 2021 rodent study investigated post-traumatic stress disorder (PTSD) susceptibility: “PTSD is an incapacitating trauma-related disorder, with no reliable therapy. We show distinct DNA methylation profiles of PTSD susceptibility in the nucleus accumbens (NAc). Data analysis revealed overall hypomethylation of different genomic CpG sites in susceptible animals. Is it possible to treat PTSD by targeting … Continue reading PTSD susceptibility?
This 2021 computational study investigated several methods of improving epigenetic clock reliability: “Epigenetic clocks are widely used aging biomarkers calculated from DNA methylation data. Unfortunately, measurements for individual CpGs can be surprisingly unreliable due to technical noise, and this may limit the utility of epigenetic clocks. Noise produces deviations up to 3 to 9 years … Continue reading Improving epigenetic clocks’ signal-to-noise ratio
This 2021 human study found: “We report on a randomized controlled clinical trial conducted among 43 healthy adult males between the ages of 50-72. The 8-week treatment program included diet, sleep, exercise and relaxation guidance, and supplemental probiotics and phytonutrients. This is the first randomized controlled study to suggest that specific diet and lifestyle interventions … Continue reading Repositioning DNA methylation
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