Non-CpG DNA 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

A strawman argument against epigenetic clocks

This 2019 review of epigenetic clocks by Washington cancer researchers repeatedly returned to an argument for randomness as a cause for aging and disease: “A time-dependent stochastic event process, like epigenetic drift, could lead to cancer formation through the accumulation of random epigenetic alterations that, through chance, eventually alter epigenetic driver gene expression leading to … Continue reading A strawman argument against epigenetic clocks

Do genes or maternal environments shape fetal brains?

This 2019 Singapore human study used Diffusion Tensor Imaging on 5-to-17-day old infants to find: “Our findings showed evidence for region-specific effects of genotype and GxE on individual differences in human fetal development of the hippocampus and amygdala. Gene x Environment models outcompeted models containing genotype or environment only, to best explain the majority of … Continue reading Do genes or maternal environments shape fetal brains?

Developmental disorders and the epigenetic clock

This 2019 UK/Canada/Germany human study investigated thirteen developmental disorders to identify genes that changed aspects of the epigenetic clock: “Sotos syndrome accelerates epigenetic aging [+7.64 years]. Sotos syndrome is caused by loss-of-function mutations in the NSD1 gene, which encodes a histone H3 lysine 36 (H3K36) methyltransferase. This leads to a phenotype which can include: Prenatal and … Continue reading Developmental disorders and the epigenetic clock

Epigenetic clock statistics and methods

This 2018 Chinese study was a series of statistical and methodological counter-arguments to a previous epigenetic clock study finding that: “Only [CpG] sites mapping to the ELOVL2 promoter constitute cell and tissue-type independent aDMPs [age-associated differentially methylated positions].” The study used external data sets and the newer epigenetic clock’s fibroblast data in its analyses to … Continue reading Epigenetic clock statistics and methods

Chronological age by itself is an outdated clinical measurement

This 2018 editorial in the New England Journal of Medicine concerned a clinical trial of an osteoporosis treatment: “When measurement of bone density was first introduced 25 years ago, absolute bone mineral density (g per square centimeter) was considered as too onerous for clinicians to understand. Ultimately, these events led to a treatment gap in … Continue reading Chronological age by itself is an outdated clinical measurement

The epigenetic clock now includes skin

The originator of the 2013 epigenetic clock improved its coverage with this 2018 UCLA human study: “We present a new DNA methylation-based biomarker (based on 391 CpGs) that was developed to accurately measure the age of human fibroblasts, keratinocytes, buccal cells, endothelial cells, skin and blood samples. We also observe strong age correlations in sorted neurons, … Continue reading The epigenetic clock now includes skin

Hijacking the epigenetic clock paradigm

This 2018 German human study’s last sentence was: “Additionally we found an association between DNAm [DNA methylation] age acceleration and rLTL [relative leukocyte telomere length], suggesting that this epigenetic clock, at least partially and possibly better than other epigenetic clocks, reflects biological age.” Statements in the study that contradicted, qualified, and limited the concluding sentence … Continue reading Hijacking the epigenetic clock paradigm

Hidden hypotheses of epigenetic studies

This 2018 UK review discussed three pre-existing conditions of epigenetic genome-wide association studies: “Genome-wide technology has facilitated epigenome-wide association studies (EWAS), permitting ‘hypothesis-free’ examinations in relation to adversity and/or mental health problems. Results of EWAS are in fact conditional on several a priori hypotheses: EWAS coverage is sufficient for complex psychiatric problems; Peripheral tissue is … Continue reading Hidden hypotheses of epigenetic studies

Measuring epigenetic changes at a single-cell level

This 2018 Canadian cell study described the development of a single-cell protocol to: “Profile primitive hematopoietic cells of mouse and human origin to identify epigenetically distinct subpopulations. Deep sampling of the CpG content of individual HSCs allowed for the near complete reconstitution of regulatory states from epigenetically defined subpopulations of HSCs and revealed a high … Continue reading Measuring epigenetic changes at a single-cell level