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 a clone of cells destined to become cancer..

It is plausible that the stochastic process inherent in epigenetic drift can induce aberrant methylation events that accumulate in normal cells and eventually induce cancer formation.

Epigenetic drift relates to a biological process that changes the DNA methylome with age via stochastic gains or losses of DNA methylation. Epigenetic drift can be understood in terms of errors in DNA methylation maintenance during DNA-replication.

The phenomenon of (epi)genetic drift is generally associated with phenotypic neutrality.

For patients who develop cancer around age 80, the most likely initiation time for the founder adenoma cell is predicted to be very early in life, roughly between the ages 15 to 20 years. This unexpected and provocative finding suggests that the optimal age-range for prevention of colorectal cancer may be in adolescence and early adulthood (and ideally through lifelong) dietary and lifestyle interventions.”


The reviewers’ strawman arguments intentionally mischaracterized aspects of the epigenetic clock. For instance, the epigenetic clock founder’s actual view on aging was declared in 2018’s The epigenetic clock theory of aging as:

“The proposed epigenetic clock theory of ageing views biological ageing as an unintended consequence of both developmental programmes and maintenance programmes, the molecular footprints of which give rise to DNAm age estimators.”

The reader wasn’t presented this information, presumably because the epigenetic clock founder’s intrinsic view conflicted with the review’s above graphic and other mischaracterizations.

Another misrepresentation was:

“In contrast to epigenetic clocks, epigenetic drift refers to a stochastic process that involves both gains and losses of the methylation state of CpG dinucleotides over time.”

A reader of the original 2013 epigenetic clock study would understand that epigenetic clocks measure “both gains and losses of methylation” as in:

“The DNA methylation levels of 193 of these markers increase with age but the remaining 160 markers show the opposite behavior.”

Who did the reviewers intend to fool with the false contrast? The real contrast was that – contrary to epigenetic drift’s randomness premise – epigenetic clocks demonstrate programmed phenomena.

Was the pressure to publish so great that the reviewers couldn’t first thoroughly educate themselves about recent developments with the epigenetic clock? For example, there was no mention of the GrimAge epigenetic clock in Statistical inferences vs. biological realities, although that study was available before this paper was initially submitted.

Epigenetic drift as the cause of aging and disease has abundant contrary evidence. The reviewers acknowledged a small bit towards the end of their directed narrative:

“We found only a small number of drift-related CpG island-gene pairs for which drift correlated positively and significantly with gene expression.

The functional consequences of epigenetic drift need to be further elucidated.”

https://cancerres.aacrjournals.org/content/early/2019/11/06/0008-5472.CAN-19-0924 “Epigenetic aging: more than just a clock when it comes to cancer” (not freely available)

Epigenetic transgenerational inheritance extends to the great-great-grand offspring

This 2019 rodent study by the Washington State University labs of Dr. Michael Skinner continued to F4 generation great-great-grand offspring, and demonstrated that epigenetic inheritance mechanisms are similar to imprinted genes:

“Epigenetic transgenerational inheritance potentially impacts disease etiology, phenotypic variation, and evolution. An increasing number of environmental factors from nutrition to toxicants have been shown to promote the epigenetic transgenerational inheritance of disease.

Imprinted genes are a special class of genes since their DNA methylation patterns are unchanged over the generation and are not affected by the methylation erasure occurring early in development. The transgenerational epigenetic alterations in the germline appear to be permanently reprogrammed like imprinted genes, and appear protected from this DNA methylation erasure and reprogramming at fertilization in the subsequent generations. Similar to imprinted genes, the epigenetic transgenerational germline epimutations appear to have a methylation erasure in the primordial germ cells involving an epigenetic molecular memory.

Comparison of the transgenerational F3 generation, with the outcross to the F4 generation through the paternal or maternal lineages, allows an assessment of parent-of-origin transmission of disease or pathology. Observations provided examples of the following:

  1. Pathology that required combined contribution of both paternal and maternal alleles to promote disease [testis and ovarian disease];
  2. Pathology that is derived from the opposite sex allele such as father to daughter [kidney disease] or mother to son [prostate disease];
  3. Pathology that is derived from either parent-of-origin alleles independently [obesity];
  4. Pathology that is transmitted within the same sex, such as maternal to daughter [mammary tumor development]; and
  5. Pathology that is observed only following a specific parent-of-origin outcross [both F4 male obesity and F4 female kidney disease in the vinclozolin lineage].”

The study showed that epigenetically inherited legacies extend to the fifth generation. Do any of us know our ancestors’ medical histories back to our great-great-grandparents?

Will toxicologists take their jobs seriously enough to look for possible effects in at least one generation that had no direct toxicant exposure?

https://www.sciencedirect.com/science/article/pii/S0012160619303471 “Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations”

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 measures but some, especially of the amygdaloid microstructure, were best explained by genotype only.

Models including DNA methylation measured in the neonate umbilical cords outcompeted the Gene and Gene x Environment models for the majority of amygdaloid measures and minority of hippocampal measures. The fact that methylation models outcompeted gene x environment models in many instances is compatible with the idea that DNA methylation is a product of GxE.

A genome-wide association study of SNP [single nucleotide polymorphism] interactions with the prenatal environments (GxE) yielded genome wide significance for 13 gene x environment models. The majority (10) explained hippocampal measures in interaction with prenatal maternal mental health and SES [socioeconomic status]. The three genome-wide significant models predicting amygdaloid measures, explained right amygdala volume in interaction with maternal depression.

The transcription factor CUX1 was implicated in the genotypic variation interaction with prenatal maternal health to shape the amygdala. It was also a central node in the subnetworks formed by genes mapping to the CpGs in neonatal umbilical cord DNA methylation data associating with both amygdala and hippocampus structure and substructure.

Our results implicated the glucocorticoid receptor (NR3C1) in population variance of neonatal amygdala structure and microstructure.

Estrogen in the hippocampus affects learning, memory, neurogenesis, synapse density and plasticity. In the brain testosterone is commonly aromatized to estradiol and thus the estrogen receptor mediates not only the effects of estrogen, but also that of testosterone.”

https://onlinelibrary.wiley.com/doi/full/10.1111/gbb.12576 “Neonatal amygdalae and hippocampi are influenced by genotype and prenatal environment, and reflected in the neonatal DNA methylome” (not freely available)

Emotional responses and BDNF methylation

This 2019 German human study found:

“A critical role of BDNF [brain-derived neurotrophic factor] methylation in human amygdala response to negative emotional stimuli, whereby:

  • High BDNF methylation rates were for the first time shown to be associated with a high reactivity in the amygdala; and
  • High BDNF methylation and high amygdala reactivity were associated with low novelty seeking.

There was no interaction or main effect of the Val66Met polymorphism on amygdala reactivity.

Our data adds evidence to the hypothesis that epigenetic modifications of BDNF can result in an endophenotype associated with anxiety and mood disorders. However, since correlations do not prove causality:

  • A direct link between human BDNF mRNA/protein levels, methylation, amygdala reactivity and psychiatric disorders is still missing, demanding further research.
  • Determining the underlying directions of the relations between BDNF methylation, amygdala reactivity, and NS [novelty seeking] cannot be accomplished based on our data and must await further research.

The fact that our results mainly involve the right amygdala is in line with previous studies. Recent reviews suggest a general right hemisphere dominance for all kinds of emotions, and, more specifically, a critical role of the right amygdala in the early assessment of emotional stimuli.

The experimental fMRI paradigm utilized a face‐processing task (faces with anger or fear expressions), alternating with a sensorimotor control task. Harm avoidance, novelty seeking, and reward dependence were measured using the Tridimensional Personality Questionnaire.”

https://onlinelibrary.wiley.com/doi/full/10.1002/hbm.24825 “The role of BDNF methylation and Val 66 Met in amygdala reactivity during emotion processing”

Reversing epigenetic T cell exhaustion

This 2019 worldwide discussion among 18 experts concerned T cell exhaustion:

“‘T cell exhaustion’ is a broad term that has been used to describe the response of T cells to chronic antigen stimulation, first in the setting of chronic viral infection but more recently in response to tumours.

Key questions remain about the potential to reverse the epigenetic programme of exhaustion and how this might affect the persistence of T cell populations.”


There were nearly a dozen viewpoints on “What do we mean by T cell exhaustion and/or dysfunction and how would you define this state?” 🙂

Answers to the question “What are the key controversies and outstanding research questions?” included:

  • “What are the cellular signalling and transcriptional pathways that drive the conversion to an exhausted T cell phenotype, and how can the chromatin and transcriptional changes of exhaustion be reversed in individual exhausted cells?
  • Whether and how we can manipulate signalling pathways to both activate and maintain T cell responses remain open questions, as does the question of whether pharmacological manipulations can reverse the epigenetic changes associated with exhaustion versus expand less-exhausted populations.
  • We need to define better the effects of the microenvironment on the induction of T cell exhaustion, the developmental trajectories of exhaustion and the point at which and extent to which exhaustion can be reversed. Understanding the consequences of unleashing T cells from exhaustion will also be crucial to designing the most effective therapeutic interventions.
  • When and how exhausted T cell populations are formed. The original view that they are terminally differentiated descendants of formerly ‘normal’ effector T cells has been challenged.
  • Whether the predysfunctional T cells themselves, or their more differentiated (and phenotypically dysfunctional) progeny, form the ultimate effector pool for control of human tumours.
  • How do the functions and states (subpopulations) of exhausted T cells change over time? Can the epigenetic state of exhaustion be reversed to form true effector or memory T cells, and is this required for improved cancer immunotherapy?
  • There is no definitive marker for exhausted T cells, although TOX may prove to be useful. Transcriptional profiles are informative, but epigenetic changes are more specific and robust. A major clinical question is whether exhausted T cells can be, or indeed need to be, reprogrammed to achieve therapeutic benefit.”

https://www.nature.com/articles/s41577-019-0221-9 “Defining ‘T cell exhaustion'” (not freely available)

Transgenerational epigenetic inheritance of thyroid hormone sensitivity

My 500th curation is a 2019 Portuguese human study of Azorean islanders:

“This study demonstrates a transgenerational epigenetic inheritance in humans produced by exposure to high TH [thyroid hormone] in fetal life, in the absence of maternal influences secondary to thyrotoxicosis. The inheritance is along the male line.

The present work took advantage of the relatively frequent occurrence of fetal exposure to high TH levels in the Azorean island of São Miguel. This is the consequence of a missense mutation in the THRB gene causing the amino-acid replacement R243Q, resulting in reduced affinity of the TH receptor beta (TRβ) for TH and thus RTHβ.

Its origin has been traced to a couple who lived at the end of the 19th century. F0 represented the third generation and F3 the sixth and seventh generation descendant.”


These researchers provided the first adequately evidenced human transgenerational epigenetic inheritance study! However, the lead sentence in its Abstract wasn’t correct:

“Evidence for transgenerational epigenetic inheritance in humans is still controversial, given the requirement to demonstrate persistence of the phenotype across three generations.”

Although found in this study, there is no “requirement to demonstrate persistence of the phenotype.” Observing the same phenotype in each generation is NOT required for human transgenerational epigenetic inheritance to exist!

Animal transgenerational studies have shown that epigenetic inheritance mechanisms may both express different phenotypes for each generation:

and entirely skip a phenotype in one or more generations!

  • Transgenerational pathological traits induced by prenatal immune activation found a F2 and F3 generation phenotype of impaired sociability, abnormal fear expression and behavioral despair – effects that weren’t present in the F1 offspring;
  • The transgenerational impact of Roundup exposure “Found negligible impacts of glyphosate on the directly exposed F0 generation, or F1 generation offspring pathology. In contrast, dramatic increases in pathologies in the F2 generation grand-offspring, and F3 transgenerational great-grand-offspring were observed.” (a disease phenotype similarly skipped the first offspring generation);
  • Epigenetic transgenerational inheritance mechanisms that lead to prostate disease “There was also no increase in prostate histopathology in the directly exposed F1 or F2 generation.” (a prostate disease phenotype skipped the first two male offspring generations before it was observed in the F3 male offspring); and
  • Epigenetic transgenerational inheritance of ovarian disease “There was no increase in ovarian disease in direct fetal exposed F1 or germline exposed F2 generation. The F3 generation can have disease while the F1 and F2 generations do not, due to this difference in the molecular mechanisms involved.” (an ovarian disease phenotype similarly skipped the first two female offspring generations before it was observed in the F3 female offspring).

Details of epigenetic inheritance mechanisms were provided in Another important transgenerational epigenetic inheritance study. Mechanisms from fetal exposure to the fungicide vinclozolin were compared with mechanisms from fetal DDT exposure, and summarized as:

The fetal exposure initiates a developmental cascade of aberrant epigenetic programming, and does NOT simply induce a specific number of DMRs [DNA methylation regions] that are maintained throughout development.

I emailed references to the studies in the first five above curations to the current study’s corresponding coauthor. They replied “What is the mechanism for the transgenerational inheritance you describe?” and my reply included a link to the sixth curation’s study.

Are there still other transgenerational epigenetically inherited effects due to fetal exposure to high thyroid hormone levels?

https://www.liebertpub.com/doi/full/10.1089/thy.2019.0080 “Reduced Sensitivity to Thyroid Hormone as a Transgenerational Epigenetic Marker Transmitted Along the Human Male Line”

Reversal of aging and immunosenescent trends

The title of this post is essentially the same as the 2019 human clinical trial:

“Epigenetic aging can be reversed in humans. Using a protocol intended to regenerate the thymus, we observed protective immunological changes, improved risk indices for many age‐related diseases, and a mean epigenetic age approximately 1.5 years less than baseline after 1 year of treatment.

This is to our knowledge the first report of an increase, based on an epigenetic age estimator, in predicted human lifespan by means of a currently accessible aging intervention.”

“Example of treatment‐induced change in thymic MRI appearance. Darkening corresponds to replacement of fat with nonadipose tissue. White lines denote the thymic boundary. Volunteer 2 at 0 (a) and 9 (b) months”

https://onlinelibrary.wiley.com/doi/full/10.1111/acel.13028 “Reversal of epigenetic aging and immunosenescent trends in humans”


Here’s a 2017 interview with the clinical trial lead author:

“You might also say that what also happened was to just postpone death from infectious diseases to after 60-65 years of age, which means that the same basic problem still remains.”


The popular press botched the facts as they usually do. I won’t link the UK Independent article because they couldn’t be bothered to even define epigenetic clock correctly.

A science journal article did a better job of explaining the study to readers. However, they often used hyperbole instead of trying to promote understanding.

Josh Mitteldorf’s blog post 1st Age Reversal Results—Is it HGH or Something Else? provided the most informative explanations:

“In 2015, Fahy finally had funding and regulatory approval to replicate his one-man trial in a still-tiny sample of ten men, aged 51-65. That it took so long is an indictment of everything about the way aging research is funded in this country; and not just aging – all medical research is prioritized according to projected profits rather than projected health benefits.”

Take care reading the post’s comments. Both non-scientist (such as Mark, Adrian, and others) and scientist commentators (such as Gustavo, Jeff, and others) attempted to hijack the discussion into their pet theories of reality in which they imagined themselves to be the definitive authorities. My discussion comment – with respect to a Mayo Clinic warning about DHEA – was: “19 instances of the word ‘might’ doesn’t lend itself to credibility.”