Chronological age by itself is an outdated clinical measurement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 patients who had strong clinical risk factors for an osteoporotic fracture (particularly age) but had T scores in the osteopenic range.

The average age of the participants in the current trial was approximately 3.5 years older than that in the Fracture Intervention Trial. Owing to the interaction between age and bone mineral density, the results of the current trial should not be extrapolated to younger postmenopausal women (50 to 64 years of age) with osteopenia.

This trial reminds us that risk assessment and treatment decisions go well beyond bone mineral density and should focus particularly on age and a history of previous fractures.”


The time has passed for physicians and clinicians to consider only chronological age when evaluating a patient’s clinical age. More effective human age measurements covering the entire person as well as their body’s components include:

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This editorial provided the history of how a still-generally-accepted set of diagnostic measurements were selected for their relative convenience instead of chosen for their efficacy. Add chronological age to such ineffective measurements.

Let’s recognize better aging and diagnostic measurements, then incorporate them. How else will we advance past uninformative averaging and unhelpful recommendations based on chronological age?

“The average age of the participants in the current trial was approximately 3.5 years older than that in the Fracture Intervention Trial. Owing to the interaction between age and bone mineral density, the results of the current trial should not be extrapolated to younger postmenopausal women (50 to 64 years of age) with osteopenia.”

https://www.nejm.org/doi/pdf/10.1056/NEJMe1812434 “A Not-So-New Treatment for Old Bones”

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A slanted view of the epigenetic clock

The founder of the epigenetic clock technique was interviewed for MIT Technology Review:

“We need to find ways to keep people healthier longer,” he says. He hopes that refinements to his clock will soon make it precise enough to reflect changes in lifestyle and behavior.”


The journalist attempted to dumb the subject down “for the rest of us” with distortions such as the headline. The varying correlation of epigenetic age to chronological age was somewhat better reported in the story:

“The epigenetic clock is more accurate the younger a person is. It’s especially inaccurate for the very old.”

The journalist inappropriately used luck as a synonym for randomness/stochasticity:

“He estimates that about 40% of the ticking rate is determined by genetic inheritance, and the rest by lifestyle and luck.”

A third example of less-than-straightforward journalism started with:

“Such personalization raises questions about fairness. If your epigenetic clock is ticking faster through no fault of your own..”

Were MIT Technology Review readers unable to comprehend a straightforward story on the epigenetic clock? What was the purpose of slants and distortions in an introductory article?

https://www.technologyreview.com/s/612256/want-to-know-when-youre-going-to-die/ “Want to know when you’re going to die?”

Epigenetic transgenerational inheritance of ovarian disease

This 2018 Washington rodent study investigated ovarian disease in F3 great-granddaughters caused by their F0 great-grandmothers’ exposures to DDT or vinclozolin while pregnant:

“Two of the most prevalent ovarian diseases affecting women’s fertility and health are Primary Ovarian Insufficiency (POI) and Polycystic Ovarian Syndrome (PCOS). POI is characterized by a marked reduction in the primordial follicle pool of oocytes and the induction of menopause prior to age 40. POI currently affects approximately 1% of female population. While genetic causes can be ascribed to a minority of patients, around 90% of POI cases are considered idiopathic, with no apparent genetic link nor known cause.

PCOS is a multi-faceted disease that affects 6-18% of women. It is characterized by infrequent ovulation or anovulation, high androgen levels in the blood, and the presence of multiple persistent ovarian cysts.

For both PCOS and POI other underlying causes such as epigenetic transgenerational inheritance of disease susceptibility have seldom been considered. Epigenetic transgenerational inheritance is defined as “the germline transmission of epigenetic information and phenotypic change across generations in the absence of any continued direct environmental exposure or genetic manipulation.” Epigenetic factors include:

  • DNA methylation,
  • Histone modifications,
  • Expression of noncoding RNA,
  • RNA methylation, and
  • Alterations in chromatin structure.

The majority of transgenerational studies have examined sperm transmission of epigenetic changes due to limitations in oocyte numbers for efficient analysis.

There was no increase in ovarian disease in direct fetal exposed F1 [grandmothers] or germline exposed F2 [mothers] generation vinclozolin or DDT lineage rats compared to controls.

The transgenerational molecular mechanism is distinct and involves the germline (sperm or egg) having an altered epigenome that following fertilization may modify the embryonic stem cells epigenome and transcriptome. This subsequently impacts the epigenetics and transcriptome of all somatic cell types derived from these stem cells.

Therefore, all somatic cells in the transgenerational [F3] animal have altered epigenomes and transcriptomes and those sensitive to this alteration will be susceptible to develop disease. The F3 generation can have disease while the F1 and F2 generations do not, due to this difference in the molecular mechanisms involved.

The epimutations and gene expression differences observed are present in granulosa cells in the late pubertal female rats at 22-24 days of age, which is long before any visible signs of ovarian disease are detectable. This indicates that the underlying factors that can contribute to adult-onset diseases like PCOS and POI appear to be present early in life.

Ancestral exposure to toxicants is a risk factor that must be considered in the molecular etiology of ovarian disease.”


1. The study highlighted a great opportunity for researchers of any disease that frequently has an “idiopathic” diagnosis. It said a lot about research priorities that “around 90% of POI cases are considered idiopathic, with no apparent genetic link nor known cause.”

It isn’t sufficiently explanatory for physicians to continue using categorization terminology from thousands of years ago. Science has progressed enough with measured evidence to discard the “idiopathic” category and express probabilistic understanding of causes.

2. One of this study’s coauthors made a point worth repeating in The imperative of human transgenerational studies: What’s keeping researchers from making a significant difference in their fields with human epigenetic transgenerational inheritance studies?

3. Parts of the study’s Discussion section weren’t supported by its evidence. The study didn’t demonstrate:

  • That “all somatic cells in the transgenerational animal have altered epigenomes and transcriptomes”; and
  • The particular “molecular mechanisms involved” that exactly explain why “the F3 generation can have disease while the F1 and F2 generations do not.”

https://www.tandfonline.com/doi/abs/10.1080/15592294.2018.1521223 “Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Ovarian Pathology and Granulosa Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Polycystic Ovarian Syndrome and Primary Ovarian Insuf[f]iency” (not freely available)

The imperative of human transgenerational studies

The coauthor of:

pointed out the opportunity for the researchers of A seasonal epigenetic effect of conception on BMI to have their work make a difference in their field:

“The ability of environmental epigenetics to promote an adaptive phenotype to cold has impacts on evolution. However, the impacts would be far greater if the phenomenon was transgenerational.

Future studies are now needed to determine whether the cold-induced thrifty metabolic phenotype is transmitted to subsequent generations. If exposure not only impacts the health of offspring, but also of all subsequent generations, the impact is significant.”


Every human alive today has observable lasting epigenetic effects caused by environmental factors:

  • During the earliest parts of our lives;
  • From our parents’ exposures and experiences before we’re conceived – many of which are inadequately researched; and
  • Potentially from some of our earlier ancestors’ exposures and experiences.

Aren’t animal studies’ evidence for epigenetic transgenerational inheritance sufficient to compel serious human follow-on research efforts by research sponsors and study designers? The same comments about epigenetic effects caused by temperature potentially inherited by multiple human generations can also be made about other environmental factors, such as:

  • Nutrition,
  • Toxins – the commentator’s usual area of study, and
  • Stress.

I hope that these researchers value their professions enough to make a difference with this or other areas of their expertise. And that sponsors won’t thwart researchers’ desires for difference-making science by putting them into endless funding queues.

https://www.nature.com/articles/s41591-018-0187-3 “Preconception cold–induced epigenetic inheritance” (not freely available)

Reversing epigenetic changes with CRISPR/Cas9

This 2018 Chinese review highlighted areas in which CRISPR/Cas9 technology has, is, and could be applied to rewrite epigenetic changes:

“CRISPR/Cas9-mediated epigenome editing holds a great promise for epigenetic studies and therapeutics.

It could be used to selectively modify epigenetic marks at a given locus to explore mechanisms of how targeted epigenetic alterations would affect transcription regulation and cause subsequent phenotype changes. For example, inducing histone methylation or acetylation at the Fosb locus in the mice brain reward region, nucleus accumbens, could affect relevant transcription network and thus control behavioral responses evoked by drug and stress.

Epigenome editing has the potential for epigenetic treatment, especially for the disorders with abnormal gene imprinting or epigenetic marks. Targeted epigenetic silencing or reactivation of the mutant allele could be a potential therapeutic approach for diseases such as Rett syndrome and Huntington’s disease.

Noncoding RNA plays important roles in gene imprinting and chromatin remodeling. CRISPR/Cas9 has been shown to be potential for manipulating noncoding RNA expression, including microRNA, long noncoding RNA, and miRNA families and clusters.

In vivo overexpression of the Yamanaka factors have proven to be able to fully or partially help somatic cells to regain pluripotency in situ. These rejuvenated cells would subsequently differentiate again to replace the lost cell types.”


The last paragraph was described in The epigenetic clock theory of aging as a promising technique:

“To date, the most effective in vitro intervention against epigenetic ageing is achieved through expression of Yamanaka factors, which convert somatic cells into pluripotent stem cells, thereby completely resetting the epigenetic clock.”

The reviewers cited three references for in vivo studies of this technique. Overall, I didn’t see that any of the review’s references were in vivo human studies.

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6079388/ “Novel Epigenetic Techniques Provided by the CRISPR/Cas9 System”

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, glia, brain, liver, and bone samples.

The skin & blood clock outperforms widely used existing biomarkers when it comes to accurately measuring the age of an individual based on DNA extracted from skin, dermis, epidermis, blood, saliva, buccal swabs, and endothelial cells. Thus, the biomarker can also be used for forensic and biomedical applications involving human specimens.

The biomarker applies to the entire age span starting from newborns, e.g. DNAm of cord blood samples correlates with gestational week.

Furthermore, the skin & blood clock confirms the effect of lifestyle and demographic variables on epigenetic aging. Essentially it highlights a significant trend of accelerated epigenetic aging with sub-clinical indicators of poor health.

Conversely, reduced aging rate is correlated with known health-improving features such as physical exercise, fish consumption, high carotenoid levels. As with the other age predictors, the skin & blood clock is also able to predict time to death.

Collectively, these features show that while the skin & blood clock is clearly superior in its performance on skin cells, it crucially retained all the other features that are common to other existing age estimators.”

http://www.aging-us.com/article/101508/text “Epigenetic clock for skin and blood cells applied to Hutchinson Gilford Progeria Syndrome and ex vivo studies”


An introduction to the study highlighted several items:

“Although the skin-blood clock was derived from significantly less samples (~900) than Horvath’s clock (~8000 samples), it was found to more accurately predict chronological age, not only across fibroblasts and skin, but also across blood, buccal and saliva tissue. A potential factor driving this improved accuracy in blood could be related to the approximate 18-fold increase in genomic coverage afforded by using Illumina 450k/850k beadarrays.

It serves as a roadmap for future clock studies, pointing towards the importance of constructing tissue or cell-type specific epigenetic clocks, to more accurately measure biological aging in the given tissue/cell-type, and therefore with the potential to be more informative of disease-risk or the success of disease interventions in the tissue or cell-type of interest.”

http://www.aging-us.com/article/101533/text “Epigenetic clocks galore: a new improved clock predicts age-acceleration in Hutchinson Gilford Progeria Syndrome patients”

Epigenetic factors affecting female rat sexual behavior

This 2018 Baltimore/Montreal rodent study found:

“If sexually naïve females have their formative sexually rewarding experiences paired with the same male, they will recognize that male and display mate-guarding behavior towards him in the presence of a female competitor. Female rats that display mate-guarding behavior also show enhanced activation of oxytocin and vasopressin neurons in the supraoptic and paraventricular hypothalamic nucleus.

We examined the effect of a lysine-specific demethylase-1 inhibitor to block the action of demethylase enzymes and maintain the methylation state of corresponding genes. Female rats treated with the demethylase inhibitor failed to show any measure of mate guarding, whereas females treated with vehicle displayed mate guarding behavior. Demethylase inhibitor treatment also blocked the ability of familiar male cues to activate oxytocin and vasopressin neurons, whereas vehicle-treated females showed this enhanced activation.”

General principles and their study-specific illustrations were:

Histone modifications are a key element in gene regulation through chromatin remodeling. Histone methylation / demethylation does not have straightforward transcriptional outcomes as do other histone modifications, like acetylation, which is almost invariably associated with transcriptional activation.

What is of vital importance in regards to histone methylation / demethylation is the pattern of methylation that is established. Patterns of methylation incorporate both methylated and demethylated residues, and are what ultimately play a role in transcriptional outcomes.

In the present study, inhibiting LSD1 demethylase enzymes disrupted the ability of cells to properly establish histone methylation / demethylation patterns, thus creating a deficit in the cells’ ability to transcribe the gene products necessary for the enhanced induction of OT, AVP, and the subsequent mate-guarding behaviors we observed. This study is the first to demonstrate a definitive role of epigenetic histone modifications in a conditioned sexual response.”

https://www.sciencedirect.com/science/article/pii/S0031938418303421 “Inhibition of lysine-specific demethylase enzyme disrupts sexually conditioned mate guarding in the female rat” (not freely available)