Sex hormones and epigenetic clocks

This 2023 human study investigated associations among sex hormones and epigenetic clocks:

“We studied associations between sex steroid hormones and DNA methylation-based (DNAm) biomarkers of age and mortality risk including Pheno Age Acceleration (AA), Grim AA, and DNAm-based estimators of Plasminogen Activator Inhibitor 1 (PAI1), and leptin concentrations.

Leptin is a peptide hormone and is associated with regulation of food intake and energy balance. Leptin also influences inflammatory processes, angiogenesis, lipolysis, and neuroplasticity.

PAI1 is a protein that is involved in tissue hemostasis. Previous studies that assessed associations between sex hormones and PAI1 protein concentrations in blood reported conflicting results.

DNAm PAI-1 was shown to be a better surrogate for lifespan than the actual plasma measure, and performs better than Grim AA regarding associations with the comorbidity-index. Another potential benefit of using DNAm-based biomarkers instead of plasma biomarkers is that the DNAm-based biomarkers represent a longer average estimate of biomarker concentration, and are not as affected by day-to-day variations that could bias results.

sex hormones and epigenetic clocks

Associations are represented by colored arrows with the lines’ thickness representing association strength. As the association was measured mainly cross-sectional, association directionality cannot be established.

  • Hormone levels were inversely associated with epigenetic estimators of mortality risk.
  • Sex Hormone Binding Globulin (SHBG) was associated with a decrease in DNAm PAI1 among men and women.
  • Higher testosterone and testosterone/estradiol ratio (TE) were associated with lower DNAm PAI and a younger epigenetic age in men.
  • A decrease in DNAm PAI1 is associated with lower mortality and morbidity risk indicating a potential protective effect of testosterone on lifespan and conceivably cardiovascular health via DNAm PAI1. “Higher testosterone and testosterone/estradiol ratio in men are associated with better epigenetic estimators of mortality risk”

Similar to a coauthor’s outstanding A rejuvenation therapy and sulforaphane where he was the lead author, this study may stay in preprint a while because it challenges current paradigms.

Remember that every truth passes through three stages before it’s recognized:

  1. It’s ridiculed; then
  2. It’s opposed; then
  3. It’s regarded as self-evident.

There may be a long lag between Stages 2 and 3 to memory-hole a fading paradigm’s damage. Don’t expect apologies, remediation, or restitution.


The goddess of destiny

A 2023 human study investigated exercise, klotho gene, and epigenetic clock relationships:

“Named after the spinner of the thread of life, klotho (KL) is involved in the aging process and may act as an anti-aging hormone in mammals. We hypothesize that circulating KL is correlated with age-associated methylation of the KL gene promoter region, and this is one reason for age-related decline in circulating KL.

202 subjects between ages 37 and 85 were included in the study. A great percentage of volunteers participated in the World Rowing Masters Regatta in Velence, Hungary. They were considered to be the trained group (TRND): n = 131; 80 males: age 59.14 ± 10.8; 51 females: age 57.24 ± 9.4. Results were compared to the sedentary group (SED): n = 71; 27 males: age 55.63 ± 13.4; 44 females: age 61.91 ± 10.5.

Circulating level of KL showed a negative correlation with chronological age in the TRND group, but not in the SED group.

klotho and exercise

Examining the relationship between circulating KL level and PhenoAge and GrimAge, KL is associated with PhenoAge acceleration in the TRND group only. It appears that higher KL can decelerate the DNA methylation-based aging process assessed by PhenoAge.

The present study revealed that circulating KL level is associated with exercise status level and general strength level, and is greatly dependent upon exercise-induced DNA methylation.” “The Circulating Level of Klotho Is Not Dependent upon Physical Fitness and Age-Associated Methylation Increases at the Promoter Region of the Klotho Gene”


Take inulin for your brain

This 2023 rodent study investigated effects of inulin on gut microbiota and brain inflammation:

“Microglia are the first immune responders in the brain. Their activation leading to neuroinflammation can promote homeostasis, but if unchecked can be pathological.

We evaluated anti-inflammatory effects of short-chain fatty acids (SCFAs) on lipopolysaccharide (LPS)-stimulated microglia from mice fed inulin, a soluble fiber fermented by intestinal microbiota to produce SCFAs, and SCFAs applied to primary microglia in vitro:

  • Feeding mice inulin increased SCFAs in the cecum and in plasma collected from the hepatic portal vein.
  • Microglia isolated from mice fed inulin and stimulated with LPS in vitro secreted less tumor necrosis factor α (TNF-α) compared to microglia from mice not given inulin.
  • Mice fed inulin and injected i.p with LPS ex vivo secretion of TNF-α by isolated microglia was lower than that secreted by microglia from mice not fed inulin and injected with LPS.


in vitro treatment of primary microglia with acetate and butyrate either alone or in combination downregulated microglia cytokine production, with effects being additive. SCFAs reduced histone deacetylase activity and nuclear factor-κB nuclear translocation after LPS treatment in vitro.

If SCFAs produced in the gut regulate microglia directly, it is likely through an epigenetic mechanism following diffusion.” “Inhibition of inflammatory microglia by dietary fiber and short-chain fatty acids”

Mice typically eat 4-5 grams of chow daily. A human equivalent of this study’s 2.5% inulin treatment would be:

  • (5,000 mg x .025) = 125 mg;
  • (125 mg x .081) = 10.125 mg;
  • (10.125 mg x 70 kg) = 709 mg.

A daily intake of < 1 gram of inulin isn’t very much. I take < 10 grams.


Week 148 of Changing to a youthful phenotype with sprouts

Ending the week with a thorough 2023 study of microwaving broccoli in a bag:

“Appropriate processing and cooking technologies can effectively improve the content of bioactive compounds in vegetables. Effects of microwave bag cooking on broccoli floret quality attributes, glucosinolates (GLSs) content and hydrolysate production were investigated in this study.

Microwave bag cooking preserved the color of florets, enhanced total phenolic and flavonoid content, as well as total chlorophyll and ascorbic acid content. The majority of microorganisms were inactivated. Floret structure was greatly altered, enhancing antioxidant capacity and promoting release of GLSs and myrosinase activity.

Fresh broccoli (Brassica oleracea L. var. italica) was purchased from a local market. Broccoli balls with uniform size, no pests and no mechanical damage were selected for the experiment. Broccoli was washed with deionized water and dried naturally before being cut at about 1 cm below the flower head. The microwave bag was filled with 25 g florets and sealed with a heat sealer.

To the best of our knowledge, microwave bag cooking was evaluated for the first time to explore effects on sulforaphane (SFN) and indole-3-carbinol (I3C) content. Microwave bag cooking at 400 W for 10 s resulted in the highest SFN content (870.18 ± 19.14 μg/g), which was about 3.99 times that of untreated florets.

sfn content

Microwave bag cooking at 800 W for 10 s resulted in the highest I3C content, which was 6.16 times that of untreated florets.

i3c content

Our findings demonstrated that I3C in supplements or vegetables also degraded quickly under various processing conditions, such as thermal processing, and that DIM and LTr1 were not only produced in acidic conditions. This filled a gap in the literature regarding effects of vegetable processing, particularly thermal treatment, on content of glucobrassicin degradation products. In brief, under suitable conditions of microwave bag cooking, content of indole hydrolyzate I3C can be significantly increased, whereas content of dimerization and trimerization products did not change as significantly as I3C.

This work demonstrated that microwave bag cooking was a quick and easy cooking method that could preserve potential health benefits of broccoli florets while also satisfying the needs of modern consumers.” “Microwave bag cooking affects the quality, glucosinolates content and hydrolysate production of broccoli florets” (not freely available) Thanks to Professor Lei Zheng for providing a copy.

Can’t replicate this study’s cooking method completely. Ziploc bags are microwavable but a little different than heat-sealed bags. I also grow a broccoli / red cabbage / mustard sprout mix.

Using 25 grams of the mix and 40% power on my 1000W microwave for 10 seconds produced a sharper taste than did the method I’ve used. Scooping the mix out of a quart bag was messy.

I put the next 25 grams on a microwavable plate that snugly fit into a sealed bag. 80% power on a 1000W microwave for 10 seconds definitely tastes more cooked.


I’ll alternate between 400W and 800W for a while to see which one I prefer. It’s as quick and easy as claimed.


Ancient parasite DNA within us

Two 2023 papers on endogenous retroviruses (ERVs) and aging relationships, starting with the Introduction section of a comprehensive study:

“Several causal determinants of aging-related molecular changes have been identified, such as epigenetic alterations and stimulation of senescence-associated secretory phenotype (SASP) factors. Although the majority of these studies describe aging determinants originating primarily from protein-coding genes, the non-coding part of the genome has started to garner attention as well.

ERVs belonging to long terminal repeat (LTR) retrotransposons are a relic of ancient retroviral infection, fixed in the genome during evolution, comprising about 8% of the human genome. As a result of evolutionary pressure, most human ERVs (HERVs) accumulate mutations and deletions that prevent their replication and transposition function. However, some evolutionarily young subfamilies of HERV proviruses, such as the recently integrated HERVK, maintain open reading frames encoding proteins required for viral particle formation.

In this study, using cross-species models and multiple techniques, we revealed an uncharacterized role of endogenous retrovirus resurrection as a biomarker and driver for aging. Specifically, we identified endogenous retrovirus expression associated with cellular and tissue aging and that the accumulation of HERVK retrovirus-like particles (RVLPs) mediates the aging-promoting effects in recipient cells. More importantly, we can inhibit endogenous retrovirus-mediated pro-senescence effects to alleviate cellular senescence and tissue degeneration in vivo, suggesting possibilities for developing therapeutic strategies to treat aging-related disorders.” “Resurrection of endogenous retroviruses during aging reinforces senescence”

This first paper’s foreword summarized their many experiments and findings:

“The study found that HERVK transcripts, viral proteins, and RVLPs were highly activated in prematurely aged human mesenchymal progenitor cells (hPMCs). This was similarly observed in aged human primary fibroblasts and hPMCs. They also discovered that decreasing silencing epigenetic marks DNA methylation and H3K9me3 while increasing H3K36me3 enabled HERVK expression.

erv aging mechanism

These observations also raise several intriguing questions:

  • HERVK is occasionally activated and eventually suppressed under physiological conditions, for example, in human embryonic cells. It would be fascinating to probe the possibility of mimicking physiological conditions in order to turn off the positive feedback between HERVK and senescence.
  • ERVs are hallmarks of aging in different species, including human, primate, and mouse. Future quantification of the absolute physiological level of ERVs across a broad population of various ages might provide further insights into the relationship between ERVs and organismal age.” “Endogenous retroviruses make aging go viral”

Previously curated papers on these subjects include:

A study of our evolutionary remnants

“Repressive epigenetic marks associated with ERVs, particularly LTRs, show a remarkable switch in silencing mechanisms, depending on evolutionary age:

  • Young LTRs tend to be CpG-rich and are mainly suppressed by DNA methylation, whereas
  • Intermediate age LTRs are associated predominantly with histone modifications, particularly histone H3 lysine 9 (H3K9) methylation.
  • Evolutionarily old LTRs are more likely inactivated by accumulation of loss-of-function genetic mutations.”

Starving awakens ancient parasite DNA within us

Reality is sometimes stranger than what fiction writers dream up. 🙂


Improve your internal environment, improve its constituents’ functions

A third update to Signaling pathways and aging:

“Sima, who was born on 28 February 2019, has lived for 47 months, surpassing the 45.5 months believed to be the oldest age recorded in scientific literature for a female Sprague-Dawley rat, the researchers say. So far, Sima has outlived her closest rival in the study by nearly six months.

‘The real point of our experiments is not so much to extend lifespan, but to extend youthspan, to rejuvenate people, to make their golden years really potentially golden years, instead of years of pain and decrepitude,’ Katcher said. ‘But the fact is, if you manage to do that, you also manage to lengthen life, and that’s not a bad side-effect.'” “Anti-ageing scientists extend lifespan of oldest living lab rat”

Whale funeral


Environmental signaling rescues aging muscle stem cells

This 2023 rodent study applied An environmental signaling paradigm of aging concepts to muscle stem cells:

“The stem cell niche environment represents an important therapeutic target to enhance tissue regeneration in aging. We decoupled age-related cell-intrinsic effects, niche-mediated cell-extrinsic effects, and changes in population dynamics of muscle stem cells (MuSCs) and two key muscle-resident cells in young and aged mice.

in vivo model

We showed that:

  1. Age-related reduction in MuSCs is not stochastic.
  2. Despite differences in transcriptomes of MuSC clusters, the effect of age on gene expression is largely uniform, suggesting that the niche environment has a fundamental role in age-related changes in MuSC gene expression.
  3. A significant fraction of changes in the transcriptome of aging MuSCs can be reversed by exposure to the young muscle environment, i.e. are niche-responsive. Given the high percentage [46.6% at a stringent cutoff of s-value < 0.05] of reversibility in gene expression, our findings indicate that age-related changes in the niche are principal drivers of resulting alterations in the MuSC transcriptome.
  4. Aging is correlated with changes at the level of chromatin accessibility and DNA methylation in MuSCs.

Plasticity of the MuSC transcriptome suggests that modulating the niche environment can be a powerful tool to restore stem cell-mediated endogenous muscle regeneration in aging. Consequently, as opposed to focusing solely on MuSCs themselves to mitigate effects of aging on MuSCs, bioengineering of the niche in its entirety may be a viable therapeutic option.” “Transcriptional reprogramming of skeletal muscle stem cells by the niche environment”

This study destroyed extremely well-funded directed research efforts that detract from science, especially those promoting irreversibility of epigenetic changes (but: Rockefeller) and randomness of pro-aging programming (but: Harvard).

These researchers showed they could do more with their ideas and careers than maintain an outdated and easily disproved status quo.

Eat broccoli sprouts to protect your brain from stroke

Starting this blog’s ninth year with a 2022 rodent study of sulforaphane neuroprotection:

“An example of endogenous neuroprotection is ischemia-resistance of the hippocampal regions comprising the CA2, CA3, CA4 and dentate gyrus subfields (here abbreviated to CA2-4,DG) which can be contrasted with the ischemia-vulnerable CA1 region, which is noted in rodents as well as humans.

As with CA2-4,DG, nuclear Nrf2 levels are also higher in the olfactory bulb, while in the cortex, striatum, and cerebellum, they are similar to ones observed in the CA1 region.

brain area comparative Nrf2 activity

We found an in vitro dose-dependent response to administration of sulforaphane on neuronal viability, with an optimal effect noted where the dose was 10 µM. A protective effect was also evident in vivo when a single 5 mg/kg dose of sulforaphane was administered intraperitoneally with delay to ischemia.

Morphology of the CA1 region stratum pyramidale was significantly improved in comparison to ischemia-operated group, with mean numbers of proper cells being 35 ± 19 and 20 ± 7, respectively, for subjects injected during ischemia or 30 min into reperfusion. Morphology of the CA2-4,DG region did not reveal change between the ischemia-operated, SFN-injected, and control groups.

We suggest that high levels of nuclear Nrf2 activity in CA2-4,DG may guarantee resistance of this region to I/R episode, while at the same time offering a potential explanation for the phenomenon of differential sensitivities of hippocampal regions. Our results are in line with the existing view that Nrf2 activation may represent a promising therapeutic strategy against cerebral ischemia.

The uniqueness of Nrf2 lies in its pleiotropic action and subsequent regulation of multiple cytoprotective pathways. This may support more efficient neuroprotection compared to single-target strategies.” “Is Nrf2 Behind Endogenous Neuroprotection of the Hippocampal CA2-4,DG Region?”

Winter beach shock therapy