Genetic factors

Epigenetic clock analysis of a clinical trial

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Memory, Stress , , ,

A 2025 paper performed post-hoc epigenetic clock analyses of a supplement and exercise clinical trial completed earlier this decade:

“We report results of a post hoc analysis among 777 participants of the DO-HEALTH trial on the effect of vitamin D (2,000 IU per day) and/or omega-3 (1 g (330 mg EPA plus 660 mg DHA from marine algae) per day) and/or a home exercise program (a strength-training exercise program performed for 30 min three times per week) on four next-generation DNA methylation (DNAm) measures of biological aging (PhenoAge, GrimAge, GrimAge2 and DunedinPACE) over 3 years. Omega-3 alone slowed the DNAm clocks PhenoAge, GrimAge2 and DunedinPACE, and all three treatments had additive benefits on PhenoAge.

Inclusion criteria were age 70 years and older, living at home, having no major health events (no cancer or myocardial infarction) in the 5 years before enrollment, having sufficient mobility to visit the study centers without help and having good cognitive function with a Mini-Mental State Examination score of at least 24. 777 provided consent for these analyses and had samples available after the application of the exclusion criteria. This group of individuals formed our analysis sample, which had the following characteristics: 59% were women; the mean age at baseline was 75 years; 30% had 25-hydroxyvitamin D (25(OH)D) levels of <20 ng ml−1; 53% were healthy agers as defined in the Nurses’ Health Study (free of major chronic diseases, disabilities, cognitive impairments and mental health limitations); and 88% were physically active (29% were active one to three times per week, and 59% were active more than three times per week). The Swiss participant subgroup represents a healthier and more active subgroup within the total DO-HEALTH population.

Overall, from baseline to year 3, standardized effects ranged from 0.16 to 0.32 units (2.9–3.8 months). In summary, our trial indicates a small protective effect of omega-3 treatment on slowing biological aging over 3 years across several clocks, with an additive protective effect of omega-3, vitamin D, and exercise based on PhenoAge.”

https://www.nature.com/articles/s43587-024-00793-y “Individual and additive effects of vitamin D, omega-3 and exercise on DNA methylation clocks of biological aging in older adults from the DO-HEALTH trial”

These epigenetic clock measurements of a subset of trial subjects was interesting, although I didn’t find it particularly relevant to what I do. I take twice as much Vitamin D and omega-3s everyday, do resistance exercises once or twice a week whenever I’ve recovered from the previous session, walk a few miles on the beach if the weather is nice, and other things.

I don’t bother with epigenetic clock measurements anymore because the free one (PhenoAge) is too variable to be personally accurate. For other clocks, it would be meaningless if all I got was a 2-3 month improvement over a three year period like this trial. Studies usually find that the most deficient subjects at the beginning are the ones that show the greatest improvements with effective treatments. Unhealthiness on any epigenetic clock parameter probably wouldn’t be my starting point, so I may not show even a one-month improvement over three years.

Dr. Goodenowe offered his opinion on the paper:

“DHA is a polyunsaturated fatty acid that is essential for maintaining youthful fluidity of the body’s membranes. While our bodies can make DHA from the essential omega-3 dietary fatty acid, as we get older, our ability to make DHA decreases and oxidative stress on our bodies increases. These two factors contribute to our membranes becoming stiffer and less pliable as we age, in other words, ‘older.’

Because getting older and losing function appear to go hand in hand, we equate aging with a loss of function. As such, we think that aging causes this loss of function, like a disease. Instead, the opposite is true, and it’s the loss of function that causes aging. To slow aging you need to focus on maintaining function.”

https://www.prevention.com/health/a63850396/vitamin-exercise-boost-longeivty-study/ “Scientists Find Taking This Vitamin Boosts Longevity, Add Years to Your Life”

Prevention magazine’s editors need to better proof their writers’ work before it gets published. Unlike the headline, the trial had nothing to do with adding years to human lifespan.

Coffee compound effects

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system, Neurochemicals, Serotonin, Stress, Telomeres , ,

Three papers continue Polyphenol Nrf2 activators themes starting with a 2025 review of chlorogenic acid:

“Chlorogenic acid may comprise between 70 and 350 mg per cup of coffee. Chlorogenic acid can reduce reactive oxygen species (ROS) levels via the upregulation of antioxidant enzymes, decreasing oxidative stress/damage due to the action of adaptive hormetic mechanisms. There is also a substantial literature of hormetic dose responses for metabolites of chlorogenic acid, such as caffeic acid and ferulic acid.

Chlorogenic acid-induced hormetic biphasic dose responses in a spectrum of experimental designs:

  1. Responses to direct exposures in a range of cell types;
  2. Preconditioning experiments in which a prior dose of chlorogenic acid protected against a subsequent stressor agent;
  3. Studies that included direct exposure, showing hormesis dose responses and then selecting the optimal hormetic dosage as a preconditioning treatment to protect against a subsequent exposure to a toxic agent; and
  4. A mixed group of experiments in which preconditioning was conducted, including several neuronal cellular models, all showing protection against the subsequent exposure to the toxic agent.

However, in the context of translating experimental data to clinical relevance, the concentrations employed in the majority of the in vitro studies with chlorogenic acid far exceeded transitory peak levels, even in heavy coffee drinkers (i.e., approximately 3 μM). In addition to the use of unrealistically high chlorogenic acid concentrations, exposures were prolonged, ranging from 1 to 3 days. These studies are of limited relevance to humans, a similar concern raised by other researchers involved with polyphenol research.


The present paper has framed the hypothesis that key coffee constituents, such as chlorogenic acid, show hormetic effects in a range of cell types and endpoints. Chlorogenic acid may affect some of the health benefits of coffee drinking via its role in GI tract health and beneficial brain-gut interaction.”

https://www.sciencedirect.com/science/article/abs/pii/S0009279724004897 “Do the hormetic effects of chlorogenic acid mediate some of the beneficial effects of coffee?” (not freely available) Thanks to Dr. Evgenios Agathokleous for providing copies of this and the following paper.

A 2024 review by the same research group was on hormetic effects of caffeic acid:

“Caffeic acid is a polyphenol present in numerous fruits and vegetables, especially in coffee. Diets contain about 5–10 to 50 milligrams per day of caffeic acid while coffee ingestion provides about another 250–600 milligrams per day. For the moderate to heavy coffee drinker this would result in an ingestion of about 600–1000 milligrams of caffeic acid from food and coffee consumption.

The present paper evaluates whether caffeic acid may act as an hormetic agent, mediating its chemoprotective effects as has been shown for related agents, such as rosmarinic acid, ferulic acid, and chlorogenic acid. Caffeic acid protective effects were mediated via the upregulation of a series of antioxidant enzymes related to activation of Nrf2.

Caffeic acid enhanced the lifespan of C. elegans along with similar observations for rosmarinic acid that can be hydrolyzed to caffeic acid. Several hundred plant-based agents can enhance lifespan in experimental models such as C. elegans, and there is a competition to find the most effective agents with potential commercial applications.

Hormetic effects typically show a 30 to 60% stimulation above control. This is far below the 2 to 3-fold greater than control detection limit for statistical significance based on human variability/bioplasticity and are often reported as false negatives.

A weight-of-evidence approach was proposed based on multiple in vivo and in vitro test results to derive a study design strategy to increase detection of hormetic effects within the clinical trial framework. Such research should explore hormetic based interactions linking protective catabolic-based adaptive responses with activation and regulation of anabolic mediated hormetic growth effects.”

https://www.tandfonline.com/doi/full/10.1080/19390211.2024.2410776 “Caffeic Acid: Numerous Chemoprotective Effects are Mediated via Hormesis” (not freely available)

A 2024 review provided an overall picture of coffee compounds’ cardiometabolic effects:

“This review provides a comprehensive synthesis of longitudinal observational and interventional studies on the cardiometabolic effects of coffee consumption.

  • Findings indicate that while coffee may cause short-term increases in blood pressure, it does not contribute to long-term hypertension risk.
  • There is limited evidence indicating that coffee intake might reduce the risk of metabolic syndrome and non-alcoholic fatty liver disease.
  • Coffee consumption is consistently linked with reduced risks of type 2 diabetes (T2D) and chronic kidney disease (CKD), showing dose-response relationships.
  • The relationship between coffee and cardiovascular disease is complex, showing potential stroke prevention benefits but ambiguous effects on coronary heart disease.
  • Moderate coffee consumption, typically ranging from 1 to 5 cups per day, is linked to a reduced risk of heart failure, while its impact on atrial fibrillation remains inconclusive. Coffee consumption is associated with a lower risk of all-cause mortality, following a U-shaped pattern, with the largest risk reduction observed at moderate consumption levels.
  • Except for T2D and CKD, Mendelian randomization studies do not robustly support a causal link between coffee consumption and adverse cardiometabolic outcomes.

Potential beneficial effects of coffee on cardiometabolic health are consistent across age, sex, geographical regions, and coffee subtypes and are multi-dimensional, involving antioxidative, anti-inflammatory, lipid-modulating, insulin-sensitizing, and thermogenic effects. Based on its beneficial effects on cardiometabolic health and fundamental biological processes involved in aging, moderate coffee consumption has the potential to contribute to extending healthspan and increasing longevity.”

https://pmc.ncbi.nlm.nih.gov/articles/PMC11493900 “Coffee consumption and cardiometabolic health: a comprehensive review of the evidence”

Nrf2 regulation

gettingwell4 5+ stars Premium, Cortisol, Epigenetics, Glutamate, Neurochemicals, Stress

This 2025 review explored what’s known so far about Nrf2 post-translational regulators:

“Nrf2 is controlled at multiple levels, including epigenetic, transcriptional, translational, and post-translational. The focus of this review is on proteins that control Nrf2 at the post-translational level because in normal cells they are of preeminent importance.

We outline mechanisms by which multiple E3 ubiquitin ligases act to repress Nrf2 expression, how derepression of Nrf2 (and induction of its target genes) by oxidative stressors occurs, and why tissue injury and endoplasmic reticulum stress downregulate Nrf2. This update also explains how Nrf2 is embedded in thiol biochemistry, and outlines signaling pathways and endogenous signaling molecules that control its activity.

Nrf2 not only positively controls the basal and/or inducible expression of a substantial number of genes in all tissues but also downregulates many genes. Estimates of the number of antioxidant/electrophile-responsive element (ARE/EpRE)-driven genes that are positively regulated by Nrf2 vary from several hundred to >2000 depending on the experimental method, species, cell type, physiology, age, sex, diet, and the magnitude of the change that is deemed to be significant.

Induction of ARE/EpRE-driven genes allows adaptation to oxidative, electrophilic, and inflammatory stress. Nrf2 positively regulates clusters of genes encoding proteins classed broadly as antioxidant, drug-, heme-, and iron-metabolizing, pentose phosphate pathway, NADPH-generating, and autophagy-related, as well as fatty acid oxidation enzymes, lipases, transcription factors, and Keap1.

Genes that are negatively regulated by Nrf2 include those encoding the cytokines IL-1β and IL-6, myosin light-chain kinase (MYLK), and NADPH oxidase 4 (NOX4). Nrf2 also regulates some microRNAs, which represents another mechanism by which Nrf2 can downregulate the expression of genes such as those encoding collagens 1A2, 3A1, and 5A1, heat shock protein 47, fibronectin, and elastin. In addition, several lipogenesis-related genes such as fatty acid synthase 1 (FASN1) and acetyl-CoA carboxylase 1 (ACC1), stearoyl-CoA desaturase (SCD1), and fatty acid elongase 6 (ELOVL6) are downregulated upon Nrf2 activation, particularly under conditions of lipid overload. Given that lipogenesis is a highly NADPH-consuming process, it seems that Nrf2 activation redirects NADPH consumption from lipid synthesis towards redox reactions, although the mechanisms underlying the negative regulation of these genes are incompletely understood.

de novo synthesized Nrf2 upon Keap1 inactivation enables a rapid increase of levels of the transcription factor in response to metabolic changes and environmental challenges, allowing cells to adapt and restore homeostasis.”

https://www.cell.com/trends/biochemical-sciences/fulltext/S0968-0004(24)00282-2 “Regulating Nrf2 activity: ubiquitin ligases and signaling molecules in redox homeostasis”

This review’s primary audience is other researchers, and it ended with 15 outstanding items that Nrf2 research hasn’t yet adequately addressed.

Reversing hair greying, Part 2

gettingwell4 4-5 stars Advanced knowledge, Cortisol, Epigenetics, Neurochemicals, Stress, Testosterone , ,

Three papers that cited the 2021 Reversing hair greying study, starting with a 2024 rodent study:

“External treatment with luteolin, but not that with hesperetin or diosmetin, alleviated hair graying in model mice. Internal treatment with luteolin also mitigated hair graying.

Both treatments suppressed the increase in p16ink4a-positive cells in bulges [senescent keratinocyte stem cells (KSCs)]. Both treatments also suppressed decreases in expression levels of endothelins in KSCs and their receptor (Ednrb) in melanocyte stem cells (MSCs), and alleviated hair graying in mice.”

https://www.mdpi.com/2076-3921/13/12/1549 “Anti-Graying Effects of External and Internal Treatments with Luteolin on Hair in Model Mice”

This study treated subjects internally and externally with luteolin and hesperetin, which are ranked #7 (effective treatment) and #14 (not an effective treatment) per Nrf2 activator rankings. I wonder what these researchers would have found if they used the #1 ranked Nrf2 activator, sulforaphane.

A 2024 review managed to cover the Nrf2 activation subject without mentioning sulforaphane:

“Certain types of hair graying can be prevented or treated by enhancing MSC maintenance or melanocyte function, reducing oxidative stress, and managing secretion and action of stress hormones.

Tactical approaches to pursue this goal may include a selective activation of the p38 MAPK–MITF axis, enhancing cellular antioxidant capacity through activating NRF2, and modulating the norepinephrine–β2AR–PKA signaling pathway.”

https://www.mdpi.com/2076-3417/14/17/7450 “Intrinsic and Extrinsic Factors Associated with Hair Graying (Canities) and Therapeutic Potential of Plant Extracts and Phytochemicals”

This reviewer also avoided citing the 2021 Sulforaphane and hair loss, although hair loss was mentioned multiple times. I suspect that institutional politics was involved, as both papers are from South Korea.

Reference 32 of this review was a 2023 review that covered mainly unintentional hair greying reversal as a side effect noted when people had pharmaceutical treatments for various diseases:

“Hair graying is a common and visible sign of aging resulting from decreased or absence of melanogenesis. It has long been thought that reversal of gray hair on a large scale is rare. However, a recent study reported that individual gray hair darkening is a common phenomenon, suggesting the possibility of large-scale reversal of gray hair.

All these treatments rely on the presence of a sufficient population of active McSCs. Maintaining a healthy population of McSCs is also an urgent problem that needs to be addressed.”

https://www.ijbs.com/v19p4588.htm “Reversing Gray Hair: Inspiring the Development of New Therapies Through Research on Hair Pigmentation and Repigmentation Progress”

I published A hair color anecdote two months into eating broccoli sprouts every day when I first noticed dark hair growing in. Since it’s been over 4 years that I’ve continued eating broccoli sprouts daily, I think it’s alright to stop referring to my continuing reversal of hair greying as an anecdote.

But it was apparently too late to address hair loss, which started before I turned 30. So now you know what to do. 🙂

A sulforaphane review

gettingwell4 0-1 star Wasted resources, Beliefs, Brain development, Epigenetics, Immune system , , ,

Here’s a 2025 review where the lead author is a retired researcher whose words readers might interpret as Science. As a reminder, unlike study researchers, reviewers are free to:

  • Express their beliefs as facts;
  • Over/under emphasize study limitations; and
  • Disregard and misrepresent evidence as they see fit.

Reviewers also aren’t obligated to make post-publication corrections for their errors and distortions. For examples:

1. After the 7. Conclusions section, there’s an 8. Afterword: I3C and DIM section. The phrase “As detailed in our earliest work on broccoli sprouts..” indicated a belief carried over from last century of the low importance of those research subjects.

Then, contrary to uncited clinical trials such as Our model clinical trial for Changing to a youthful phenotype with broccoli sprouts and Eat broccoli sprouts for DIM, “Broccoli sprouts had next to no indole glucosinolates.” And in the middle of downplaying I3C and DIM research, they stated: “There are 149 clinical studies on DIM and 11 on I3C listed on clinicaltrials.gov, suggesting a good safety profile. Potential efficacy and mode of action in humans are a subject of intense current investigation, though definitive answers will not come for some time.” 🧐

2. In the 3. Sulforaphane section, they asserted: “Glucosinolates such as glucoraphanin are ‘activated’ or converted to isothiocyanates such as sulforaphane by an enzyme called myrosinase, which is present in that same plant tissue (e.g., seed, sprout, broccoli head, or microgreen) and/or in bacteria that all humans possess in their gastrointestinal tracts.” and cited a 2016 book they coauthored that I can’t access.

The first 2021 paper of Broccoli sprout compounds and gut microbiota didn’t assert that “all humans” had certain gut microbiota that converted glucosinolates to isothiocyanates. That paper instead stated: “Human feeding trials have shown inter-individual variations in gut microbiome composition coincides with variations in ITC absorption and excretion, and some bacteria produce ITCs from glucosinolates.”

3. Nearly half of their cited references were in vitro cancer papers. I rarely curate those types of studies because of their undisclosed human-irrelevant factors. For example, from the second paper of Polyphenol Nrf2 activators:

Bioavailability studies reveal that maximum concentrations in plasma typically do not exceed 1 µM following consumption of 10–100 mg of a single phenolic compound, with the maximum concentration occurring typically less than 2 h after ingestion, then dropping quickly thereafter. In the case of the in vitro studies assessed herein, and with few exceptions, most of the studies employed concentrations >10 µM with some studies involving concentrations in the several hundred µM range, with the duration of exposure typically in the range of 24–72 h, far longer duration than the very short time interval of a few minutes to several hours in human in vivo situations.

applsci-15-00522-g001-550

https://www.mdpi.com/2076-3417/15/2/522 “The Impact of Sulforaphane on Sex-Specific Conditions and Hormone Balance: A Comprehensive Review”

Nrf2 activator rankings

gettingwell4 5+ stars Premium, Epigenetics, Stress ,

A 2024 cell study compared and contrasted findings of previous plant compound Nrf2 inducer studies with a newer assay type:

“Various plants have been reported to contain compounds that promote transcriptional activity of Nuclear factor erythroid 2-related factor 2 (Nrf2) to induce a set of xenobiotic detoxifying enzymes, such as NAD(P)H-quinone acceptor oxidoreductase 1 (NQO1), via the antioxidant response element (ARE). An ARE luciferase reporter assay was recently developed to specifically assess Nrf2 induction potency of compounds.

33 compounds were sorted in the order of their transcriptional activity of Nrf2. CD value is the concentration of a compound required to double the basal activities of individual enzymes or luciferase activity.

nrf2 induction

This study is the first to examine consistency of the transcriptional activity of Nrf2 evaluated using ARE reporter and NQO1 assays for multiple compounds. Future comparisons of CD values by each assay across cell types may be used to demonstrate consistency between the assays, as well as to reveal the factors that influence Nrf2 induction potency.”

https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-024-07038-6 “Nrf2 induction potency of plant-derived compounds determined using an antioxidant response element luciferase reporter and conventional NAD(P)H-quinone acceptor oxidoreductase 1 activity assay”

A 2019 ranking of sulforaphane with 18 other Nrf2 activators was curated in Part 2 of Rejuvenation therapy and sulforaphane, and pointed out bioavailability differences:
OMCL2019-2716870.006

It [sulforaphane] is not only a potent Nrf2 inducer but also highly bioavailable [around 80%], so that modest practical doses can produce significant clinical responses. Other Nrf2 activators [shown in the above image] not only lack potency, but also lack the bioavailability to be considered as significant intracellular Nrf2 activators.”

This study attempted to explain differences in the two assay findings with numerous “may” and “could” statements. Okay.

But if you want to activate your body’s endogenous detoxification and antioxidant systems with a natural plant compound, sulforaphane remains the number one choice.

PXL_20241223_185836159

TFEB and autophagy

gettingwell4 2-3 stars Required further work, Stress ,

Two 2024 papers that cited Precondition your defenses with broccoli sprouts, starting with an in vitro study of influences on auditory cell function:

“Although various studies have focused on the effect of oxidative stress on the inner ear as an inducer of age-related hearing loss (ARHL), there are no effective preventive approaches for ARHL.

We focused on the function of TFEB and the impact of intracellular ROS as a potential target for ARHL treatment in a NaAsO2-induced auditory premature senescence model. Our results suggested that short exposure to NaAsO2 leads to DNA damage, lysosomal damage and mitochondrial damage in auditory cells, triggering temporary signals for TFEB transport into the nucleus and, as a result, causing insufficient autophagic flux and declines in lysosomal function and biogenesis and mitochondrial quality.

41420_2024_2139_Fig6_HTML

This is the first report to indicate that the inactivation of TFEB directly causes oxidative stress (NaAsO2)-induced premature auditory senescence and SASP induction via decreases in autophagic flux and lysosomal dysfunction, with a lowered pH at the transcriptional level and, as a consequence, ROS production with decreasing mitochondrial quality in auditory cells. The activator of TFEB might have a pivotal antiaging effect in the inner ear.”

https://www.nature.com/articles/s41420-024-02139-4 “Premature senescence is regulated by crosstalk among TFEB, the autophagy lysosomal pathway and ROS derived from damaged mitochondria in NaAsO2-exposed auditory cells”

These researchers used exposure concentrations and durations that had no relevance to humans. Human irrelevance made it difficult to assess the above graphic that shows both TFEB activation and inactivation as stress-related. “No effective preventive approaches for ARHL” was asserted as a given, although “TFEB activation via transport into the nucleus contributes to anti-senescence activity in auditory cells and represents a new therapeutic target for ARHL” was also stated.

Just like the two papers in Eat broccoli sprouts for your hearing, preconditioning’s importance wasn’t investigated. So this study didn’t have findings about how mild TFEB activation or inactivation might precondition auditory cells for other stress that might damage hearing.

Next is a review of muscle regeneration and autophagy:

“Satellite cells, also known as muscle stem cells when activated, are essential for muscle repair. These adult stem cells typically remain in a dormant state. In response to tissue injury, these cells are rapidly activated and divided to generate new stem cells, which proliferate to form myoblasts, which further differentiate into myocytes to repair damaged muscle tissue. However, muscle regeneration can be significantly impaired under various conditions due to dysfunctional satellite cell activity.

mTORC1 activity is suppressed during amino acid starvation, leading to autophagy activation. Under these conditions, TFEB, TFE3, and MITF translocate to the nucleus, where they enhance the transcription of genes involved in autophagy and lysosomal function. When nutrients are abundant, mTORC1 suppresses autophagy. This inhibition ensures that resources are directed toward growth and proliferation rather than cellular recycling.

Chronic injuries are typically associated with sustained metabolic or oxidative stress, leading to prolonged or impaired autophagy. While autophagy serves a compensatory and beneficial role in acute injuries, its role in chronic muscle diseases is more complex. On the one hand, autophagy alleviates oxidative stress and mitigates aging. On the other hand, dysregulated autophagy may contribute to muscle fibrosis and loss of muscle mass.

The function of autophagy varies across different stages of satellite cell activity. Autophagy:

  1. Maintains cellular homeostasis by clearing damaged organelles.
  2. Preserves the number of satellite cells by antagonizing apoptosis.
  3. Sustains the quiescence of satellite cells by reducing reactive oxygen species (ROS).
  4. Promotes the activation of satellite cells by supplying energy.
  5. Facilitates the differentiation of satellite cells by mitochondrial remodeling.”

ijms-25-11901-g003-550

https://www.mdpi.com/1422-0067/25/22/11901 “Autophagy in Muscle Regeneration: Mechanisms, Targets, and Therapeutic Perspective”

I’ve curated a few other of the 110 papers that cited the 2020 “Sulforaphane activates a lysosome-dependent transcriptional program to mitigate oxidative stress” over the years, to include:

Sulforaphane’s effects on autism and liver disease;

Bridging Nrf2 and autophagy; and

Eat broccoli sprouts to maintain your cells.

Polyphenol Nrf2 activators

gettingwell4 2-3 stars Required further work, Acetylcholine, Amygdala, Cerebrum, Cortisol, Dopamine, Epigenetics, Glutamate, Hippocampus, Hypothalamus, Immune system, Limbic system, Memory, Neurochemicals, Oxytocin, Serotonin, Stress, Vasopressin , , , , ,

Two 2024 reviews by the same group that published Sulforaphane in the Goldilocks zone investigated dietary polyphenols’ effects as “hormetic nutrients”:

“Polyphenols display biphasic dose–response effects by activating at a low dose the Nrf2 pathway resulting in the upregulation of antioxidant vitagenes [see diagram]. We aimed to discuss hormetic nutrients, including polyphenols and/or probiotics, targeting the Nrf2 pathway and vitagenes for the development of promising neuroprotective and therapeutic strategies to suppress oxidative stress, inflammation and microbiota deregulation, and consequently improve cognitive performance and brain health.

antioxidants-13-00484-g001

Hormetic nutrition through polyphenols and/or probiotics targeting the antioxidant Nrf2 pathway and stress resilient vitagenes to inhibit oxidative stress and inflammatory pathways, as well as ferroptosis, could represent an effective therapy to manipulate alterations in the gut microbiome leading to brain dysfunction in order to prevent or slow the onset of major cognitive disorders. Notably, hormetic nutrients can stimulate the vagus nerve as a means of directly modulating microbiota-brain interactions for therapeutic purposes to mitigate or reverse the pathophysiological process, restoring gut and brain homeostasis, as reported by extensive preclinical and clinical studies.”

https://www.mdpi.com/2076-3921/13/4/484 “Hormetic Nutrition and Redox Regulation in Gut–Brain Axis Disorders”

I’m not onboard with this study’s probiotic assertions because most of the cited studies contained unacknowledged measurement errors. Measuring gut microbiota, Part 2 found:

“The fecal microbiome does not represent the overall composition of the gut microbiome. Despite significant roles of gut microbiome in various phenotypes and diseases of its host, causative microbes for such characteristics identified by one research fail to be reproduced in others.

Since fecal microbiome is a result of the gut microbiome rather than the representative microbiome of the GI tract of the host, there is a limitation in identifying causative intestinal microbes related to these phenotypes and diseases by studying fecal microbiome.”

These researchers also erroneously equated isothiocyanate sulforaphane’s Nrf2-activating mechanisms with polyphenols activating Nrf2.

This research group did better in clarifying polyphenols’ mechanisms in a review of hormetic dose-response effects of the polyphenol rosmarinic acid:

“This article evaluates whether rosmarinic acid may act as a hormetic agent, mediating its chemoprotective effects as has been shown for similar agents, such as caffeic acid, a derivative of rosmarinic acid.

Rosmarinic acid enhanced memory in institute of cancer research male mice in the Morris water maze (escape latency).

untitled

Of importance in the evaluation of rosmarinic acid are its bioavailability, metabolism, and tissue distribution (including the capacity to affect and/or cross the BBB and its distribution and half-life within the brain). In the case of polyphenols, including rosmarinic acid, they are typically delivered at low doses in the diet and, in most instances, they do not escape first-pass metabolism, with the prominent chemical forms being conjugates of glucuronides and sulfates, with or without methylation.

These conjugated metabolites are chemically distinct from the parent compound, showing considerable differences in size, polarity, and ionic form. Their biological actions are quite different from the parent compound.

Bioavailability studies reveal that maximum concentrations in plasma typically do not exceed 1 µM following consumption of 10–100 mg of a single phenolic compound, with the maximum concentration occurring typically less than 2 h after ingestion, then dropping quickly thereafter. In the case of the in vitro studies assessed herein, and with few exceptions, most of the studies employed concentrations >10 µM with some studies involving concentrations in the several hundred µM range, with the duration of exposure typically in the range of 24–72 h, far longer duration than the very short time interval of a few minutes to several hours in human in vivo situations.

We strongly recommend that all experiments using in vitro models to study biological responses to dietary polyphenols use only physiologically relevant flavonoids and their conjugates at appropriate concentrations, provide evidence to support their use, and justify any conclusions generated. When authors fail to do this, referees and editors must act to ensure that data obtained in vitro are relevant to what might occur in vivo.”

https://www.degruyter.com/document/doi/10.1515/med-2024-1065/html “The chemoprotective hormetic effects of rosmarinic acid”

Failed aging paradigms

gettingwell4 2-3 stars Required further work, Brain development, Epigenetics, Memory , , , ,

A 2024 paper with 81 coauthors presented different views of aging:

“This article highlights the lack of consensus among aging researchers on fundamental questions such as the definition, causes, and onset of aging as well as the nature of rejuvenation. Our survey revealed broad disagreement and no majority opinion on these issues.

We obtained 103 responses (∼20% of which were submitted anonymously). The respondents included 29.8% professors, 25% postdoctoral fellows, 22.1% graduate students, 13.5% industry professionals, and 9.6% representing other categories (a total of eight additional groups).

When does aging begin? At 20 years (22%), gastrulation (18%), conception (16.5%), gametogenesis (13%), 25 years (11%), birth (8%), 13 years (5%), and 9 years (4%). Nobody chose the only remaining option (30 years).

m_pgae499f3

It is clear from responses that aging remains an unsolved problem in biology. While most scientists think they understand the nature of aging, apparently their understanding differs. Where some may stress the importance of targeting underlying mechanisms, others focus on ameliorating the phenotypes.”

https://academic.oup.com/pnasnexus/article/3/12/pgae499/7913315?login=false “Disagreement on foundational principles of biological aging”

I’ll assert that these researchers were unable to incorporate information outside of their chosen paradigm. This would explain why only 18% understood the embryonic stage of gastrulation as aging’s start, although the 2022 paper Epigenetic profiling and incidence of disrupted development point to gastrulation as aging ground zero in Xenopus laevis provided epigenetic clock evidence that:

“It is not birth, marriage, or death, but gastrulation which is truly the most important time in your life.”

I’ve cited Josh Mitteldorf’s work about aging a few times. His paradigm of aging is in his 2017 book Cracking the Aging Code: The New Science of Growing Old – And What It Means for Staying Young that:

“Aging has an evolutionary purpose: to stabilize populations and ecosystems.”

However, there isn’t evidence of such causal inheritance mechanisms that would begin an organism’s aging during embryogenesis, i.e., that an embryo’s development of aging elements at gastrulation is causally affected by population and ecosystem factors.

Dr. Goodenowe recently had a casual conversation Episode 8 – Perpetual Health, Exploring The Science Behind Immortality where he asserted items such as:

“What we’re all fighting is entropy. Entropy is the tendency of all things to reach a level of randomness. Aging is not a disease. It’s just apathy and entropy. The body just doesn’t care – people don’t pay attention.

This notion that we are programmed for death is wrong. We’re not programmed to die. We actually teach ourselves to die. The body learns how to die, so as your function decreases, it adjusts. It appears to be programmed because of the association with chronological age.”

I haven’t seen any of his papers that put these and his other assertions up for review. For example, I doubt the entropy-caused randomness assertion would survive peer review per Stochastic methylation clocks?:

“Entropic theories of aging have never been coherent, but they are nevertheless experiencing a resurgence in recent years, primarily because neo-Darwinist theories of aging are all failing. I find this ironic, because the neo-Darwinist theories arose precisely because scientists realized that the Second Law of Thermodynamics does not apply to living systems.”

The funny thing about failed aging paradigms is that quite a few of their treatments improve healthspan, but not lifespan. If they don’t “target aging underlying mechanisms” they “ameliorate aging phenotypes.” None so far have positively affected both human healthspan and lifespan.

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An elevator pitch for plasmalogen precursors

gettingwell4 4-5 stars Advanced knowledge, Acetylcholine, Dopamine, Epigenetics, Glutamate, Hippocampus, Immune system, Limbic system, Lower brain, Memory, Neurochemicals, Serotonin, Stress, Thalamus , , ,

An excerpt from the latest video at Dr. Goodenowe’s Health Matters podcast, Episode 7 “The Truth about Parkinson’s”, starting at 50:30:

“What’s exciting about this community medicine focus that we’ve switched to which basically says: How do we develop technologies in a way that they can be incorporated into a community model versus a pharmaceutical drug model? People can actually do I would say self-experiment just the way you self-experiment with your own diet because these are fundamentally dietary nutrition molecules.

Could you give me an elevator pitch because there are probably people listening who are thinking what is this plasmalogen precursor and for sure how is it having this dramatic effect?

Plasmalogens are the most important nutrient that nobody knows about. Normally you don’t know about it because the body is usually pretty good at making them. What makes plasmalogens unique is that your body makes them kind of like cannon fodder, the first group of people that go into war. Your body throws them out for destruction. They absorb oxidative stress and get destroyed in the process.

They’re stored in your cell membranes. 50% of the membranes of your heart are these plasmalogen molecules. When your heart gets inflamed, what your heart does is it dumps these plasmalogens out of its membranes to douse the flame of inflammation. After inflammation is under control, your body naturally builds these things back up again.

But if you have an inability to make enough plasmalogens, these inflammation events knock you down and keep you down. So plasmalogen precursors are critical for maintaining high levels of plasmalogens across your body, not just in your brain (30% of the lipids in your brain) but in your heart, your lungs, your kidneys.”

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A heterochromatin loss theory of aging? Or just an unhealthy system?

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Telomeres , ,

A 2024 rodent study investigated epigenetic effects of loosening compacted chromatin:

“We show using a novel mouse strain, (TKOc), carrying a triple knockout of three methyltransferases responsible for H3K9me3 deposition, that the inducible loss of H3K9me3 in adulthood results in premature aging. TKOc mice exhibit:

  • Reduced lifespan;
  • Lower body weight;
  • Increased frailty index;
  • Multi-organ degeneration;
  • Transcriptional changes with significant upregulation of transposable elements; and
  • Accelerated epigenetic age.

TKOc survival

Through simultaneous depletion of Setdb1 and Suv39h1/2 methyltransferases, crucial to formation of constitutive heterochromatin, our model analyzes consequential transcription changes including a potential source of genomic instability by activation of endogenous mobile genetic elements, specifically transposable elements.

These findings reveal the importance of epigenetic regulation in aging, and suggest that interventions targeting epigenetic modifications could potentially slow down or reverse age-related decline.”

https://www.biorxiv.org/content/10.1101/2024.07.24.604929v1.full “Loss of H3K9 trimethylation leads to premature aging”

Many of these findings could be restated without viewing them as age-related, i.e.: failure to maintain an adult’s methyltransferase system results in a loss of health. For example, an unhealthy methyltransferase system indicated by parameters like homocysteine levels (not mentioned) can be reversed to healthy function regardless of age. Healthy vs. unhealthy system function wasn’t the paradigm these researchers operated under, though.

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Eat broccoli sprouts to reduce knee pain?

gettingwell4 2-3 stars Required further work, Epigenetics ,

A 2024 preprint published results of feasibility trial NCT03878368:

“High glucosinolate broccoli soup is a novel approach to managing osteoarthritis (OA) that is widely accessible and can be used on a large scale. This study shows that it is an acceptable way of delivering dietary bioactives and has potential for therapeutic benefit.

Limitations of the study:

1. COVID-19 curtailed data collection and restricted sample size below that originally planned, however we remained able to derive meaningful interpretation and meet our original study aims.

2. The study had a short time scale (12 weeks). A longer study would be useful to understand how a long-term intervention might be accepted, important for chronic conditions such as OA.

3. The full sample size fell short of the number anticipated, therefore we were unable to use the data to provide a reliable estimate of sample size for a full trial.

4. Participants were excluded if they did not like broccoli to maximise compliance and retention, and so a food intervention should account for this in future developments. While most patients tolerated the soups well, two patients withdrew because they did not like the soup.”

https://www.medrxiv.org/content/10.1101/2024.06.20.24309233v1.full-text “The BRoccoli In Osteoarthritis (BRIO study) – A randomised controlled feasibility trial to examine the potential protective effect of broccoli bioactives, (specifically sulforaphane), on osteoarthritis”

The glucoraphanin dose used was the highest of three tested in 2017 via NCT02300324:

“This study seeks to quantify the exposure of human tissues to glucoraphanin and sulforaphane following consumption of broccoli with contrasting Myb28 genotypes. Myrosinases are intentionally denatured during soup manufacture. Threefold and fivefold higher levels of sulforaphane occur in the circulation following consumption of Myb28V/B and Myb28V/V broccoli soups, respectively.

6b

Myb28V/V and Myb28B/V broccoli soups contained 452 ± 10.6 μmoles glucoraphanin per 300 mL portion and 280 ± 8.8 μmoles glucoraphanin per 300 mL portion respectively, approximately five- and threefold greater glucoraphanin levels compared to Myb28B/B broccoli soup that contained 84 ± 2.8 μmoles glucoraphanin per 300 mL.

The percentage of sulforaphane excreted in 24 h relative to the amount of glucoraphanin consumed varies among volunteers from 2 to 15%, but does not depend on the broccoli genotype.”

https://onlinelibrary.wiley.com/doi/10.1002/mnfr.201700911 “Bioavailability of Glucoraphanin and Sulforaphane from High-Glucoraphanin Broccoli”

Unlike these two papers, I don’t depend primarily on my gut microbiota for results. Microwaving 3-day-old broccoli sprouts to 60°C to create 80% bioavailable sulforaphane then immediately eating it is way more efficient. If depending on an individual’s gut microbiota to convert glucoraphanin into sulforaphane, the best that can be expected is 15% bioavailability.

Don’t think an osteoarthritis clinical trial that depends on a person’s gut microbiota could have steady, predictable results when there could be more than 700% variability (2% to 15%) among subjects’ sulforaphane conversions. If a treatment subject doesn’t have relief from knee pain, there would have to be additional methods to detect that subject’s effective sulforaphane dose based on their gut microbiota conversion ability. Would these researchers suggest that subject change their gut microbiota? What study has reliable results for that?

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Astaxanthin and aging

gettingwell4 2-3 stars Required further work, Epigenetics, Immune system, Stress ,

A 2023 rodent study investigated two NRF2-activating compounds for their effects in increasing median and maximum lifespan:

“In genetically heterogeneous (UM-HET3) mice, the Nrf2 activator astaxanthin (Asta) extended the median male lifespan by 12%. Astaxanthin (Asta) is a naturally occurring xanthophyll carotenoid that is an efficient Nrf2 activator, with potent antioxidant activity, broad health applications, and excellent safety.

Asta is distributed systemically and incorporated into cellular membranes, where it spans and stabilizes the lipid bilayer and reduces lipid peroxidation. Asta localizes in mitochondria and protects against mitochondrial dysfunction.

It has anti-inflammatory properties, showing equivalent efficacy to prednisolone in an animal model. Geroprotective mechanisms of Asta regulate FOXO3, Nrf2, Sirt1, and Klotho, and the influence of Asta on autophagy via modulation of AMPK (a direct upstream regulator of mTOR), PI3K/Akt, and MAPK (JNK and p38) signaling pathways.

The present Interventions Testing Program (ITP) study is the first evaluation of Asta in a mammalian lifespan model, so the target dose of 4000 ppm in the diet is based on chronic mammalian studies other than lifespan. Despite the fact that the average diet contained 1840 ppm Asta (only 46% of the target), median lifespans of male UM-HET3 mice were significantly improved.astaxanthin male survival

Asta and dimethyl fumarate (DMF) are both Nrf2 inducers; while both had low concentrations sometimes in the diet, we used about 30 times more Asta, which may explain why it increased the lifespan in males while DMF had no effect. Amounts of DMF in the diet averaged 35% of the target dose, which may explain the absence of lifespan effects.”

https://link.springer.com/article/10.1007/s11357-023-01011-0 “Astaxanthin and meclizine extend lifespan in UM‑HET3 male mice; fisetin, SG1002 (hydrogen sulfide donor), dimethyl fumarate, mycophenolic acid, and 4‑phenylbutyrate do not significantly affect lifespan in either sex at the doses and schedules used”

This study repeated an astaxanthin supplier’s claims without investigating its low bioavailability issues mentioned in Astaxanthin bioavailability. No explanations were forthcoming for unintentional low doses of astaxanthin and DMF in the treatment chows.

A human equivalent for the intended astaxanthin dose was 22 mg (4000 ppb x .081 x 70 kg), whereas the actual dose human equivalent was 10 mg (1840 ppb x .081 x 70 kg). Dose/response studies weren’t performed, so no conclusions could be drawn as to whether the target dose or other astaxanthin doses may be optimal for increasing lifespan.

A previous ITP study of another commercial NRF2 activator (PB125) found no lifespan benefits. Maybe one day, ITP or others will come around to testing sulforaphane that has 80% bioavailability (regardless of sex) and dose/response studies, which should end the uncertainty about NRF2’s anti-aging effects.

How to choose your medical professional

gettingwell4 4-5 stars Advanced knowledge, Beliefs, Epigenetics, Immune system, Primal Therapy, Stress , , ,

Two+ decades ago (before smart phones) I wrote a series of short books entitled How To Choose Your  Lawyer, ..Accountant, ..Financial Advisor. My customers were mainly public libraries.

This is a short post on choosing doctors, although I’ve fired all my doctors and don’t have one. Everything that’s happened this decade has made me wonder why I trusted doctors in the first place.

1. It takes certain behavioral quirks for doctors to assert they know better than you do about what is good for you. These behaviors usually have nothing to do with these doctors’ patients, but patients somehow believe doctors.

These behaviors are almost always doctors’ act-outs of early-life traumas of unfulfilled needs. Pain keeps people from feeling their actual histories, though, so we don’t deal with our real histories therapeutically until we absolutely have to.

If your doctor listens to you at all, it’s only because they are constantly vigilant for some way to fulfill their own unsatisfied needs. But that neither resolves anything for them, as an early need can’t be satisfied years later, nor has anything to do with what you need from a medical professional.

2. If you’ve read extensively about an area and have questions, a doctor may know less than you. That won’t keep them from gaslighting you due to 1. above, but it does keep you from getting what you need from them. Discussing facts you know with a medical professional who is intentionally ignorant about a medical subject gets you nowhere.

3. If your doctor has not publicly disclaimed their advocacy of this decade’s misguided genetic therapy, they are compromised and can’t be trusted. It doesn’t matter what else they said, because they weren’t honest about what they knew or should have known, as revealed by their actions or inactions.

For example, two studies published in June 2024 established that:

  • Neurologic issues (68% increase in depression, and a 44% increase in anxiety / dissociative / stress-related / somatoform disorders) followed COVID gene therapy: https://www.nature.com/articles/s41380-024-02627-0 “Psychiatric adverse events following COVID-19 vaccination: a population-based cohort study in Seoul, South Korea” (2,027,353 people)
  • COVID gene therapy increased the risk of mild cognitive impairment 138% and the risk of Alzheimer’s by 23%: https://academic.oup.com/qjmed/advance-article-abstract/doi/10.1093/qjmed/hcae103/7684274 “A potential association between COVID-19 vaccination and development of Alzheimer’s disease” (558,017 people). These graphics showed rapidly increasing MCI and AD incidences. The study’s analysis showed incidence increases could not have happened by chance.

ea3f75cb-a071-4cc9-9bd8-0609d0ad8961_1466x890

A doctor’s only honest response to this malfeasance is to publicly apologize, and tell their trusting patients they will make it up to them by providing free healthcare to help mitigate results of their unprofessional conduct. If they tell you something else, it’s a distraction from consequences that are beyond words.

Eat broccoli sprouts to support muscle growth

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system ,

A 2024 rodent study investigated sulforaphane’s effects on skeletal muscle:

“Sulforaphane (SFN) shows a promising application in skeletal muscle protection and recovery from muscle atrophy and damage. However, limited work has focused on the role of SFN in maintaining the balance of protein and lipid metabolism in skeletal muscle.

The current work investigates effects of SFN at an everyday consumption level on protein and lipid metabolism in skeletal muscle. Investigating SFN at lower levels over an extended period more closely resembles human consumption habits. Four-week-old mice received SFN at a dosage of 1 mg per kilogram of body weight per day (1 mg/kg/d BW) using i.p. injection (SFN1 group) and 3 mg/kg/d BW (SFN3 group) for eight weeks, equivalent to concentrations of 0.14 μM and 0.42 μM.

Histological analysis was performed for the Longissimus dorsi [the largest back muscle]. LD muscle fiber diameter and cross-section area was significantly increased in the SFN3 group, not in the SFN1 group.

SFN muscle growth

The levels of triglycerides and total cholesterol in the LD muscle were found to be decreased in both SFN groups.

This study reported, for the first time, that SFN administration increased peroxisome activity and enhanced the peroxisomal protein shuttle, which supports enhanced peroxisomal fatty acid β-oxidation. SFN redirects the flux of fatty acid to be utilized through β-oxidation in peroxisomes and mitochondria to support muscle growth. Furthermore, SFN treatment influenced lipid and protein metabolism related pathways including AMPK signalling, fatty acid metabolism signalling, cholesterol metabolism signalling, PPAR signalling, peroxisome signalling, TGFβ signalling, and mTOR signalling.”

https://portlandpress.com/bioscirep/article/doi/10.1042/BSR20240084/234562/Sulforaphane-enhanced-muscle-growth-by-promoting “Sulforaphane enhanced muscle growth by promoting lipid oxidation through modulating key signaling pathways”

A human equivalent to this study’s 3 mg daily dose is (3 mg x .081) x 70 kg = 17 mg, albeit doses were intraperitoneally injected. An oral 17 mg is a common sulforaphane floor dose in human studies, and is approximately what I get from eating 60 grams of a microwaved broccoli / red cabbage / mustard 3-day-old sprouts mix daily.

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