Genetic factors

Take responsibility for your one precious life – Trained innate immunity

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

This 2020 review subject was the normal progression of our immune systems:

“Age-related alterations in the immune system result in high susceptibility to infections, increased risk of hospitalization and mortality. Defects in adaptive immunity underlie the markedly low vaccine efficiency in the elderly. Despite reduced cellular functions, a systemic increase in inflammatory markers, so-called inflammaging, is observed in aged individuals.

Trained immunity is a newly emerging concept that showed that innate immune cells possess non-specific immunological memory established through epigenetic and metabolic reprogramming upon encountering certain pathogenic stimuli.

Novel approaches targeting innate immunity to improve host responses are crucial to evade the consequences of the aged immune system. It is an emerging concept that innate immune cells can manifest memory-like properties that are not antigen-specific and exhibit enhanced responsiveness upon later challenges with heterologous stimuli. Whether trained immune responses change as people age is yet to be explored.”

https://academic.oup.com/intimm/advance-article/doi/10.1093/intimm/dxaa052/5885077 “Overcoming immune dysfunction in the elderly: trained immunity as a novel approach”

Previous papers by this review’s corresponding coauthor were curated in:

There’s no reason to rely entirely on the review’s elaborate vaccination schemes to develop trained immunity. Take responsibility for your one precious life and Train your immune system every day!

Eat broccoli sprouts for your hair!

gettingwell4 4-5 stars Advanced knowledge, Acetylcholine, Epigenetics, Immune system, Memory, Neurochemicals, Stress, Testosterone , ,

A trio of papers, with the first a 2017 review exploring broccoli sprout compounds’ effects on head hair:

“Skin appendages, notably hair follicles (HFs), can be exposed to high levels of reactive oxygen species (ROS), which are generated through metabolic reactions occurring mostly in the mitochondria, peroxisomes, and endoplasmic reticulum, as well as in the plasma membrane. Despite their involvement in redox stress and cellular damage, ROS also have key roles in physiological signalling processes, including but not limited to, control of stem cell quiescence / differentiation, regulation of innate and adaptive immune responses and importantly, normal HF development.

HFs are composed of a series of concentric keratinocyte layers with a central hair shaft, all of which are encapsulated by a mesenchymal connective tissue sheath. Within this structure is an area known as the ‘bulge’, housing a population of epithelial and melanocyte stem cells. The hair bulb, the lowermost portion of the HF, contains transient amplifying cells that produce rapidly proliferating matrix keratinocytes that give rise to various cell types of the inner root sheath and hair shaft itself.

Putative impact of NRF2 activation on protection against hair disorders:

  1. Accumulation of excess ROS within crucial HF compartments (i.e. bulb and bulge) can be induced by endogenous and exogenous stressors associated with androgenetic alopecia (AGA), alopecia areata (excessive mast cell degranulation), chemotherapy, UV exposure, and even physiological processes such as melanogenesis.
  2. In the HFSCs [hair follicle stem cells] of the bulge, this can lead to reduced FOXP1 signaling, increased senescence and P21-mediated telogen retention, contributing to hair ageing.
  3. In the hair bulb, negative consequences of excessive ROS can include reduced matrix keratinocyte proliferation and Bcl-2 expression, coupled to increased p53 activity and apoptosis. This redox imbalance may also stimulate dermal papilla-derived TGF-b1 release associated with AGA.
  4. NRF2 activation via SFN [sulforaphane] can induce expression of numerous downstream targets, hence suggesting the potential to counteract excessive ROS and associated pathologies, for example via enhanced clearance of reactive species, detoxification, NADPH generation, and GSH maintenance.
  5. In addition, NRF2 may down-regulate genes that would negatively impact on proliferation and stimulate apoptosis.
  6. Ultimately, activation of NRF2 has the potential to protect against HF miniaturization, chemotherapy-induced apoptosis, HFSC aging, and hair greying, through maintenance of normal redox homeostasis.

Whereas eumelanin (black) is involved in natural UV protection by reducing generation of free radicals, pheomelanin (red) can trigger generation of ROS. It would certainly be interesting to determine whether NRF2 activity is therefore higher in individuals with red as opposed to black hair, in order to mitigate any negative impact from higher ROS generation.

Modulation of NRF2 activity is an attractive approach for further study in prevention of hair greying and HFSC ageing. The remarkable prospect for NRF2 activators in modulating other oxidative stress-linked disease states, strongly advocates for development of NRF2 targeting as a novel strategy in modulating redox-associated disorders of the HF.”

https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201700029 “Oxidative stress management in the hair follicle: Could targeting NRF2 counter age‐related hair disorders and beyond?” (not freely available)

This review was cited in a 2020 Exploring the possibility of predicting human head hair greying from DNA using whole-exome and targeted NGS data study:

“This study aimed to assess the potential of genetic data to predict hair greying in a population of nearly 1000 individuals from Poland. Most prediction information was brought by age alone. Genetic variants explained < 10% of hair greying variation, and the impact of particular SNPs on prediction accuracy was found to be small.

Study population included 673 males (67.4%) and 325 (32.6%) females. Mean age of participants was 30.5 ± 8.8.

Hair greying was recorded in 14.3% of individuals aged 18–30, and prevalence of grey hair was noted to be significantly higher in young males when comparing to young females (17.8 and 9.2%, respectively). Incidence of grey hair increased to 29.5% in the group of people aged 18–40 years, and was 84.2% when people aged ≥40 years were considered.

Because pleiotropy is so common, it would be impossible to predict natural phenotypes avoiding genes involved in determination of pathological phenotypes. The penetrance of individual SNP variants is usually low, and they altogether can only explain a small fraction of predisposition to disease.

Prediction of hair greying status solely based on genetic information is currently impossible.”

A 2020 review had a pertinent evaluation scheme:

“Geroprotectors are pharmacological agents that decrease the rate of aging and extend lifespan. We proposed a set of primary and secondary selection criteria for potential geroprotectors. Primary criteria:

  1. Life extension in experiments with wild type animal models. The geroprotector should prolong life of the model beyond the intact maximum lifespan, protecting it from one or more mechanisms of aging.
  2. Improvement of molecular, cellular, and physiological biomarkers to a younger state, or slow down progression of age-related changes in humans.
  3. Most potential geroprotectors are preventive only when applied at relatively high concentrations. The lifespan-extending dose should be several orders of magnitude less than the toxic dose.
  4. Minimal side effects at the therapeutic dosage at chronic application.
  5. The potential benefit of taking a geroprotector may come after a long period. Potential geroprotectors should initially improve some parameters of health-related quality of life: physical, mental, emotional, or social functioning of the person.”

https://www.mdpi.com/2076-3921/9/6/529/htm “Terpenoids as Potential Geroprotectors”

IMG_20200822_064852

Aging as a normal disease

gettingwell4 4-5 stars Advanced knowledge, Brain development, Epigenetics, Immune system, Memory, Stress , ,

This 2018 review explained:

“Aging is the sum of all age-related diseases. Aging and its diseases are inseparable, as these diseases are manifestations of aging.

An aged appearance (e.g., grey hair, wrinkles, cushingoid body types and loss of muscles) are manifestations of pre-diseases. For example, an aged appearance may reflect hypercortisolism, sarcopenia, osteoporosis, skin pre-diseases.

Instead of healthy aging, we could use the terms pre-disease aging or decelerated aging. Treatments are generally more effective at pre-disease stages, associated with hyper-function, than at disease stages, associated with functional decline.

The decision to treat or not to treat is often determined by whether it is possible to treat.

A treatment that slows aging increases both healthspan (subclinical period) and lifespan, whereas a treatment that increases lifespan (e.g., coronary bypass, defibrillation) is not necessarily increase healthspan. The goal of both anti-aging therapies and preventive medicine is to extend healthspan (by preventing diseases), thus extending total lifespan.

The fact that aging is an obligatory part of the life of all organisms is not important. Aging can be treated as a pre-disease to prevent its progression to diseases. Aging does not need to be defined as a disease to be treated.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6286826/ “Disease or not, aging is easily treatable”



Sleep

gettingwell4 2-3 stars Required further work, Acetylcholine, Amygdala, Beliefs, Brainstem, Cerebrum, Cortisol, Epigenetics, Hippocampus, Hypothalamus, Immune system, Limbic system, Lower brain, Memory, Neurochemicals, Stress, Testosterone, Vasopressin , , , , , , ,

If you can stand the woo of two Californians trying to outwoo each other, listen to these five podcasts with a sleep scientist.

https://peterattiamd.com/matthewwalker1/

“Ambien, sedation, hypnotives, are not sleep.

Sleep is a life support system. It’s the Swiss army knife of health.

Lack of sleep is like a broken water pipe in your home that leaks down into every nook and cranny of your physiology.

Sleep research is not being transmitted to clinical practice.”

I live on the US East Coast. Hyperbole in normal conversations outside of urban centers is an exception.

It’s different on the West Coast. For example:

  • Interviewer assertions regarding heart rate variability should be compared and contrasted with Dead physiological science zombified by psychological research evidence that:

    “A broad base of further evidence was amassed within human cardiac, circulatory, and autonomic physiology such that the hypotheses do not work as described.”

  • Interviewer favorable comments for MDMA (Ecstasy) “to deal with issues of underlying trauma, anxiety, and depression.”

Eat broccoli sprouts for your skin!

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

This 2020 Swiss review subject was the interaction of Nrf2 activators and skin:

“The electrophile and Nrf2 activator dimethyl fumarate (DMF) is an established and efficient drug for patients suffering from the common inflammatory skin disease psoriasis. DMF is being tested for pharmacological activity in several other inflammatory skin conditions.

dmf

Psoriasis is a chronic inflammatory skin disease affecting 2–4% of the population and plaque psoriasis is the most common type, affecting about 90% of all patients. As about 30% of all patients suffer from moderate and severe psoriasis, there is a strong need for efficient systemic treatment options with few side effects.

SFN [sulforaphane] blocks NF-κB activity by several mechanisms. SFN oxidizes IκB, thereby inhibiting its phosphorylation and downstream NF-κB activation, but also targets specific cysteine residues of p50/p65, causing a reduction in DNA binding.

More indirect effects have also been suggested. SFN induces HO-1 expression via Nrf2, which in turn inhibits NF-κB. The isothiocyanate can also react with and oxidize components of cellular redox buffers, such as glutathione and thioredoxin, which are required to retain NF-κB’s DNA-binding capacity.

NLRP3 is believed to be critically involved in common diseases, whereas its role in immunity is rather minor. The mechanisms underlying NLRP3 inflammasome activation are of high medical interest.

Electrophiles can directly inhibit inflammasome activation. SFN inhibits activation of NLRP3 in the absence of NRF2 expression in a very fast manner, suggesting that transcriptional effects are not relevant for NLRP3 inhibition. SFN inhibits NLRP3 even in KEAP1 knockout cells.

All these results demonstrate that electrophiles can inhibit the inflammasome pathway in a direct manner, perhaps via the modification of reactive cysteine residues of inflammasome proteins or those which regulate activation of these complexes.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7072181/ “Electrophiles against (Skin) Diseases: More Than Nrf2”

These reviewers focused on a pharmaceutical. Read this article for progress made on a generic:

“Biogen is expected to appeal this ruling against its Tecfidera patent protection, which is not due to expire until 2028. Its list price is reported to be about $2,026 for a two-week (14 day) supply at 120 mg.

‘The District Court decision clears the legal pathway for us to bring our dimethyl fumarate product to market, and we are working with the FDA to accelerate our regulatory approval target action date, which currently is November 16.'”

Broccoli or Sulforaphane: Is It the Source or Dose That Matters? listed 15 mouse studies and 4 human studies of sulforaphane treatments of skin diseases in Supplementary Material Table S3.

From Novel Nrf2 activators from microbial transformation products inhibit blood–retinal barrier permeability in rabbits:

“The cysteine residue of sulforaphane works as a weak electrophile and it interacts with cysteine residues of Keap1. Dimethyl fumarate is also a weak electrophile.

Nrf2 activity was evaluated by NQO1 induction activity in Hepa1c1c7 cells. RS9 was the most potent and the concentration needed to double (CD) the specific Nrf2 activity was 0.2 nM. The CD values for bardoxolone methyl, sulforaphane and dimethyl fumarate were 0.9 nM, 154.4 nM and 13.3 μM respectively.”

1. This review didn’t mention dimethyl fumarate’s NQO1 induction CD value because..? It’s one of Nrf2 signaling pathway’s main studied parameters, along with HO-1. For example, from Autism biomarkers and sulforaphane:

“This time point was chosen based on our earlier observations of kinetics of upregulation of Nrf2-dependent genes by SF, and was expected to capture increased mRNA production of both very fast (HO-1) and relatively slow (NQO1) responders.”

2. What about adverse effects? From Sulforaphane and RNAs:

“DMF is the most successful Nrf2 activator, FDA-approved in 2013 for the treatment of relapsing remitting multiple sclerosis. However, DMF causes leukopenia and other side-effects.

Bardoxolone cleared Phase II clinical trials for the treatment of advanced chronic kidney disease and type 2 diabetes mellitus, but was halted in Phase III trials due to cardiovascular concerns.”

3. What about prevention mechanisms for skin problems? Skin care isn’t just cancer prevention.

So – what can a person do to treat an inflammation problem in our largest organ, our skin?

  • Pay $2,026 every two weeks to take a daily 120 mg dose of a brand name pharmaceutical?
  • Wait around for some hypothetical future “development of new tailor-made molecules and drugs for the many inflammatory conditions which are associated with Nrf2, NF-κB and inflammasomes”?
  • Try other treatments that just address symptoms, not causes?

Or eat daily clinically-relevant broccoli sprout dosages for < $500 a year?

Sulforaphane clinical trials and COVID-19

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

A plethora of articles have been published this year on how researchers’ favorite topics can / may / should / could / will fix COVID-19. This one was different in that relevant clinical trials were both completed and already underway before a Madness of Crowds behavioral contagion infected us:

“It is crucial to understand the most appropriate context for introducing an anti-inflammatory therapy to complement an antiviral therapy. Such therapy must control inflammation without altering the ability of the host to mount an efficient adaptive immune response against the virus.

We propose that boosting endogenous cellular defenses by targeting the cytoprotective transcription factor Nrf2 (gene name NFE2L2) will promote the resolution of COVID-19 associated inflammation and also restore redox homeostasis and facilitate tissue repair.

The isothiocyanate sulforaphane (SFN) is the most potent naturally occurring NRF2 activator, with well-documented antioxidant and anti-inflammatory effects. The high bioavailability of SFN makes it an excellent candidate for alleviating excessive anti-inflammatory responses and protecting the lungs.

Even though Nrf2 is the primary mediator, additional factors contribute to the anti-inflammatory effects of SFN. SFN inhibits NF-κB, inhibitor of NF-κB kinase subunit β (IKKβ), and STAT3.

By regulating the endogenous cytoprotective systems, Nrf2 may have a more physiological role in achieving a balance between the beneficial and adverse effects of inflammation. Nrf2 inhibits IL-6 and IL-1β gene expression.

Antioxidant and cytoprotective effects of Nrf2 activation are long-lasting and persist for several days after inducer elimination. They are mediated by enzymes that, in contrast to small molecules, have long half-lives and are not consumed, and are instead regenerated during the reactions which they catalyze.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359808/ “Can Activation of Nfr2 Be a Strategy against COVID-19?”

The paper also documented in vitro, animal, and non-clinical human Nrf2 activator studies relevant to causes and effects.

A cherry-picked DNA methylation study

gettingwell4 0-1 star Wasted resources, Epigenetics, Immune system, Stress , , ,

This 2020 US/Sweden/Denmark human study measured twins during their old age:

“We evaluate individual differences in DNA methylation at individual CpG sites across the methylome across 10 years in two Scandinavian samples of same‐sex aging twins. We test two competing hypotheses about the longitudinal stability and change in DNA methylation:

  1. The contribution of genetic influences changes with age, reflecting diminishing influence across time; and
  2. Nonshared factors accumulate in importance, signaling an increasing diversity of response to environmental exposures.

Understanding epigenetic changes over time in the elderly may identify pathways of decline or plasticity (e.g., maintenance or even boosts in functioning) during the aging process and help with elucidating the biology of aging and survival.

Across time, stability in methylation is primarily due to genetic contributions, while novel experiences and exposures contribute to methylation differences. Elevated genetic contributions at age‐related methylation sites suggest that adaptions to aging and senescence may be differentially impacted by genetic background.”

https://onlinelibrary.wiley.com/doi/full/10.1111/acel.13197 “A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation”

Swedish subject measurements were taken at ages 62 and 72. Danish subject measurements were taken at ages 76 and 86.

One epigenetic clock that used 2019 technology was favored over three others, including Horvath’s 2013 original clock. For some reason this study didn’t use his 2018 skin-and-blood clock that had vastly improved technology such as an 18-fold increase in genomic coverage with Illumina 450k/850k bead arrays.

These researchers’ intentions became evident with:

“The 353 Horvath clock sites were selected as best predictors of chronological age using multiple tissues. The 71 Hannum clock sites best predicted age (adjusted for sex, BMI) based on methylation observed in whole blood while the 514 sites from the Zhang prediction model relied on methylation observed in blood and saliva samples (Zhang et al., 2019).

The current findings of moderately higher heritabilities in the Zhang and Hannum sites versus the other clock sites may be in part due to our use of blood tissue.”

The 18-fold increase improved accuracy in blood for the 2018 Horvath clock. Could these researchers ignore it and claim they did their due diligence in 2019 and 2020?

A larger issue was this study’s duality paradigm of either heritability or environment being solely responsible for observed changes. Consider what A blood plasma aging clock found at ages 60 and 78 peaks:

The above changes were due to life stage. Josh Mitteldorf did his usual excellent job of providing contexts for that study with New Aging Clock based on Proteins in the Blood, including:

“The implication is that a more accurate clock can be constructed if it incorporates different information at different life stages. None of the Horvath clocks have been derived based on different CpG sites at different ages, and this suggests an opportunity for a potential improvement in accuracy.”

Weren’t changes in subjects’ life stages relevant to their epigenetic changes? Why wouldn’t their life stages have been among the causes of observed effects?

Sulforaphane and RNAs

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

This 2020 Texas review subject was long non-coding RNAs:

“We review the emerging significance of long non-coding RNAs (lncRNA) as downstream targets and upstream regulators of the Nrf2 signaling pathway, a critical mediator of diverse cellular processes linked to increased cell survival.

It is believed that more than 3% of human genes are regulated by the Nrf2/Keap1 pathway. In addition to the classical cytoprotective and oxidative stress response genes transactivated by Nrf2, emerging evidence suggests a role for non-coding transcript regulation at the level of noncoding RNAs, [which] far outnumber protein-coding genes in the human genome.

One important distinction between miRNAs and lncRNAs is that the latter are often species-specific, meaning that a human lncRNA typically cannot be studied in the mouse or rat, and vice versa.

Sulforaphane (SFN) acts via multiple mechanisms to modulate gene expression, including the induction of Nrf2-dependent signaling. In addition to the established canonical targets of Nrf2, such as NQO1 and HMOX1, SFN altered the expression of multiple lncRNAs.

Given that SFN induces NMRAL2P [a lncRNA pseudogene] and several other lncRNAs in colon cancer cells, further studies are warranted on their respective roles as upstream regulators and/or downstream targets of Nrf2 signaling.

Pharmacological modulation of Nrf2 is considered a viable strategy against chronic conditions that are accompanied by oxidative stress and inflammation:

  • DMF [dimethyl fumurate] is the most successful Nrf2 activator, FDA-approved in 2013 for the treatment of relapsing remitting multiple sclerosis. However, DMF causes leukopenia and other side-effects.
  • Bardoxolone cleared Phase II clinical trials for the treatment of advanced chronic kidney disease and type 2 diabetes mellitus, but was halted in Phase III trials due to cardiovascular concerns.
  • SFN is relatively unstable at room temperature.

We used reported bioinformatics approaches to search for putative ARE [antioxidant response element] sequences among the entire set of 16,000+ annotated human lncRNAs. 13,285 promoter regions contained one or more potential binding sites for Nrf2.”

https://www.sciencedirect.com/science/article/pii/S0304383520303670 “Emerging crosstalk between long non-coding RNAs and Nrf2 signaling”

This study hyped lncRNAs in that only 7 have been validated as Nrf2 targets, and 8 validated as Nrf2 regulators. For regulators, “protein and/or miRNA interacting partners are yet to be fully corroborated” as well.

Also, there’s no need for a “SFN is relatively unstable at room temperature” problem. Just create sulforaphane right before consuming it.

Twice a day I microwave an average 65.5 grams of 3-day-old broccoli sprouts immersed in 100 ml water with a 1000W microwave on full power for 35 seconds to ≤ 60°C. After microwaving I transfer broccoli sprouts to a strainer, and wait five minutes to allow further myrosinase hydrolization of glucoraphanin and other glucosinolates into sulforaphane and other healthy compounds.

Eat sauerkraut today!

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

This 2017 Spanish article reviewed health benefits of sauerkraut:

“During cabbage shredding and fermentation, a disruption of cabbage cells occurs, and GLS [glucosinolates] are hydrolyzed by myrosinase enzyme to a variety of GLS breakdown products. In particular, glucobrassicin is hydrolyzed into indol-3-carbinol (I3C) by myrosinase.

As the pH decreases during cabbage fermentation, I3C reacts nonenzymatically with ascorbic acid to yield ascorbigen (ABG). Studies have shown that ABG is the main GLS breakdown compound in sauerkraut, and it is present at levels between 3 and 18 μmol/100 g fw.

The antioxidant activity observed for sauerkraut in all studies was higher than that observed in raw cabbage.

It has been reported that doses between 53 and 150 μmol of ITCs [isothiocyanates] are enough to display anticarcinogenic effects. Taking into account that the content of ITCs in sauerkraut is in the range 22 μmol/100 g fw, it could be assumed that a weekly consumption of 200–250 g of sauerkraut would provide effective ITC doses to exert cancer chemopreventive effects.

Many studies reported that LAB [lactic acid bacteria] isolated from sauerkraut are potential probiotics.”

https://www.sciencedirect.com/science/article/pii/B9780128023099000248 “Sauerkraut: Production, Composition, and Health Benefits” (not freely available)

This introductory article presented interesting facts, but oversold sauerkraut. Dose and other conditional dependencies in order to achieve health and disease prevention benefits seemed to be beyond its scope.

A more considered view was offered in Fermented Food and Non-Communicable Chronic Diseases which referenced this article:

“Clinical data about the effects of sauerkraut on the human organism, health and disease are scarce. There is knowledge concerning particular compounds in sauerkraut and their impacts on diseases; however, a literature search revealed mostly cell line or rat experiments with very limited conclusions for humans.”

Earlier this month I started eating refrigerated sauerkraut twice a day with microwaved broccoli sprouts. I mix in three heaping teaspoons each time, and finish a 50 oz (1418 g) container in a week.

The mixture tastes better than just microwaved broccoli sprouts. It requires more chewing, which assists myrosinase hydrolization of broccoli sprout glucosinolates into sulforaphane and other healthy compounds.

Although sauerkraut isn’t a primary source, there may be beneficial amounts of probiotics etc. that increase what I get with broccoli sprouts and supplements.

I also started making my own sauerkraut using the commercial product’s juice as a starter. I add garlic but not salt. No results yet.

Transgenerational epigenetic inheritance of epimutations

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My 600th curation is a 2020 rodent study from Dr. Michael Skinner’s labs at Washington State University:

“Numerous environmental toxicants have been shown to induce the epigenetic transgenerational inheritance of disease and phenotypic variation. Alterations in the germline epigenome are necessary to transmit transgenerational phenotypes.

In previous studies, the pesticide DDT and the agricultural fungicide vinclozolin were shown to promote the transgenerational inheritance of sperm differential DNA methylation regions, non-coding RNAs and histone retention, which are termed epimutations. The current study was designed to investigate the developmental origins of the transgenerational differential histone retention sites (called DHRs) during gametogenesis of the sperm.

In addition to alterations in sperm DNA methylation and ncRNA expression previously identified, the induction of DHRs in the later stages of spermatogenesis also occurs. This novel component of epigenetic programming during spermatogenesis can be environmentally altered and transmitted to subsequent generations.

While the DHR may be consistent and present between the stages of development, the histone modifications may be altered. Several of the core histone retention sites absent in the DHRs had altered histone methylation. This adds a level of complexity to the potential role of histone retention in that it may be not only the retention, but also the alterations in histone epigenetic modifications.

The DHRs had positional associations with genes and the major functional categories were signaling, metabolism and transcription.

In the event the embryo stem cell population has a modified epigenetics and corresponding transcriptome, then all somatic cells derived from the stem cell population will have an altered cascade of epigenetic and gene expression programming to result in adult differentiated cells with altered epigenetics and transcriptomes. Previous observations have demonstrated in older adult human males alterations in histone retention develop and are associated with infertility.

Similar observations have also been provided for the development of differential DNA methylation regions (DMRs) induced by environmental toxicants such as DDT and vinclozolin. Since DHRs have a similar developmental programming, other epigenetic processes such as ncRNA are also anticipated to be similar.”

https://www.sciencedirect.com/science/article/pii/S0012160620301834 “Developmental origins of transgenerational sperm histone retention following ancestral exposures”

This study, like its dozens of predecessors performed year after year by this research facility, provided evidence for mechanisms of epigenetic transgenerational inheritance. The studied F3 generation members were great-grand-offspring, the first generation to have no direct exposure to DDT and vinclozolin.

As pointed out in A compelling review of epigenetic transgenerational inheritance:

“During the 1950s, the entire North American population was exposed to high levels of the pesticide DDT, when the obesity rate was < 5% of the population. Three generations later, the obesity frequency in North America is now ~45% of the population.”

There are varieties of mischaracterizations and hand-waving denials of epigenetically-inherited diseases. People don’t want to hear about and read proof that something we did or experienced disfavored our children, who unwittingly passed resultant problems on to their children, and which furthered on to their children’s children.

Take responsibility for your one precious life – Vitamin D3

gettingwell4 4-5 stars Advanced knowledge, Brain development, Epigenetics, Immune system, Memory, Stress , , , , , , ,

Where to start among 6,489 studies and reviews published during the past five years, results from a PubMed search of “dihydroxyvitamin D3.” How about:

“Vitamin D plays a fundamental role in body calcium and phosphorous homeostasis, ensuring proper functioning of the skeletomuscular system. Pleiotropic activities include:

  • Anti-inflammatory and immunomodulatory properties (predominantly downregulation of adaptive and upregulation of innate immunity);
  • An important role in reproduction, pregnancy, placental functions and fetal and child development;
  • Important in neurodevelopment as well as in the functioning of the adult central and peripheral nervous system;
  • Regulation of global metabolic and endocrine homeostasis and the functions of different endocrine organs, as well as in the functioning of the cardiovascular system;
  • Inhibits malignant transformation, tumor progression and has anti-cancer properties on a variety of tumors;
  • Formation of the epidermal barrier and hair cycling; and
  • Ameliorating effects on skin cancer and on proliferative and inflammatory cutaneous diseases.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6342654/ “The serum vitamin D metabolome: What we know and what is still to discover”

Or maybe:

“A study in 6,275 American children and adolescents aged 1–21 years showed that 61% were 25-(OH)D3 insufficient and 9% deficient. In adults, up to 40% are 25-(OH)D3 insufficient and 6% deficient.

Once adequate vitamin D values are reached, to further preserve adequate vitamin D levels in adults, the IOM [Institute of Medicine] recommends a daily dose of 600 IU per day, while the Endocrine Society recommends a dose of 600–2000 IU per day (according to the amount of sunlight the individual is exposed to). There seems to be no additional health benefit in doses higher than 4000 IU/day.

Vitamin D supplementation was protective against acute respiratory tract infections in a 25-(OH)D3 deficient population, especially in those receiving daily or weekly supplementation. However, in children this protective effect could not be reproduced.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7281985/ “Vitamin D’s Effect on Immune Function”

Not to forget Advanced glycation end products alter steroidogenic gene expression by granulosa cells: an effect partially reversible by vitamin D:

“This study suggests that there is a relationship between AGEs (advanced glycation end products) and their receptors (RAGE and sRAGE) with vitamin D. Understanding the interaction between AGEs and vitamin D in ovarian physiology could lead to a more targeted therapy for the treatment of ovarian dysfunction.”

Or similarities to broccoli sprouts’ main effect of Nrf2 signaling pathway activation:

“1,25(OH)2D3 plays a role in delaying aging by upregulating Nrf2, inhibiting oxidative stress and DNA damage, inactivating p53‐p21 and p16‐Rb signaling pathways, and inhibiting cell senescence and SASP.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6516172/ “1,25‐Dihydroxyvitamin D exerts an antiaging role by activation of Nrf2‐antioxidant signaling and inactivation of p16/p53‐senescence signaling”

Why do we insist on giving ourselves non-communicable diseases?

I recently paid $22.53 after tax for a nearly two-year supply:

A better use of one’s money would be..?

My June 2020 serum 25-OH Vitamin D measurement was 76 on a scale of 0 to 100 from taking a total of 3,400 IU daily. It’s fat-soluble, so I take it along with 1 gram flax oil each time.

Take responsibility for your own one precious life.

Take responsibility for your one precious life – Zinc

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

This 2020 review highlighted earlier clinical data on zinc:

  • “Zinc is known to modulate antiviral and antibacterial immunity and regulate inflammatory response.
  • Zinc possesses anti-inflammatory activity by inhibiting NF-κB signaling and modulation of regulatory T-cell functions.
  • The most critical role of zinc is demonstrated for the immune system.
  • Zinc regulates proliferation, differentiation, maturation, and functioning of leukocytes and lymphocytes.

Alteration of zinc status significantly affects immune response resulting in increased susceptibility to inflammatory and infectious diseases including acquired immune deficiency syndrome, measles, malaria, tuberculosis, and pneumonia. Zinc status is associated with the prevalence of respiratory tract infections in children and adults.

In view of the high prevalence of zinc deficiency worldwide (up to 17%), its impact on population health is considered as a significant issue. Certain groups of people, including infants, especially preterm ones, and elderly, are considered to be at high risk of zinc deficiency and its adverse effects.

Zinc was shown to have a significant impact on viral infections through modulation of viral particle entry, fusion, replication, viral protein translation and further release for a number of viruses including those involved in respiratory system pathology. Increasing intracellular Zn levels through application of Zn ionophores significantly alters replication of picornavirus, the leading cause of common cold.

The results of systematic analysis confirmed the efficiency of intake of at least 75 mg/day Zn in reduction of pneumonia symptom duration but not severity, with the response being more pronounced in adults than in children.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7255455/ “Zinc and respiratory tract infections: Perspectives for COVID-19”

The review noted a 2014 rodent cell study which found:

“Labile zinc, a tiny fraction of total intracellular zinc that is loosely bound to proteins and easily interchangeable, modulates the activity of numerous signaling and metabolic pathways. Dietary plant polyphenols such as the flavonoids quercetin and epigallocatechin-gallate act as antioxidants and as signaling molecules. The activities of numerous enzymes that are targeted by polyphenols are dependent on zinc.

We have demonstrated the capacity of quercetin and epigallocatechin-gallate to rapidly increase labile zinc. The polyphenols transport zinc cations across the plasma membrane independently of plasma membrane zinc transporters.

The ionophore activity of dietary polyphenols may underlay the raising of labile zinc levels triggered in cells by polyphenols and thus many of their biological actions.”

https://pubs.acs.org/doi/10.1021/jf5014633 “Zinc Ionophore Activity of Quercetin and Epigallocatechin-gallate: From Hepa 1-6 Cells to a Liposome Model” (not freely available)

I get EGCG from drinking 4-5 cups of green tea every day, and 65 mg zinc from supplements. Microwave broccoli to increase flavonoid levels demonstrated 108.5% to 129.8% increases in quercetin and kaempferol levels from microwaving grocery-store broccoli. Microwaving 3-day-old broccoli sprouts may be expected to increase my worst-case calculation of daily 134 mg total flavonoids.

I’ve taken quercetin intermittently per Preliminary findings from a senolytics clinical trial. I’m changing that to take 100 mg quercetin daily.

Take responsibility for your own one precious life.

Autism biomarkers and sulforaphane

gettingwell4 4-5 stars Advanced knowledge, Brain development, Epigenetics, Immune system, Stress , ,

This 2020 US human study investigated autism improvements with sulforaphane:

“Autism Spectrum Disorder (ASD) is one of the most common neurodevelopmental disorders that, in the United States, is currently estimated to affect 1 out of 59 children who are 8 years old. Despite decades of research and advances in our knowledge of etiologies of ASD, treatments and biomarkers for ASD remain limited.

The primary diagnosis of ASD still relies on observational tools that are by nature subjective. There are currently no drugs approved to treat core symptoms of ASD, nor are there any studies using SF [sulforaphane] in genetic mouse models of ASD.

In our previous placebo-controlled, double-blinded, randomized clinical trial, daily administration of SF for 4-18 weeks substantially improved behavioral abnormalities of the majority of 26 young males with moderate to severe ASD without significant toxicity. The multi-functional phytochemical sulforaphane affects many biochemical abnormalities associated with ASD.

We investigated potential molecular markers from three ASD-associated physiological pathways that can be affected by sulforaphane:

  1. Redox metabolism / oxidative stress;
  2. Heat shock response; and
  3. Immune dysregulation / inflammation

in peripheral blood mononuclear cells (PBMCs) from healthy donors and patients with ASD.

Three representative Nrf2 [nuclear factor erythroid 2-related factor 2]-dependent enzymes:

  1. AKR1C1 [aldo-keto reductase family 1 member C1];
  2. NQO1 [dehydrogenase quinone 1]; and
  3. HO-1 [heme oxygenase]

were significantly induced by 6 h of 2 μM or 5 μM SF ex vivo treatments in PBMCs from healthy donors. This time point was chosen based on our earlier observations of kinetics of upregulation of Nrf2-dependent genes by SF, and was expected to capture increased mRNA production of both very fast (HO-1) and relatively slow (NQO1) responders.

There was no concentration-dependence in induction of any genes examined, with higher (5 μM) concentration of SF even showing a slightly diminished effect for induction of AKR1C1 and NQO1. Although this concentration is achievable in vivo, more typical peak concentrations of SF (and its metabolites) in human plasma are 1-2 μM.

SF ex vivo pre-treatment significantly decreased the LPS [lipopolysaccharides]-stimulated inflammatory gene (

  • COX-2,
  • TNF-α,
  • IL-6 and
  • IL-1β

) expression levels in PBMCs from healthy donors.

As a pilot study for a clinical trial of SF in children with ASD, we evaluated the same biomarkers from the ex vivo studies in 10 young males with ASD, 6-12 years of age, who received SF (in the form of a dietary supplement containing GR [glucoraphanin] and myrosinase), 2.2 μmol/kg/d for 14 days. Grouping by broad functionality (e.g. cytoprotective or pro-inflammatory), differences from baseline were highly significant.

asd gene expression

Individually none is sufficiently specific or sensitive, but when grouped by function as two panels, these biomarkers show promise for monitoring pharmacodynamic responses to sulforaphane in both healthy and autistic humans, and providing guidance for biomedical interventions. We conducted this study in the context of ASD, however our findings have broader implications and suggest that these biomarkers can be used in any study involving an intervention with SF.

Major signaling pathways for protective mechanisms against ASD by SF:

  • (a) Keap1/Nrf2/ARE pathway,
  • (b) NF-κB inflammatory pathway,
  • (c) Heat-shock responses.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7118069/ “Biomarker Exploration in Human Peripheral Blood Mononuclear Cells for Monitoring Sulforaphane Treatment Responses in Autism Spectrum Disorder”

This was a pilot study. Does sulforaphane treat autism? was its follow-on clinical trial.

Broccoli sprouts and sulforaphane aren’t panaceas. Their research is becoming more intensive and focused, though.

Measuring sulforaphane plasma compounds

gettingwell4 0-1 star Wasted resources, Epigenetics ,

This 2020 Australian human study investigated methods of measuring sulforaphane plasma compounds:

“A simplified methodology to allow high-throughput LC–MS [Liquid Chromatography-Mass Spectrometry] analysis of plasma samples for measurement of sulforaphane and its metabolites is described. Analysis time is greatly reduced by employing fast chromatography and simple plasma extraction procedure.

Participants were observed consuming four Broccomax capsules, each containing 30 mg of broccoli seed extract and a dose of 8 mg of sulforaphane, as per manufacturer certificate of analysis, resulting in a total dose of 32 mg of sulforaphane (120 mg of broccoli seed extract).

Mean peak of combined metabolites from our study (0.9 and 1 μM) using 120 mg of broccoli seed extract (~32 mg of SFN) was similar to work by Fahey et al. who investigated pharmacokinetics of 350 mg of purified broccoli seed powder (mean 1.3 μM ± 0.5 μM), though our dose was almost three-times less. Pharmacokinetic profiles of our study mirrored those of Fahey et al. in that excretion was complete 8 hrs after consumption. Our intervention peaked slightly later (~2hrs), than that of Fahey (~1 hr), likely due to our use of a capsule rather than liquid.”

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7070302/ “Measuring Sulforaphane and Its Metabolites in Human Plasma: A High Throughput Method”

This study was thin on comparing their n = 2 results to previous work. Here are comparables from Broccoli or Sulforaphane: Is It the Source or Dose That Matters?


These researchers set up a strawman by stating a false comparison:

“Our dose was almost three-times less.”

The compared study was the n = 10 subjects row above, which stated its dose as:

“200 μmol of SF was contained in about 350 mg of SF-αCD powder dissolved in 25 mL of distilled water, which subjects were given to drink upon arrival at the clinic.”

If the current study wanted a true comparison, they would measure and compare sulforaphane dose weights or amounts:

  • https://pubchem.ncbi.nlm.nih.gov/compound/sulforaphane lists sulforaphane’s molecular weight as 177.3 g / mol.
  • A 5.64 μmol sulforaphane amount (.001 / 177.3) equals a 1 mg weight of sulforaphane.
  • 200 μmol / 5.64 μmol = 35 mg sulforaphane used in the compared study.

But these researchers couldn’t even do that! They asserted a 32 mg sulforaphane dose “per manufacturer certificate of analysis” when they had the resources to do otherwise!

What kind of study design would go to all the trouble of measuring plasma sulforaphane metabolite outputs, but not measure their sulforaphane input dose???

Had they closely read the compared study, they may have also noticed that its commercial supplement, Prostaphane, was tested to verify stated dosage. These researchers could have done the same with Broccomax.

Are sulforaphane supplements better than microwaved broccoli sprouts?

gettingwell4 4-5 stars Advanced knowledge, Anterior cingulate cortex, Beliefs, Cerebrum, Epigenetics, Glutamate, Hippocampus, Immune system, Limbic system, Lower brain, Memory, Neurochemicals, Stress, Thalamus , , , , ,

Armando asked a good question in Upgrade your brain’s switchboard with broccoli sprouts:

“Is there any way to consume sulphorafane in a supplement form? Rather than have to jump so many hops to consume it from broccoli.”

That blog post referenced a 2017 study, whose sulforaphane amount was:

“100 µmol [17.3 mg] sulforaphane as standardized broccoli sprout extract in the form of 2 gel capsules.”

One answer in A pair of broccoli sprout studies was No:

  • “Plasma and urinary levels of total SFN [sulforaphane] metabolites were ~3–5 times higher in sprout consumers compared to BSE [broccoli sprout extract] consumers.
  • In sprout consumers, plasma concentrations were 2.4-fold higher after consuming the second dose than after the first dose.
  • Calculated SFN bioavailability from broccoli sprouts exceeded 100%.”

That study was from 2015, though. Are better products than broccoli sprout extracts available now?

Image from the US Library of Congress

During Week 5 of Changing an inflammatory phenotype with broccoli sprouts, back in May when I still believed impossible things like we would:

I contacted a distributor of a dried broccoli sprout powder for evidence of their claim:

“Independent assays confirm that EnduraCELL yields more Sulforaphane per gram and per dose than any other broccoli sprout ingredient available! These assays showed that EnduraCell yields around 3.5 times more SULFORAPHANE than the next highest broccoli sprout product.”

I’ve asked three times for the lab assays. They declined each time to provide the data. In correspondence the company founder said:

“Each 700 mg capsules yields around 15mg sulforaphane.”

The company founder has written several reviews, one of which is entitled Sulforaphane and Other Nutrigenomic Nrf2 Activators: Can the Clinician’s Expectation Be Matched by the Reality? In Section 6.5 Sulforaphane it stated:

“By calculation, MYR [myrosinase]-active whole broccoli sprout supplement yielding 1% SFN could deliver 10 mg SFN per gram of powder, corresponding to ~12 grams of fresh broccoli sprouts (dried powder retains ~8% moisture).“

The 2017 study’s dosage of “100 µmol [17.3 mg] sulforaphane as standardized broccoli sprout extract” weighed a gram or less, for a 1.73% sulforaphane yield. A broccoli sprout powder may have a 15 mg / 700 mg = 2.14% sulforaphane yield.

Using calculations from Estimating daily consumption of broccoli sprout compounds and Our model clinical trial for Changing to a youthful phenotype with broccoli sprouts, I eat 131 grams of 3-day-old broccoli sprouts daily. That would be 131 g / 12 = 10.9 grams of a broccoli sprout powder.

The equivalent sulforaphane dosage would be 10.9 g x 21.4 mg per gram = 233.3 mg! That’s obviously too high. What isn’t right?

Subsequent investigation of a distributor’s site found this table:

autism sprout powder

The study referenced for equivalence was Sulforaphane treatment of autism spectrum disorder (ASD). Calculations:

  • The 100 µmol sulforaphane amount for 90 kg participants weighed 17.73 mg per https://pubchem.ncbi.nlm.nih.gov/compound/sulforaphane.
  • The equivalent broccoli sprout powder sulforaphane yield is 0.01773 / 3.6 g = 0.4925%. That’s 5 mg of sulforaphane per gram of broccoli sprout powder.
  • 0.4925% / 2.14 % = 0.23. Decrementing the above sulforaphane weight gives 233.3 mg x .23 = 54 mg.

The answer to my question What isn’t right? I relied on private correspondence rather than what a vendor publicly disclosed.

I’m not particularly concerned about analytical uncertainties for myself. Whatever the numbers are, microwaving techniques for fresh broccoli sprouts increase them.

I immerse 3-day-old broccoli sprouts in 100 ml distilled water, then microwave them on 1000W full power for 35 seconds to ≤ 60°C (140°F) per Microwave broccoli to increase sulforaphane levels. Worst-case estimates are 52 mg sulforaphane with microwaving.

My answer to Armando’s question would be No for sulforaphane supplements. I’d consider a whole broccoli sprout powder after lab assays were personally verified.