DNA methylation

Peripheral vs. brain epigenetic measurements

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

This 2023 human study investigated associations of peripheral and brain epigenetic measurements:

“Evaluating DNA methylation of brain tissue is challenging owing to the issue of tissue specificity. Consequently, peripheral surrogate tissues are used, resulting in limited progress compared with other epigenetic studies.

Averaging data for each CpG across individuals, saliva–brain correlation (r = 0.90) was higher than that for blood–brain (r = 0.87) and buccal–brain (r = 0.88) comparisons. Among individual CpGs, blood had the highest proportion of CpGs correlated to the brain at nominally significant levels (19.0%), followed by saliva (14.4%) and buccal (9.8%). However, cross-database correlations of correlation coefficients revealed relatively low brain vs. blood: r = 0.27, saliva: r = 0.18, and buccal: r = 0.24.

The majority of methylation in the brain is most likely not synchronized with methylation in the periphery. Despite this, variable CpGs that correlate in the brain and periphery, although in small numbers, may have biological relevance, and could be useful for inferring brain methylation from peripheral tissues. This study has six major limitations.”

https://www.nature.com/articles/s41398-023-02370-0 “Cross-tissue correlations of genome-wide DNA methylation in Japanese live human brain and blood, saliva, and buccal epithelial tissues”

Real science is messy. Hypotheses are experimentally reevaluated many, many times under varying conditions. I skip over studies where researchers don’t provide meaningful limitation clauses.

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Sex hormones and epigenetic clocks

gettingwell4 2-3 stars Required further work, Epigenetics, Telomeres, Testosterone , ,

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

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

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

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

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

sex hormones and epigenetic clocks

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

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

https://www.medrxiv.org/content/10.1101/2023.02.16.23285997v1.full “Higher testosterone and testosterone/estradiol ratio in men are associated with better epigenetic estimators of mortality risk”

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

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

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

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

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The goddess of destiny

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

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

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

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

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

klotho and exercise

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

The present study revealed that circulating KL level is associated with exercise status level and general strength level, and is greatly dependent upon exercise-induced DNA methylation.”

https://www.mdpi.com/2073-4425/14/2/525 “The Circulating Level of Klotho Is Not Dependent upon Physical Fitness and Age-Associated Methylation Increases at the Promoter Region of the Klotho Gene”

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Ancient parasite DNA within us

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

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

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

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

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

https://www.cell.com/cell/fulltext/S0092-8674(22)01530-6 “Resurrection of endogenous retroviruses during aging reinforces senescence”

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

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

erv aging mechanism

These observations also raise several intriguing questions:

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

https://academic.oup.com/lifemedi/advance-article/doi/10.1093/lifemedi/lnad001/6982772 “Endogenous retroviruses make aging go viral”

Previously curated papers on these subjects include:

A study of our evolutionary remnants

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

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

Starving awakens ancient parasite DNA within us

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

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Environmental signaling rescues aging muscle stem cells

gettingwell4 5+ stars Premium, Epigenetics, Immune system, Stress , ,

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

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

in vivo model

We showed that:

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

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

https://www.nature.com/articles/s41467-023-36265-x “Transcriptional reprogramming of skeletal muscle stem cells by the niche environment”

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

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

Blinded by their paradigm?

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

This 2022 human study investigated another type of aging clock:

“The glycan clock of age, based entirely on immunoglobulin G (IgG) N-glycans, can predict biological age with high accuracy. Unlike DNA methylation, glycosylation of IgG does not predict chronological age with high accuracy.

Heritability analysis of plasma glycans revealed that the majority of traits have high heritability estimates, indicating a tight genetic control of glycosylation. To better understand genetic and environmental factors influencing glycan clock variation, we performed a heritability analysis on data from two cohorts included in the TwinsUK registry.

Glycosylation is a series of enzymatic reactions in which carbohydrates are attached to other molecules (e.g., proteins or lipids) resulting in formation of complex carbohydrates and glycoconjugates commonly referred to as ‘glycans.’ Glycosylation of IgG antibody is especially interesting as it dramatically affects its function, and acts as a molecular switch between pro- and anti-inflammatory immune responses.

Heritability of the glycan clock was estimated to decompose observed phenotypic variance into three latent sources of variation:

  • A—additive genetic variance [red] represents cumulative impact of genes;
  • C—shared/common environment variance [purple] results from influences to which both members of a twin pair are exposed; and
  • E—unique environment variance [green] is events occurring to one twin but not the other, and includes measurement error.

fcell-10-982609-g002

Despite tight genetic control of the IgG glycome:

  • Heritability analysis of the glycan clock revealed only a moderate genetic contribution averaging around 39% [A, left side].
  • Including age of the individuals as a covariate in heritability analysis averaged 71% heritability estimates [B, right side].
  • Mean time difference was 7.5 years for points 1 and 2, and 6 years for points 2 and 3.

Observed increase in the genetic component could be a consequence of chronological age as a shared environmental variance characteristic for every individual and determined by their genetic makeup and epigenetic regulation.”

https://www.frontiersin.org/articles/10.3389/fcell.2022.982609/full “Heritability of the glycan clock of biological age”

Although A rejuvenation therapy and sulforaphane was cited, these researchers missed its central premise: Pro-aging epigenetic programming is directional and not purely random. Contrasting their above graphic’s heritability estimates of 39% with the age-regressed, right side’s average 71% could hardly have been more clear in illustrating this fact.

This study instead stated “Aging in general leads to epigenetic mediated deregulation of genes.” This weak sauce accompanied speculations such as “supports the notion that the glycan clock can be rejuvenated by simple lifestyle choices.”

Researchers almost always want to claim being first in finding x, y, or z. These researchers could have done that in this glycan clock study by highlighting an outstanding finding. So what happened?

An alternate explanation to their paradigm blinding them could be sponsor expectations, peer pressures, etc. I’ll ask them about it, and will update here with their response.

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Eat broccoli sprouts to epigenetically regulate histones

gettingwell4 5+ stars Premium, Epigenetics, Immune system, Stress , , ,

Five papers on beneficial effects from sulforaphane inhibiting histone deacetylases (HDACs), starting with a 2022 rodent cell study:

“Sulforaphane (SFN) has tissue specificity for subtypes of HDACs that are downregulated. For example:

  • In breast cancer cells, HDAC1-3 are inhibited by SFN to induce cell apoptosis;
  • In skin cells, HDAC1-4 are regulated by SFN [anti-skin cancer]; and
  • In the cochlea, SFN inhibits HDAC2, 4, and 5 [attenuates hearing loss].

In the present study, SFN significantly inhibited HDAC2, 3, and 5 expression and HDACs activity in cardiomyocytes, thereby increasing H3 acetylation levels in the Nrf2 promoter and upregulating Nrf2 expression. Mechanism by which SFN prevents Ang II-induced cardiomyocyte apoptosis:

  • Ang II activates oxidative stress by increasing ROS leading to inflammation, oxidative stress and fibrosis in cardiomyocytes.
  • SFN prevents Ang II-induced cardiomyocyte apoptosis by inhibiting HDACs to activate Nrf2 and downstream antioxidant genes.

aging-14-204247-g007

SFN activates Nrf2 by inhibiting HDACs expression and activation.”

https://www.aging-us.com/article/204247/text “Sulforaphane inhibits angiotensin II-induced cardiomyocyte apoptosis by acetylation modification of Nrf2”

A 2021 rodent study found:

“SFN significantly attenuated diabetes-induced renal fibrosis in vivo. SFN inhibited diabetes-induced increase in HDAC2 activity.

Bone morphologic protein 7 (BMP-7) has been shown to reduce renal fibrosis induced by transforming growth factor-beta1. SFN protects against diabetes-induced renal fibrosis through epigenetic up-regulation of BMP-7.”

dmj-2020-0168f7

https://e-dmj.org/journal/view.php?doi=10.4093/dmj.2020.0168 “Sulforaphane Ameliorates Diabetes-Induced Renal Fibrosis through Epigenetic Up-Regulation of BMP-7”

A 2019 human osteosarcoma cell study found:

“SFN inhibits mTOR in a concentration- and time-dependent manner. This inhibition occurs in the presence or in the absence of NRF2.

SFN inhibits HDAC6 and decreases catalytic activity of AKT, which partially explains the mechanism by which SFN inhibits mTOR.”

https://www.sciencedirect.com/science/article/pii/S0944711319302284 “The isothiocyanate sulforaphane inhibits mTOR in an NRF2-independent manner”

A 2022 review cited a 2018 cell study:

“HDAC expression and activity are dysregulated in various diseases including asthma, chronic obstructive pulmonary disease, cancer, cardiac hypertrophy, and neurodegenerative and psychological disorders. HDAC inhibitors could be a potential therapeutic target for many diseases.

In hypertension, aortic stiffness is usually increased and vascular smooth muscle cells (VSMCs) contribute to vascular stiffness. We used VSMCs to test the degree of acetylation of histones in this study.

Sulforaphane weakly inhibited HDAC2 and effectively inhibited HDAC9.”

https://www.sciencedirect.com/science/article/pii/S0006295222002052 “Zinc-dependent histone deacetylases: Potential therapeutic targets for arterial hypertension”

https://www.sciencedirect.com/science/article/abs/pii/S0753332217364636 “Inhibition of class IIa histone deacetylase activity by gallic acid, sulforaphane, TMP269, and panobinostat” (not freely available)

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Do broccoli sprouts treat gout and kidney stones?

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

This 2022 rodent study investigated glucoraphanin’s effects on reducing uric acid:

“Hyperuricemia is a chronic disease characterized by abnormally elevated serum uric acid levels. Sulforaphane could lower uric acid by decreasing urate synthesis and increasing renal urate excretion in hyperuricemic rats.

A hyperuricemia model was established by administering feedstuffs with 4% potassium oxonate and 20% yeast. Forty male Sprague–Dawley rats were randomly divided into the normal control, hyperuricemia, allopurinol, and sulforaphane groups. Animals were treated by oral gavage for six consecutive weeks, and then phenotypic parameters, metabolomic profiling, and metagenomic sequencing were performed.

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We identified succinic acid and oxoglutaric acid as critical host-gut microbiome co-metabolites. Sulforaphane improved diversity of microbial ecosystems and functions, as well as metabolic control of the kidney. Sulforaphane exerted its renoprotective effect through epigenetic modification of Nrf2 and interaction between gut microbiota and epigenetic modification in hyperuricemic rats.

Limitations of this study include:

  1. We used glucoraphanin bioactivated with myrosinase for our experiments. Future experiments may directly involve sulforaphane.
  2. Bioinformatics analysis resulted in speculations that require further experimental testing.
  3. Further investigation of interactions between microbiota and the host epigenome is still needed.”

https://www.sciencedirect.com/science/article/pii/S209012322200251X “Sulforaphane-driven reprogramming of gut microbiome and metabolome ameliorates the progression of hyperuricemia”

It was a stretch to label treatment subjects as the “sulforaphane group” by claiming “Glucoraphanin (10 mg/kg) was metabolized to SFN by myrosinase as described in previous studies.” Both this and the referenced 2014 study “(RS)-glucoraphanin purified from Tuscan black kale and bioactivated with myrosinase enzyme protects against cerebral ischemia/reperfusion injury in rats” measured glucoraphanin and myrosinase, but not sulforaphane.

A human equivalent to this study’s daily glucoraphanin intake of 10 mg / kg weight would be (.162 x 10 mg) x 70 kg = 113 mg. Whether 10 mg was dry or wet weight wasn’t disclosed.

If 10 mg was wet, 113 mg is a little more than twice our model clinical trial’s average glucoraphanin intake of 51 mg fresh weight from eating 30 grams / day of super sprouts. In April 2020’s Understanding a clinical trial’s broccoli sprout amount, a study coauthor said:

“We considered 30 g and 60 g to be 1/2 and 1 portion per day, respectively, of broccoli sprouts. When we carried out tests with consumers, previous to the bioavailability studies, higher amounts per day were not easy to consume and to get eaten by participants.”

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Broccoli sprouts activate the AMPK pathway, Part 4

gettingwell4 4-5 stars Advanced knowledge, Cerebrum, Dopamine, Epigenetics, Hippocampus, Immune system, Limbic system, Memory, Neurochemicals, Stress , , , , ,

Today someone viewed the 2020 Part 3 of Broccoli sprouts activate the AMPK pathway which lacked citations at the time. Checking again, here are three citing 2022 papers, starting with a review:

“Nrf2 is an important transcription factor that regulates expression of a large number of genes in healthy and disease states. Nrf2 regulates expression of several key components of oxidative stress, mitochondrial biogenesis, mitophagy, autophagy, and mitochondrial function in all organs of the human body, and in the peripheral and central nervous systems.

Overall, therapeutic drugs including sulforaphane that target Nrf2 expression and Nrf2/ARE pathway are promising. This article proposes additional research in Nrf2’s role within Parkinson’s disease, Huntington’s disease, and ischemic stroke in preclinical mouse models and humans with age-related neurodegenerative diseases.”

https://www.sciencedirect.com/science/article/pii/S1568163722001982 “Role of Nrf2 in aging, Alzheimer’s and other neurodegenerative diseases” (not freely available) Thanks to Dr. P. Hemachandra Reddy for providing a copy.

One of the Part 3 study’s coauthors contributed to this very detailed review:

“Due to observed overlapping cellular responses upon AMPK or NRF2 activation and common stressors impinging on both AMPK and NRF2 signaling, it is plausible to assume that AMPK and NRF2 signaling may interdepend and cooperate to readjust cellular homeostasis.

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The outcome and underlying signaling events of AMPK-NRF2 crosstalk may diverge between:

  1. in vitro and in vivo studies (one cell type in isolation vs inter-organ crosstalk in living organisms);
  2. Different cell types/organs/organisms of different cultivation conditions, genetic background, age or sex;
  3. Different stress-regimens (chronic vs acute, nature of stress (lipotoxicity, redox stress, xenobiotic, starvation, etc));
  4. Different modes of Nrf2 or AMPK activation and inhibition (genetic vs pharmacological, constitutive vs transient/intermittent, systemic vs organ-specific, electrophilic vs PPI, allosteric vs covalent, or pan vs subtype-specific);
  5. Different target genes with distinct promoter and enhancer structure; or
  6. Different timing of activation.

The latter should deserve increased attention as Nrf2 is one of the most cycling genes under control of the circadian clock. Feeding behavior, metabolism and hence AMPK activity follow and substantiate the biological clock, indicating an entangled circadian regulation of metabolic and redox homeostasis.”

https://www.sciencedirect.com/science/article/pii/S089158492200497X “AMPK and NRF2: Interactive players in the same team for cellular homeostasis?”

A third citing paper was a study of lens cells that provided an example of similar metformin effects noted in Part 2 of Broccoli sprouts activate the AMPK pathway:

“Loss of Nrf2 and Nrf2 antioxidant genes expression and activity in aging cells leads to an array of oxidative-induced deleterious responses, impaired function, and aging pathologies. This deterioration is proposed to be the primary risk factor for age-related diseases such as cataracts.

AMPK regulates energy at physiological levels during metabolic imbalance and stress. AMPK is a redox sensing molecule, and can be activated under cellular accumulation of reactive oxygen species, which are endogenously produced due to loss of antioxidant enzymes.

The therapeutic potential of AMPK activation has context-dependent beneficial effects, from cell survival to cell death. AMPK activation was a requisite for Bmal1/Nrf2-antioxidants-mediated defense, as pharmacologically inactivating AMPK impeded metformin’s effect.

Using lens epithelial cell lines (LECs) of human or mouse aging primary LECs along with lenses as model systems, we demonstrated that metformin could correct deteriorated Bmal1/Nrf2/ARE pathway by reviving AMPK-activation and transcriptional activities of Bmal1/Nrf2, resulting in increased antioxidants enzymatic activity and expression of Phase II enzymes. Results uncovered crosstalk between AMPK and Bmal1/Nrf2/antioxidants mediated by metformin for blunting oxidative/aging-linked pathobiology.”

https://www.mdpi.com/2073-4409/11/19/3021/htm “Obligatory Role of AMPK Activation and Antioxidant Defense Pathway in the Regulatory Effects of Metformin on Cellular Protection and Prevention of Lens Opacity”

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If you were given a lens to see clearly, would you accept it?

gettingwell4 4-5 stars Advanced knowledge, Amygdala, Brainstem, Cerebrum, Cortisol, Epigenetics, Hippocampus, Hypothalamus, Limbic system, Locus coeruleus, Lower brain, Memory, Neurochemicals, Primal Therapy, Serotonin, Stress , , , , , , , ,

Two papers, starting with a 2022 rodent study of maternal behaviors’ effects on offspring physiologies:

“Early life adversity (ELA) is a major risk factor for development of pathology. Predictability of parental care may be a distinguishing feature of different forms of ELA.

We tested the hypothesis that changes in maternal behavior in mice would be contingent on the type of ELA experienced, directly comparing predictability of care in the limited bedding and nesting (LBN) and maternal separation (MS) paradigms. We then tested whether predictability of the ELA environment altered expression of corticotropin-releasing hormone (Crh), a sexually-dimorphic neuropeptide that regulates threat-related learning.

MS was associated with increased expression of Crh-related genes in males, but not females. LBN primarily increased expression of these genes in females, but not males.”

https://www.sciencedirect.com/science/article/pii/S2352289522000595 “Resource scarcity but not maternal separation provokes unpredictable maternal care sequences in mice and both upregulate Crh-associated gene expression in the amygdala”

I came across this first study by it citing a republished version of 2005 epigenetic research from McGill University:

“Early experience permanently alters behavior and physiology. A critical question concerns the mechanism of these environmental programming effects.

We propose that epigenomic changes serve as an intermediate process that imprints dynamic environmental experiences on the fixed genome resulting in stable alterations in phenotype. These findings demonstrate that structural modifications of DNA can be established through environmental programming and that, in spite of the inherent stability of this epigenomic marker, it is dynamic and potentially reversible.”

https://www.tandfonline.com/doi/full/10.31887/DCNS.2005.7.2/mmeaney “Environmental programming of stress responses through DNA methylation: life at the interface between a dynamic environment and a fixed genome”

This post commemorates the five-year anniversary of Dr. Arthur Janov’s death. Its title is taken from my reaction to his comment on Beyond Belief: Symptoms of hopelessness. Search his blog for mentions of the second paper’s coauthors, Drs. Meaney and Szyf.

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Measuring epigenetic DNA causes

gettingwell4 5+ stars Premium, Epigenetics, Immune system, Stress , , ,

This 2022 human cell study investigated DNA methylation and aging:

“Models based on DNA methylation can be used to predict the age of biological samples, but their interpretability is limited due to the lack of causal inferences. Neither existing epigenetic clocks nor DNA methylation changes are enriched in causal CpG sites. Causal CpGs include similar numbers of sites that contribute to aging and protect against it, yet their combined contribution negatively affects age-related traits.

One general approach for developing anti-aging interventions is to identify molecular changes during aging and use these changes as targets to modulate the aging process. A similar idea has also been applied to evaluate potential longevity interventions. However, this logic is intrinsically flawed, as correlation does not imply causation, and age-related changes are not necessarily causal to age-associated declines.

We developed a framework for integrating causal knowledge into epigenetic clock models and constructed DamAge and AdaptAge that measure age-related damaging and adaptive changes, respectively. DamAge acceleration is associated with various adverse conditions (e.g., mortality risk), whereas AdaptAge acceleration is related to beneficial adaptations.

causality clocks

We found that transcription factor (TF)-binding sites of BRD4 and CREB1 are enriched with CpG sites whose methylation levels promote healthy longevity, and TF-binding sites for HDAC1 are enriched with CpG sites whose methylation levels decrease healthy longevity.

  • BRD4 contributes to cell senescence and promotes inflammation, and higher DNA methylation at BRD4 binding sites may inhibit the downstream effects of BRD4 and promote healthy longevity.
  • CREB1 is related to type II diabetes and neurodegeneration, and mediates the effect of calorie restriction. Our data suggest that higher methylation at CREB1-binding sites may support its longevity effects.
  • HDAC1 is a histone deacetylase, and its activity increases with aging and may promote age-related phenotypes. Increased DNA methylation at HDAC1 binding sites may causally inhibit healthy longevity.

Our causality-informed clock models provide novel insights into the aging mechanisms and testing interventions that delay aging and reverse biological age.”

https://www.biorxiv.org/content/10.1101/2022.10.07.511382v1 “Causal Epigenetic Age Uncouples Damage and Adaptation”

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How to measure biological age?

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

As mentioned in Week 127, I had biological age measured earlier this month, and received five reports two days ago on Sunday. Part of the company’s process is to follow up their reports (intrinsic aging, immune aging, pace of aging, telomere length, weight loss) with a consulting session to review and interpret, which lasted an hour yesterday.

Part of our conversation revolved around comparing my measurements with other customers. These people are a different population than people usually sampled for aging and other biomarkers, because people who pay to get their biological age measured probably actionably want to improve it.

We’ll see which items I asked the consultant to pass on to the company produce responses, and which interfere with their business or they’re too busy to get back to me. I offered more than a half-dozen specifics, but held back on items I didn’t think the consultant would adequately communicate.

I didn’t argue with the consultant’s recommendations for quercetin supplementation (at 4% bioavailability?) as part of a treatment for senescence (not measured in any of the reports?). I didn’t offer to follow-up with studies demonstrating yeast cell wall β-glucan (new to the consultant) effects on immune report findings here in my 19th year of taking it every day.

I did argue with their recommendation to take DHEA-S. I changed my mind about taking it a year and a half ago, but left blog posts up such as Take responsibility for your one precious life – DHEA for evidence that I’m learning.

Epigenetic clocks per The epigenetic clock theory of aging generally view biological aging as “an unintended consequence of both developmental programmes and maintenance programmes, the molecular footprints of which give rise to DNAm [DNA methylation] age estimators.”

So what would be appropriate anti-aging actions for customers to take? Should customers try to emulate youthful biological markers, and supplement DHEA-S to impact serum levels of insulin-like growth factor 1?

I don’t think so. Our bodies never evolved feedback mechanisms to determine “Time to stop the growth programs, you’ve survived to reproduction age.” Older people achieving teenagers’ DHEA-S levels and activating IGF-1 pathways, pretty much guarantees further biological aging as “an unintended consequence of both developmental programmes and maintenance programmes.”

It’s too early to recommend these biological aging measurements. We’ll see where it goes.

One good thing is the company wants their customers to tell them everything about what they’re doing. I exercise at least a half hour every day, eat Avena nuda oats for breakfast and AGE-less chicken vegetable soup for dinner, and take the following:

Before breakfast
– 3-day-old microwaved broccoli / red cabbage / mustard sprouts started from 10.7 grams of seeds, with nothing else an hour before or after
– Yeast cell wall β-glucan (Glucan 300), 1500 mg, with nothing else an hour before or after

Breakfast, lunch, and dinner
– Hyaluronic acid, Nature’s Lab, 1 serving total
– Boron, Swanson Triple Boron Complex, 9 mg total

Breakfast and dinner
– Acetyl-L-carnitine, 1 g total
– Balance oil, which blends linoleic acid 1400 mg with linolenic acid 350 mg, 2 times
– Betaine anhydrous, 3 g total
– Glucosamine hydroxychloride 1.5 g total, with chondroitin sulfate 1.2 g total
– Taurine, 2 g total
– 3-day-old Avena sativa oat sprouts started from 20 g seeds, 2 times

Breakfast only
– Minerals and vitamins, RDA mainly, Kirkland Signature Daily Multi
– D3 25 mcg
– Calcium alpha-ketoglutarate 1 g

Lunch only
– Vitamin K2 MK-7 600 mcg

Dinner only
– D3 50 mcg
– Zinc monomethionine 30 mg with 0.3 mg copper
– Lutein 25 mg with 5 mg zeaxanthin

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An inflammation clock

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

Here are six 2022 papers that either cited the second study of Variable aging measurements, or provided further evidence for its findings. Let’s start with a citing study:

“This study aimed to investigate expression patterns and prognostic values of the inflammatory aging clock (iAge) in glioblastoma (GBM), and its relations with stem cells. Similar to epigenetic clocks and transcriptomic clocks, iAge could track multifaceted aging phenotypes and have clinical significance in translation medicine.

iAge was positively correlated with chronological age, and highly associated with immune cells and inflammatory activities. iAge could serve as a prognostic biomarker for overall survival, and could precisely predict GBM stem cells stemness.

We identified the physiological importance and function of iAge in GBM, and provided novel insights into how iAge is a critical event for development of GBM.”

https://www.frontiersin.org/articles/10.3389/fgene.2022.925469/full “Inflammatory aging clock: A cancer clock to characterize the patients’ subtypes and predict the overall survival in glioblastoma”

Beginning with a human osteoporosis study, five papers investigated cytokine CXCL9, which the iAge study found to be “clearly actionable as shown by our experiments in CXCL9 where we can reverse aging phenotypes.”

“We assessed whether levels of CXCL9 and CXCL10 were elevated in human serum samples of older adults who had incident hip fractures. Our findings revealed higher serum levels of CXCL9 in pre-fracture blood samples of men with subsequent hip fractures, compared with their non-fracture controls. There was no such difference in CXCL9 serum levels between cases and controls in women.

Serum CXCL9 improved the prediction of osteoporotic hip fracture in men. The association between CXCL10 and hip fracture risk was not statistically significant in either sex.

While our epidemiologic findings are supported by experimental data providing the mechanistic pathway for CXCL9 in regulating osteoclast recruitment, further studies are needed to confirm validity of our findings and determine their generalizability to other study populations. Underlying biological mechanisms that limit our findings to men but not women require further investigation.”

https://asbmr.onlinelibrary.wiley.com/doi/10.1002/jbmr.4646 “CXCL9 Predicts the Risk of Osteoporotic Hip Fracture in a Prospective Cohort of Chinese Men—A Matched Case–Control Study”

Two immune-mediated skin diseases, with a vitiligo review:

“Current findings emphasize the critical role of immune cells and their mediators in the immunopathogenesis of vitiligo. IFN-γ [interferon gamma] is the primary cytokine mediator that activates the JAK/STAT pathway, causing keratinocytes to produce the key chemokines CXCL9 and CXCL10.

Interactions between immune and non-immune cells finally result in apoptosis of melanocytes. Additional investigations of these pathways may provide an opportunity for finding possible therapeutic targets, as there are currently no targeted biological drugs available for treatment of vitiligo.”

https://www.mdpi.com/2227-9059/10/7/1639/htm “Current Concepts of Vitiligo Immunopathogenesis”

and a study of psoriasis:

“CXCL9 is an important chemokine involved in T cell recruitment, and is up-regulated in plasma of patients with psoriasis. Increased CXCL9 expression can aggravate the progression of psoriasis.

cxcl9 expression

IL-1β and CXCL9 were up-regulated and CLDN8 was down-regulated in psoriasis with statistically significant differences. Identification of potential key molecular markers and signaling pathways provides potential research directions for further understanding molecular mechanisms of psoriasis.”

https://www.wjgnet.com/2307-8960/full/v10/i18/5965.htm “Identification of potential key molecules and signaling pathways for psoriasis based on weighted gene co-expression network analysis”

Two lung-related studies, first, an editorial for a human lung transplant study that isn’t freely available:

“CXCL9 and CXCL10 are chemokines that bind to the shared receptor CXCR3, potentiating T cells, mononuclear cells, and natural killer (NK) cells. Previous studies demonstrated that presence of these chemokines in bronchoalveolar lavage samples preceded development of chronic lung allograft dysfunction (CLAD).

Acute rejection and acute lung injury are known risk factors to the development of CLAD, yet this study found that increased risk was dependent on the presence of CXCL9/CXCL10 plasma elevation. Early identification of patients at risk, possibly during the active inflammatory phase, rather than once abnormal wound healing pathways dominate resulting in irreversible injury, provides an attractive opportunity for intervention.”

https://onlinelibrary.wiley.com/doi/10.1111/ajt.17135 “CXCL9 and CXCL10 plasma levels: Potential keys to unlocking CLAD risk”

and a study of smoking effects:

“We collected blood samples from 78 healthy male volunteers aged 18–60, including non-smokers (n = 30), current smokers (n = 30), and ex-smokers (n = 18). Expression levels of CXCL9/MIG [monokine induced by IFN-γ] and sIL-6R significantly increased after smoking, and continued to increase after quitting smoking.

cxcl9 smoking

Changes in related cytokines after smoking cessation are mainly restorative, while some cytokines further strengthen the trend of smoking-related changes.”

https://www.mdpi.com/1420-3049/27/12/3715/htm “Effects of Smoking on Inflammatory-Related Cytokine Levels in Human Serum”

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Natural sulforaphane effects

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

This 2022 rodent cell study used the natural form of sulforaphane to replicate experiments performed with mixtures of its natural and unnatural forms:

“Natural sulforaphane (SFN) exists as a single enantiomer with a RS absolute configuration. Most studies focusing on its biological activities, in particular its anti-inflammatory and antioxidant activities, have been conducted using its racemic (rac) form. rac-SFN has shown these effects in several in vitro and in vivo models.

(R)-sulforaphane

These findings demonstrate that (R)-SFN was able to:

  • Modulate inflammatory response and oxidative stress induced by LPS stimulation in murine peritoneal macrophages;
  • Reduce pro-inflammatory enzyme expression (iNOS, COX-2 and mPGES-1) and cytokine production (IL-1β, IL-6, IL-17, IL-18 and TNF-α);
  • Inhibit MAPK, JAK2/STAT-3, and canonical and non-canonical inflammasome signaling pathways;
  • Reduce NO and ROS levels and up-regulate the Nrf-2/HO-1 axis; and
  • Modulate epigenetic changes through histone methylation (H3K9me3) and deacetylation (H3K18ac).

(R)-SFN could be a new epinutraceutical compound useful for management of several immunoinflammatory diseases.”

https://www.mdpi.com/1424-8247/15/8/966/htm “Immunomodulatory Effects of (R)-Sulforaphane on LPS-Activated Murine Immune Cells: Molecular Signaling Pathways and Epigenetic Changes in Histone Markers”

PXL_20220902_101717612

Epigenetic effects of plasma concentrate

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

“We use data from a safety study (n = 18, mean age 74) to investigate whether human umbilical cord plasma concentrate (hereinafter Plasma Concentrate) injected weekly (1 ml intramuscular) into elderly human subjects over a 10-week period affects different biomarkers, including epigenetic age measures, standard clinical biomarkers of organ dysfunction, mitochondrial DNA copy number (mtDNA-CN), and leukocyte telomere length.

More than 20 clinical biomarkers were significantly and beneficially altered. Telomere length and mtDNA-CN were not significantly affected by treatment.

An increase in entropy means that the methylome becomes noisier. We found that entropy was significantly decreased after treatment. Decreased entropy may implicate rejuvenation of the epigenetic landscape after plasma concentrate treatments.

changes in methylation entropy

Treatment reduced DNA methylation-based GrimAge by an average of 0.82 years, suggesting a reduction in morbidity and mortality risk. By contrast, no significant results could be observed for epigenetic clocks that estimate chronological age.

Our study lends credence to the notion that there are youth-promoting factors in the secretome of umbilical cord plasma. This conclusion has also been reached by other researchers that have provided treatment with stem cells, which do not work by plasma dilution but primarily by providing humoral factors and changing the microenvironment of cells and tissues. While there may be youth-promoting microvesicles or humoral factors that are at work, we do not want to rule out the possibility that it is ‘young and undamaged’ albumin that leads to the improvements noted, especially in light of recent evidence for such a mechanism.

This first human epigenetic clock study of plasma concentrate treatments revealed age-reversal effects according to a well-established DNA methylation-based estimator of morbidity and mortality risk. Future placebo-controlled replication studies are warranted with a larger number of participants over a longer study period, which our laboratory has undertaken to pursue.”

https://onlinelibrary.wiley.com/doi/10.1111/acel.13696 “Umbilical cord plasma concentrate has beneficial effects on DNA methylation GrimAge and human clinical biomarkers”

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