Lifespan Uber Correlation

This 2022 study developed new epigenetic clocks:

“Maximum lifespan is deemed to be a stable trait in species. The rate of biological function decline (i.e., aging) would be expected to correlate inversely with maximum species lifespan. Although aging and maximum lifespan are intimately intertwined, they nevertheless appear in some investigations to be distinct processes.

Some cytosines conserved across mammals exhibit age-related methylation changes so consistent that they were used to successfully develop cross-species age predictors. In a similar vein, methylation levels of some conserved cytosines correlate highly with species lifespan, leading to the development of highly accurate lifespan predictors. Surprisingly, little to no commonality is found between these two sets of cytosines.

We correlated the intra-species age correlation with maximum lifespan across mammalian species. We refer to this correlation of correlations as Lifespan Uber Correlation (LUC).

We overlapped genes from the LUC signature with genes found in human genome-wide association studies (GWAS) of various pathologies and conditions. With all due caution, we report that some genes from the LUC signature were those highlighted by GWAS to be associated with type II diabetes, stroke, chronic kidney disease, and breast cancer.

Human aging genes vs mammalian LUC

We used the subset of CpGs found to be significant in our LUC to build age estimators (epigenetic clocks). We demonstrated that these clocks are able to capture effects of interventions that are known to alter age as well as lifespan, such as caloric restriction, growth hormone receptor knockout, and high-fat diet.

We found that Bcl11b heterozygous knockout mice exhibited an increased epigenetic age in the striatum. BCL11B is a zinc finger protein with a wide range of functions, including development of the brain, immune system, and cardiac system.

This gene is also implicated in several human diseases including, but not limited to, Huntington disease, Alzheimer’s diseases, HIV, and T-cell malignancies. BCL11B plays an important role in adult neurogenesis, but is less studied in the context of lifespan disparities in mammals.

Bcl11b knockout affected both DNA methylation and mRNA expression of LUC genes. Our current study does not inform us about the potential role of Bcl11b in aging processes during adulthood since observed patterns could be attributed to developmental defects.

We are characterizing other genetic and non-genetic interventions that perturb the LUC clocks. These we will feature in a separate report that will uncover biological processes regulated by LUC cytosines and their associated genes.” “Divergent age-related methylation patterns in long and short-lived mammals”


Gut microbiota’s positive epigenetic effects

Three papers with the first a 2021 review:

“Gut microbiota along with their metabolites are involved in health and disease through multiple epigenetic mechanisms including:

  • Affecting transporter activities, e.g. DNA methyltransferases (DNMTs), histone methyltransferases (HMTs), histone acetyltransferases (HATs), and histone deacetylases (HDACs);
  • Providing methyl donors to participate in DNA methylation and histone modifications; and
  • miRNAs that can lead to gene transcriptional modifications.


These mechanisms can participate in a variety of biological processes such as:

  • Maturation of intestinal epithelial cells (IECs);
  • Maintenance of intestinal homeostasis;
  • Inflammatory response;
  • Development of metabolic disorders; and
  • Prevention of colon cancer.” “Dissecting the Interplay Mechanism between Epigenetics and Gut Microbiota: Health Maintenance and Disease Prevention”

A second 2022 review added subjects such as crotonate (aka unsaturated butyrate):

“Studies are carving out potential roles for additional histone modifications, such as crotonylation and ethylation, in facilitating crosstalk between microbiota and host. Lysine crotonylation is a relatively less studied histone modification that is often enriched at active promoters and enhancers in mammalian cells.

While addition or removal of crotonyl motifs can be catalyzed by specialized histone crotonyltransferases and decrotonylases, HATs and HDACs have also been reported to exhibit histone crotonyl-modifying activity. Microbiota stimulate multiple types of histone modifications and regulate activity of histone-modifying enzymes to calibrate local and extra-intestinal chromatin landscapes.” “Epigenetic regulation by gut microbiota”

A third 2021 review added subjects such as broccoli sprout compounds’ epigenetic effects:

“Glucosinolates are converted into isothiocyanates (ITCs) by bacteria that regulate host epigenetics. Levels of ITCs produced following broccoli consumption are highly dependent on the functional capacity of individual microbiomes, as much interindividual variability exists in gut microbiota composition and function in humans.

Sulforaphane inhibits HDAC activity both in vitro and in vivo, and protects against tumor development. Microbial-mediated production of ITCs represents a strong diet-microbe interaction that has a direct impact on host epigenome and health.” “The interplay between diet, gut microbes, and host epigenetics in health and disease”

Clearing the channel


The aryl hydrocarbon signaling pathway

I’ll emphasize this densely packed 2021 review’s broccoli sprout compounds / gut microbiota / health interactions:

“The aryl hydrocarbon receptor (AhR) senses cues from environmental toxicants and physiologically relevant dietary/microbiota-derived ligands. AhR signaling mediates bidirectional host-microbiome interactions in a wide range of cellular functions in a ligand-, cell type-, species-, and context-specific manner.

Brassicaceae family plants are rich sources of glucobrassicin, the glucosinolate precursor of indole-3-carbinol (I3C). Glucobrassicin can be enzymatically hydrolyzed and converted into I3C by myrosinase, which is present in intact plant cells and gut microbiota.

I3C activates AhR but exhibits low binding affinity. However, in acidic conditions found in the stomach, I3C undergoes acid condensation reaction to generate a variety of more potent AhR ligands, such as 3,3′-diindolylmethane (DIM).

AhR activation by natural AhR ligands (e.g., I3C) has been shown to prevent pathogenic gut microbial dysbiosis by altering gut microbiome composition in mice with colitis. Depletion of AhR ligands in the diet decreased α diversity of gut microbiota, while I3C supplementation restored microbiota composition.

I3C treatment is effective for treating IBD patients, partly by upregulating IL-22. Targeting AhR could modulate the amplitude and duration of IL-22 signaling to treat IBD patients.

Administration of I3C or DIM significantly reduced the number of tumors in the cecum and small intestine. Supplementation of I3C reduces the number of colorectal tumors in WT, but not in AhR null mice.


Gut microbiota and diet are major sources of AhR ligands that influence the whole body, including gut, liver, brain, and the immune system. Many human diseases are associated with decreased circulating levels of AhR ligands, partly due to dysbiosis.

The ability of AhR signaling to regulate self-renewal and differentiation of intestinal stem cells intrinsically or extrinsically has recently been brought into the spotlight.” “Diet–Host–Microbiota Interactions Shape Aryl Hydrocarbon Receptor Ligand Production to Modulate Intestinal Homeostasis”

Young hawk


Every baby needs a sugar mama

This 2021 in vitro study examined butyrate producers:

“Butyrate produced by gut microbiota has multiple beneficial effects on host health. Oligosaccharides derived from host diets, and glycans originating from host mucus, are major sources of its production.

Butyrate is the major energy source for epithelial cells in the distal colon, induces differentiation of colonic regulatory T cells, and functions as an inhibitor of host histone deacetylase. These activities are essential for documented beneficial properties of butyrate, including anti-inflammation, gut immune homeostasis, inhibition of proliferation, and induction of apoptosis of colorectal cancer cells.

FOS-type oligosaccharides (kestose, nystose, fructooligosaccharide) were metabolized by only 6 of 14 butyrate-producing strains tested:

Growth of butyrate producers

Faecalibacterium prausnitzii, which is the most abundant butyrate producer in the healthy human gut, metabolized only FOS-type oligosaccharides among tested oligosaccharides. Anaerostipes spp. exhibited a similar pattern, except that A. caccae metabolized kestose but not nystose.

Glycoside hydrolase (GH)32 enzymes exhibiting FOS degradation activities were conserved in all six strains metabolizing FOS, and in three of the eight strains that did not metabolize FOS. This suggests that GH32 enzymes in those three strains are not actively used in metabolism.

The present study highlighted that even if functional genes are present in microbes, they are sometimes unable to metabolize substrates. This should be carefully considered in metagenomic studies to understand metabolic potential of gut microbiota.” “Characterization of fructooligosaccharide metabolism and fructooligosaccharide-degrading enzymes in human commensal butyrate producers”

These researchers had some work to do to show that selected strains’ characteristics were representative of their species. This post’s title was excerpted from Citation 37.


Nrf2 and circadian rhythm

This 2021 rodent study investigated aging’s effects:

“We investigated aging consequences on temporal patterns of antioxidant defenses, molecular clock machinery, and blood pressure.

We observed circadian rhythms of catalase (CAT) and glutathione peroxidase (GPx) mRNA expression, as well as ultradian rhythms of Nrf2 mRNA levels, in the hearts of young adult rats. We also found circadian oscillations of CAT and GPx enzymatic activities, reduced glutathione (GSH), and BMAL1 protein.

Aging abolished rhythms of CAT and GPx enzymatic activities, phase-shifted rhythm acrophases of GSH and BMAL1 protein levels, and turned circadian the ultradian oscillation of Nrf2 expression.

aging changes Nrf2 oscillation

Moreover, aging phase-shifted the circadian pattern of systolic blood pressure. In conclusion, aging modifies temporal organization of antioxidant defenses and blood pressure, probably as a consequence of disruption in the circadian rhythm of the clock’s transcriptional regulator, BMAL1, in heart.” “Aging disrupts the temporal organization of antioxidant defenses in the heart of male rats and phase shifts circadian rhythms of systolic blood pressure” (not freely available)

A human equivalent to this study’s 3-month-old young adult group is around 19 years. The older group’s 22-month age is roughly equivalent to a 68-year-old human.

Couldn’t say whether Nrf2 oscillations flattening out with age is specific to heart tissue, or is a more general trend. I’m pretty sure that humans have to make good things happen while aging, because bad things are pre-programmed.

I came across this study from a citation trail of a comment to Eat broccoli sprouts for your workouts. I didn’t curate the mentioned study because one of its coauthors tainted it by designing and supervising Problematic rodent sulforaphane studies.

How would you answer the comment’s question?

Repairs needed: The story of 2021


Resistant starch, β-glucan, and inulin

This 2021 paper reported results of two related human clinical trials:

“Lean and prediabetic overweight/obese men were included in two randomized crossover studies. In one study, participants received supplements of either long-chain inulin+resistant starch (INU+RS), INU or maltodextrin (placebo, PLA) the day prior to a clinical investigation day. The second trial studied beta glucan+RS (BG+RS) versus BG and PLA.

1. In lean men, INU+RS increased breath hydrogen and fasting plasma butyrate, which was accompanied by increased energy expenditure, carbohydrate oxidation, and peptide YY, and decreased postprandial glucose concentrations compared to PLA.

In prediabetic men, INU+RS increased plasma acetate compared to INU or PLA, but did not affect metabolic parameters.

The three supplements were:

  • INU: 12 g long-chain inulin in combination with 5.43 g maltodextrin to make it isocaloric.
  • INU+RS: 12 g of long-chain inulin in combination with 9.39 g 80% resistant starch RS2 granular potato starch.
  • PLA: 11.43 g maltodextrin.

2. BG+RS increased plasma butyrate compared to PLA in prediabetic individuals, but did not affect other fermentation/metabolic markers in both phenotypes.

The three supplements were:

  • BG: 35.25 g 34% yeast beta glucan with 5.43 g maltodextrin to make it isocaloric.
  • BG+RS: 35.25 g 34% yeast beta glucan in combination with 9.39 g 80% RS2 granular potato starch.
  • PLA: 11.43 g maltodextrin + 13.1 g protein and 4.58 g fat, same type and amounts as in the beta glucan product.

Effects of one-day consumption with a ‘slowly fermentable’ complex INU or BG alone, or INU or BG combined with a more ‘rapidly fermentable’ RS on substrate and energy metabolism were studied. These fiber mixtures were selected based on a high distal colonic acetate and total SCFA production in a validated in vitro model of the human colon.

Further research should study whether longer-term supplementation periods are required to elicit beneficial metabolic health in prediabetic individuals.” “Fiber mixture-specific effect on distal colonic fermentation and metabolic health in lean but not in prediabetic men”

The Discussion section related these findings to other research. Not sure how these researchers determined a trial time period. As Reviewing clinical trials of broccoli sprouts and their compounds pointed out:

“Biomarkers of effect need more time than biomarkers of exposure to be influenced by dietary treatment.”


Sulforaphane vs. too much oxygen

This 2021 rodent study investigated perinatal effects of hyperoxia and sulforaphane:

“We demonstrated that early-life oxidant-induced acute lung injury had significant consequences later in life on NRF2-dependent respiratory syncytial virus (RSV) susceptibility in mice. We also determined that increased antioxidant conditions in utero potentially contribute to a decreased risk of postnatal airway disease as we found that prenatal antioxidant sulforaphane (SFN) protected developing lungs from bronchopulmonary dysplasia (BPD)-like oxidative pathogenesis in mice.

Unexpectedly, our results indicated that prenatal SFN-mediated postnatal protection against BPD-like phenotypes are not NRF2-dependent. Prenatal SFN markedly improved hyperoxia-caused severe BPD-like lung injury parameters in Nrf2−/− pups while we observed relatively marginal protection by in utero SFN in hyperoxia-resistant Nrf2+/+ pups.

SFN is a strong NRF2 and ARE gene inducer for cytoprotection by NRF2 stabilization. However, SFN also acts through other mechanisms, including NF-κB inhibition, MAPK activation, and histone deacetylase inhibition for anti-inflammation, chemoprevention, apoptosis, and autophagy.

Our study provided new insights into infant oxidant lung injury severity influence on persistence of pulmonary morbidity and therapeutic intervention for NRF2 agonists. Our results also provided justification for further studies on feto–placental barrier crossing of SFN metabolites and SFN-triggered molecular and epigenetic aspects of maternal cues for barrier and fetal lung signaling.” “Murine Neonatal Oxidant Lung Injury: NRF2-Dependent Predisposition to Adulthood Respiratory Viral Infection and Protection by Maternal Antioxidant”

This study’s oral human-equivalent dose for treatment dams was 9 mg sulforaphane (1.67 mg x .081 x 70 kg) every other day during the last half of pregnancy. A small dose per How much sulforaphane is suitable for healthy people?

“The daily SFN dose found to achieve beneficial outcomes in most of the available clinical trials is around 20-40 mg.”


Eat broccoli sprouts for your workouts

This 2021 human study investigated effects of pre- and post-workout glucoraphanin intake:

“The tablet used in this study contained 30 mg of glucoraphanin, a precursor of sulforaphane (SFN), which is converted to SFN in the intestinal lumen by intestinal microflora. Subjects took one tablet of SFN supplement per meal, three times a day. Healthy men without exercise habits, smoking, or medication were included in the experiment:

eccentric exercise subjects

Pain on palpation reached its peak 1–2 days after exercise and recovered to baseline 5 days after exercise. Muscle soreness on palpation and range of motion were significantly lower 2 days after exercise in the sulforaphane group:

range of motion

Serum malondialdehyde, an indicator of exercise-induced oxidative stress, showed significantly lower levels 2 days after exercise in the sulforaphane group. SFN intake may protect the balance of antioxidant capacity and suppress excessive oxidative stress caused by exercise.

Continuation of SFN intake – from 2 weeks before and up to 4 days after eccentric exercise – suppressed exercise-induced oxidative stress and inhibited muscle soreness and muscle damage. To our knowledge, this study is the first to analyze these effects of SFN in humans.” “Effect of a sulforaphane supplement on muscle soreness and damage induced by eccentric exercise in young adults: A pilot study”

This study found that four days wasn’t enough time for 19-to-23-year-old men to fully recover from bicep eccentric exercise, regardless of glucoraphanin treatment or control group status. What’s an appropriate exercise recovery time? found a similar result using taurine as treatment with 20-to-33-year-old recreationally fit men who didn’t fully recover from bicep eccentric exercise after three days.

These researchers referenced Autism biomarkers and sulforaphane to acknowledge that this study’s 30 mg of glucoraphanin three times daily wasn’t sufficient to fully activate Nrf2 signaling pathways:

When SFN was added to PBMCs of healthy subjects in ex vivo experiments, NQO1 expression was increased, while HO-1 was not increased at a low SFN concentration (0.5 µM). However, when 2 or 5 µM of SFN was added to PBMCs, both NQO1 and HO-1 gene expression were increased. Concentration of the SFN supplement may be a reason why the amount of supplementation used in our protocol did not increase HO-1 expression.”

I create isothiocyanates by microwaving 3-day-old broccoli / red cabbage / mustard sprouts at 1000 W to 60°C (140°F) shortly before eating them. Unlike this study, I don’t depend on metabolism after the stomach to produce isothiocyanates from glucosinolates:

  • Less dependence on these subjects’ gut microbiota for sulforaphane production would have reduced a source of dose variability. Broccoli sprout compounds and gut microbiota first paper reviewed that subject.
  • Glucoraphanin intake with nothing else an hour before and after would have also reduced chances of sulforaphane loss by reacting with food. See Week 19 item 2 for two studies that found eating protein, fats, and fiber along with broccoli sprouts lowered isothiocyanates’ bioavailability.

Still, this was a step forward in research. Have fun with New Year’s resolutions.