Almost all of the cells in your body have the same genes, but they display different forms and functions in different tissues because of epigenetic differences.
Epigenetics is a fairly new science.
The word was first coined in 1942 by Conrad Waddington, in whose Edinburgh lab my mother was principal researcher and portrait painter (1). I remember him, hazily, and a host of brilliant scientists who tumbled through my childhood like white water. They included Aubrey Manning, Charlotte Auerbach, Goro Eguchi and Tokindo Okada, who I drove around Edinburgh on the back of my first motorbike long before he became Director of the National Institute of Basic Biology in Okazaki.
Conrad gifted me a copy of his coffee-table book ‘Behind Appearances’, which I loved. I eventually exchanged it for a trompe l’oeil version carved in wood, which served as conceptual kindling in an open fireplace for many years.
Waddington’s beautiful schematic of the epigenetic landscape, which I believe was influenced by quantum physics probability diagrams of the time, was fundamentally correct; and in the decades that followed much of the machinery that underpins that landscape has been fleshed out.
As we form in utero and after, initially pluripotent cells roll down the epigenetic valleys and at various bifurcation points, by turning different genes up or down, become precursors for the roughly 200 cell types that make up a person.
It’s a highly coordinated and self-referencing cellular pintable, and the volume controls for those genes are modified during development and subsequently throughout life by epigenetic markers, of which more later. These markers are influenced by internal and external factors. The science of the modification of gene expression by epigenetic markers and the way those markers are influenced by internal and external factors is epigenetics, and its core subject is the epigenome.
Unlike the genome which is predominantly static, the epigenome is dynamic and changes rapidly in response to environmental cues, acting as a buffer between nature and nurture.
Many of these changes are adaptative and positive, such as the metabolic and health benefits that accrue from physical exercise (2, 3). Others may be positive in the short term (ie in utero) but deleterious in the longer term (after birth).
This is the basis for the Developmental Origins of Heath and Disease (DOHaD) hypothesis referenced in previous posts (ie 4-6). It has given rise to the commonly expressed idea that you are what your mother and possibly what your father and grandmother ate; and although it is not all about eating, maternal nutrition and nutrition in general are clearly important.
As far back as 2011, a well-regarded team at the University of Alabama started working on an ‘epigenetic diet’ (7). By this they meant a diet replete with nutrients known to favorably modify the epigenome and to provide positive health outcomes. This diet included isothiocyanates such as sulphurophane (8), isoflavones, stilbenes, curcuminoids, catechins and other polyphenols (9, 10) and latterly prebiotic fibers, via postbiotic production (11).
All of the compounds occur almost exclusively in plant-based foods and are well represented in, for example, the notoriously healthy Mediterranean and Viking diets. Other dietary constituents such as dietary lipids exert epigenetic effects also, and present an interestingly nuanced picture (ie 12). (Clue: omega 3 HUFA’s good, omega 6 HUFA’s not so good).
Phyto- and other nutrients modify the availability and binding to DNA of three epigenetic markers; methyl and acetyl groups (which are structurally quite similar), and micro-RNA’s (13). The markers exert their effects on genes by altering the structure of DNA, a macro-molecule which is intrinsically dynamic. You could almost say it breathes.
At different stages in the growth of cells different sections of their DNA open up and become active or close down and become quieter, depending on local requirements. Here is where the markers come in. Acetylation of histones around the DNA enables it to open up and become active, thereby increasing gene expression. Methylation generally decreases gene expression, partly by switching off gene promoter sections and partly by folding DNA more tightly around its histone core.
Acetyl groups, methyl groups and the micro-RNA’s all interact at the epigenetic level (14), and as outlined above are all accessible via dietary means (13-18); because they are all involved in energy, nutrient and stress sensing (including psychological stress, 19), and thereby maintaining internal homeostasis (ie 20).
A lot of the research is obviously pre-clinical.
One beautiful example is found in protein-restricted pregnant female rats. Protein restriction reduces the availability of methyl groups. Reduced methylation opens up the promoter section of a gene that codes for glucocorticoid receptors, increasing the numbers of those receptors in the tissues of the offspring, including its liver.
The point of increased glucocorticoid receptors in the young of protein-restricted rats is to accelerate the maturation of tissues when protein is scarce, so that a small neonate can still be born with functional lungs. Unfortunately, the increased number of receptors amplifies the liver’s response to stress hormones and increases gluconeogenesis, making them prone to metabolic disorder in later life (21).
Some epigenetic changes are multi-generational. Young rats raised by methyl-depleted mothers are more reactive and anxious, and their chemistry and behaviour cast a shadow on their offspring who become similarly affected (21-23); creating what is effectively a culturally embedded shift. This likely explains some (but not all) of the racial disparities seen in public health outcomes (24).
Similar patterns develop in humans.
Women at risk of pre-term birth were formerly given synthetic glucocorticoids to prevent infant respiratory distress syndrome. This exposes the developing fetus to increased glucocorticoids, as does maternal stress during pregnancy. After birth these children ‘inherit’ the same risks as the protein-restricted rodents do: an epigenetic increase in blood pressure, tendency to overweight and metabolic disorder, and an inability to deal with stress (25-28).
On the positive side, there is evidence that an epigenetically rich diet consumed by parents might, by re-configuring their children’s DNA, protect them in later life against environmental challenges (29).
The idea that changes induced by dietary / environmental cues can be transmitted to subsequent generations has been described as a kind of neo-Lamarckism (30, 31). Lamarckism certainly influenced me, in a pseudo-epigenetic way; my geneticist father was absent for long periods during my childhood, working in Russia to help undo the destruction wreaked by the pseudo-epigeneticist Trofim Lysenko.
Other epigenetic changes, which occur within the individual over time, are age-related.
Age-related reductions in methylation rates at many DNA sites (32) have been characterized as an epigenetic clock, which measure aspects of biological ageing and age-related disease and death, including time to death (ie 33-36). This holds out the prospect of modifying deep ageing with dietary measures designed to affect epigenetic markers, and thus gene expression, shifting the epigenome, the proteome and cellular function back to an earlier and healthier pattern.
While the first clock was discovered in blood cells, subsequent research found clocks in different tissues, running at different rates depending on life experiences. In sun-aged skin, for example, the epigenetic clock is fast.
It is not entirely certain that modifying epigenetic clocks will change the ageing process. Stopping the station clock, for example, does nothing to affect the running of trains, the printing of timetables and the tidal movements of commuters. The epigenetic clock may drive clinical signs of the ageing process, it may be driven by them, or both might have a deeper driver.
But let’s assume, for the moment, that turning the epigenetic clocks back has anti-ageing effects. How would you do that?
DNA methylation is a reversible process catalysed by a well-defined group of enzymes, and depends on the availability of methyl groups. These cannot be synthesized in the body and must be obtained from the diet, making them essential micronutrients.
An inadequate dietary supply of methyl groups is very damaging. It is clinically measured as hyperhomocysteinemia, which is an independent risk factor for many serious diseases and in that sense accelerates the ageing process. Hyperhomocysteinaemia is toxic in its own right; but in the background, methyl group depletion and hyperhomocysteinemia cause extensive epigenetic dysregulation (37), which is likely as or more serious.
Sources of methyl groups include the amino acid methionine, the amino acid variant betaine, the B vitamin folate and the B-like compound choline. These methyl group donors occur in a wide range of basic foods, making it easy to obtain sufficient methyl groups from any pre-transitional (ie normal) diet. This is also true for B vitamins 2, 3, 6 and 12, which are all involved in methyl (one-carbon) metabolism.
Teleologically, the fact that methyl group donors occur in a very wide range of foods can be thought of as a safety feature, and underlies the importance of this simple -CH3 group. Socially and politically, the fact that hyperhomocystenaemia has become rather common (38, 39), is another indictment of the industrial diet which causes so much disease and death today.
Eating more methyl groups is a reasonable component in any anti-ageing strategy, and can be achieved by adding an effective donor such as betaine to your already phytonutrient-rich diet.
Be reasonable; excessive doses might well be counter-productive (40-42). As a rough guide, take enough betaine to drop your plasma homocysteine levels towards the lower end of the range found in healthy persons, ie circa 5 micromoles per liter.
Overdosing and forcing homocysteine levels lower is not recommended. DNA hypermethylation of tumor-suppressor genes, for example, might be counter-productive (ie 42, 43) if a latent cancer is already present and your many anti-cancer defenses have been degraded by your modern diet and lifestyle. Chronic inflammation disturbs methylation profiles (44) and is well known to predispose to cancer (ie 45), so Balance oil has a place here.
Smoking and alcohol disturb one-carbon metabolism, and could therefore be thought of as epigenetic anti-factors (46, 47).
There are age-related changes in histone acetylation too (48), and there is evidence linking falling acetylation with some (but not all) age-related problems (49, 50). Acetyl groups are removed from the histones around DNA by the enzyme histone deacetylase (HDAC), which is blocked very effectively by the short chain fatty acid butyrate (ie 51). Butyrate supplementation might therefore have some anti-ageing effects.
While butyrate occurs in small amounts in foods such as butter and cheese, the most significant albeit indirect dietary source is prebiotic fiber. These fibers do not contain butyrate, but once ingested they are broken down by probiotic bacteria in the large bowel in a fermentation reaction – which produces butyrate.
Intakes of prebiotic fibers have declined dramatically in the post-transitional era, and a lack of fiber has been associated with a 30% increased risk of early death (52) from a range of non-communicable degenerative diseases. This is a remarkable acceleration of the ageing process and so, although I believe most scientists in this area would caution against mega-doses of butyrate, increasing your intake of prebiotic fibers and therefore butyrate might be another way to turn epigenetic clocks back (ie 51, 53, 54).
The available data suggest that a daily intake of between 10 and 20 grams of prebiotic fiber would restore a pre-transitional microbiota (52, 55, 56), and improve your health- and lifespan (57).
The general dietary approach outlined here is designed to combine phytonutrients which modulate epigenetic markers in a protective manner (ie 58-60), with a healthy supply of those markers from the diet. It would be expected to undo much of the damage caused by the industrial diet, and to reduce the risk of many degenerative diseases.
That is already a potent anti-ageing effect, and a highly self-referential one.
Nutritional scientists used to think in terms of classical pharmacological mechanisms, borrowed from pharmaceutical pharmacology. In Newtonian nutrition, a polyphenol (for example) acted by inhibiting an enzyme (ie 61). In a more relativistic world (62) that polyphenol also exerts epigenetic effects, reducing the production of that enzyme (ie 63, 64). And it interacts with microbiotal species (ie 65, 66) which respond to each other and then exert secondary / tertiary effects in the gut and elsewhere, generating epigenetic effects of their own.
Swallowing a capsule of green tea extract, a tablespoon of fish and/or olive oil or a pinch of spice sends ripples through the body which reach into multiple tissues and cells, modifying their behaviour before reflecting and refracting in a therapeutic salsa which is flavoured by almost everything else you eat, and do (67). This is nutri-epigenomics; and there is increasing evidence that it is important (68).
‘When we try to pick out anything by itself, we find it hitched to everything else in the Universe.’ (69)
Eating an epigenetic diet should keep you healthier for longer, and give the next generation the best chance of fulfilling their biological potential (70-73). Or you could live on fast foods, die young and book an XXL coffin (74).
Take a moment for self-referral: (75 & 76, best consumed together).
Next week: When the gut-brain connection short-circuits …
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