The inherently complex and multifaceted nature of the biological aging process makes any attempt at providing biological arguments in favor or against potential anti-aging effects of specific diets rather difficult. To start with, selecting a suitable method for quantifying the biological age of an organism is a more daunting task than may seem at first. However, with the advent of novel biomarkers and measurement techniques, the past few years have provided tools for comparison and evaluation and therefore shed some light on the biomolecular mechanisms that underlie the observed health benefits of certain diets. In the upcoming series of articles, we will take a more in-depth look at these mechanisms for each individual diet and use available empirical evidence as potential guidelines to better inform dietary choices, starting today with caloric restriction (CR).
One highlight of such novel biomarkers is the recent advent of epigenetic clocks as tools for measuring biological age, currently seen as the best such tool due to their strong correlation with chronological age and all-cause mortality . Though there are some differences among them, these epigenetic clocks all base their predictions on the DNA methylation status of a specific set of CpG dinucleotides. The most important ones currently in use are Horvath’s clock, which measures 353 CpGs using DNA extracted from any tissue, Hannum’s clock, measuring 71 CpGs from whole blood DNA samples, Levine’s PhenoAge clock, which alongside DNA methylation also takes into account clinical factors like glucose or C-reactive protein levels or white blood cell count, and finally, GrimAge, which also factors in lifestyle elements such as smoking on top of DNA methylation levels[2,3,4,5].
Commonly defined as the reduction of caloric intake in a diet by 20-50% without changing the macronutrient composition, CR and its anti-aging effects is a topic we already briefly addressed in last month’s article. We would like to further develop the points we made there by focusing on the three main categories of epigenetic signatures impacted by CR: (a) DNA methylation, (b) microRNAs or miRNAs, and (c) histone modifications.
a. DNA methylation
The addition of methyl groups to nucleotides, primarily to cytosine residues within CpG dinucleotides, is considered the most important and is therefore the most well-documented of the epigenetic markers. While global methylation levels are known to decrease with old age, certain genomic regions, most commonly gene promoters, become hypermethylated [6,7]. Hypermethylation of these promoter regions has in turn been associated with gene silencing .
A study performed on human and mouse cell lines showed that the effects of CR on the transcriptomic profile are mediated by the differential expression of the SIRT1 (sirtuin-1) gene, a histone deacetylase which this study concludes might have an indirect role on DNA methylation profiles as well; this conclusion is also confirmed in other studies that do not specifically focus on CR [9,10,11]. Interestingly enough, DNA methylation changes mediated by CR seemingly persist long after the return to normal caloric intake; this finding is supported by evidence from both mice models and humans who were prenatally exposed to famine conditions [12,13]. The impact of CR on biological age was evaluated based on blood samples from participants of the CALERIE Study, finding a significant slowing of the aging process based on the DunedinPACE clock [14,15].
This type of epigenetic marker represents small non-coding RNAs that modulate post-transcriptional gene expression by either repressing translation or triggering the degradation of mRNA . Though not yet proved in humans, there is evidence of CR having significant health benefits and increasing anti-aging biomarkers in mice and rhesus monkeys. This has been documented across multiple tissue types, including skeletal muscle, vascular endothelium, brain and colon [17,18,19,20].
c. Post-translational histone modifications (PTHMs)
The last major category of epigenetic modifications consists of chemical alterations to histones, the proteins that DNA coils around. These modifications most commonly include methylation, acetylation, ubiquitination and phosphorylation. The subsequent implications of their presence and changes are complex and differ based on the modified histone, the modified residue and the exact nature of the modification, but most commonly come in the form of transcriptional activation or repression of specific genes or groups of genes .
In regards to decelerating the aging process, it is thought that the most impactful type of PTHM is the deacetylation of lysine residues by a family of enzymes called sirtuins . One study, in particular, has proven that, in an in vitro simulation of CR-like conditions performed on human lung fibroblast cultures, the sirtuin SIRT1 is involved in histone acetylation and methylation causing chromatin remodeling of the p16 promoter. This promoter in turn suppresses the expression of p16INK4a, known to be an inducer of cellular senescence . Similarly, the regulation of hTERT, a gene involved in telomere maintenance and oncogenesis, was shown to be in part caused by histone modifications in human WI-38 fibroblast cultures under the same simulated CR conditions . Other age-related histone modifiers have been documented in CR studies on yeast and mice, including NAT4 and Histone Deacetylase 2, respectively [25,26].
Caloric restriction’s health benefits and its anti-aging potential are backed up by decades of preclinical and clinical research. It affects a wide range of molecular pathways involved in the aging process, including cellular senescence, oncogenesis, nutrient sensing and many others. Since its implementation generally requires quantitative rather than qualitative changes to one’s diet, we also find it to be a rather approachable anti-aging intervention for the general public. Next time, we will take a look at another well-studied dietary regime, the ketogenic diet.