Calorie restriction and mutations: what mice revealed

Calorie restriction and mutations appear to be more closely connected than previously appreciated. Mice consuming about 30% fewer calories accumulated fewer somatic mutations across several tissues as they aged. The most unexpected difference was not concentrated in highly active genes, but in parts of the genome that cells barely transcribe.

Somatic mutations arise throughout life. DNA is damaged, copied and repaired, and these processes occasionally leave permanent sequence changes behind. Unlike inherited variants, somatic mutations are acquired by individual cells and are not passed to offspring. Most are harmless, but some can disrupt genes and contribute to diseases such as cancer.

Calorie restriction is one of the most reproducible interventions known to extend lifespan in laboratory animals. A different question, however, has remained open: does it also alter the rate at which mutations accumulate across the genome?

Fewer mutations across different tissues

Marta Grońska-Pęski and colleagues compared mice under calorie restriction with animals allowed to eat without the same restriction. To detect rare mutations, they used high-fidelity duplex DNA sequencing.

The method takes advantage of the fact that the two complementary strands of an original DNA molecule contain the same genuine genetic change. Many sequencing errors, by contrast, appear on only one strand. Requiring agreement between the two makes it possible to measure somatic mutations present at extremely low frequencies.

The researchers analyzed bulk liver and kidney tissue, isolated hepatocytes, and cerebellar neurons. The size of the effect differed among sample types, but the direction was consistent: calorie-restricted mice carried a lower genome-wide somatic mutation burden.

Both single-base substitutions and small insertions and deletions were reduced. The effect was stronger in liver cells than in kidney or brain samples.

This therefore was not a change confined to one gene or one particular type of DNA alteration. The dietary intervention affected mutation accumulation across a substantial fraction of the genome and in several distinct tissues and cell types.

The surprising signal in quiet DNA

One result was particularly counterintuitive.

In liver and kidney cells, the reduction in mutation burden was greatest in transcriptionally inactive genomic regions — stretches of DNA containing no active genes or genes that were not being used by that particular cell.

One possible explanation involves DNA repair. Actively transcribed regions already receive preferential attention from some repair systems because DNA damage can interfere with transcription. If calorie restriction primarily lowers the amount of DNA damage arising throughout the genome, relatively inactive regions might show the larger improvement because they start with less intensive repair.

That interpretation is plausible, but the study does not establish it as the mechanism.

The investigators also found that calorie restriction reduced the contribution of SBS5, a mutational signature. A mutational signature is a characteristic pattern of DNA changes that acts as a molecular footprint of the processes producing mutations. SBS5 is widespread in mammalian tissues and contributes substantially to the gradual accumulation of single-base substitutions with age, although the biological process behind it remains poorly understood.

The intervention therefore changed more than the total number of mutations. It also altered the activity of one of the background mutational processes that continuously leaves marks in mammalian genomes.

The result applies to mice subjected to a substantial, roughly 30% reduction in calorie intake. It does not demonstrate that the same intervention reduces somatic mutation accumulation in humans, nor does it show that a lower mutation burden is responsible for the longevity effects of calorie restriction observed in animals.

What it does establish is more specific. At least in mice, age-related somatic mutation accumulation is not simply a fixed consequence of time passing. Its rate can be modified by a physiological intervention. Even relatively quiet regions of the genome carried a detectable record of the conditions in which the cells had lived.