Long-term caloric restriction has a small effect on the DNA methylation measure of the pace of aging

By Pooja Toshniwal PahariaReviewed by Danielle Ellis, B.Sc.Feb 13 2023

In a recent letter published in Nature Aging, researchers assessed the impact of caloric restriction (CR) on biological aging among the comprehensive assessment of the long-term effects of reducing the intake of energy (CALERIE) randomized controlled trial participants.

Background

Several therapies have been identified to increase biological aging in humans. The intervention trials require months to years for clinical translation, but age-related processes take years to decades to cause illness. Measures that can summarize age-associated biological pathway alterations can overcome the challenge. Biological age quantification measures that can estimate future illness, morbidity, and death and also detect age-associated short-term changes could be used as alternate endpoints in interventional trials on aging.

According to the geroscience hypothesis, therapies that can retard or reverse age-associated molecular changes could prevent or delay the onset of chronic illnesses and increase lifespan. Caloric restriction by reducing calorie intake without altering intake of important nutrients could alter age-associated molecular changes such as deoxyribonucleic acid (DNA) methylation (DNAm) and, therefore, increase the lifespan.

About the trial

In the present study, researchers reported findings of the CALERIE trial, which was performed to assess the impact of restricting the caloric intake by 25.0% over two years among healthy adult individuals with body mass index <27.90 kg m⁻², comprising males aged 21 to 50 years, and premenopausal females aged 21 to 47 years).

The CALERIE trial was conducted at three clinical centers in the United States to deliver therapy with known age-retarding properties in animals. The trial comprised 220 non-obese adults, randomized in a 2:1 ratio to 25.0% caloric restriction diets (intervention) and ad libitum diets (control) diets for two years.

CR levels were quantified based on energy needs (determined semi-annually based on the two-week doubly labeled water (DLW) periods). Blood DNAm analysis information was obtained for 197 individuals, of which 128 and 69 individuals were on CR diets and control diets, respectively. DNA methylation assays were performed using the blood specimens of the CALERIE randomized controlled clinical trial participants, and the data were merged with secondary information from the clinical trial.

Biological aging was measured based on blood DNA methylation changes using algorithms published previously based on molecular changes underlying the age-associated gradual system integration losses. The first-generation DNAm clocks, such as the Horvath clock and Hannum clock, were used for comparing samples of differently aged individuals.

The intent-to-treat (ITT) analysis was performed using second-generation DNA methylation clocks such as the GrimAge and PhenoAge that improved aging quantification by emphasizing death risk differences rather than age-associated differences, and the third-generation DunedinPACE clock for measuring measure the speed of aging, using the repeated-measures analysis of covariance (ANCOVA) method.

DNAm PCs/PC clocks were used to evaluate test-retest reliability. Follow-up assessments of dose-response effects and the treatment-on-the-treated (TOT) effects were conducted at one year and two years post-intervention. The TOT effects were evaluated using the instrumental variables (IV) approach. The study participants also received individual-level and intensive group behavioral counseling sessions once weekly. The sensitivity analyses evaluated leukocyte count alterations by the CALERIE therapy, and sex-based differences in therapy effects. The extent of weight loss was compared to an estimated weight loss trajectory of 16% loss of weight within one year with subsequent maintenance.

Results

The average age of the study participants was 38.0 years, 77.0% of them were White, and 70.0% of them were female. The methods proposed to quantify biological aging used in the study could estimate aging-associated health deterioration and death. CALERIE intervention retarded aging, as determined using the DunedinPACE DNA methylation clock, but significant age-associated alterations measured using the PhenoAge and GrimAge clocks were not observed. The therapy effects were small; however, the modest retardation of aging observed could profoundly impact public health.

CR treatment lowered participants’ DunedinPACE within one year, with the effect maintained over two years. No dose-response effects were observed using the GrimAge and PhenoAge clocks; however, individuals attaining greater CR experienced more profound DunedinPACE reductions. The sensitivity analysis yielded similar results. DunedinPACE showed high test-retest reliability and correlated strongly with aging endpoints in validation studies.  

Most of the CALERIE trial participants could not attain the prescribed caloric restriction of 25%. Despite the imperfect adherence, therapy group participants showed considerable loss of weight and associated body compositional alterations, with improved cardiovascular health and retardation of age-associated physiological alterations.

Conclusion

Overall, the study findings showed that CALERIE trial intervention retarded the aging process, as determined by the DunedinPACE clock, whereas the GrimAge and PhenoAge DNA methylation clocks were not significantly affected by CR.

The findings underpinned the geroscience hypothesis and highlighted DunedinPACE as a reliable aging measure for further clinical trials. However, long-term follow-up assessments are needed to investigate whether CR-induced DunedinPACE reductions could translate into greater lifespan and prevent diseases.