Aging and Geroscience: Putting epigenetic biomarkers to the test for clinical trials
Reliable biomarkers are needed to test the effectiveness of interventions intended to improve health and extend lifespan.
- Internal Medicine Section on Gerontology and Geriatrics, Wake Forest School of Medicine, United States
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, United States
Geroscience is a developing discipline based on the premise that health can be improved by targeting aging. This hypothesis is supported by evidence that interventions (such as changes in diet) can improve the health and extend the lifespan of various animal models (López-Otín et al., 2013). Clinical trials are underway to test the geroscience hypothesis in humans (Barzilai et al., 2016). Definitive tests of the hypothesis must demonstrate reduced rates of age-related diseases and death, but the length of time and size of trial needed to test the hypothesis are both substantial. Therefore, objective, quantifiable characteristics of the aging process – known as biomarkers – that can be tracked in clinical trials are needed for the field to progress.
Useful biomarkers should meet several criteria: i) their measurement should be reliable and feasible; ii) they should be relevant to aging; iii) they should robustly and consistently predict trial endpoints, such as functional ability, disease, or death; and iv) they should be responsive to interventions such as treatments targeting aging biology (Justice et al., 2018). Practically speaking, this means that a change in the level of a biomarker should parallel changes in the susceptibility to disease, age of death, or loss of function. Interventions that target aging and support the geroscience hypothesis should therefore also lead to changes in these biomarkers, which will be reflected in the incidence or severity of age-related diseases and functional decline.
Biomarkers based on DNA methylation levels look promising. Briefly, these biomarkers quantify the proportion of cells in which a gene locus is methylated. Small but consistent changes in the methylation of some loci occur in organisms with older ages, and early methods for estimating age using epigenetics took advantage of these chronologic changes (Hannum et al., 2013; Horvath, 2013). However, critics argue that while these ‘clocks’ may be associated with chronological age, it is uncertain whether they reflect meaningful change in the context of interventions affecting the underlying biology.
Estimators based on the levels of DNA methylation are now being developed to detect a myriad of disease states and predict mortality and adverse health events, and each is unique to its calibration method. A few of these estimators are calibrated to detect aging-related outcomes, which makes them attractive as possible biomarkers for clinical trials in geroscience. Now, in eLife, Daniel Belsky (Columbia University) and colleagues in the United States, the United Kingdom, Denmark and New Zealand report the development of a new epigenetic biomarker called Dunedin Pace of Aging methylation (DunedinPoAm) that is able to detect how aging phenotypes change over time (Belsky et al., 2020).
The new biomarker relies on a composite measure called the Pace of Aging that was developed by Belsky and colleagues several years ago (Belsky et al., 2015). The Pace of Aging is calculated based on a number of age-related phenotypic changes that occur over time. In the new work this measure was used to calibrate and validate a DNA-wide methylation clock in four independent cohorts. This is in contrast to previous approaches in which methylation biomarkers were calibrated using endpoints such as chronological age, death, environmental exposure or other biomarkers.
Is DunedinPoAm developed to the point where it could be relied upon as a biomarker for clinical trials targeting biological aging? Figure 1 shows four criteria that are used to evaluate DNA methylation as a biomarker. DunedinPoAm appears to satisfy the first three criteria. It remains to be seen if it can satisfy the fourth, which involves being responsive to interventions. One of the cohorts used to validate the new approach consisted of middle-aged, non-obese adults enrolled in the CALERIE trial. This trial tested the effects of caloric restriction – an intervention that has been successful in animal models – over a period of two years. DunedinPoAm was able to predict changes in the Pace of Aging measure in the control group, but not in the group that had been calorie restricted. However, it remains to be seen whether interventions which affect aging biology change DunedinPoAm in a way that is consistent with the phenotypic changes observed in the trial.
Figure 1
Assessing DNA methylation biomarkers for use in clinical trials in geroscience.
How do five DNA methylation-based biomarkers (listed in row 1) fare when assessed against four biomarker criteria for clinical trials targeting aging (listed in column 1)? All five biomarkers meet the first three criteria, but none as yet satisfy the fourth criterion. Row 2 lists how each biomarker was calibrated. Horvath and Hannum are both epigenetic age estimators (Horvath, 2013; Hannum et al., 2013); GrimAge is a mortality estimator (Lu et al., 2019); PhenoAge is a health and lifespan biomarker (Levine et al., 2018); and DunedinPoAm is an estimator of change in aging phenotype over time (Belsky et al., 2020).
Testing the geroscience hypothesis in clinical trials is still in its early days, so it is not surprising that DunedinPoAm does not yet meet the primary criterion for an aging biomarker. However, emerging evidence suggests that methylation state may change with intervention. Data from two small clinical studies, with fewer than 15 people in the control and intervention groups, suggest that methylation-based biomarkers just might meet the minimum burden of proof (Chen et al., 2019; Fahy et al., 2019). However, the acid test for any biomarker will be whether changes in its levels predict differences in the rate of chronic disease accumulation or progression, death or other clinical trial endpoints. This will require a large study like the planned Targeted Aging with MEtformin (TAME) trial, which will last for over four years and include 3000 test subjects. This trial will test the effects of metformin, a drug currently used to treat type 2 diabetes, on FDA-informed clinical disease endpoints and functional ability. Trials like this will provide a platform for discovery, data sharing, and widescale biomarker validation to accelerate the pace of progress in geroscience.
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Metformin as a tool to target agingCell Metabolism 23:1060–1065.https://doi.org/10.1016/j.cmet.2016.05.011
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Stephen B Kritchevsky
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- Version of Record published: June 9, 2020 (version 1)
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© 2020, Justice and Kritchevsky
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Aging and Geroscience: Putting epigenetic biomarkers to the test for clinical trials
eLife 9:e58592.
https://doi.org/10.7554/eLife.58592
Further reading
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- Epidemiology and Global Health
Background:
The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania and continued local transmission.
Methods:
To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo district on the coastal mainland from 2016 to 2018.
Results:
Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to the rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias, suggests ongoing low-level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes.
Conclusions:
Our data support importation as a main source of genetic diversity and contribution to the parasite population in Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive to malaria reemergence due to susceptible hosts and competent vectors.
Funding:
This research was funded by the National Institutes of Health, grants R01AI121558, R01AI137395, R01AI155730, F30AI143172, and K24AI134990. Funding was also contributed from the Swedish Research Council, Erling-Persson Family Foundation, and the Yang Fund. RV acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 program supported by the European Union. RV also acknowledges funding by Community Jameel.
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- Epidemiology and Global Health
- Microbiology and Infectious Disease
Background: Few national-level studies have evaluated the impact of 'hybrid' immunity (vaccination coupled with recovery from infection) from the Omicron variants of SARS-CoV-2.
Methods: From May 2020 to December 2022, we conducted serial assessments (each of ~4000-9000 adults) examining SARS-CoV-2 antibodies within a mostly representative Canadian cohort drawn from a national online polling platform. Adults, most of whom were vaccinated, reported viral test-confirmed infections and mailed self-collected dried blood spots to a central lab. Samples underwent highly sensitive and specific antibody assays to spike and nucleocapsid protein antigens, the latter triggered only by infection. We estimated cumulative SARS-CoV-2 incidence prior to the Omicron period and during the BA.1/1.1 and BA.2/5 waves. We assessed changes in antibody levels and in age-specific active immunity levels.
Results: Spike levels were higher in infected than in uninfected adults, regardless of vaccination doses. Among adults vaccinated at least thrice and infected more than six months earlier, spike levels fell notably and continuously for the nine months post-vaccination. By contrast, among adults infected within six months, spike levels declined gradually. Declines were similar by sex, age group, and ethnicity. Recent vaccination attenuated declines in spike levels from older infections. In a convenience sample, spike antibody and cellular responses were correlated. Near the end of 2022, about 35% of adults above age 60 had their last vaccine dose more than six months ago, and about 25% remained uninfected. The cumulative incidence of SARS-CoV-2 infection rose from 13% (95% CI 11-14%) before omicron to 78% (76-80%) by December 2022, equating to 25 million infected adults cumulatively. However, the COVID-19 weekly death rate during the BA.2/5 waves was less than half of that during the BA.1/1.1 wave, implying a protective role for hybrid immunity.
Conclusions: Strategies to maintain population-level hybrid immunity require up-to-date vaccination coverage, including among those recovering from infection. Population-based, self-collected dried blood spots are a practicable biological surveillance platform.
Funding: Funding was provided by the COVID-19 Immunity Task Force, Canadian Institutes of Health Research, Pfizer Global Medical Grants, and St. Michael's Hospital Foundation. PJ and ACG are funded by the Canada Research Chairs Program.
