Besides this latest clock, LinAge, the mild, short term CR study also found it impacts the third generation clock, DunedinPace. Other methylation studies have also found positive impacts from CR.
Generally, think it’s about what the different clocks are designed to be able to pick up and the limitations of the older, second gen clocks and what they hence are not able to pick up.
The key thing is that the latest (third generation) clocks like Dunedin are PACE clocks - they are designed to identify the rate of aging*.
The older, second generation clocks like Pheno and Grim are AGE clocks, they are designed to predict total, cumulative biological age.
So Dunedin provides a short term, current snap shot of raging rates, while Grim and Pheno are the cumulative effects of a person entire lifetime.
More holistically:
Caloric restriction (CR), defined as lessening caloric intake without depriving essential nutrients4, results in changes in molecular processes that have been associated with aging, including DNA methylation (DNAm)5,6,7, and is established to increase healthy lifespan in multiple species8,9
Caloric restriction delays age-related methylation drift (Ref 5)
https://www.nature.com/articles/s41467-017-00607-3
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism (Ref 6)
Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions (Ref 7)
https://www.cell.com/cell-metabolism/fulltext/S1550-4131(17)30168-7?
More in detail
You are right that this mild, 2 year (so not yet long term) CR study found that:
CALERIE intervention slowed the pace of aging, as measured by the DunedinPACE DNAm algorithm, but did not lead to significant changes in biological age estimates measured by various DNAm clocks including PhenoAge and GrimAge.
At the same time
However, these DNAm measures were developed using different methods and reflect different models of aging. The PhenoAge and GrimAge clocks [both only second generation clocks] were developed to predict mortality risk at a single timepoint in mixed-age and older adults. This approach quantifies aging as a static construct of risk accumulated across the lifetime. In contrast, DunedinPACE [a third generation clock] was developed to predict multi-system physiological decline over two decades of follow-up from early adulthood to midlife. This approach quantifies aging as a dynamic construct reflecting change in risk accumulation.
Said differently
A third generation of DNAm measures of aging are referred to as pace-of-aging measures. In contrast to first- and second-generation DNAm clocks [such as PhenoAge and GrimAge], which aim to quantify how much aging has occurred up to the time of measurement, [third generation clocks like DunedinPACE] pace-of-aging measures aim to quantity how fast the process of aging-related deterioration of system integrity is proceeding.
DunedinPACE may therefore be more sensitive than PhenoAge and GrimAge to changes induced by 2 yr of CALERIE intervention.
Treatment effect estimates may therefore represent a lower-bound of the true impact of CALERIE intervention on biological aging.
Our dose–response and TOT analyses indicated that participants who achieved higher doses of CR experienced more pronounced reductions in DunedinPACE.
The finding that CR modified DunedinPACE in a randomized controlled trial supports the geroscience hypothesis, building on evidence from small and uncontrolled studies14,15,16 and contrasting with reports that biological aging may not be modifiable17
Above is from this paper published last year by Yale in Nature Aging - it’s a good read about both CR and how to think about first vs second bs third generation clocks and how they can be used in clinical clinical trials (and in N=1 biohacking):
Effect of long-term caloric restriction on DNA methylation measures of biological aging in healthy adults from the CALERIE trial
https://www.nature.com/articles/s43587-022-00357-y#ref-CR5
And now there is also the new clock published this week showing effect of even just the mild CR: 2 years of mild caloric restriction significantly reduces biological age
See also here for a lot of color how these later, 3rd gen rate of aging clocks have a lot of advantages vs the older 2nd gen cumulative amount of age clocks:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8853656/