High circulating triglycerides (TG), carried by triglyceride-rich-lipoproteins (TRL),
are associated with insulin resistance, obesity, metabolic syndrome, and type 2 diabetes
and are considered a major risk factor for cardiovascular disease. Although strategies
that lower TG and TRL to improve cardiometabolic outcomes are of major interest, there
are still many unknowns that impede therapeutic development and thwart therapeutic
success. For example, what increases the susceptibility of certain individuals to
unfavorable lipid profiles? And why are some study participants more responsive to
diet and lifestyle interventions? While considerable efforts have been made to identify
genetic variants that may account for metabolic changes across individuals, variants
with functional significance are rare, and those that have been identified do not
fully explain the high variability of lipid profiles. Hence, attention has been refocused
towards the epigenetic regulation—highly dynamic and heritable changes in gene function
without changes in DNA sequence—of genes involved in lipid and lipoprotein metabolism.
While many studies have linked altered epigenetic processing of key metabolic genes
to distinct metabolic phenotypes [reviewed in (1)], whether specific epigenetic marks
can predict the success of lifestyle interventions remains unknown. In the present
study, Li et al show that study participants with higher levels of DNA methylation
(DNAm) in the first intron of carnitine palmitoyltransferase 1 A (CPT1A)—the rate
limiting enzyme in mitochondrial fatty acid uptake and oxidation—show greater improvements
in TG and TRL when adhering to a low-fat weight-loss diet (2). Therefore, this study
reports an important observation for the first time and directly links altered epigenetic
processing of a key lipid metabolism gene to favorable lipid profiles following diet
modification.
DNAm of cytosine residues within CpG islands in promoter regions and other cis regulatory
DNA elements is a highly dynamic epigenetic mark associated with chromatin remodeling
and gene transcription. In the present study, Li et al were motivated by recent findings
from epigenome-wide associations studies linking increased levels of CPT1A DNAm to
reduced CPT1A expression and increased circulating TG and TRL (3). In a separate study,
dietary fat appears to modify CPT1A DNAm (4), leading the authors to hypothesize that
adjusting dietary fat intake could alter the relationship between CPT1A DNAm and circulating
lipid profiles. This study leveraged the POUNDS lost trial: a 2-year randomized clinical
trial comparing the ability of 4 diets with varying macronutrient content to promote
weight loss. In brief, the study involved 811 overweight adults that were assigned
to either (1) 20% fat, 15% protein, 65% carbohydrate; (2) 20% fat, 25% protein, 55%
carbohydrate; (3) 40% fat, 15% protein, 45% carbohydrate; or (4) 40% fat, 25% protein,
35% carbohydrate (5). DNAm was assessed in 538 study participants by high-resolution
methyl-capture sequencing and presented as percent of methylation over a given CpG
containing region. Importantly, standard (eg, TG, total cholesterol, high-density
lipoprotein cholesterol, and low-density lipoprotein cholesterol) and specialized
(eg, very low density lipoprotein with or without apolipoprotein C-III) lipids were
measured. Notably, the authors found that individuals with a higher baseline level
of regional DNAm at CPT1A had lower circulating TG, consistent with previous studies
(3). In addition, the authors report for the first time that higher CPT1A DNAm was
associated with even greater reductions in total TG and TRL, including very low density
lipoprotein particles without apolipoprotein C-III. Although the data presented do
not probe the molecular mechanisms leading to these observations, the findings show
for the first time that baseline methylation levels of distinct regions of a lipid
processing gene can predict changes in the metabolic parameters following dietary
intervention. Since CPT1A is primarily involved in fatty acid catabolism, Li et al's
findings suggest that reduced dietary lipids alter the transcriptional regulation
of CPT1A to increase fatty acid oxidation, leading to reduced circulating lipids within
their associated lipoprotein class.
DNAm is one of the best-characterized, yet controversial, epigenetic marks. Although
the prevailing dogma links DNAm to reduced transcription factor (TF) binding and transcriptional
repression, with the advent of more sensitive techniques it has become clear that
this model needs to be revisited. Recent models suggest that (1) TFs bind to methylated
CpGs to activate transcription, (2) DNAm is a consequence of TF binding, and (3) in
some cases DNAm does not influence TF binding [reviewed in (6)]. Therefore, the outcomes
of DNAm are largely dependent on the specific TFs and baseline transcriptional state
within a cell. In the present study, the authors show that higher levels of DNAm within
intron 1 of CPT1A are associated with lower circulating lipids, which suggests that
CPT1A expression, and hence lipid catabolism, is increased. While this directionality
is plausible, given our evolving understanding of the dynamic role of DNAm in transcriptional
regulation, our interpretation of the study is limited due to the lack of CPT1A expression
data. In addition, the dynamic methylation within intron 1 of the CPT1A gene suggests
that this region is actively modified in response to nutrient, and specifically dietary
lipid, status, but why remains unclear. Since intron 1 contains putative lipogenic
TF binding sites (eg, SREBP1c), future studies aimed at determining the effect of
DNAm on the binding of specific TFs within the CPT1A gene would be particularly informative.
Comparison of chromatin structure and accessibility (eg, ATAC seq) within the CPT1A
gene in response to dietary changes would be even more powerful and could highlight
novel lipid-sensitive regulatory elements to dramatically transform our understanding
of the nutrient–epigenome interface.
Overall, Li et al present intriguing findings that hold promise for the development
of precision dietary intervention approaches. While further studies are needed to
determine mechanism, evidently CPT1A is dynamically regulated in response to metabolic
status, and its methylation could be used to assess which dietary interventions might
have the most favorable effects on circulating lipids to mitigate the association
with cardiometabolic disease in susceptible individuals.
Disclosures
The authors have no conflicts of interest or disclosures to declare.