HACS————HACS|導(dǎo)讀：
DNA methylation in genes of longevity-regulating pathways: association with obesity and metabolic complications.
|背景介紹：
Improvements in health care and nutrition, more efficient infrastructure and access to basic supplies have been increasing life expectancy worldwide, leading to a shift towards older populations (Methods for Life Expectancy and Healthy Life Expectancy, WHO (2014)).
However, this extended lifespan is associated with an increase in the prevalence of age-related diseases.
On the other hand, obesity and its comorbidities have been reported to decrease longevity and accelerate aging.
comorbidities ：co-existed diseases
For example, a recent report has associated obesity with shorter longevity; where normal-weight men lived on average about six years more than morbidly obese men, whereas morbidly obese women tended to live two years less than normal-weight women.
morbid[?m??rb?d]:adj, suggesting an unhealthy mental state;(ill)
Similarly, there is a relationship between obesity-related diseases and mortality or years of life lost (YLL).
It has been estimated that obesity-related diseases increase lessened life years by 0.2 to 11.7 years depending on age BMI, gender and ethnic background.
Aging is an unavoidable physiological process, characterized by a progressive decline of functions in tissues and organs and is a risk factor for several pathological conditions including metabolic and cardiovascular diseases, neurodegenerative disorders and cancer.
In this context, aging is considered a major factor contributor to abdominal(belly) obesity, insulin resistance, type 2 diabetes and metabolic syndrome .
Interestingly, cases of extreme longevity exhibit a healthier phenotype associated to a lower prevalence of overweight and obesity, and lower blood pressure.
Mechanisms involved in the aging process are diverse and include genomic instability, telomere shortening, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered cellular senescence, loss of proteostasis, and epigenetic changes.
proteostasis: Proteostasis involves a highly complex interconnection of pathways that influence the fate of a protein from synthesis to degradation. As individual components are affected, the others adjust accordingly to maintain normal function.(normal level of proteins)
Longevity regulating pathways encompass several genes and associated signaling pathways that can modulate processes such as autophagy, protein synthesis, nutrient sensing, mitochondrial function, oxidative stress, among others .
Some of the signaling pathways more intrinsically associated with longevity are those of the Insulin/Insulin Like Growth Factor (IGF-1) system, mammalian target of rapamycin (mTOR) and Sirtuin 1 (SIRT1).
In invertebrate species, it has been demonstrated that a reduced signaling in insulin/IGF-1 can increase lifespan .
invertebrate[?n?v??rt?br?t]：any animal lacking a backbone or notochord; the term is not used as a scientific classification；adj. lacking a backbone or spinal colum.
On the other hand, mTOR is a sensor that integrates environmental and intracellular signals.
It has been shown that, the inhibition of mTORC1 with rapamycin increases lifespan in several animal models, which opens the door to new therapeutic approaches focused on aging.
Moreover, sirtuins also play a key role in longevity, where brain-specific Sirt1-overexpressing transgenic mice show significant life span extension, and aged mice exhibit phenotypes consistent with a delay in aging.
SIRT1 can be modulated by caloric restriction, which extends lifespan in several organisms, and is the target of resveratrol, which has the ability to extend the lifespan of yeast, worms, and flies.
resveratrol[?rez?ver?trɑl]：a compound found in red grapes, mulberries, peanuts, and certain plants, used medicinally as an antioxidant and anti-inflammatory 白藜蘆醇; 在紅葡萄、桑園、花生等植物中的化合物，在醫(yī)藥上作為抗氧化劑和抗炎藥使用；
Altered epigenetic landscapes have been described in relation to aging.
One of the most studied epigenetic mechanisms is DNA methylation, a dynamic process that controls genomic integrity and transcriptional activity.
DNA methylation consists in the addition of a methyl group at the carbon 5 position of cytosine ring to obtain 5-methylcitosine, occurs at specific sites and can vary along cycles of life.
Changes in DNA methylation affects crucial processes such as chromatin states, gene expression, and cell renewal, among others.
In general terms, CpG methylation within promoters can lead to transcriptional repression and promoter regions from highly expressed genes are hypomethylated.
However, gene expression could be also affected by changes in DNA methylation in regions such as 5` UTR, 3` UTR or gene body, although the mechanism is less understood.
During aging, mammalian cells undergo global DNA hypomethylation, especially at repetitive transposable sequences, which mostly occurs in a stochastic manner, as well as local DNA hypermethylation.
stochastic[st?'k?st?k]: being or having a random variable
Therefore, DNA hypomethylation appears to be a key factor associated to aging and longevity processes.
Our group has previously reported that the methylation levels of 55 CpG sites in white blood cells were significantly associated with age.
In older subjects, global DNA methylation patterns have been correlated with frailty, which is related with the relaxation of the epigenetic control impacting in functional decline.
frailty[?fre?lti]： he state of being weak in health or body (especially from old age)
In contrast to germ-line inherited genetic mutations, DNA methylation is theoretically reversible due to the action environmental factors, which opens the door to modulate aging-related epigenetic marks through specific lifestyle and dietary interventions.
The use of epigenetic techniques and algorithms could predict the risk of a disease considering inter-individual epigenetic variability and be useful to prevent disease progression.
The aim of this study is to analyze DNA methylation patterns of genes involved in longevity regulating pathways in young and old subjects that exhibit metabolic alterations in order to understand the implication of these epigenetic DNA signatures in the development of aging-related metabolic complications.
|核心內(nèi)容：
Aging is the main risk factor for most chronic diseases.
Epigenetic mechanisms, such as DNA methylation (DNAm) plays a pivotal role in the regulation of physiological responses that can vary along lifespan.
The aim of this research was to analyze the association between leukocyte DNAm in genes involved in longevity and the occurrence of obesity and related metabolic alterations in an adult population.
leukocyte [ 'lju:k?usait ]:blood cells that engulf and digest bacteria and fungi; an important part of the body's defense system
Subjects from the MENA cohort (n=474) were categorized according to age (<45 vs 45>) and the presence of metabolic alterations: increased waist circumference, hypercholesterolemia, insulin resistance, and metabolic syndrome.
The methylation levels of 58 CpG sites located at genes involved in longevity‐regulating pathways were strongly correlated (FDR‐ adjusted< 0.0001) with BMI.
Fifteen of them were differentially methylated (p<0.05) between younger and older subjects that exhibited at least one metabolic alteration.
Six of these CpG sites, located at MTOR (cg08862778), ULK1 (cg07199894), ADCY6 (cg11658986), IGF1R (cg01284192), CREB5 (cg11301281), and RELA (cg08128650), were common to the metabolic traits, and CREB5, RELA, and ULK1 were statistically associated with age.
In summary, leukocyte DNAm levels of several CpG sites located at genes involved in longevity‐ regulating pathways were associated with obesity and metabolic syndrome traits, suggesting a role of DNAm in aging‐related metabolic alterations.
● RESULTS ●
DNA methylation in genes of longevity-regulating pathways in relation to BMI
Longevity and lifespan are influenced by genetics, the environment, and lifestyle.
As phenotypes can vary substantially among individuals, we analyzed if DNA methylation of genes involved in longevity-regulating pathways is deregulated in presence of metabolic alterations.
These genes were identified by using KEGG database (“Longevity-regulating pathway”).
A first analysis was performed by correlating all DNA methylation sites across the 450K array with BMI.
Among the 13,268 CpGs significantly associated with BMI (p<0.05), we focused on the 58 methylation sites that located in genes participating in the longevity regulating pathway (FDR-adjusted p-value <0.0001)
Hereafter, 25 of these CpG sites were statistically significant (p<0.05) between younger (<45 y) and older subjects (≥45 y), and genomic and statistical data of these 25 CpG sites are shown (Tables 2-3).
In a second step, we decided to perform a search of this 25 CpG sites in public repositories such as Gene Expression Omnibus (GEO) databases with metabolic phenotypes related to our study population (Supplementary Table 2).
This analysis was conducted in four tissues such as PBMC (peripheral blood mononuclear cells), liver biopsies, subcutaneous and visceral fat to evaluate the methylation state in selected CpG sites (Table 4).
GSE76399 compared insulin resistant and insulin sensitive individuals in PBMC, whereas GSE65057 compared obese and nonobese individuals in liver samples.
In liver tissue from obese subjects, 13 CpG sites were hypomethylated showing a similar pattern in comparison to our results (blue lines in Table 4). In adipose tissue, we found only a hypermethylation for cg07199894 in ULK1 gene in omental fat and hypo-methylation for cg11322849 (INS), cg14844401 (ADCY5) and cg14323456 (RHEB) in subcutaneous fat, but it is important to note that sample size, gender and BMI were very different among studies.
It is noteworthy that we found more coincidence between our results (that were based on the CpGs that were differential according to BMI) and the study comparing the methylation patterns between obese and non-obese subjects in liver, than to the study performed in PBMC (similar to our cells) but which compared insulin resistant versus insulin sensitive individuals.
Another important difference between our study and the GSE76285 performed also in PBMC is that the population studied in GSE76285 was composed by subjects with extreme obesity (BMI >35), which makes difficult to find the same CpGs in both studies.
Methylation levels in longevity-regulating pathways and metabolic alterations
From those 25 CpG sites that were differentially methylated among age categories, a second filter was applied.
Subjects were categorized according the presence of metabolic alterations and the new selection was made based in those CpGs that were either hypo- or hypermethylated according to age and metabolic traits, in the same direction: those CpGs that were hypomethylated in the disease must be also hypomethylated with age, and vice versa.
To perform this analysis, binary categories were created (absence or presence of the condition) as previously described: Abdominal obesity, hypercholesterolemia, insulin resistance and metabolic syndrome.
Fifteen CpG sites were positively associated with abdominal/belly obesity: cg08862778 (MTOR), cg11322849 (INS), cg07199894 (ULK1), cg14844401 (ADCY5), cg20300093 (ADCY5), cg11658986 (ADCY6), cg04149773 (ADCY6), cg14862787 (CREB5), cg11301281 (CREB5), cg05792022 (FOXO1), cg14267811 (TSC1), cg02823066 (IGF1), cg01284192 (IGF1R), cg08128650 (RELA), cg24061580 (PRKAG2) (Figure 1). Of these 15 CpG sites, cg07199894 (ULK1) was the only hypermethylated.
Figure 1. Methylation levels of CpGs located at genes of the longevity‐regulating pathway in relation to waist circumference categories after age and sex adjustments.
Normal waist circumference vs High waist circumference levels, p<0.01**; p<0.001***; p<0.0001****. Cut‐off value between both groups was 102 cm for men and 88 cm for women.
Thirteen CpG were positively associated with hypercholesterolemia: cg08862778 (MTOR), cg07199894 (ULK1), cg11658986 (ADCY6), cg04149773 (ADCY6), cg06223834 (ADCY9), cg18237616 (RHEB), cg05792022 (FOXO1), cg01781374 (CAMK4), cg11301281 (CREB5), cg14267811 (TSC1), cg08128650 (RELA), cg01284192 (IGF1R), cg24061580 (PRKAG2) (Figure 2).
Figure 2. Methylation levels of CPGs located at genes of the longevity‐regulating pathway in relation to total cholesterol categories after age and sex adjustments. Normal cholesterol vs High cholesterol levels, p<0.05*; p<0.01**; p<0.001***; p<0.0001****. Cut‐off value between both groups was 200 mg/dl of total cholesterol in plasma.
Twelve CpG sites were associated with HOMA index: cg08862778 (MTOR), cg11322849 (INS), cg07199894 (ULK1), cg11658986- cg04149773 (ADCY6), cg14862 787-cg11301281 (CREB5), cg05792022 (FOXO1), cg14844401 (ADCY5), cg01284192 (IGF1R), cg02823066 (IGF1), cg08128650 (RELA) (Figure 3).
Figure 3. Methylation levels (beta values mean ± SEM) of CPGs located at genes of the longevity‐regulating pathway in relation to HOMA‐index categories after age and sex adjustments. Normal HOMA‐index vs High HOMA‐index levels, p<0.05*; p<0.01**; p<0.001***; p<0.0001****. Cut‐off value between both groups was a 2.4 HOMA‐IR index, higher levels was considered insulin resistant.
Finally, eleven CpG sites were associated with metabolic syndrome: cg08862778 (MTOR), cg11322849 (INS), cg07199894 (ULK1), cg11658986- cg04149773 (ADCY6), cg14862787-11301281 (CREB5), cg14844401-cg20300093 (ADCY5), cg01284192 (IGF1R) and cg08128650 (RELA) (Figure 4).
Figure 4. Methylation levels (beta values mean ± SEM) of CPGs located at genes of the longevity‐regulating pathway in relation to Metabolic Syndrome categories after age and sex adjustments. Non‐Metabolic syndrome vs Metabolic syndrome, p<0.05*; p<0.01**; p<0.001***; p<0.0001****. Metabolic syndrome was defined as the presence of three of five criteria: large waist circumference reduced HDL‐c, hypertriglyceridemia, hypertension and fasting hyperglycemia.
In an attempt to define age-specific CpG sites, we decided to perform a characterization in the older subjects according to their metabolic phenotype.
Starting from the 58 CpG sites associated with BMI residing in longevity regulating genes in the whole population (FDR<0.0001), and using the same criteria to split the population based on metabolic parameters as previously described, we observed that new CpG sites (blue lines in Table 5) appear differentially methylated in hyperglycemia, insulin resistance and hypertriglyceridemia but not in hypercholesterolemia.
Interestingly, 8 CpGs (cg11322849, cg07199894, cg14862787, cgcg14844401, cg01091261, cg06223834, cg08128650, cg04149773 in gray lines, Table 5) coincide when the whole population and the old sub-population are analyzed, which suggests that these genes could have a greater impact in metabolic regulation (Table 5).
Moreover, PRKAG2 (cg20406576) and EHMT2 (cg00210002) are hypomethylated in subjects with hyperglycemia, HOMA-IR ≥2.5 and hypertriglyceridemia.
In the case of IRS1 (cg21511036), AKT1S1 (cg03813033), ADCY2 (cg12566890 and EHMT2 (cg00210002) are hypomethylated, whereas AKT1 (cg01749142), FOXO3 (15283498), are hypermethylated in subjects with insulin resistance and hypertriglyceridemia.
In a second step, PathDIP was used to perform a pathway enrichment analysis and address the impact of these epigenetic marks on longevity-related molecular processes.
This analysis showed that those CpG sites associated with the occurrence of metabolic alterations contributed significantly to the regulation of longevity regulating pathways (Table 6).
Moreover, multiple linear regressions adjusted by LARS (least-angle regression) were performed to determine which CpG sites contributed in a significant way to the metabolic traits.
The resulting models show that the identified CpG sites have an important impact in abdominal obesity measured as waist circumference (adjusted r2 :0.341), and also in insulin resistance expressed as HOMA-index (adjusted r2 :0.153) (Table 6).
As mentioned before, a total of 15 CpG sites are hypoor hypermethylated in older subjects, but only six of these CpG sites are common for all the metabolic alterations previously described (Figure 5).
Figure 5. Venn diagram showing the common CpG sites differentially methylated between the different metabolic disturbances.
In a second approach, correlations between methylation levels and age were made for the six CpG sites located at the genes MTOR, ULK1, ADCY6, IGFR1, CREB5 and RELA.
In the case of cg08128650 (RELA) and cg11301281 (CREB5), methylation levels negative correlated with age, while cg07199984 (ULK1) showed a significant positive correlation (Figure 6).
Figure 6. Correlations between DNA methylation levels (beta values) at CpGs located at genes of the longevity‐regulating pathway and age, after sex adjustment. In (A) cg08128650, RELA, (B) cg11301281, CREB5, and (C) cg07199894, ULK1 (n=474 subjects).
Considering that a small number of common CpG sites are significant associated with age and r2 adjusted values are small, we decided to create a z-score that includes those 25 CpG sites differentially methylated according to age previously described (Table 3) and a linear regression was performed analyzing this z-score with age, adjusted by BMI (Figure 7).
Figure 7. Relation between Z‐scores of methylation levels and age. Values reflect the significant change in Z‐scores from CpG methylation (25 CpG sites, n=474) according age, after BMI adjustment.
This analysis showed a statistically significant association with age (r2 :0.098, p<0.0001), where older subjects presented hypomethylation in CpG sites related to genes involved in longevity-regulating pathways.
DISCUSSION :
Longevity is considered the survival up to advanced ages.
Long-lived people are those who exceeds ≥90 years and in some cases, are individuals who have stabilized or avoided age-related diseases .
On the other hand, aging is an unavoidable process, characterized by a progressive decline of functions in tissues and organs and is associated to mortality .
Up to date, several GWAS and linkage and candidate gene association studies have identified genetic variants, such as those for apoliprotein E (APOE) and forkhead box O3 (FOXO3A), that have been consistently associated with longevity .
In the case of APOE, APOE ε2 isoform decrease the risk of cardiovascular disease and APOE ε4 isoform limits longevity [30] and FOXO3 is linked to insulin/insulin-like growth factor 1 (IGF1) signaling [31].
Another classic genetic model of increased lifespan in mammals is the growth hormone receptor (GHR) knock-out mouse, as well as its corresponding genetic defect in humans (Laron syndrome), which is characterized by extreme insulin sensitivity and protection to cancer [32,33].
These studies suggest that genetic variants are important contributors to the variability in longevity, but it is important to find other regulators of the longevity process.
In this context, epigenetic modifications seem to be crucial in aging and longevity processes since they can integrate genetic and environmental factors The present study has identified fifteen CpG sites that whose methylation levels showed statistical differences between younger and older subjects that exhibited at least one metabolic alteration and were significantly associated with longevity-regulating pathways.
As expected, in our population study, older subjects were more prone to develop metabolic alterations, where no gender differences were found.
According to the enrichment pathway analysis and linear regression models, a total of six CpG sites (located at the genes MTOR, ADCY6, IGFR1, ULK1, CREB5 and RELA) were common to individuals that exhibited at least one metabolic alteration related to aging.
One of these CpG sites (cg08862778) is located at MTOR gene, which codifies the mammalian target of rapamycin (mTOR), a serine/threonine protein kinase that can form two complexes: mTORC1 and mTORC2 [34].
This protein can regulate protein translation, protein homeostasis and cellular growth due to its capacity as energy sensor [34].
mTOR can be negatively regulated by rapamycin and caloric restriction, and inhibition of mTORC1 activity is known to increase lifespan in yeast, nematodes, flies and mice [35].
In humans, no associations have been found in SNPs for mTOR complex components in cases of extreme longevity [36], however, mTOR has been shown to be deregulated in several aging-related pathologies such as obesity, diabetes, cardiovascular disease and cancer [34].
Higher levels of mTOR and a chronic activation of mTORC1 in tissues from obese mice and humans appears to play a key role in the development of insulin resistance and type 2 diabetes, which is supported by the results of treatments with metformin, which is known to negatively regulate the action of mTOR [37].
Our results show that cg08862778 (MTOR) is hypomethylated in older subjects and also, in those subjects who exhibit abdominal obesity, hypercholesterolemia, insulin-resistance and/or metabolic syndrome.
This CpG site is located in a genomic region known as “Transcription start sites” (TSS200) that belong to the promoter region [38], and could be associated with an upregulation of MTOR, but this need to be demonstrated since there is evidence for cases where hypomethylation is associated with gene upregulation in autoimmune diseases [39,40] and early stages of tumorigenesis.
A second CpG site hypomethylated in older subjects (cg11658986) is located in the first exon of ADCY6 gene.
ADCY6 encodes adenylyl cyclase 6, a key protein in the synthesis of cyclic AMP from ATP [41].
ADCY family encodes at least 9 closely related isoforms (1-9) and shares a large sequence homology [42] with functions on learning and memory, olfaction and cardiac contractility [43], but up to date, there is no evidence in metabolism.
Nevertheless, genome-wide association studies have shown that ADCY3 polymorphisms (rs2033655 and rs1968482) are associated with obesity [44] and other SNPs are involved in proximal gene regulation through changes in DNA methylation [45] .
Another CpG hypomethylated site corresponds to cg01284192, located in the body of IGF1R gene.
This gene encodes a receptor that binds insulin-like growth factor with high affinity and plays a key role in cell growth and survival control.
It is overexpressed in several types of cancer and has been implicated in the transformation into malignant cells and cell survival promotion [46].
Although it should be necessary to measure IGF1R expression levels, IGF1R gene has been reported to be hypomethylated in placentas exposed to maternal impaired glucose tolerance, which suggests its potential implication in fetal programming [47].
Additionally, heterozygous loss-of-function mutations in the IGF1R were found to be enriched in the cohort of Ashkenazi Jewish centenarians compared to controls [48].
All these sets of evidences suggest IGF1R as a possible candidate gene in aging-related processes [48].
Our results show that three of six CpG sites differentially methylated (in RELA, CREB5 and ULK1 genes) also correlated with age.
Methylation levels for cg08128650, located in the body of the RELA gene, are associated negatively with age.
RELA encodes a transcription factor known as p65, a subunit of NF-κB [49].
This complex is involved in cellular response against several stimuli such as stress, cytokines, UV radiation, oxidized LDL and some bacterial or viral antigens [50].
Methylation at RelA subunit can modulate DNA binding and transcriptional activity, and a deregulation of NFkB, mainly a constitutively activation, is associated with inflammatory and tumorigenesis development [51,52].
The hypomethylation of RELA that we have found supports its role; never- theless, DNA methylation within the gene body is less understood and requires further analysis.
A second differentially methylated site is cg11301281, which exhibits a negative association with age and is located in the 5′ UTR of CREB5 gene.
CREB5 encodes cyclic AMP-responsive element binding protein 5, a key factor in cell growth, proliferation, differentiation and cell cycle control [53].
Up-regulation of CREB5 is associated with metastatic process [54], inflammatory response genes and modulation of immune responses [55–57].
It is well known that aging is associated with an inflammatory state that contributes to the pathogenesis of several diseases.
Transcriptomic and epigenetic analyses in nonagenarian men revealed that CREB5 methylation was related to inflammatory response genes in a gender-specific manner [58].
In comparison with our results, we did not find gender differences, but our age spectrum is wider and cannot be compared with a nonagenarian population.
A third CpG (cg07199984, located in the TSS200 region of ULK1 gene) was hypermethylated in older individuals.
ULK1 encodes Unc-51 Like Autophagy Activating Kinase 1 (ULK1), a serine/threonine-protein kinase involved in autophagy in response to starvation [59].
Autophagy is a cellular degradation and recycling process that is highly conserved in all eukaryotes [55] and is associated with an extension in lifespan [60].
Under conditions of amino acid starvation or mTOR inhibition, ULK1 phosphorylates Beclin-1 to let a complete induction of autophagy [61, 62].
Autophagy has a key role in lipid homeostasis after lipid mobilization lowering their potential toxicity [63, 64] and it is well stablished that autophagy dysfunction is linked to aging-related pathologies such as Alzheimer′s disease and type 2 diabetes [65].
Our results show a hypermethylation that could disrupt transcription factor binding to the gene, suggesting a potential silencing of ULK1 transcription and inhibition of autophagy [66].
This result is related also to the hypomethylation reported for cg08862778 at MTOR gene, which suggests mTOR activation which can promote lower levels of autophagy [67,68].
In an attempt to evaluate age-specific CpGs, we perform a similar analysis taking into account only old subjects, but we did not identify the same results in CpGs associated with BMI.
身體質(zhì)量指數(shù)是BMI指數(shù)(身體質(zhì)量指數(shù)，簡(jiǎn)稱體質(zhì)指數(shù))，是目前國(guó)際上常用的衡量人體胖瘦程度以及是否健康的一個(gè)標(biāo)準(zhǔn)。
計(jì)算公式為：BMI=體重（千克）除以身高（米）的平方。
成人標(biāo)準(zhǔn)值是BMI18.5-23.9才算標(biāo)準(zhǔn)體重。
We thought that differences between analyzing the whole population and subjects divided by age, are due to different exposures along the lifetime and due to this is not a follow-up study.
However, in the young population we can identify a few CpGs in comparison with old subjects, which suggests that aging is driving methylation changes.
When older subjects are analyzed as a separate group, we identified two genes that are differentially methylated in metabolic disturbances, and also are associated with BMI in the whole population, suggesting a potential role in metabolic disturbances.
IRS1 belongs to the Insulin receptor substrate 1, and DNA promotor methylation and expression in human adipose tissue are related to fat distribution and metabolic traits [69].
EHMT1 gene codifies a histone methyltransferase to promote transcriptional repression; a key process in gene regulation associated to aging, and also is associated to the control of brown adipose cell fate and thermogenesis [70,71].
The epigenome, including DNA methylation signatures, undergoes a notable changes during the lifetime and undoubtedly can influence the aging process [19].
For this reason, epigenetic clocks are promising biomarkers of aging [72].
Recently, it has been developed a DNAm age estimator based on 391 CpG sites [73].
This epigenetic clock allows to track the dynamic aging of cells and can be used as a quantitative biomarker of chronological age[73].
In our work, we designed a zscore including individual z-scores from 25 CpG sites, showing that older subjects presented hypomethylated in CpG sites associated with longevity-regulating pathways, which supports the genomic hypomethylation hypothesis, but age-related changes in DNA methylation occurs in specific regions or at specific sites in the genome [74].
Z-scores can be useful predictors because they normalize variables and eliminate a number of the sources of variance in raw values [75].
These results could be related to epigenetic clocks that allow to calculate the acceleration of aging and predict the risk of age-related diseases, cognitive and physical decline, among others [76, 77].
One of the remaining challenges in DNA methylation is identify causal pathways that contribute to functional changes and unravel potential mechanisms, but it is important to address the limitations of this type of research.
DNA methylation microarrays were performed in buffy coat, which is a mixture of circulating white cells.
To circumvent this problem, the results have been corrected using the Houseman procedure [78].
On the other hand, gene expression (mRNA) levels should be determined in order to properly evaluate the impact of the epigenetic changes.
To elucidate the mechanisms, it is key to contextualize gene expression with its impact in disease development [79] and taking into consideration other mechanisms (non-coding RNAs, chromatin reorganization, histone modifications) that can also modulate the aging process.
Microarrays have the limitation of including only a small amount of the CpGs present in each gene, but it is an affordable technique that can detect individual CpGs in 99% of known genes including 5`UTR, 3`UTR, coding regions and island shores, moreover, Infinium Human Methylation 450K (Illumina) platforms results has a good correlate when has been analyzed by pyrosequencing [80–83].
For this reason, it could be interesting to analyze the methylation status of the whole sequence of the specific genes of interest through specific techniques such as PCR and sequencing, bead array, pyrosequencing, methylation specific PCR [84]) to confirm the differential patterns.
In an attempt to compare our results with those from existing databases available in GEO, a public repository of databases, we identified some common patterns in metabolic tissues, particularly in the liver of obese and non-obese individuals, which in turn reinforces our findings and suggests that the CpGs identified in the present study could be used as potential biomarkers.
In the case of aging-longevity methylation studies, it is important evaluate lifestyle and dietary factors, such as methyl donor intake, and study folate metabolism in these subjects to obtain accurate conclusions [85].
Nevertheless, if DNA methylation assays are robust in blood samples, it is feasible the development of epigenetic biomarkers as a method for diagnosis and personalized treatments through a noninvasive approach [86], especially considering the fact that during aging the genome shift towards to a global hypomethylation and hypermethylation in specific sites.
In brief, this study has identified several CpG sites that are differentially methylated between younger and older adults and are associated with metabolic dysfunctions.
In summary, our data support that differentially methylated sites could be involved in the promotion of a proaging phenotype in those subjects older than 45 years old and in those who exhibit metabolic disturbances.
Beyond the limitations of this research and after further validation, these CpG sites could be used as markers of premature aging, especially in the context of obesity and related metabolic diseases.
This set of methylation-based biomarkers could be useful in the implementation of new personalized preventing strategies and in the measurement of outcomes to demonstrate the effectiveness of treatments targeting longevity pathways.
簡(jiǎn)版：
Mechanisms involved in the aging process are diverse and include genomic instability, telomere shortening, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered cellular senescence, loss of proteostasis, and epigenetic changes.
