DNA-methylation-based telomere length estimator: comparisons with measurements from flow FISH and qPCR

Health insurance and epigenetic aging: Trends in a United States adult population

Background

Health insurance plays an important role in reducing morbidity and mortality. Still, there is limited data examining the relationships of health insurance with biomarkers of aging that reflect morbidity and mortality risk.

Methods

We conducted a cross-sectional study of United States adults using data from the National Health and Nutrition Examination Survey (NHANES) to examine the relationships of health insurance with seven DNA methylation-based biomarkers of aging (epigenetic age): HannumAge, HorvathAge, SkinBloodAge, PhenoAge, GrimAge2, DNAm Telomere Length, and DunedinPoAm.

Results

Our analyses included 2315 participants with available health insurance and epigenetic aging data (mean [sd] age, 65.1 [9.3] years). Compared to the uninsured, having health insurance was associated with a 2.25-year lower GrimAge2 (95 %CI: -3.49, -1.02, P = 0.001) and a slower DunedinPoAm pace of aging (β = -0.04, 95 %CI: -0.06, -0.02, P < 0.001) in basic demographic-adjusted models. GrimAge2 (β = -1.42, 95 %CI: -2.75, -0.09, P = 0.04) and DunedinPoAm (β = -0.03, 95 %CI: -0.06, -0.01, P = 0.02) relationships were attenuated after additional adjustments for general health, body mass index (BMI), education, occupation, and poverty-to-income ratio. Model estimates were larger if insurance plans were more comprehensive and included dental coverage and/or single service plans. When considering categories of insurance, similar trends were observed with private insurance and public insurance plans (i.e. Medicare, Medicaid/CHIP, and other government plans), although private insurance relationships were more often statistically significant.

Conclusion

Our findings suggest that epigenetic aging measures may be useful for examining the relationship between health insurance and population health, with potential implications for policy decisions.

Sensory impairments and epigenetic aging: insights from self-rated hearing and vision in United States adults

Sensory impairments are common with aging, but studies examining the relationships of these impairments with DNA methylation-based biomarkers of aging, strong predictors of morbidity and mortality, remain sparse. We investigated whether subjective measures of sensory impairment are associated with epigenetic age biomarkers. We conducted a cross-sectional analysis in a representative sample of 2344 U.S. adults from the 1999-2000 and 2001-2002 cycles of the National Health and Nutrition Examination Survey (NHANES). We examined the relationships of self-rated auditory and vision function with seven epigenetic aging biomarkers: HannumAge, HorvathAge, SkinBloodAge, PhenoAge, GrimAge2, DNA methylation telomere length, and DunedinPoAm. We adjusted for potential confounders including chronological age, other demographics, lifestyle factors, and general health. In adjusted survey-weighted models, self-reported deafness was associated with a significantly higher GrimAge2 (β = 4.19-years, 95% CI 2.29, 6.09, P = 0.004) and DunedinPoAm (β = 0.07, 95% CI 0.04, 0.09, P = 0.002) compared to good hearing. Deafness was also associated with significantly higher GrimAge2 estimates of TIMP1 (β = 459.51, 95% CI 287.00, 632.03 P = 0.002) and marginally higher estimated levels of ADM (β = 10.06, 95% CI 1.76, 18.36, P = 0.03), CRP (β = 0.34, 95% CI 0.11, 0.56, P = 0.01), and cigarette pack-years (β = 6.55, 95% CI 2.62, 10.47, P = 0.01). No associations were observed with self-rated vision. We describe associations of self-rated deafness with accelerated epigenetic aging, as measured by GrimAge2 and DunedinPoAm. These results provide a foundation for future research exploring epigenetic biomarkers as tools for predicting and understanding the biological processes underlying sensory impairments like deafness.

Associations of epigenetic aging with self-rated health, access to care, and healthcare utilization in a representative sample of United States adults

BACKGROUND

Health status is closely linked to both healthcare access and utilization. While previous research has identified associations between health status and DNA methylation-based biomarkers of aging (epigenetic aging), studies exploring these relationships in the context of healthcare access and utilization remain limited. To address this gap, we analyzed cross-sectional associations in a representative sample of 2,343 U.S. adults from the 1999-2000 and 2001-2002 cycles of the National Health and Nutrition Examination Survey (NHANES). Our study examined the relationships of self-rated health status, healthcare access, and healthcare utilization with seven epigenetic aging biomarkers: HannumAge, HorvathAge, SkinBloodAge, PhenoAge, GrimAge2, DNAm Telomere Length (DNAmTL), and DunedinPoAm.

RESULTS

After adjusting for chronological age, demographics, lifestyle factors, and health insurance, participants with good-excellent self-rated health had a 1.58-year lower PhenoAge (95% CI - 2.54, - 0.62 P = 0.006) and a 1.16-year lower GrimAge2 (95% CI - 1.80, - 0.53, P = 0.004) than participants with poor-fair health. Participants who reported having a routine place where they received healthcare had a lower GrimAge2 (β = - 1.44-years, 95% CI - 2.66, - 0.22, P = 0.03) than participants without a routine healthcare location. Participants with ≥ 10 healthcare visits in the prior year had a shorter DNAmTL (β = - 0.05-kb, 95% CI - 0.09, - 0.01, P = 0.02) than participants with < 10 visits. After including additional adjustments for estimated leukocyte proportions, participants who were hospitalized overnight in the prior year had a shorter DNAmTL (β = - 0.05-kb, 95% CI - 0.08, - 0.01, P = 0.02) than non-hospitalized individuals.

CONCLUSIONS

Our findings reinforce previous reports linking better health status to lower epigenetic aging and provide new evidence of associations of epigenetic aging with measures of healthcare access and utilization. If validated, these findings suggest that epigenetic aging biomarkers may be useful in studying disease processes and assessing health outcomes related to access and utilization.

Dietary inflammatory index (DII) and telomere length: a systematic review

Dietary intake influences inflammation and may impact telomere length (TL), a biomarker of biological aging. However, the relationship between the inflammatory potential of the diet and TL remains unclear. This review systematically assessed whether higher Dietary Inflammatory Index (DII) scores, indicative of pro-inflammatory diets, are associated with shorter TL. Searches in PubMed, Embase, Scopus, Web of Science, and Cochrane up to October 2024 identified nine eligible studies, involving 123,923 participants (53% women), aged 9-80 years. Seven studies were cross-sectional, and two were longitudinal, with follow-ups of 5-10 years. Most studies (n = 4) examined adult and older adult populations of both sexes. DII values ranged from -6.48 (anti-inflammatory) to 3.98 (pro-inflammatory). None included all DII parameters, and three adjusted for energy intake. Four studies linked higher DII to shorter TL, focusing on European adults with and without cardiovascular risk, healthy American adults, and Chinese older adults with mild cognitive impairment. This systematic review presents limited data to provide a definitive conclusion on the association between higher DII and shorter TL. Additional studies that address the limitations identified in this review are needed.

Immigrant status and citizenship relationships with epigenetic aging in a representative sample of United States adults

BACKGROUND

Immigrant status and citizenship influence health and well-being, yet their associations with DNA methylation (DNAm)-based biomarkers of aging - key predictors of healthspan and lifespan, also known as epigenetic aging - remain underexplored.

METHODS

Using a representative sample of 2,336 United States (U.S.) adults from the 1999-2000 and 2001-2002 cycles of the National Health and Nutrition Examination Survey (NHANES), we analyzed cross-sectional associations of immigrant status and U.S. citizenship with seven epigenetic aging biomarkers: HannumAge, HorvathAge, SkinBloodAge, PhenoAge, GrimAge2, DNAm Telomere Length, and DunedinPoAm.

RESULTS

After adjusting for demographic factors, immigrants had 2.53-year lower GrimAge2 measures (95%CI: -3.44, -1.63, p < 0.001) compared to non-immigrants. U.S. citizens had 1.98-year higher GrimAge2 measures (95%CI: 0.66, 3.30, p = 0.005) compared to non-citizens. The GrimAge2 associations with immigrant status (β = -1.04-years, 95%CI: -1.87, -0.21, p = 0.02) and citizenship (β = 1.35-years, 95%CI: 0.38, 2.32, p = 0.02) were attenuated after adjusting for other lifestyle/health variables. Immigrant status and citizenship were associated with estimated levels of several GrimAge2 DNAm component proteins, including adrenomedullin and C-reactive protein.

CONCLUSION

Our results support the paradigm of the immigrant mortality advantage and highlight the potential value of epigenetic age measures in studying socioeconomic and broader factors influencing citizen and immigrant health.

Comparing Veteran and Nonveteran Epigenetic Aging in a Representative Sample of United States Adults

INTRODUCTION

Military service can significantly impact human health, with research showing that veterans experience higher mortality rates than the general population. However, limited data exist on the relationships of veteran status with biomarkers of aging that may precede clinical illness and mortality.

METHODS

Using survey-design weighted generalized linear regression models, we examined the cross-sectional relationship of self-reported veteran status with DNA methylation (DNAm)-based biomarkers of aging (epigenetic age) in a representative sample of 2344 U.S. adults participating in the 1999-2000 and 2001-2002 cycles of the National Health and Nutrition Examination Survey. We tested 7 epigenetic aging markers: HannumAge, HorvathAge, SkinBloodAge, PhenoAge, GrimAge2, DNAm Telomere Length (TL), and DunedinPoAm.

RESULTS

After adjusting for basic demographics, veterans had marginally greater SkinBloodAge (β = 0.86 years, 95% CI: -0.10, 1.81, P = .08) and GrimAge2 (β = 0.71 years, 95% CI: -0.07, 1.49, P = .07) measures when compared to nonveterans. Similar SkinBloodAge (β = 1.00 years, 95% CI: -0.01, 2.00, P = .05) and GrimAge2 (β = 0.69 years, 95% CI: -0.14, 1.52, P = .09) relationships were observed in fully-adjusted models where missing health and lifestyle covariates were imputed. Compared to nonveterans, veterans also had higher DNAm-estimated blood levels of GrimAge2-components hemoglobin A1c (β = 0.006, 95% CI: 0.0005, 0.01, P = .03) and protein TIMP1 (β = 71.14, 95% CI: 8.28, 134.01, P = .03) in basic demographic-adjusted models. In fully-adjusted imputed models (β = 96.40, 95% CI: -15.05, 207.85, P = .08) and complete case models (β = 98.66, 95% CI: -25.24, 222.55, P = .099), the TIMP1 relationships remained marginally significant.

CONCLUSIONS

Our marginal results support existing veteran morbidity and mortality literature while suggesting a modest utility of epigenetic aging biomarkers for further understanding veteran health. As veterans represent an important subset of the population and are a priority in federal government budgets, future research in this area holds the potential for significant public health and policy impact.

The multi-omics signatures of telomere length in childhood

BACKGROUND

Telomere length is an important indicator of biological age and a complex multi-factor trait. To date, the telomere interactome for comprehending the high-dimensional biological aspects linked to telomere regulation during childhood remains unexplored. Here we describe the multi-omics signatures associated with childhood telomere length.

METHODS

This study included 1001 children aged 6 to 11 years from the Human Early-life Exposome (HELIX) project. Telomere length was quantified via qPCR in peripheral blood of the children. Blood DNA methylation, gene expression, miRNA expression, plasma proteins and serum and urinary metabolites were measured through microarrays or (semi-) targeted assays. The association between each individual omics feature and telomere length was assessed in omics-wide association analyses. In addition, a literature-guided, sparse supervised integration method was applied to multiple omics, and latent components were extracted as predictors of child telomere length. The association of these latent components with early-life aging risk factors (child lifestyle, body mass index (BMI), exposure to smoking, etc.), were interrogated.

RESULTS

After multiple-testing correction, only two CpGs (cg23686403 and cg16238918 at PARD6G gene) out of all the omics features were significantly associated with child telomere length. The supervised multi-omics integration approach revealed robust associations between latent components and child BMI, with metabolites and proteins emerging as the primary contributing features. In these latent components, the contributing molecular features were known as involved in metabolism and immune regulation-related pathways.

CONCLUSIONS

Findings of this multi-omics study suggested an intricate interplay between telomere length, metabolism and immune responses, providing valuable insights into the molecular underpinnings of the early-life biological aging.

Association between phenotypic age and mortality risk in individuals with obesity: a retrospective cohort study

Objective

This study investigates the association between phenotypic age acceleration (PAA) and all-cause and cause-specific mortality in obese individuals.

Methods

Data were drawn from the National Health and Nutrition Examination Survey (NHANES) between 1999 and 2018, including 9,925 obese adults (BMI ≥ 30 kg/m2). PAA, defined as phenotypic age exceeding chronological age, was assessed using clinical biomarkers. Kaplan-Meier survival analysis and Cox proportional hazards models were used to assess the relationship between PAA and all-cause, cardiovascular, and cancer mortality, adjusting for covariates such as age, gender, race, lifestyle, and health status. Subgroup and sensitivity analyses were performed to ensure the robustness of the findings.

Results

During a median follow-up of 10.6 years, 1,537 deaths were recorded, including 419 from cardiovascular disease and 357 from cancer. PAA was significantly associated with all-cause mortality (HR = 1.84, 95% CI: 1.64-2.06), cardiovascular mortality (HR = 1.86, 95% CI: 1.50-2.31), and cancer mortality (HR = 1.47, 95% CI: 1.17-1.85). These associations remained significant after adjusting for multiple variables, and sensitivity analyses confirmed the robustness of the results.

Conclusion

PAA is an independent predictor of all-cause, cardiovascular, and cancer mortality in obese individuals. This study highlights the importance of PAA in mortality risk assessment and health management in the obese population.

DNA methylation-based telomere length is more strongly associated with cardiovascular disease and long-term mortality than quantitative polymerase chain reaction-based telomere length: evidence from the NHANES 1999-2002

BACKGROUND

Telomere length (TL) serves as a pivotal gauge of cellular aging, with shorter TL linked to various age-related ailments. Recently, a DNA methylation-based TL estimator, known as DNAmTL, has emerged as a novel TL measurement tool. Our current investigation scrutinized the correlation between DNAmTL and the risks of cardiovascular disease (CVD) and enduring mortality among middle-aged and elderly individuals.

METHODS

We enrolled a nationwide, population-based cohort of subjects from the National Health and Nutrition Examination Survey spanning 1999 to 2002, possessing data on both DNAmTL and quantitative polymerase chain reaction-based TL (qPCRTL). Logistic regression models and Cox proportional hazards models were employed to evaluate the associations of DNAmTL with CVD risk and mortality, respectively.

RESULTS

The cohort comprised 2532 participants, with a weighted CVD prevalence of 19.06%. Notably, each one-kilobase increase in DNAmTL was linked to a 53% diminished CVD risk [odds ratio (OR): 0.47, 95% confidence interval (CI): 0.23-0.95, P = 0.035]. Over a median follow-up period of 206 months, 1361 deaths were recorded (53.75%), with 590 (23.30%) ascribable to CVD. Individuals with the lengthiest DNAmTL exhibited a 36% lower risk of all-cause mortality (hazard ratio (HR): 0.64, 95% CI: 0.49-0.85, P = 0.002) and a 35% decrease in CVD mortality (HR: 0.65, 95% CI: 0.43-0.98, P = 0.044) compared to those with shortest DNAmTL. Notably, a stronger association with age was observed for DNAmTL compared to qPCRTL (r = -0.58 vs. r = - 0.25). Analysis of receiver operating characteristic (ROC) curves suggested superior predictive performance of DNAmTL over qPCRTL for CVD (area under curve (AUC): 0.63 vs. 0.55, P < 0.001), all-cause (AUC: 0.74 vs. 0.62, P < 0.001), and CVD mortality (AUC: 0.75 vs. 0.64, P < 0.001).

CONCLUSION

Longer DNAmTL was positively correlated with reduced CVD risk and long-term mortality in middle-aged and elderly cohorts. Notably, DNAmTL outperformed qPCRTL as an aging biomarker in the stratification of CVD risks and mortality.

Bronchial cell epigenetic aging in a human experimental study of short-term diesel and ozone exposures

Blood-based, observational, and cross-sectional epidemiological studies suggest that air pollutant exposures alter biological aging. In a single-blinded randomized crossover human experiment of 17 volunteers, we examined the effect of randomized 2-h controlled air pollution exposures on respiratory tissue epigenetic aging. Bronchial epithelial cell DNA methylation 24 h post-exposure was measured using the HumanMethylation450K BeadChip, and there was a minimum 2-week washout period between exposures. All 17 volunteers were exposed to ozone, but only 13 were exposed to diesel exhaust. Horvath DNAmAge [Pearson coefficient (r) = 0.64; median absolute error (MAE) = 2.7 years], GrimAge (r = 0.81; MAE = 13 years), and DNAm Telomere Length (DNAmTL) (r = -0.65) were strongly correlated with chronological age in this tissue. Compared to clean air, ozone exposure was associated with longer DNAmTL (median difference 0.11 kb, Fisher's exact P-value = .036). This randomized trial suggests a weak relationship of ozone exposure with DNAmTL in target respiratory cells. Still, causal relationships with long-term exposures need to be evaluated.

DNA methylation-based estimators of telomere length show low correspondence with paternal age at conception and other measures of external validity of telomere length

In humans, DNA methylation (DNAm) based estimators of telomere length (TL) have been shown to better predict TL-associated variables (e.g., age, sex, and mortality) than TL itself. The biological significance of DNAm-based estimators of TL (DNAmTL) is unclear. In vitro DNAmTL shortens with cell replications, even when telomerase is maintaining TL. Telomerase is typically suppressed in humans, except in testes. Accordingly, sperm TL increases with age, and offspring with greater paternal age at conception (PAC) have longer TL. Thus, we expect that PAC associations with DNAmTL can shed light on whether in vivo cell replications in the presence of high telomerase activity (production of sperm) shorten DNAmTL or if PAC-lengthened TL causes lengthened DNAmTL. In a pre-registered analysis, using data from 1733 blood samples from the Philippines, we examined the association between paternal age at conception (PAC) and offspring DNAmTL. We did not find an association between PAC and DNAmTL but found a positive association of paternal grandfather's age at father's conception predicting grandchild's DNAmTL. In post hoc analyses, we examined how DNAmTL versus qPCR-measured TL (qPCR-TL) correlated with measures typically associated with TL. Contrary to previous findings, on almost all measures of external validity (correlations with parental TLs, southern blot TL, and age), qPCR-TL outperformed DNAmTL. The "kilobase" units of DNAm-based estimators of TL showed considerable deviations from southern blot-derived kilobase measures. Our findings suggest that DNAmTL is not a reliable index of inherited aspects of TL and underscores uncertainty about the biological meaning of DNAmTL.

Unveiling the epigenetic impact of vegan vs. omnivorous diets on aging: insights from the Twins Nutrition Study (TwiNS)

BACKGROUND

Geroscience focuses on interventions to mitigate molecular changes associated with aging. Lifestyle modifications, medications, and social factors influence the aging process, yet the complex molecular mechanisms require an in-depth exploration of the epigenetic landscape. The specific epigenetic clock and predictor effects of a vegan diet, compared to an omnivorous diet, remain underexplored despite potential impacts on aging-related outcomes.

METHODS

This study examined the impact of an entirely plant-based or healthy omnivorous diet over 8 weeks on blood DNA methylation in paired twins. Various measures of epigenetic age acceleration (PC GrimAge, PC PhenoAge, DunedinPACE) were assessed, along with system-specific effects (Inflammation, Heart, Hormone, Liver, and Metabolic). Methylation surrogates of clinical, metabolite, and protein markers were analyzed to observe diet-specific shifts.

RESULTS

Distinct responses were observed, with the vegan cohort exhibiting significant decreases in overall epigenetic age acceleration, aligning with anti-aging effects of plant-based diets. Diet-specific shifts were noted in the analysis of methylation surrogates, demonstrating the influence of diet on complex trait prediction through DNA methylation markers. An epigenome-wide analysis revealed differentially methylated loci specific to each diet, providing insights into the affected pathways.

CONCLUSIONS

This study suggests that a short-term vegan diet is associated with epigenetic age benefits and reduced calorie intake. The use of epigenetic biomarker proxies (EBPs) highlights their potential for assessing dietary impacts and facilitating personalized nutrition strategies for healthy aging. Future research should explore the long-term effects of vegan diets on epigenetic health and overall well-being, considering the importance of proper nutrient supplementation.

TRIAL REGISTRATION

Clinicaltrials.gov identifier: NCT05297825.

DNA methylation-based telomere length is associated with HIV infection, physical frailty, cancer, and all-cause mortality

Telomere length (TL) is an important indicator of cellular aging. Shorter TL is associated with several age-related diseases including coronary heart disease, heart failure, diabetes, osteoporosis, and cancer. Recently, a DNA methylation-based TL (DNAmTL) estimator has been developed as an alternative method for directly measuring TL. In this study, we examined the association of DNAmTL with cancer prevalence and mortality risk among people with and without HIV in the Veterans Aging Cohort Study Biomarker Cohort (VACS, N = 1917) and Women's Interagency HIV Study Cohort (WIHS, N = 481). We profiled DNAm in whole blood (VACS) or in peripheral blood mononuclear cells (WIHS) using an array-based method. Cancer prevalence was estimated from electronic medical records and cancer registry data. The VACS Index was used as a measure of physiologic frailty. Models were adjusted for self-reported race and ethnicity, batch, smoking status, alcohol consumption, and five cell types (CD4, CD8, NK, B cell, and monocyte). We found that people with HIV had shorter average DNAmTL than those without HIV infection [beta = -0.25, 95% confidence interval (-0.32, -0.18), p = 1.48E-12]. Greater value of VACS Index [beta = -0.002 (-0.003, -0.001), p = 2.82E-05] and higher cancer prevalence [beta = -0.07 (-0.10, -0.03), p = 1.37E-04 without adjusting age] were associated with shortened DNAmTL. In addition, one kilobase decrease in DNAmTL was associated with a 40% increase in mortality risk [hazard ratio: 0.60 (0.44, 0.82), p = 1.42E-03]. In summary, HIV infection, physiologic frailty, and cancer are associated with shortening DNAmTL, contributing to an increased risk of all-cause mortality.

Biological aging markers in blood and brain tissue indicate age acceleration in alcohol use disorder

BACKGROUND

Alcohol use disorder (AUD) is associated with increased mortality and morbidity risk. A reason for this could be accelerated biological aging, which is strongly influenced by disease processes such as inflammation. As recent studies of AUD show changes in DNA methylation and gene expression in neuroinflammation-related pathways in the brain, biological aging represents a potentially important construct for understanding the adverse effects of substance use disorders. Epigenetic clocks have shown accelerated aging in blood samples from individuals with AUD. However, no systematic evaluation of biological age measures in AUD across different tissues and brain regions has been undertaken.

METHODS

As markers of biological aging (BioAge markers), we assessed Levine's and Horvath's epigenetic clocks, DNA methylation telomere length (DNAmTL), telomere length (TL), and mitochondrial DNA copy number (mtDNAcn) in postmortem brain samples from Brodmann Area 9 (BA9), caudate nucleus, and ventral striatum (N = 63-94), and in whole blood samples (N = 179) of individuals with and without AUD. To evaluate the association between AUD status and BioAge markers, we performed linear regression analyses while adjusting for covariates.

RESULTS

The majority of BioAge markers were significantly associated with chronological age in all samples. Levine's epigenetic clock and DNAmTL were indicative of accelerated biological aging in AUD in BA9 and whole blood samples, while Horvath's showed the opposite effect in BA9. No significant association of AUD with TL and mtDNAcn was detected. Measured TL and DNAmTL showed only small correlations in blood and none in brain.

CONCLUSIONS

The present study is the first to simultaneously investigate epigenetic clocks, telomere length, and mtDNAcn in postmortem brain and whole blood samples in individuals with AUD. We found evidence for accelerated biological aging in AUD in blood and brain, as measured by Levine's epigenetic clock, and DNAmTL. Additional studies of different tissues from the same individuals are needed to draw valid conclusions about the congruence of biological aging in blood and brain.

Experimental and Computational Approaches to Measure Telomere Length: Recent Advances and Future Directions

PURPOSE OF REVIEW

The length of telomeres, protective structures at the chromosome ends, is a well-established biomarker for pathological conditions including multisystemic syndromes called telomere biology disorders. Approaches to measure telomere length (TL) differ on whether they estimate average, distribution, or chromosome-specific TL, and each presents their own advantages and limitations.

RECENT FINDINGS

The development of long-read sequencing and publication of the telomere-to-telomere human genome reference has allowed for scalable and high-resolution TL estimation in pre-existing sequencing datasets but is still impractical as a dedicated TL test. As sequencing costs continue to fall and strategies for selectively enriching telomere regions prior to sequencing improve, these approaches may become a promising alternative to classic methods. Measurement methods rely on probe hybridization, qPCR or more recently, computational methods using sequencing data. Refinements of existing techniques and new approaches have been recently developed but a test that is accurate, simple, and scalable is still lacking.

Associations between the New DNA-Methylation-Based Telomere Length Estimator, the Mediterranean Diet and Genetics in a Spanish Population at High Cardiovascular Risk

Biological aging is a relevant risk factor for chronic diseases, and several indicators for measuring this factor have been proposed, with telomere length (TL) among the most studied. Oxidative stress may regulate telomere shortening, which is implicated in the increased risk. Using a novel estimator for TL, we examined whether adherence to the Mediterranean diet (MedDiet), a highly antioxidant-rich dietary pattern, is associated with longer TL. We determined TL using DNA methylation algorithms (DNAmTL) in 414 subjects at high cardiovascular risk from Spain. Adherence to the MedDiet was assessed by a validated score, and genetic variants in candidate genes and at the genome-wide level were analyzed. We observed several significant associations (p < 0.05) between DNAmTL and candidate genes (TERT, TERF2, RTEL1, and DCAF4), contributing to the validity of DNAmTL as a biomarker in this population. Higher adherence to the MedDiet was associated with lower odds of having a shorter TL in the whole sample (OR = 0.93; 95% CI: 0.85-0.99; p = 0.049 after fully multivariate adjustment). Nevertheless, this association was stronger in women than in men. Likewise, in women, we observed a direct association between adherence to the MedDiet score and DNAmTL as a continuous variable (beta = 0.015; SE: 0.005; p = 0.003), indicating that a one-point increase in adherence was related to an average increase of 0.015 ± 0.005 kb in TL. Upon examination of specific dietary items within the global score, we found that fruits, fish, "sofrito", and whole grains exhibited the strongest associations in women. The novel score combining these items was significantly associated in the whole population. In the genome-wide association study (GWAS), we identified ten polymorphisms at the suggestive level of significance (p < 1 × 10-5) for DNAmTL (intergenics, in the IQSEC1, NCAPG2, and ABI3BP genes) and detected some gene-MedDiet modulations on DNAmTL. As this is the first study analyzing the DNAmTL estimator, genetics, and modulation by the MedDiet, more studies are needed to confirm these findings.

Connections between cross-tissue and intra-tissue biomarkers of aging biology in older adults

Background

Saliva measures are generally more accessible than blood, especially in vulnerable populations. However, connections between aging biology biomarkers in different body tissues remain unknown.

Methods

The present study included individuals (N = 2406) who consented for saliva and blood draw in the Health and Retirement Telomere length study in 2008 and the Venous blood study in 2016 who had complete data for both tissues. We assessed biological aging based on telomere length in saliva and DNA methylation and physiology measures in blood. DNA methylation clocks combine information from CpGs to produce the aging measures representative of epigenetic aging in humans. We analyzed DNA methylation clocks proposed by Horvath (353 CpG sites), Hannum (71 CpG sites), Levine or PhenoAge, (513 CpG sites), GrimAge, (epigenetic surrogate markers for select plasma proteins), Horvath skin and blood (391 CpG sites), Lin (99 CpG sites), Weidner (3 CpG sites), and VidalBralo (8 CpG sites). Physiology measures (referred to as phenotypic age) included albumin, creatinine, glucose, [log] C-reactive protein, lymphocyte percent, mean cell volume, red blood cell distribution width, alkaline phosphatase, and white blood cell count. The phenotypic age algorithm is based on parametrization of Gompertz proportional hazard models. Average telomere length was assayed using quantitative PCR (qPCR) by comparing the telomere sequence copy number in each patient's sample (T) to a single-copy gene copy number (S). The resulting T/S ratio was proportional to telomere length, mean. Within individual, relationships between aging biology measures in blood and saliva and variations according to sex were assessed.

Results

Saliva-based telomere length showed inverse associations with both physiology-based and DNA methylation-based aging biology biomarkers in blood. Longer saliva-based telomere length was associated with 1 to 4 years slower biological aging based on blood-based biomarkers with the highest magnitude being Weidner (β = - 3.97, P = 0.005), GrimAge (β = - 3.33, P < 0.001), and Lin (β = - 3.45, P = 0.008) biomarkers of DNA methylation.

Conclusions

There are strong connections between aging biology biomarkers in saliva and blood in older adults. Changes in telomere length vary with changes in DNA methylation and physiology biomarkers of aging biology. We observed variations in the relationship between each body system represented by physiology biomarkers and biological aging, particularly at the DNA methylation level. These observations provide novel opportunities for integration of both blood-based and saliva-based biomarkers in clinical care of vulnerable and clinically difficult to reach populations where either or both tissues would be accessible for clinical monitoring purposes.

DNA methylation variations and epigenetic aging in telomere biology disorders

Telomere Biology Disorders (TBDs) are characterized by mutations in telomere-related genes leading to short telomeres and premature aging but with no strict correlation between telomere length and disease severity. Epigenetic alterations are also markers of aging and we aimed to evaluate whether DNA methylation (DNAm) could be part of the pathogenesis of TBDs. In blood from 35 TBD cases, genome-wide DNAm were analyzed and the cases were grouped based on relative telomere length (RTL): short (S), with RTL close to normal controls, and extremely short (ES). TBD cases had increased epigenetic age and DNAm alterations were most prominent in the ES-RTL group. Thus, the differentially methylated (DM) CpG sites could be markers of short telomeres but could also be one of the mechanisms contributing to disease phenotype since DNAm alterations were observed in symptomatic, but not asymptomatic, cases with S-RTL. Furthermore, two or more DM-CpGs were identified in four genes previously linked to TBD or telomere length (PRDM8, SMC4, VARS, and WNT6) and in three genes that were novel in telomere biology (MAS1L, NAV2, and TM4FS1). The DM-CpGs in these genes could be markers of aging in hematological cells, but they could also be of relevance for the progression of TBD.

A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator

BACKGROUND

The field of epigenomics holds great promise in understanding and treating disease with advances in machine learning (ML) and artificial intelligence being vitally important in this pursuit. Increasingly, research now utilises DNA methylation measures at cytosine-guanine dinucleotides (CpG) to detect disease and estimate biological traits such as aging. Given the challenge of high dimensionality of DNA methylation data, feature-selection techniques are commonly employed to reduce dimensionality and identify the most important subset of features. In this study, our aim was to test and compare a range of feature-selection methods and ML algorithms in the development of a novel DNA methylation-based telomere length (TL) estimator. We utilised both nested cross-validation and two independent test sets for the comparisons.

RESULTS

We found that principal component analysis in advance of elastic net regression led to the overall best performing estimator when evaluated using a nested cross-validation analysis and two independent test cohorts. This approach achieved a correlation between estimated and actual TL of 0.295 (83.4% CI [0.201, 0.384]) on the EXTEND test data set. Contrastingly, the baseline model of elastic net regression with no prior feature reduction stage performed less well in general-suggesting a prior feature-selection stage may have important utility. A previously developed TL estimator, DNAmTL, achieved a correlation of 0.216 (83.4% CI [0.118, 0.310]) on the EXTEND data. Additionally, we observed that different DNA methylation-based TL estimators, which have few common CpGs, are associated with many of the same biological entities.

CONCLUSIONS

The variance in performance across tested approaches shows that estimators are sensitive to data set heterogeneity and the development of an optimal DNA methylation-based estimator should benefit from the robust methodological approach used in this study. Moreover, our methodology which utilises a range of feature-selection approaches and ML algorithms could be applied to other biological markers and disease phenotypes, to examine their relationship with DNA methylation and predictive value.

Telomere length and epigenetic clocks as markers of cellular aging: a comparative study

Telomere length (TL) and DNA methylation-based epigenetic clocks are markers of biological age, but the relationship between the two is not fully understood. Here, we used multivariable regression models to evaluate the relationships between leukocyte TL (LTL; measured by qPCR [n = 635] or flow FISH [n = 144]) and five epigenetic clocks (Hannum, DNAmAge pan-tissue, PhenoAge, SkinBlood, or GrimAge clocks), or their epigenetic age acceleration measures in healthy adults (age 19-61 years). LTL showed statistically significant negative correlations with all clocks (qPCR: r =  - 0.26 to - 0.32; flow FISH: r =  - 0.34 to - 0.49; p < 0.001 for all). Yet, models adjusted for age, sex, and race revealed significant associations between three of five clocks (PhenoAge, GrimAge, and Hannum clocks) and LTL by flow FISH (p < 0.01 for all) or qPCR (p < 0.001 for all). Significant associations between age acceleration measures for the same three clocks and qPCR or flow FISH TL were also found (p < 0.01 for all). Additionally, LTL (by qPCR or flow FISH) showed significant associations with extrinsic epigenetic age acceleration (EEAA: p < 0.0001 for both), but not intrinsic epigenetic age acceleration (IEAA; p > 0.05 for both). In conclusion, the relationships between LTL and epigenetic clocks were limited to clocks reflecting phenotypic age. The observed association between LTL and EEAA reflects the ability of both measures to detect immunosenescence. The observed modest correlations between LTL and epigenetic clocks highlight a possible benefit from incorporating both measures in understanding disease etiology and prognosis.

Inhibiting the Priming for Cancer in Li-Fraumeni Syndrome

Simple Summary

Li-Fraumeni Syndrome (LFS) is a rare cancer pre-disposition syndrome associated with a germline mutation in the TP53 tumour suppressor gene. People with LFS have a 90% chance of suffering one or more cancers in their lifetime. No treatments exist to reduce this cancer risk. This paper reviews the evidence for how cancers start in people with LFS and proposes that a series of commonly used non-cancer drugs, including metformin and aspirin, can help reduce that lifetime risk of cancer.

Abstract

The concept of the pre-cancerous niche applies the ‘seed and soil’ theory of metastasis to the initial process of carcinogenesis. TP53 is at the nexus of this process and, in the context of Li-Fraumeni Syndrome (LFS), is a key determinant of the conditions in which cancers are formed and progress. Important factors in the creation of the pre-cancerous niche include disrupted tissue homeostasis, cellular metabolism and chronic inflammation. While druggability of TP53 remains a challenge, there is evidence that drug re-purposing may be able to address aspects of pre-cancerous niche formation and thereby reduce the risk of cancer in individuals with LFS.

Comparing qPCR and DNA methylation-based measurements of telomere length in a high-risk pediatric cohort

Various approaches exist to assess population differences in biological aging. Telomere length (TL) is one such measure, and is associated with disease, disability and early mortality. Yet, issues surrounding precision and reproducibility are a concern for TL measurement. An alternative method to estimate TL using DNA methylation (DNAmTL) was recently developed. Although DNAmTL has been characterized in adult and elderly cohorts, its utility in pediatric populations remains unknown. We examined the comparability of leukocyte TL measurements generated using qPCR (absolute TL; aTL) to those estimated using DNAmTL in a high-risk pediatric cohort (N = 269; age: 8–13 years, 83% investigated for maltreatment). aTL and DNAmTL measurements were correlated with one another (r = 0.20, p = 0.001), but exhibited poor measurement agreement and were significantly different in paired-sample t-tests (Cohen’s d = 0.77, p < 0.001). Shorter DNAmTL was associated with older age (r = −0.25, p < 0.001), male sex (β = −0.27, p = 0.029), and White race (β = −0.74, p = 0.008). By contrast, aTL was less strongly associated with age (r = −0.13, p = 0.040), was longer in males (β = 0.31, p = 0.012), and was not associated with race (p = 0.820). These findings highlight strengths and limitations of high-throughput measures of TL; although DNAmTL replicated hypothesized associations, aTL measurements were positively skewed and did not replicate associations with external validity measures. These results also extend previous research in adults and suggest that DNAmTL is a sensitive TL measure for use in pediatric populations.