Centenarians consistently present a younger epigenetic age than their chronological age with four epigenetic clocks based on a small number of CpG sites

Protocol for the San Diego Nathan Shock Center Clinical Cohort: a new resource for studies of human aging

INTRODUCTION

While it is well recognised that aging is a heterogeneous process, our understanding of the determinants of biological aging and its heterogeneity remains unclear. The San Diego Nathan Shock Center (SD-NSC) Clinical Cohort aims to establish a resource of biospecimens and extensive donor clinical data such as physical, cognitive and sensory function to support other studies that aim to explore the heterogeneity of normal human aging and its biological underpinnings.

METHODS AND ANALYSIS

The SD-NSC Clinical Cohort is composed of 80 individuals across the adult human lifespan. Strict inclusion and exclusion criteria are implemented to minimise extrinsic factors that may impede the study of normal aging. Across three visits, participants undergo extensive phenotyping for collection of physical performance, body composition, cognitive function, sensory ability, mental health and haematological data. During these visits, we also collected biospecimens including plasma, platelets, peripheral blood mononuclear cells and fibroblasts for banking and future studies on aging.

ETHICS AND DISSEMINATION

Ethics approval from the UC San Diego School of Medicine Institutional Review Board (IRB #201 141 SHOCK Center Clinical Cohort, PI: Molina) was obtained on 11 November 2020. Written informed consent is obtained from all participants after objectives and procedures of the study have been fully explained. Congruent with the goal of establishing a core resource, biological samples and clinical data are made available to the research community through the SD-NSC.

Heritability of Gene Expression Measured from Peripheral Blood in Older Adults

The contributions of genetic variation and the environment to gene expression may change across the lifespan. However, few studies have investigated the heritability of blood gene expression in older adults. The current study therefore aimed to investigate this question in a community sample of older adults. A total of 246 adults (71 MZ and 52 DZ twins, 69.91% females; mean age-75.79 ± 5.44) were studied. Peripheral blood gene expression was assessed using Illumina microarrays. A heritability analysis was performed using structural equation modelling. There were 5269 probes (19.9%) from 4603 unique genes (23.9%) (total 26,537 probes from 19,256 genes) that were significantly heritable (mean h2 = 0.40). A pathway analysis of the top 10% of significant genes showed enrichment for the immune response and ageing-associated genes. In a comparison with two other gene expression twin heritability studies using adults from across the lifespan, there were 38 out of 9479 overlapping genes that were significantly heritable. In conclusion, our study found ~24% of the available genes for analysis were heritable in older adults, with only a small number common across studies that used samples from across adulthood, indicating the importance of examining gene expression in older age groups.

The CEPH aging cohort and biobank: a valuable collection of biological samples from exceptionally long-lived French individuals and their offspring for longevity studies

The increasing aging of the human population is currently and for the coming decades a major public health issue in many countries, requiring the implementation of global public health policies promoting healthy and successful aging. Individuals are not equal in the face of aging and some can present exceptional healthspan and/or lifespan, which are notably influenced by both genetic and environmental factors. Research and studies on human aging, healthy aging and longevity should rely in particular on cohorts of long-lived individuals, also including biological samples allowing studies on the biology of aging and longevity. In this manuscript, we provide for the first time a complete description of the CEPH (Centre d'Etude du Polymophisme Humain) Aging cohort, an exceptional cohort recruited during the 90s to 2000s, including more than 1700 French long-lived individuals (≥ 90 years old) born between 1875 and 1916 as well as for some of them their siblings and offspring. Among the participants, 1265 were centenarians, including 255 semi-supercentenarians ([105-110] years old) and 25 supercentenarians (≥ 110 years old). The available anthropometric, epidemiologic and clinical data for the cohort participants are described and especially the collection of blood-derived biological samples associated with the cohort which includes DNA, cryopreserved cells and cell lines, plasma, and serum. This biological collection from the first cohort of centenarians in the world is an inestimable resource for ongoing and future molecular, cellular, and functional studies aimed at deciphering the mechanisms of human (successful) aging and longevity.

Building Minimized Epigenetic Clock by iPlex MassARRAY Platform

Epigenetic clocks are valuable tools for estimating both chronological and biological age by assessing DNA methylation levels at specific CpG dinucleotides. While conventional epigenetic clocks rely on genome-wide methylation data, targeted approaches offer a more efficient alternative. In this study, we explored the feasibility of constructing a minimized epigenetic clock utilizing data acquired through the iPlex MassARRAY technology. The study enrolled a cohort of relatively healthy individuals, and their methylation levels of eight specific CpG dinucleotides in genes SLC12A5, LDB2, FIGN, ACSS3, FHL2, and EPHX3 were evaluated using the iPlex MassARRAY system and the Illumina EPIC array. The methylation level of five studied CpG sites demonstrated significant correlations with chronological age and an acceptable convergence of data obtained by the iPlex MassARRAY and Illumina EPIC array. At the same time, the methylation level of three CpG sites showed a weak relationship with age and exhibited a low concordance between the data obtained from the two technologies. The construction of the epigenetic clock involved the utilization of different machine-learning models, including linear models, deep neural networks (DNN), and gradient-boosted decision trees (GBDT). The results obtained from these models were compared with each other and with the outcomes generated by other well-established epigenetic clocks. In our study, the TabNet architecture (deep tabular data learning architecture) exhibited the best performance (best MAE = 5.99). Although our minimized epigenetic clock yielded slightly higher age prediction errors compared to other epigenetic clocks, it still represents a viable alternative to the genome-wide epigenotyping array.

Decelerated Epigenetic Aging in Long Livers

Epigenetic aging is a hot topic in the field of aging research. The present study estimated epigenetic age in long-lived individuals, who are currently actively being studied worldwide as an example of successful aging due to their longevity. We used Bekaert's blood-based age prediction model to estimate the epigenetic age of 50 conditionally "healthy" and 45 frail long-livers over 90 years old. Frailty assessment in long-livers was conducted using the Frailty Index. The control group was composed of 32 healthy individuals aged 20-60 years. The DNA methylation status of 4 CpG sites (ASPA CpG1, PDE4C CpG1, ELOVL2 CpG6, and EDARADD CpG1) included in the epigenetic clock was assessed through pyrosequencing. According to the model calculations, the epigenetic age of long-livers was significantly lower than their chronological age (on average by 21 years) compared with data from the group of people aged 20 to 60 years. This suggests a slowing of epigenetic and potentially biological aging in long livers. At the same time, the obtained results showed no statistically significant differences in delta age (difference between the predicted and chronological age) between "healthy" long livers and long livers with frailty. We also failed to detect sex differences in epigenetic age either in the group of long livers or in the control group. It is possible that the predictive power of epigenetic clocks based on a small number of CpG sites is insufficient to detect such differences. Nevertheless, this study underscores the need for further research on the epigenetic status of centenarians to gain a deeper understanding of the factors contributing to delayed aging in this population.

An evidence-based debate on epigenetics and immunosenescence in COVID-19

Immunosenescence contributes to the decline of immune function leading to a reduced ability to respond to severe coronavirus disease 2019 (COVID-19) in elderly patients. Clinical course of COVID-19 is widely heterogeneous and guided by the possible interplay between genetic background and epigenetic-sensitive mechanisms underlying the immunosenescence which could explain, at least in part, the higher percentage of disease severity in elderly individuals. The most convincing evidence regards the hypomethylation of the angiotensin-converting enzyme 2 (ACE2) promoter gene in lungs as well as the citrullination of histone H3 in neutrophils which have been associated with worsening of COVID-19 outcome in elderly patients. In contrast, centenarians who have showed milder symptoms have been associated to a younger "epigenetic age" based on DNA methylation profiles at specific genomic sites (epigenetic clock). Some large prospective studies showed that the acceleration of epigenetic aging as well as the shortening of telomeres were significantly associated with lymphopenia and poor outcome suggesting prognostic biomarkers in elderly COVID-19 patients. Furthermore, randomized clinical trials showed that statins, L-arginine, and resveratrol could mediate anti-inflammatory effects via indirect epigenetic interference and might improve COVID-19 outcome. Here, we discuss the epigenetic-sensitive events which might contribute to increase the risk of severity and mortality in older subjects and possible targeted therapies to counteract immunosenescence.

Discovering Biological Mechanisms of Exceptional Human Health Span and Life Span

Humans age at different rates and families with exceptional longevity provide an opportunity to understand why some people age slower than others. Unique features exhibited by centenarians include a family history of extended life span, compression of morbidity with resultant extension of health span, and longevity-associated biomarker profiles. These biomarkers, including low-circulating insulin-like growth factor 1 (IGF-1) and elevated high-density lipoprotein (HDL) cholesterol levels, are associated with functional genotypes that are enriched in centenarians, suggesting that they may be causative for longevity. While not all genetic discoveries from centenarians have been validated, in part due to exceptional life span being a rare phenotype in the general population, the APOE2 and FOXO3a genotypes have been confirmed in a number of populations with exceptional longevity. However, life span is now recognized as a complex trait and genetic research methods to study longevity are rapidly extending beyond classical Mendelian genetics to polygenic inheritance methodologies. Moreover, newer approaches are suggesting that pathways that have been recognized for decades to control life span in animals may also regulate life span in humans. These discoveries led to strategic development of therapeutics that may delay aging and prolong health span.

Biomarkers of aging

Aging biomarkers are a combination of biological parameters to (i) assess age-related changes, (ii) track the physiological aging process, and (iii) predict the transition into a pathological status. Although a broad spectrum of aging biomarkers has been developed, their potential uses and limitations remain poorly characterized. An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research: How old are we? Why do we get old? And how can we age slower? This review aims to address this need. Here, we summarize our current knowledge of biomarkers developed for cellular, organ, and organismal levels of aging, comprising six pillars: physiological characteristics, medical imaging, histological features, cellular alterations, molecular changes, and secretory factors. To fulfill all these requisites, we propose that aging biomarkers should qualify for being specific, systemic, and clinically relevant.

Longevity, Centenarians and Modified Cellular Proteodynamics

We have shown before that at least one intracellular proteolytic system seems to be at least as abundant in the peripheral blood lymphocytes of centenarians as in the same cells of young individuals (with the cells of the elderly population showing a significant dip compared to both young and centenarian cohorts). Despite scarce published data, in this review, we tried to answer the question how do different types of cells of longevous people-nonagenarians to (semi)supercentenarians-maintain the quality and quantity of their structural and functional proteins? Specifically, we asked if more robust proteodynamics participate in longevity. We hypothesized that at least some factors controlling the maintenance of cellular proteomes in centenarians will remain at the "young" level (just performing better than in the average elderly). In our quest, we considered multiple aspects of cellular protein maintenance (proteodynamics), including the quality of transcribed DNA, its epigenetic changes, fidelity and quantitative features of transcription of both mRNA and noncoding RNAs, the process of translation, posttranslational modifications leading to maturation and functionalization of nascent proteins, and, finally, multiple facets of the process of elimination of misfolded, aggregated, and otherwise dysfunctional proteins (autophagy). We also included the status of mitochondria, especially production of ATP necessary for protein synthesis and maintenance. We found that with the exception of the latter and of chaperone function, practically all of the considered aspects did show better performance in centenarians than in the average elderly, and most of them approached the levels/activities seen in the cells of young individuals.

An ELOVL2-Based Epigenetic Clock for Forensic Age Prediction: A Systematic Review

The prediction of chronological age from methylation-based biomarkers represents one of the most promising applications in the field of forensic sciences. Age-prediction models developed so far are not easily applicable for forensic caseworkers. Among the several attempts to pursue this objective, the formulation of single-locus models might represent a good strategy. The present work aimed to develop an accurate single-locus model for age prediction exploiting ELOVL2, a gene for which epigenetic alterations are most highly correlated with age. We carried out a systematic review of different published pyrosequencing datasets in which methylation of the ELOVL2 promoter was analysed to formulate age prediction models. Nine of these, with available datasets involving 2298 participants, were selected. We found that irrespective of which model was adopted, a very strong relationship between ELOVL2 methylation levels and age exists. In particular, the model giving the best age-prediction accuracy was the gradient boosting regressor with a prediction error of about 5.5 years. The findings reported here strongly support the use of ELOVL2 for the formulation of a single-locus epigenetic model, but the inclusion of additional, non-redundant markers is a fundamental requirement to apply a molecular model to forensic applications with more robust results.

A Blood-Based Molecular Clock for Biological Age Estimation

In the last decade, extensive efforts have been made to identify biomarkers of biological age. DNA methylation levels of ELOVL fatty acid elongase 2 (ELOVL2) and the signal joint T-cell receptor rearrangement excision circles (sjTRECs) represent the most promising candidates. Although these two non-redundant biomarkers echo important biological aspects of the ageing process in humans, a well-validated molecular clock exploiting these powerful candidates has not yet been formulated. The present study aimed to develop a more accurate molecular clock in a sample of 194 Italian individuals by re-analyzing the previously obtained EVOLV2 methylation data together with the amount of sjTRECs in the same blood samples. The proposed model showed a high prediction accuracy both in younger individuals with an error of about 2.5 years and in older subjects where a relatively low error was observed if compared with those reported in previously published studies. In conclusion, an easy, cost-effective and reliable model to measure the individual rate and the quality of aging in human population has been proposed. Further studies are required to validate the model and to extend its use in an applicative context.