A novel sampling design to explore gene-longevity associations: the ECHA study

Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging

Background

Aging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration.

Recent Advances

In this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today.

Critical Issues

Although the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types.

Future Directions

We critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.

Enhanced longevity and metabolism by brown adipose tissue with disruption of the regulator of G protein signaling 14

Disruption of the regulator for G protein signaling 14 (RGS14) knockout (KO) in mice extends their lifespan and has multiple beneficial effects related to healthful aging, that is, protection from obesity, as reflected by reduced white adipose tissue, protection against cold exposure, and improved metabolism. The observed beneficial effects were mediated by improved mitochondrial function. But most importantly, the main mechanism responsible for the salutary properties of the RGS14 KO involved an increase in brown adipose tissue (BAT), which was confirmed by surgical BAT removal and transplantation to wild-type (WT) mice, a surgical simulation of a molecular knockout. This technique reversed the phenotype of the RGS14 KO and WT, resulting in loss of the improved metabolism and protection against cold exposure in RGS14 KO and conferring this protection to the WT BAT recipients. Another mechanism mediating the salutary features in the RGS14 KO was increased SIRT3. This mechanism was confirmed in the RGS14 X SIRT3 double KO, which no longer demonstrated improved metabolism and protection against cold exposure. Loss of function of the Caenorhabditis elegans RGS-14 homolog confirmed the evolutionary conservation of this mechanism. Thus, disruption of RGS14 is a model of healthful aging, as it not only enhances lifespan, but also protects against obesity and cold exposure and improves metabolism with a key mechanism of increased BAT, which, when removed, eliminates the features of healthful aging.

Analysis of Case-Parent Trios Using a Loglinear Model with Adjustment for Transmission Ratio Distortion

Transmission of the two parental alleles to offspring deviating from the Mendelian ratio is termed Transmission Ratio Distortion (TRD), occurs throughout gametic and embryonic development. TRD has been well-studied in animals, but remains largely unknown in humans. The Transmission Disequilibrium Test (TDT) was first proposed to test for association and linkage in case-trios (affected offspring and parents); adjusting for TRD using control-trios was recommended. However, the TDT does not provide risk parameter estimates for different genetic models. A loglinear model was later proposed to provide child and maternal relative risk (RR) estimates of disease, assuming Mendelian transmission. Results from our simulation study showed that case-trios RR estimates using this model are biased in the presence of TRD; power and Type 1 error are compromised. We propose an extended loglinear model adjusting for TRD. Under this extended model, RR estimates, power and Type 1 error are correctly restored. We applied this model to an intrauterine growth restriction dataset, and showed consistent results with a previous approach that adjusted for TRD using control-trios. Our findings suggested the need to adjust for TRD in avoiding spurious results. Documenting TRD in the population is therefore essential for the correct interpretation of genetic association studies.

SIRT3 regulates progression and development of diseases of aging

The mitochondrial sirtuin SIRT3 is a protein deacylase that influences almost every major aspect of mitochondrial biology, including nutrient oxidation, ATP generation, reactive oxygen species (ROS) detoxification, mitochondrial dynamics, and the mitochondrial unfolded protein response (UPR). Interestingly, mice lacking SIRT3 (SIRT3KO), either spontaneously or when crossed with mouse models of disease, develop several diseases of aging at an accelerated pace, such as cancer, metabolic syndrome, cardiovascular disease, and neurodegenerative diseases, and, thus, might be a valuable model of accelerated aging. In this review, we discuss functions of SIRT3 in pathways involved in diseases of aging and how the lack of SIRT3 might accelerate the aging process. We also suggest that further studies on SIRT3 will help uncover important new pathways driving the aging process.

Decreased SIRT3 in aged human mesenchymal stromal/stem cells increases cellular susceptibility to oxidative stress

Sirtuin3 (SIRT3) is an important member of the sirtuin family of protein deacetylases that is localized to mitochondria and linked to lifespan extension in organisms ranging from yeast to humans. As aged cells have less regenerative capacity and are more susceptible to oxidative stress, we investigated the effect of ageing on SIRT3 levels and its correlation with antioxidant enzyme activities. Here, we show that severe oxidative stress reduces SIRT3 levels in young human mesenchymal stromal/stem cells (hMSCs). Overexpression of SIRT3 improved hMSCs resistance to the detrimental effects of oxidative stress. By activating manganese superoxide dismutase (MnSOD) and catalase (CAT), SIRT3 protects hMSCs from apoptosis under stress. SIRT3 expression, levels of MnSOD and CAT, as well as cell survival showed little difference in old versus young hMSCs under normal growth conditions, whereas older cells had a significantly reduced capacity to withstand oxidative stress compared to their younger counterparts. Expression of the short 28 kD SIRT3 isoform was higher, while the long 44 kD isoform expression was lower in young myocardial tissues compared with older ones. These results suggest that the active short isoform of SIRT3 protects hMSCs from oxidative injury by increasing the expression and activity of antioxidant enzymes. The expression of this short isoform decreases in cardiac tissue during ageing, leading to a reduced capacity for the heart to withstand oxidative stress.

Glomerular filtration rate in the elderly and in the oldest old: correlation with frailty and mortality

The equations for estimating kidney function have become very popular in the last decade. However, the clinical and prognostic meaning of these measures may be very different in older populations. Two cohorts of people aged 65-89 years (older sample) and 90 or more (oldest old sample) were used to investigate the prognostic significance of estimated glomerular filtration rate (eGFR). Additionally, we also investigated whether combining frailty and eGFR may improve the accuracy of frailty in predicting mortality. We found that lower eGFR values were significantly more frequent among frail subjects in both groups. eGFR < 30 was associated with increased risk for all-cause mortality either in subjects aged 65-89 years (HR = 3.71, 95% CI = 1.23-11.2) or in those aged 90 or more (HR = 1.53, 95% CI = 1.05-2.23). In the latter group, a not significant trend for increasing mortality was also observed among people with eGFR > 60 (HR = 1.28, 95% CI = 0.72-2.26). In addition, the oldest old subjects with eGFR > 60 and eGFR < 30 had the lowest hand-grip strength and ADL values. Combining eGFR and frailty status significantly improved the accuracy of frailty in predicting mortality only in the older sample. In conclusion, a U-shaped relationship exists between eGFR and mortality in the oldest old, but not in older individuals. Our findings suggest that eGFR needs to be adjusted for muscle mass/physical performance when estimating kidney function in people aged 90 or more. Nevertheless, in subjects aged 65-89 years, eGFR may improve the accuracy of frailty status in predicting prognosis, thus suggesting that eGFR may represent an additional dimension of frailty syndrome.

Gender-specific association between FSHR and PPARG common variants and human longevity

Men and women have different life expectancies. Not unexpectedly, several genes involved in life span determination have been found to influence the probability of achieving longevity differently in men and women. This investigation examines the association between longevity and polymorphisms of follicle-stimulating hormone receptor (FSHR, Asn680Ser polymorphism) and peroxisome proliferator-activated receptor gamma (PPARG, Pro12Ala polymorphism), two genes that previous investigations suggested may exert a gender-specific influence on human longevity. A sample of 277 individuals (mean age, 82.9±5.7years) was recruited in 2000. On the basis of mortality data collected in 2009, the sample was divided into two groups of subjects surviving over 90 years (long-lived) or not (controls). The frequency of the FSHR 680 Ser/Ser genotype was significantly higher in the sample of long-lived women compared to controls, indicating that the FSHR 680 Ser/Ser genotype may favor survival to more than 90 years of age only in women (odds ratio [OR]=4.21; 95% confidence interval [CI], 1.10-16.10, p=0.036). In contrast, the frequency of the PPARG Pro/Ala genotype was significantly higher in the sample of male subjects who died before 90 years of age than in the long-lived, suggesting that carrying the PPARG Pro/Ala genotype may prevent the attainment of advanced age only in men (OR=0.13; 95% CI, 0.02-0.79; p=0.03). We then searched the literature for studies reporting a differential role for the genetic component in male and female longevity. To do this, we selected longevity genes with a gender-specific effect. A review of the studies showed that genetic factors tend to have a greater relevance in determining longevity in men than in women. The possible impact of this phenomenon is discussed.

Transmission ratio distortion: review of concept and implications for genetic association studies

Transmission ratio distortion (TRD) occurs when one of the two alleles from either parent is preferentially transmitted to the offspring. This leads to a statistical departure from the Mendelian law of inheritance, which states that each of the two parental alleles is transmitted to offspring with a probability of 0.5. A number of mechanisms are thought to induce TRD such as meiotic drive, gametic competition, and embryo lethality. TRD has been extensively studied in animals, but the prevalence of TRD in humans remains largely unknown. Nevertheless, understanding the TRD phenomenon and taking it into consideration in many aspects of human genetics has potential benefits that have not been sufficiently emphasized in the current literature. In this review, we discuss the importance of TRD in three distinct but related fields of genetics: developmental genetics which studies the genetic abnormalities in zygotic and embryonic development, statistical genetics/genetic epidemiology which utilizes population study designs and statistical models to interpret the role of genes in human health, and population genetics which is concerned with genetic diversity in populations in an evolutionary context. From the perspective of developmental genetics, studying TRD leads to the identification of the processes and mechanisms for differential survival observed in embryos. As a result, it is a genetic force which affects allele frequency at the population, as well as, at the organismal level. Therefore, it has implications on genetic diversity of the population over time. From the perspective of genetic epidemiology, the TRD influence on a marker locus is a confounding factor which has to be adequately dealt with to correctly interpret linkage or association study results. These aspects are developed in this review. In addition to these theoretical notions, a brief summary of the empirical evidence of the TRD phenomenon in human and mouse studies is provided. The objective of our paper is to show the potentially important role of TRD in many areas of genetics, and to create an incentive for future research.

Epidemiological, genetic and epigenetic aspects of the research on healthy ageing and longevity

Healthy ageing and longevity in humans result from a number of factors, including genetic background, favorable environmental and social factors and chance.

In this article we aimed to overview the research on the biological basis of human healthy ageing and longevity, discussing the role of epidemiological, genetic and epigenetic factors in the variation of quality of ageing and lifespan, including the most promising candidate genes investigated so far. Moreover, we reported the methodologies applied for their identification, discussing advantages and disadvantages of the different approaches and possible solutions that can be taken to overcome them. Finally, we illustrated the recent approaches to define healthy ageing and underlined the role that the emerging field of epigenetics is gaining in the search for the determinants of healthy ageing and longevity.

A cross-section analysis of FT3 age-related changes in a group of old and oldest-old subjects, including centenarians' relatives, shows that a down-regulated thyroid function has a familial component and is related to longevity

Background: several studies suggest that a decreased thyroid activity might be favourable in oldest-old subjects and that subclinical thyroid hyperfunction may be detrimental.

Objectives: to verify whether declining levels of circulating thyroid hormones may contribute to longevity.

Design: cross-sectional observational study.

Setting: all subjects were born in Calabria (southern Italy) and their ancestry in the region was ascertained up to the grandparents.

Subjects: six hundred and four home-dwelling subjects (301 females, 303 males), divided into three groups: 278 individuals 60–85 years old; 179 children or nieces/nephews of centenarians who are 60–85 years old; 147 individuals older than 85 years.

Methods: thyroid function parameters were measured in the frame of a comprehensive geriatric assessment.

Results: FT3 and FT4 levels were negatively associated with age. Lower levels of FT3, FT4 and TSH were found in centenarians’ children and nieces/nephews with respect to age-matched controls. Indeed, being a relative of centenarians qualified as an independent correlate of thyroid parameters.

Conclusions: age-related subtle thyroid hypofunction (either due to a familial component or due to a reset of the thyroid function occurring between the sixth and the eighth decade of life) appears to be related to longevity.

Handgrip strength: indications of paternal inheritance in three European regions

BACKGROUND

Handgrip strength is an indicator of overall muscle strength. Poor handgrip strength is a risk factor for disability and mortality. We aimed to investigate the pattern of inheritance of handgrip strength in a sample of parent-offspring pairs from three different European regions in Denmark, France, and Italy.

METHODS

In this substudy of the European Challenge for Healthy Aging study, handgrip strength was measured in 290 subjects aged 90 years and older and in one of their offspring.

RESULTS

When all pairs were considered together, parental and offspring handgrip strength were weakly correlated (r = .16; p < .01). However, paternal-offspring correlation was significantly higher than maternal-offspring correlation (r = .26; confidence interval [CI]: 0.11-0.41 versus r = .03; CI: -0.14 to 0.19; p = .04). This difference was particularly marked for daughters (r = -.07; CI: -0.29 to 0.16 for mother-daughter correlation versus r = .31; CI: 0.11-0.49 for father-daughter; p = .01) compared with sons (r = .12; CI: -0.13 to 0.36 for mother-son correlation versus r = .25; CI: 0.00-0.46 for father-son; p = .47). Father-daughter correlation remained higher than mother-daughter when analyses were performed with 144 nondependent parents (r = .32; CI: 0.04; 0.55 versus r = -.25; CI: -0.61 to 0.21; p = .03). These results were similarly observed in the three regions of the study, where mean levels of handgrip strength strongly differed.

CONCLUSIONS

It suggests that age-related effects on functional health among women could be mediated more through the paternal line than the maternal.

Power assessment for genetic association study of human longevity using offspring of long-lived subjects

Recently, an indirect genetic association approach that compares genotype frequencies in offspring of long-lived subjects and offspring from random families has been introduced to study gene-longevity associations. Although the indirect genetic association has certain advantages over the direct association approach that compares genotype frequency between centenarians and young controls, the power has been of concern. This paper reports a power study performed on the indirect approach using computer simulation. We perform our simulation study by introducing the current Danish population life table and the proportional hazard model for generating individual lifespan. Family genotype data is generated using a genetic linkage program for given SNP allele frequency. Power is estimated by setting the type I error rate at 0.05 and by calculating the Armitage's chi-squared test statistic for 200 replicate samples for each setting of the specified allele risk and frequency parameters under different modes of inheritance and for different sample sizes. The indirect genetic association analysis is a valid approach for studying gene-longevity association, but the sample size requirement is about 3-4 time larger than the direct approach. It also has low power in detecting non-additive effect genes. Indirect genetic association using offspring from families with both parents as nonagenarians is nearly as powerful as using offspring from families with one centenarian parent. In conclusion, the indirect design can be a good choice for studying longevity in comparison with other alternatives, when relatively large sample size is available.