Somatic mutation and aging

The Impact of Genes and Environment on Brain Ageing in Males Aged 51 to 72 Years

Magnetic resonance imaging data are being used in statistical models to predicted brain ageing (PBA) and as biomarkers for neurodegenerative diseases such as Alzheimer's Disease. Despite their increasing application, the genetic and environmental etiology of global PBA indices is unknown. Likewise, the degree to which genetic influences in PBA are longitudinally stable and how PBA changes over time are also unknown. We analyzed data from 734 men from the Vietnam Era Twin Study of Aging with repeated MRI assessments between the ages 51-72 years. Biometrical genetic analyses "twin models" revealed significant and highly correlated estimates of additive genetic heritability ranging from 59 to 75%. Multivariate longitudinal modeling revealed that covariation between PBA at different timepoints could be explained by a single latent factor with 73% heritability. Our results suggest that genetic influences on PBA are detectable in midlife or earlier, are longitudinally very stable, and are largely explained by common genetic influences.

Evaluating the impact of age on immune checkpoint therapy biomarkers

Both tumors and aging alter the immune landscape of tissues. These interactions may play an important role in tumor progression among elderly patients and may suggest considerations for patient care. We leverage large-scale genomic and clinical databases to perform comprehensive comparative analysis of molecular and cellular markers of immune checkpoint blockade (ICB) response with patient age. These analyses demonstrate that aging is associated with increased tumor mutational burden, increased expression and decreased promoter methylation of immune checkpoint genes, and increased interferon gamma signaling in older patients in many cancer types studied, all of which are expected to promote ICB efficacy. Concurrently, we observe age-related alterations that might be expected to reduce ICB efficacy, such as decreases in T cell receptor diversity. Altogether, these changes suggest the capacity for robust ICB response in many older patients, which may warrant large-scale prospective study on ICB therapies among patients of advanced age.

Evolution of aging and death: what insights bacteria can provide

Several unresolved issues, paradoxes, and information voids characterize the field of evolution of aging. The recent discovery of aging-like phenomenon in Escherichia coli, marked by asymmetric segregation of damaged components, particularly protein aggregates, has created a number of new possibilities that remain underexplored. Bacterial systems can potentially throw light on issues such as: whether evolution of aging and evolution of death are different phenomena; whether aging is inevitable for life or is an evolved strategy; whether there could be selection for aging or aging is a pleiotropic effect of some other selection; what are the possible mechanisms of antagonistic pleiotropy, if any; and whether there are mechanisms of aging that are conserved throughout the hierarchy of life. Bacterial aging itself is underexplored and least understood as of now, but even scratching the surface appears to reveal things that may compel us to revise some of the classical concepts about evolution of aging. This warrants more focused and innovative inquiry into aging-like processes in bacteria.

Somatic mutations in aging, cancer and neurodegeneration

The somatic mutation theory of aging posits that the accumulation of mutations in the genetic material of somatic cells as a function of time results in a decrease in cellular function. In particular, the accumulation of random mutations may inactivate genes that are important for the functioning of the somatic cells of various organ systems of the adult, result in a decrease in organ function. When the organ function decreases below a critical level, death occurs. A significant amount of research has shown that somatic mutations play an important role in aging and a number of age related pathologies. In this review, we explore evidence for increases in somatic nuclear mutation burden with age and the consequences for aging, cancer, and neurodegeneration. We then review evidence for increases in mitochondrial mutation burden and the consequences for dysfunction in the disease processes.

Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS

Aging is a complex multifactorial phenomenon, which is believed to result from the accumulation of cellular damage to biological macromolecules. Peroxisomes recently emerged as another important source of reactive oxygen species (ROS) production in addition to mitochondria. However, the role of these organelles in the process of aging is still not clear. The aim of this study was to characterize the changes in protein expression profiles of young (10 weeks old) versus old (18 months old) mouse liver peroxisome-enriched fractions. We have applied shotgun proteomic approach based on liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with iTRAQ (isobaric tags for relative and absolute quantitation) labeling that allows comparative quantitative multiplex analysis. Our analysis led to identification and quantification of 150 proteins, 8 out of which were differentially expressed between two age groups at a statistically significant level (p<0.05), with folds ranging from 1.2 to 4.1. These proteins involved in peroxisomal β-oxidation, detoxification of xenobiotics and production of ROS. Noteworthy, differences in liver proteome have been observed between as well as within different age groups. In conclusion, our subproteomic quantitative study suggests that mouse liver proteome is sufficiently maintained until certain age.

The L84F polymorphism in the O6-Methylguanine-DNA-Methyltransferase (MGMT) gene is associated with increased hypoxanthine phosphoribosyltransferase (HPRT) mutant frequency in lymphocytes of tobacco smokers

OBJECTIVES

O-methylguanine-DNA-methyltransferase (MGMT) is a crucial DNA repair protein that removes DNA adducts formed by alkylating mutagens. Several coding single nucleotide polymorphisms (cSNPs) in the MGMT gene have been reported. Their biological significance, however, is not known.

METHODS

We used a newly modified cloning HPRT mutant lymphocyte assay to test the hypothesis that inheritance of the L84F and I143V coding single nucleotide polymorphism in the MGMT gene is associated with increases in HPRT mutant frequency in lymphocytes of individuals exposed to alkylating agents. In addition, we expanded and sequenced 109 mutant clones to test the hypothesis that the mutation spectrum would shift to a larger percentage of base substitutions and G-->A transition mutations in cells with L84F and I143 V coding single nucleotide polymorphisms.

RESULTS

We observed no significant effect for the I143 V coding single nucleotide polymorphism on mutant frequency. In contrast, we observed a significant increase in mutant frequency (P<0.01) in lymphocytes from smokers with the 84F coding single nucleotide polymorphism compared with smokers homozygous for the referent L84 wild-type allele. A multiple regression analysis indicated that the mutant frequency increased significantly as a function of the 84F coding single nucleotide polymorphism and smoking, according to the model; mutant frequency (x10)=0.90+0.618 (84F polymorphism)+0.46 (smoking) with R=0.22. Mutation spectra analysis revealed an apparent increase, which was short of statistical significance (P=0.08), in base substitutions in cells with the 84F polymorphism.

CONCLUSIONS

These new data suggest that the 84F coding single nucleotide polymorphism may alter the phenotype of the MGMT protein, resulting in suboptimal repair of O-methylguanine lesions after exposure to alkylating agents.

Changes in DNA repair during aging

DNA is a precious molecule. It encodes vital information about cellular content and function. There are only two copies of each chromosome in the cell, and once the sequence is lost no replacement is possible. The irreplaceable nature of the DNA sets it apart from other cellular molecules, and makes it a critical target for age-related deterioration. To prevent DNA damage cells have evolved elaborate DNA repair machinery. Paradoxically, DNA repair can itself be subject to age-related changes and deterioration. In this review we will discuss the changes in efficiency of mismatch repair (MMR), base excision repair (BER), nucleotide excision repair (NER) and double-strand break (DSB) repair systems during aging, and potential changes in DSB repair pathway usage that occur with age. Mutations in DNA repair genes and premature aging phenotypes they cause have been reviewed extensively elsewhere, therefore the focus of this review is on the comparison of DNA repair mechanisms in young versus old.

Aging is no longer an unsolved problem in biology

For much of the 20th century, the accumulation of a considerable amount of information about the processes of aging did not reveal the underlying mechanisms. Toward the end of that century, the biological basis for aging became very much clearer. It became apparent that the best strategy for animals' survival was to develop to an adult, but not to invest resources in maintaining the body, or soma, indefinitely. In their natural environment, animals do not survive environmental hazards (predators, disease, starvation, and drought) to reach a long life span. There is thus a trade-off between the investment of resources in reproduction, and the survival time of the soma. At a stroke, this solves the problem of different rates of aging in different species, because those that develop and reproduce fast also have short life spans, and those that develop and reproduce slowly have long life spans. This difference is due to actual resources invested in the maintenance of the adult soma. There is now much evidence that long-lived mammals have much more efficient maintenance mechanisms than short-lived mammals. Thus, aging can be defined as the eventual failure of maintenance. It also became apparent that many different maintenance mechanisms exist, and that these depend on very many genes and a considerable investment in metabolic resources. Most individual theories of aging revolve around the failure of a given maintenance system, but as there are many of these, it is likely that most of the important theories have some degree of truth. A broad interpretation of the different degenerative changes during senescence should therefore be adopted, with the major conclusion that aging is multicausal. It is also evident that the evolved design of many components of complex animals is incompatible with indefinite survival. We can therefore conclude that this evolved design is intrinsically related to the fact of aging. This in turn means that aging cannot be reversed, although it may be modulated, as, for example, by calorie restriction.

Genotype profiles of loci encoding DNA repair enzymes in newborn and elderly populations: no evidence of association with longevity

The comparison of genotype frequencies between neonates and elderly populations can aid in the identification of loci, and polymorphisms within those loci, that affect longevity. Here we have compared genotype frequencies of seven polymorphisms at four loci involved in DNA repair between a cohort of newborns (n = 290) and a retired population (average age at sampling 70.02 years; n = 430) who have suffered a lifetime of DNA damage from normal, metabolic processes, and on whom selection on DNA repair gene variants may be expected to have acted. No differences in genotype frequencies at the four SNP loci were seen, indicating that there is no evidence of association with longevity in this population. Significant differences in frequency of certain repeat sizes at three microsatellite loci were detected. However, since there is no known functional consequence of these repeat lengths, the action of selection cannot yet be ascribed.

Making ends meet in old age: DSB repair and aging

Accumulation of somatic mutations has long been considered as a major cause of aging and age-related diseases such as cancer. Genomic rearrangements, which arise from aberrant repair of DNA breaks, are the most characteristic component of the mutation spectra in aging cells and tissues. The studies conducted in the past few years provide further support for the role of DNA double-strand break (DSB) repair in aging and cellular senescence. Evidence was obtained that in addition to accumulation of mutations the efficiency and fidelity of repair declines with age. We propose that DNA damage and age-related decline of DNA repair form a vicious cycle leading to amplification of damage and progression of aging, and discuss a hypothesis on how the interplay between the two pathways of DSB repair, homologous recombination and nonhomologous end joining, may contribute to the aging process.

The close relationship between biological aging and age-associated pathologies in humans

In the last 100 years, there has accumulated a vast amount of information about the changes that accompany aging in a wide range of animal species. At the same time, there has been extensive documentation of the onset and characteristics of age-associated pathologies of humans and other mammals. It is argued that the totality of all this information is interrelated and provides a very extensive description of the deleterious changes in molecules, cells, tissues, and organs, which accompany both aging and many age-associated diseases. The accumulation of damage is in DNA, proteins, membranes, and organelles, as well as the formation of insoluble protein aggregates. The evolved design of many organ systems, such as the cardiovascular system, the brain, and the eye, are incompatible with indefinite survival. The eventual failure to maintain the integrity of tissues and organs is the end result of the multiple causes of aging.

Spontaneous mutation in Big Blue mice from fetus to old age: tissue-specific time courses of mutation frequency but similar mutation types

Transgenic mouse mutation detection systems permit rapid determination of the frequency and type of mutations allowing direct examination of mutational markers for aging, neurodegeneration, and cancer. The Big Blue transgenic mouse mutation detection system was used to determine the frequency and nature of spontaneous mutations versus age in multiple tissue types. Nuclear DNA was extracted from whole fetus at 13.5 days postcoitus (dpc) and from six tissues postbirth (cerebellum, forebrain, thymus, liver, adipose tissue, and male germline) of Big Blue transgenic mice at four ages: 10 days and at 3, 10, and 25 months postbirth. Forty million total plaque-forming units (pfu) were screened. The time course of mutation frequency with age had a significantly different shape in different tissues (P < 10(-6)). By 13.5 dpc, the whole fetus mutation frequency had already started increasing from the theoretical zero at conception to a value that was about one-half the mid-adulthood (3-10 months) average. From 10 days to 3 months, mutation frequency increased significantly in liver (P = 0.007) and showed an increasing trend in cerebellum, forebrain, and thymus. From 3 to 10 months, there was no significant change in mutation frequency in any tissue examined. From 10 to 25 months, the mutation frequency increased significantly in liver (P < 10(-6)) and adipose tissue (P = 0.002), but not in the other tissues examined (cerebellum, forebrain, and male germline). It is of interest that the mutation frequency in the male germline is consistently the lowest, remaining essentially unchanged in old age. The spectrum of mutation types was unaltered with age, tissue type and gender, although, as previously reported, tandem GG-->TT mutations are tissue specific and show significant increases with age and certain hotspots (Buettner VL et al. [1999]: Environ Mol Mutagen 33:320-324; Hill KA et al. [2003]: Mutat Res 534:173-186). The spectrum of mutation types was generally the same for all tissue types, despite the tissue-specific increases in mutation frequency with age. These data provide a useful reference for future studies of endogenous and exogenous mutagenesis.

What the papers say: Where is the somatic mutation that causes aging?

It has been proposed that somatic mutations make major contributions to aging. The first paper, based on a gene knock-in mouse, supports a contributory role for mutation in mtDNA in aging, but does not support a damaged-mtDNA-producing-more-damaged-mtDNA hypothesis. The second paper indicates some GC-rich sequences in the nuclear DNA are more sensitive to oxidative damage than mtDNA. As a result, key genes involved in brain function and mitochondrial function are progressively inactivated with age. Failure in these nucleus-encoded mitochondrial genes may be a primary reason for mitochondrial failure in old age.

An age-induced switch to a hyper-recombinational state

There is a strong correlation between age and cancer, but the mechanism by which this phenomenon occurs is unclear. We chose Saccharomyces cerevisiae to examine one of the hallmarks of cancer--genomic instability--as a function of cellular age. As diploid yeast mother cells aged, an approximately 100-fold increase in loss of heterozygosity (LOH) occurred. Extending life-span altered neither the onset nor the frequency of age-induced LOH; the switch to hyper-LOH appears to be on its own clock. In young cells, LOH occurs by reciprocal recombination, whereas LOH in old cells was nonreciprocal, occurring predominantly in the old mother's progeny. Thus, nuclear genomes may be inherently unstable with age.

Does dietary sugar and fat influence longevity?

Simultaneous consideration of the influence of the different types of carbohydrates and fats in human diets on mortality rates (especially the diseases of aging), and the probable retardation of such diseases by caloric restriction (CR) leads to the hypothesis that restriction of foods with a high glycemic index and saturated or hydrogenated fats would avoid or delay many diseases of aging and might result in life extension. Many of the health benefits of CR might thereby be available to humans without the side effects or unacceptability of semi-starvation diets.

Coronary atherosclerosis and somatic mutations: an overview of the contributive factors for oxidative DNA damage

Coronary artery disease (CAD) is a multifactorial process that appears to be caused by the interaction of environmental risk factors with multiple predisposing genes. Genetic research on CAD has traditionally focused on investigation aimed at identifying disease-susceptibility genes. Recent evidence suggests that somatically acquired DNA mutations may also contribute significantly to the pathogenesis of the disease, underlining the similarity between atherosclerotic and carcinogenic processes. The generation of oxidative stress has been emphasized as an important cause of DNA damage in atherosclerosis. This review highlights some of the major atherogenic risk factors as likely mediators in the oxidative modification of DNA. It also examines the hypothesis that an increase in oxidative stress may derive from "oxidatively" damaged mitochondria. Accordingly, further research in this field should be given high priority, since increased somatic DNA damage could be an important pathogenic factor and an additional prognostic predictor, as well as a potential target for therapeutic strategies in coronary artery disease.

Large accumulation of mRNA and DNA point modifications in a plant senescent tissue

Although nucleic acids are the paradigm of genetic information conservation, they are inherently unstable molecules that suffer intrinsic and environmental damage. Oxidative stress has been related to senescence and aging and, recently, it has been shown that mutations accumulate at high frequency in mitochondrial DNA with age. We investigated RNA and DNA modifications in cork, a senescent plant tissue under high endogenous oxidative stress conditions. When compared to normally growing young tissue, cork revealed an unexpected high frequency of point modifications in both cDNA (Pn = 1/1784) and nuclear DNA (Pn = 1/1520). Cork should be viewed as a mosaic of genetically heterogeneous cells. This has biological implications: it supports somatic mutation models for aging and challenges 'single cDNA clone' as descriptor for the molecular genetics of senescent tissues.