Aging as a genomic-epigenomic dance

By Vince Giuliano

Much of what we observe in aging appears to come about through accumulated genomic damage, or through aging-related epigenomic mechanisms. This blog entry explores the relationship of genomics to epigenomics with respect to diseases and aging.

Some of the material presented here has been covered before from differing viewpoints and a number of newer 2011 publications are cited here for the first time.  My intention is to present an integrated viewpoint of the topic so I don’t hesitate to refer to relevant past blog entries.

For background on genomic damage as an irreversible source of aging you can see Brendan Hussey’s blog entry The Nuclear DNA Damage/Mutation Theory of Aging.  I have written a number of blog entries relating epigenetics to various facets of aging including the introduction to this topic Epigenetics, epigenomics and aging, the recent entry Longevity of stem cells and the roles of stem cells in aging, The epigenetic regulation of telomeres, Stochastic epigenetic evolution – a new and different theory of evolution, aging and disease susceptibility, DNA methylation, personalized medicine and longevity,and Epigenetics of cancer and aging.  And in my treatise, one of the main theories of aging discussed is Programmed Epigenomic Changes.  Finally, in my most recent blog entry Longevity of stem cells and the roles of stem cells in aging, among other maters I outline how epigenetic interventions in adult stem cells could possibly contribute to longer human lifespans.

Increasingly, the epigenetics paradigm is supplementing or even displacing the genetics paradigm when considering diseases and aging

There is a major shift in how things are being looked at – from a purely genomic viewpoint to a much more subtle and complex genomic-epigenomic viewpoint.  This shift that has become clear during the lifetime of this blog.  Looking for simple associations between genetic variants and diseases has generally turned out to be a disappointing exercise.  The associations, when they exist, usually turn out to be weak.  An in only very rare circumstances is there a one-to-one relationship between a gene variant and a disease.  See Victor’s recent blog entry Kinase Inhibition – A Magic Bullet? A lot more is needed to explain aging and disease susceptibilities than can be found in the genome by itself.

This newer viewpoint is central to a number of publications in recent years such as Epigenetics: molecular mechanisms and implications for disease , Interactions between genes and the environment. Epigenetics in allergy, The role of epigenetics in aging and age-related diseases, Epigenetic factors in aging and longevity, The Janus face of DNA methylation in aging,   Epigenetics and its implications for plant biology 2. The ‘epigenetic epiphany’: epigenetics, evolution and beyond, Epigenetics and cancer, 2nd IARC meeting, Lyon, France, 6 and 7 December 2007, Epigenetics, disease, and therapeutic interventions, Epigenetic regulation of gene expression in the inflammatory response and relevance to common diseases, Epigenetic reprogramming: enforcer or enabler of developmental and Epigenetics and human disease.

With aging there is accumulated genomic damage and global changes in epigenetic markers.  While each of these phenomena by themselves can be used as the basis for constructing a comprehensive theory of aging, they appear to affect each other in complex feedback relationships

Accumulating evidence suggests that the genomic and epigenomic theories of aging are not mutually exclusive but are highly complementary.  Indeed, accumulated genomic damage is likely to be causative of aging-related epigenomic changes, and conversely, epigenomic changes may well have important genomic consequences.

The relationships between genomic damage, epigenomic changes and aging are explored in the excellent 2009 review publication The ageing epigenome: damaged beyond repair? By David Sinclair and Philipp Oberdoerffer.  “Of all the proposed causes of ageing, DNA damage remains a leading, though still debated theory. Unlike most other types of age-related cellular damage, which can hypothetically be reversed, mutations in DNA are permanent. Such errors result in the accumulation of changes to RNA and protein sequences with age, and are tightly linked to cellular senescence and overall organ dysfunction.”

Continuing: “Over the past few years, an additional, more global role has emerged for the contribution of DNA damage and genomic instability to the ageing process. We, and others have found that DNA damage and the concomitant repair process can induce genome-wide epigenetic changes, which may promote a variety of age-related transcriptional and functional changes. Here, we discuss the link between DNA damage, chromatin alterations and ageing, an interplay that explains how seemingly random DNA damage could manifest in predictable phenotypic changes that define ageing, changes that may ultimately be reversible(ref).”

Going on: “most life-forms share common weak spots that become increasingly susceptible to failure over time. One such “Achilles’ Heel” is the genome, a fragile and highly conserved structure that accumulates a wide range of damaging alterations with age, despite continuous surveillance and repair (Garinis et al. 2008; Lombard et al. 2005; Vijg 2004). Recent work extends the impact of genomic defects to an age-associated deregulation of the epigenome (reviewed in (Oberdoerffer and Sinclair 2007)), suggesting that the accumulation of DNA damage and genomic instability with age may be a critical contributor to the ageing process, though perhaps in a more indirect and complex way than first proposed. — The accrual of genomic defects can affect cellular function on many levels. For example, mutations in coding regions of DNA can cause abnormal protein expression or function, and chromosomal translocations and rearrangements can result in apoptosis, tumor formation or senescence (Campisi 2005). — DNA damage and its repair have also been linked to wide-ranging chromatin alterations that surround the sites of damage and may affect a large number of genomic loci, including coding regions and structural components (Downs et al. 2007 (ref).”

“Like mutations, epigenomic changes to chromatin are a conserved hallmark of ageing (Oberdoerffer and Sinclair 2007). A major difference, though, is that epigenetic changes are theoretically reversible. This is due to the fluid nature of chromatin, a complex packaging system, in which DNA is wrapped around a protein core of four different histone dimers, forming the basic building blocks of chromatin called nucleosomes. — This highly dynamic form of nuclear organization influences both DNA stability and gene-expression patterns (Cheutin et al. 2003; Grewal and Jia 2007) and its level of compaction can be modulated through a variety of reversible chemical modifications of histones or modifications of DNA itself (Kouzarides 2007). Amongst the most prominent posttranslational modifications are histone acetylation and histone or DNA methylation. The enzymes that catalyze those changes are comprehensively referred to as chromatin modifiers. Histone acetylation renders chromatin accessible for transcriptional regulators and DNA binding factors, whereas histone and DNA methylation have the opposite effect, although certain types of histone methylation are linked to active transcription (Kouzarides 2007). Highly compacted, transcriptionally silent chromatin is generally referred to as “heterochromatin”, whereas the more accessible chromatin is “euchromatin”. –  The potential of DNA damage to affect cell function both through direct alterations to the DNA sequence and through indirect, epigenetic changes in chromatin structure puts it at a critical position to influence the ageing of eukaryotes. In this review we will highlight recent progress in both fields, focusing on newly discovered links between chromatin, genome instability and ageing(ref).”

Not only can genomic damage lead to epigenomic changes but the converse is also highly likely to be true

The blog entry Homicide by DNA methylation discusses a hypothesis that lifelong DNA methylation could lead to devastating gene mutations. “The May 2009 publication by Alexander L. Mazin from Lomonosov Moscow State University is entitled Suicidal function of DNA methylation in age-related genome disintegration and presents a very dark view of DNA methylation as possibly being at the heart of the aging process. — “The proposed model considers DNA methylation as the generator of 5mC > T transitions that induce 40–70% of all spontaneous somatic mutations of the multiple classes at CpG and CpNpG sites and flanking nucleotides in the p53, FIX, hprt, gpt human genes and some transgenes.” “The accumulation of 5mC-dependent mutations explains: global changes in the structure of the vertebrate genome throughout evolution; the loss of most 5mC from the DNA of various species over their lifespan and the Hayflick limit of normal cells; the polymorphism of methylation sites, including asymmetric mCpNpN sites; cyclical changes of methylation and demethylation in genes. The suicidal function of methylation may be a special genetic mechanism for increasing DNA damage and the programmed genome disintegration responsible for cell apoptosis and organism aging and death.”

“The theory is plausible. DNA methylation is known to be capable of exercising mutagenic and epigenetic effects. Multiple publications discuss mutations in relationship to methylation in CpG sites within genes(ref)(ref)(ref). In a previous paper DNA Cytosine Methylation Produces CpG and CpNpG Hotspots for Various Types of Mutations in Human Genes Mazin stated “The evidence is presented that both CpG and CpNpG sites of DNA methylation and their 5`-, 3`-neighboring nucleotides are hotspots not only for 5mC>T transitions, but also for most types of mutations. 40-70% of all spontaneous mutations are found at these sites, and mutation frequencies at the hotspots are 10-40 times higher than the average for the genes studied. 52-77% of CpG sites could be lost because of relict germ-line 5mC>T substitutions, and 10-20% of somatic mutations result in the emergence of new sites of methylation in these genes. Various mutagenes induce significant changes in mutation spectra at sites of methylation. Thus, one of the basic functions of DNA methylation is mutation destruction of most host genes that responsible for human genetic diseases, aging, and cancer.”

Early-age epigenetic imprints may lead to pathologies later in life

The case for DNA methylation contributing to aging is made above.  Another quite different case is made in the 2010 publication The Janus face of DNA methylation in aging reports “Aging is arguably the most familiar yet least-well understood aspect of human biology. The role of epigenetics in aging and age-related diseases has gained interest given recent advances in the understanding of how epigenetic mechanisms mediate the interactions between the environment and the genetic blueprint. While current concepts generally view global deteriorations of epigenetic marks to insidiously impair cellular and molecular functions, an active role for epigenetic changes in aging has so far received little attention. In this regard, we have recently shown that early-life adversity induced specific changes in DNA methylation that were protected from an age-associated erasure and correlated with a phenotype well-known to increase the risk for age-related mental disorders. This finding strengthens the idea that DNA (de-)methylation is controlled by multiple mechanisms that might fulfill different, and partly contrasting, roles in the aging process.”

There are many other examples of how early epigenetic imprints can affect health and disease susceptibilities later in life.  See for example the 2011 publication Epigenetic Gene Promoter Methylation at Birth Is Associated With Child’s Later Adiposity,  “CONCLUSIONS Our findings suggest a substantial component of metabolic disease risk has a prenatal developmental basis. Perinatal epigenetic analysis may have utility in identifying individual vulnerability to later obesity and metabolic disease.”

While histone acetylation and DNA methylation appear to be major epigenetic markers of aging, there are others as well, in particular expression of microRNAs

An introduction to miRNAs can be found in my blog entry MicroRNAs, diseases and yet-another view of aging. From the 2010 publication Epigenetic Regulation of Aging: “The recent discovery of mammalian microRNAs (miRNAs) as a new member of gene regulation mechanisms has qualified them for inclusion in the field of epigenetics. These miRNAs are endogenous, small (~22 nucleotides), single-stranded, and non-coding RNAs that pair with the 3´ untranslated region (3′UTR) of their specific target messenger RNA (mRNA). Usually, the pairing results in a repression of protein expression and the promotion of target mRNA degradation (Guil and Esteller, 2009). They play a more decisive role in chromatin structure control by directly targeting the post-transcriptional regulation of key factors involved in the epigenetic control of chromatin remodelers.”

From my MicroRNA blog entry: “Of special interest to me is yet-another view of aging in which miRNAs play the lead roles. Quoting again from the Gen article, “Eugenia Wang, Ph.D., professor at the University of Louisville, has proposed that miRNAs have a critical role in “a universal or system-specific programmatic shift of signaling control” that occurs at mid-life and brings about a decline in cellular health status associated with aging, which may precipitate increased risk of late-life diseases. In her presentation, she will review the hypothesis that the changes in expression of most if not all aging-related genes are controlled by underlying hubs and the belief that miRNAs, acting as molecular master switches, are candidate hubs.”

Patterns of epigenetic shifts characterize the entire lifecycle of a complex organism from conception to death

This is an important point that is often not well understood.  Since all body cells have the same genes, the differences between these cells are epigenetic.  An epigenetic program controls the progressive cell-type differentiation that leads from embryonic stem cells eventually into the development of a complex organism.  I believe such a program continues to generate what we call aging, this being the essence of my 13th theory of aging Programmed Epigenomic Changes.  This theory dovetails in many dimensions with the 14th theory of aging, Stem Cell Supply Chain Breakdown. I point out that not all scientists agree with this point.  Aubrey de Gray, for example, has argued with me that the epigenetic developmental program ends with adulthood and that further aging related changes are due to the accumulation of damage.

The 2011 publication Epigenetic Predictor of Age supports my viewpoint. “From the moment of conception, we begin to age. A decay of cellular structures, gene regulation, and DNA sequence ages cells and organisms. DNA methylation patterns change with increasing age and contribute to age related disease. Here we identify 88 sites in or near 80 genes for which the degree of cytosine methylation is significantly correlated with age in saliva of 34 male identical twin pairs between 21 and 55 years of age. Furthermore, we validated sites in the promoters of three genes and replicated our results in a general population sample of 31 males and 29 females between 18 and 70 years of age. The methylation of three sites—in the promoters of the EDARADD, TOM1L1, and NPTX2 genes—is linear with age over a range of five decades. Using just two cytosines from these loci, we built a regression model that explained 73% of the variance in age, and is able to predict the age of an individual with an average accuracy of 5.2 years. In forensic science, such a model could estimate the age of a person, based on a biological sample alone. Furthermore, a measurement of relevant sites in the genome could be a tool in routine medical screening to predict the risk of age-related diseases and to tailor interventions based on the epigenetic bio-age instead of the chronological age.”

The epigenetic development program is not simple since, as well as genetic factors, environmental factors, present, past and inherited, affect the epigenome.  See Epigenetics and environment: a complex relationship. “The epigenomes of higher organisms constantly change over time. Many of these epigenetic changes are necessary to direct normal cellular development and differentiation in the developing organism. However, developmental abnormalities may occur in response to inappropriate epigenetic signaling that occurs secondarily to still poorly understood causes. In addition to genetic and stochastic influences on epigenetic processes, epigenetic variation can arise as a consequence of environmental factors.”

There is progress in understanding how reversible epigenetic changes are maintained in the process of cell replication

The 2011 publication Stable transmission of reversible modifications: maintenance of epigenetic information through the cell cycle reports “Even though every cell in a multicellular organism contains the same genes, the differing spatiotemporal expression of these genes determines the eventual phenotype of a cell. This means that each cell type contains a specific epigenetic program that needs to be replicated through cell divisions, along with the genome, in order to maintain cell identity. The stable inheritance of these programs throughout the cell cycle relies on several epigenetic mechanisms. In this review, DNA methylation and histone methylation by specific histone lysine methyltransferases (KMT) and the Polycomb/Trithorax proteins are considered as the primary mediators of epigenetic inheritance. In addition, non-coding RNAs and nuclear organization are implicated in the stable transfer of epigenetic information. Although most epigenetic modifications are reversible in nature, they can be stably maintained by self-recruitment of modifying protein complexes or maintenance of these complexes or structures through the cell cycle.”

Age-related disease states appear to occur when there is a coincidence of genetic predisposition and inherited or acquired epigenetic factors

From the 2010 publication Epigenetic Regulation of Aging: “Interactions linking environmental and genetic factors offer possible explanations for why autoimmunity afflicts certain individuals and not others. Autoimmunity is believed to develop when genetically predisposed individuals encounter epigenetic modifications in response to environmental factors and aging. Age-associated changes in DNA methylation (hypomethylation) are a striking mechanism connecting senescence and autoimmunity (Yung and Julius, 2008). For example, global hypomethylation has been found in rheumatoid arthritis synovial fibroblasts that are phenotypically activated. Moreover, it is possible to obtain these activated and hypomethylated fibroblasts in vitro, where more than a hundred genes were up-regulated with an enhanced level of protein expression. These overexpressed proteins included growth factors and receptors, extracellular matrix proteins, adhesion molecules, and matrix-degrading enzymes, confirming the role of these epigenetic mechanisms in the pathophysiology of rheumatoid arthritis (Karouzakis et al., 2009).”

I believe that the view that diseases arise from what happens when epigenetics meets genetics is now becoming mainline.  “Epidemiological evidence and data from animal studies have linked maternal diet with susceptibility to metabolic disorders (obesity, glucose intolerance, type II diabetes) and related diseases (atherosclerosis, cardiovascular diseases) or mental disorders in adulthood. The environmental factors that may affect epigenetic status during adult life in humans can be categorized as those connected with diet, living place and/or workplace, pharmacological treatments, and unhealthy habits. The degree of exposure of a tissue to a specific environmental factor can also determine its ability to induce specific epigenetic alterations within that tissue(ref).”

Dietary substances can generate epigenetic shifts that can combat age-related diseases and possibly slow overall aging

This point is made in the 2011 blog entry Cancer, epigenetics and dietary substances .  “Green tea, olive oil, blueberries, garlic and broccoli are among foods that work to reverse epigenetic changes that create susceptibility to cancers. A number of recent research publications relate to complex epigenetic conditions that lead to cancers – conditions that typically involve DNA methylation and histone acetylation. A number of other recent publications point out how many of these conditions are reversible via dietary inputs of substances that are old friends to many of my readers – substances like olive oil, blueberries, garlic, green tea, curcumin and resveratrol. Indeed, this new research is providing deep insight into why certain dietary polyphenols are effective in preventing cancers via their epigenetic actions.”  The blog entry cites a large number of publications supporting these claims.

“Dietary factors including folate, methionine, choline, beatine, and vitamins B2, B6, and B12 contribute to SAM production. Dietary restriction in methyl donors and genetic polymorphism in folate metabolism have been associated with abnormal DNMT expression, global DNA hypomethylation, and increased cancer risk (Vaissiere et al., 2009). — The effect of specific environmental factors (diet, living place and/or workplace, pharmacological treatments, and unhealthy habits) on the epigenetic status of adult organisms has been widely reported (Figure 2) (Aguilera et al., 2010; Feinberg, 2007). As commented before, folic acid intake is necessary for the remethylation of homocysteine, a key chemical reaction for SAM production. Deficiencies in dietary folate result in numerous health alterations that are most evident when they occur during embryonic development, but may also be noted during adult life (Keyes et al., 2007). It is also known that dietary polyphenols from green tea and genistein from soybean are thought to prevent cancer by means of epigenetic mechanisms (Fang et al., 2007). Organosulphur compounds from garlic as well as the isothyocyanates from cruciferous vegetables have a capacity to alter histone acetylation and HDAC activity, and a putative role has been proposed in cancer chemoprevention(ref).”

Although not directly formulated in terms of epigenetics, many other of my blog entries highlight the importance of epigenetic factors in driving longevity and possible lifestyle and dietary epigenetic interventions that could foster health and longevity.  I mention as examples the blog entries  Public health longevity developments – focus on foods and Diabetes Part 2: Lifestyle, dietary and supplement interventions.  I have also focused on research related to certain important plant-derive phyto-substances which generate important epigenetic health effects including resveratrol(ref)(ref),curcumin(ref)(ref), folic acid, valproic acid, caffeic acid, rosmarinic acid, ginger, and some of the the phyto-ingredients in olive oil, walnuts, chocolate, hot peppers, and blueberries.  In traditional folk medicine most of these substances were reputed to be “good for you,” without knowledge of exactly how or why.  Now we are increasingly talking about them in terms of their specific epigenetic impacts.  And there are the suggested lifestyle and dietary supplement anti-aging regimens in my treatise.

Final Comments

It appears there are a number of bad-news messages from the viewpoint of healthy longevity: irreversible genomic damage occurs with aging through several mechanisms, cell-specific epigenetic programs drive constant aging, age-related epigenomic changes create genomic damage, and the genetic-epigenetic aging and disease-inducing juggernaut so far appears unstoppable.

Yet, there appear also to be some good-news messages: genetic and epigenetic factors work together to drive aging changes, negative and age-related epigenetic changes appear to be reversible, and a number of already-known lifestyle and dietary factors appear to affect epigenetics in a way to slow disease and aging processes.  Further, knowledge about the new genomics-epigenomics paradigm is being accumulated ever-more rapidly.

The uncertain news is whether knowledge we still have to acquire and technologies still on the horizon will enable us to overcome issues of age-related genomic damage.  I am thinking, for example of knowledge about DNA repair mechanisms and technologies like safe high-fidelity induced pluripotent stem cells.  And perhaps new paradigms of understanding will arise that are now completely invisible to us.  What we know we still don’t know is vast compared to what we know.  And what we currently have no inkling about could be infinite.

So from where we are now, we don’t know what the limits of epigenetic anti-aging interventions will be.  Stay tuned for the next exciting episode!  I intend to  be in the game for the long ride.