20130606
Carlos López-Otín, Maria A. Blasco, Linda Partridge, Manuel Serrano, Guido Kroemer
https://www.cell.com/cell/fulltext/S0092-8674%2813%2900645-4

Evolution does not create order and simplicity, but instead randomly creates whatever intricate mess that happens to survive by chance or advantage. The hallmarks of aging is a human endeavor to create a learning tool that improves comprehension of the evolutionary mess we have been handed.

It is valuable to reduce the effects of aging to prevent aging related disease, so we attempt to categorize somatic and stem cell damage that occurs with time:

genomic instability
telomere attrition
epigenetic alterations
loss of proteostasis
deregulated nutrient-sensing
mitochondrial dysfunction
cellular senescence
stem cell exhaustion
altered intercellular communication

Part of the challenge is unraveling ways in which these hallmarks are related to each other.

Cancer and aging share common origins: the accumulation of cellular damage. Thus, the categorization of the underlying mechanisms that drive cancer, by Hanahan and Weinberg in 2000, and again in 2011, has also helped give insight into the hallmarks of aging.

For example, “atherosclerosis and inflammation involve uncontrolled cellular overgrowth or hyperactivity.”

Each hallmark meets the following criteria:

1. manifested during normal aging
2. experimental aggravation should accelerate aging
3. experimental amelioration should retard aging

The last criterion is the most difficult to achieve. It's possible that amelioration of one hallmark can also reduce the others.

Evolution is not a master designer. The concept “survival of the fittest” is only part of the evolutionary pressure. Evolution does not select for the perfection of a singular organism, but instead optimizes the continuation of its brethren. Hence the existence of organism traits that favor reproductive fitness over longevity, such as altruistic behavior.

So why does aging even exist? One explanation is that of pleiotropic genes. Pleiotropy is where one gene influences more than one phenotypic trait. The antagonistic pleiotropy hypothesis states that a gene that can express both a beneficial and detrimental phenotype will be preserved if its benefit outweighs the detriment. An example is high testosterone in human males, which increases fitness in early life, while also increasing the risk of prostate cancer with age. Consider that life expectancy beyond 40 was something very uncommon, just a few centuries ago (Song and Johnson 2018)¹⁾:

“To die of old age is a death rare, extraordinary, and singular, and therefore so much less natural than the others: it is the last and most extreme sort of dying […] And therefore my opinion is that when once forty years old, we should consider it as an age to which very few arrive […] and since we have exceeded the ordinary bounds which make the just measure of life, we ought not to expect to go much further.” (Michel de Montaigne 16th century)

There is also a certain irony that we are in competition with our own genes for survival. Genes are more likely to survive in an evolutionary sense, if the gene is used in multiple biological functions. A mutation of a pleiotropic gene is less likely to be compatible in all the dependent functions requiring it for assembly. Thus, a pleiotropic gene is selfish at the cost of the adaptability of a species to its environment. Also at the cost of a continuation of deleterious phenotypes such as aging.

There is much diversity, including a few genetic outliers. The hydra and the naked mole rat are species that don't age the way other organisms do. Their chance of death does not noticeably increase with age. “The nonsenescent life history of Hydra implies levels of maintenance and repair that are sufficient to prevent the accumulation of damage for at least decades after maturity … A high proportion of stem cells, constant and rapid cell turnover, few cell types, a simple body plan, and the fact that the germ line is not segregated from the soma are characteristics of Hydra that may make nonsenescence feasible.” (Schaible et al 2015)²⁾ It may be possible in the future to genetically modify a mammal, or a human, with a much longer lifespan. Maybe one way of doing so, is by being a master designer, and simplifying the convoluted mess that evolution has created.

Different theories of why aging exists are covered well by Song and Johnson:
https://www.mdpi.com/2073-4425/9/4/201/htm

Exogenous and endogenous threats drive genetic lesions. Endogenous threats include ROS (Reactive Oxygen Species), replication errors, and spontaneous reactions. Exogenous threats include anything from the environment, such as radiation. These legions are mostly fended by various repair and integrity-checking mechanisms in the cells.

Increasing the effectiveness of these mechanisms in mice has been shown to increase healthspan, as in the case of transgenic mice with an overexpression of BubR1.

Mutated or dysfunctional or senescent cells can be cleared by apoptosis or by the immune system. However, the number of senescent cells accumulate with age.

Genetic lesions are “highly diverse and include point mutations, translocations, chromosomal gains and losses, telomere shortening, and gene disruption caused by the integration of viruses or transposons.”

(the following just covers transposons)

Repetitive elements may comprise over two-thirds of the genome. (Koning et al 2011)³⁾ These are thought to be caused by mobile genetic elements such as retrotransposons, which cause gene duplication events.

Transposons are selfish genetic elements, yet serve functions that are still being discovered.

Mitochondria are the aerobic power generators of a cell. Different cell types have different number of mitochondria, from zero in a red blood cell, to thousands in a liver cell.

Mitochondria is theorized to have been an independent organism that was absorbed by a larger organism, ending in a symbiosis from which we evolved. Thus, mitochondria have their own DNA, referred to as mtDNA.

MtDNA does not follow the rules of Mendelian inheritance. With rare exception, mtDNA is inherited exclusively from the mitochondria in the maternal egg cell. Because of the nature of this inheritance, even though there were many different mtDNA types at one time in history, there is now only one. Thus there was a single woman, referred to as Mitochondrial Eve from which all other women have inherited their mtDNA.

Over time, many of the genes in mtDNA were replaced or incorporated as genes in the cell nucleus. The mitochondrial genes located in the cell nucleus are transcribed and translated into proteins that are then imported into the mitochondria from the cytoplasm. There are around 1100 genes that are imported from the nucleus into the mitochondria in this way. Around a quarter of these, around 250, are for the maintenance and expression of the genes in the mitochondria.

There are 37 genes left in the mtDNA of humans, where it takes the form of a supercoiled circle. “This raises a question: why would eukaryotic cells invest more than 250 proteins to be able to make just a handful of them inside mitochondria? This question is intimately linked to another one: why mtDNA has been so carefully maintained during evolution?”

Also, unlike nuclear DNA, which has a single copy of its genome, there are many copies of mtDNA within a mitochondria. As noted earlier, there are many mitochondria per cell. “The actual number of mtDNA varies between cell types and is dependent on the energy demands within each cell. Any mutations in the mtDNA can co-exist with wild-type copies, a condition called heteroplasmy. The mutant mtDNAs do not exert a biochemical phenotype on a cell until the mutant load reach a certain level. The threshold of mutant/wild type can vary depending on the specific mutation and the cell type.” (Lee and Wei 2011)⁴⁾

“Although mtDNA was initially considered to be naked, unprotected, and vulnerable to damage, research over the last decades has shown that mtDNA is protein-coated and packaged into nucleoids.” (Szczepanowska and Trifunovic 2015)⁵⁾ Nonetheless, the protection is not as effective, and the mutation rate for somatic mtDNA is several orders of magnitude greater than that of nuclear DNA.

Originally, the Mitochondrial Theory of Aging proposed that oxidative damage increased exponentially with time: “Accumulation of these mtDNA mutations could result in dysfunction of the respiratory chain, leading to increased ROS production in mitochondria and subsequent accumulation of more mtDNA mutations. This vicious cycle has been proposed to account for an increase in oxidative damage during aging, which leads to the progressive decline of cellular and tissue functions as a result of insufficient supply of energy and increased susceptibility to apoptosis.” (Lee and Wei 2011)⁶⁾

When oxidative damage to DNA occurs and is not correctly repaired, there is one point mutation that happens more frequently. Oxidative damage to DNA can thus be traced as larger percentages of G → T mutations. Mounting evidence suggests the mutations occur during errors in mtDNA synthesis, rather than oxidative damage, and that the mutations that are seen to accumulate, occurred early in life: “Our results indicate that most somatic mtDNA mutations occur as replication errors during the rapid amplification of mtDNA during embryo-genesis and do not result from damage accumulation in adult life.” (Payne et al 2011)⁷⁾ “A continuously dividing tissue like liver may show a different pattern of accumulation of mtDNA point mutations with age in comparison with a postmitotic tissue such as brain or heart.” (Payne et al 2011)⁸⁾

“…given that there are hundreds of genes in nuclear genome bigger that the whole mtDNA, it is remarkable how this small piece of DNA can cause so many different metabolic diseases, be causatively linked to numerous age-associated disease and influence aging process itself.” (Szczepanowska and Trifunovic 2015)⁹⁾

Is there a separate process for maintaining mtDNA integrity in germ-line cells? There must be a way of keeping mutations in check, if lineages of mtDNA are so well kept that it is possible to trace populations by their mtDNA to a mitochondrial eve.

Not only does DNA decline, but so does the nucleus that surrounds it. The nuclear lamina provides a scaffold for tethering chromatin and protein complexes that maintain genomic stability. If genes that make up the nuclear lamins are mutated, accelerated aging can occur, as in the case of a mutated prelamin A (aka progerin) which causes Hutchinson-Gilford and Nestor-Guillermo progeria syndromes. Laminar progerin has also been detected in normal human aging, and may be linked to telomere dysfunction. A decline in the levels of another laminar protein, Lamin B1, has been found to be useful as a marker for cell senescence.

In mice with progeria syndrome, treatments that reduce the effects of the disease have increased lifespan, including stem cell therapy that corrects the LMNA mutation. “Further studies are necessary to validate the idea that reinforcement of the nuclear architecture can delay normal aging.”

The protective end caps of DNA molecules are called telomeres, and they shorten with cell divisions or some strand repairs. Telomerase is an enzyme that can add length to the telomeres, but it is not produced in most somatic cells. Loss of telomeres has been shown to be the cause of cellular senescence.

DNA repair machinery is unable to see the end of the DNA double helix because telomeres are covered by shelterin. Damage to the telomeres is thus irreparable, even in the presence of telomerase, and also causes cellular senescence and apoptosis. In animal models, both deficiency in telomerase or shelterin components leads to loss of tissue-regenerative capability.

Genetically modified animals with shortened or lengthened telomeres lead shorter or longer lifespans, respectively. Premature aging of telomerase-deficient mice can be reverted by reactivating telomerase in the already aged mice. “Moreover, normal physiological aging can be delayed without increasing the incidence of cancer in adult wild-type mice by pharmacological activation or systemic viral transduction of telomerase. In humans, recent meta-analyses have indicated a strong relation between short telomeres and mortality risk, particularly at younger ages.”

Chromatin is composed of DNA and the proteins that help package and protect it. The packaging is made of histone proteins, which are like tupperware for DNA. Changes in the chromatin affect how DNA is expressed. Gene expression, which includes running a program coded for morphogenesis and growth, continues to change with age.

Chromatin changes include histone methylation and acetylation, with research showing that aging brings about consistent regions that have increased or decreased amounts of these molecular markers. The question unanswered is if the changes are a continuation of the morphogenic program, or if the changes are haphazard degradation of the chromatin in certain regions that are susceptible. “Like stem cell reprogramming, our results suggest that reestablishment of epigenetic marks lost during aging might help “reset” the developmental age of animal cells.” (Jin et al 2011)¹⁰⁾

Histone modifications affect the way genes are expressed: “A histone modification is a covalent post-translational modification (PTM) to histone proteins which includes methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation. The PTMs made to histones can impact gene expression by altering chromatin structure or recruiting histone modifiers.” ¹¹⁾

Scientists have a lot to cover in understanding gene expression as a function of chromatin modification. However, there is a principle that a tightly packed region of chromatin keeps the DNA inaccessible to other molecules, such as the machinery that would transcript the DNA into RNA. There are regions of tightly-packed chromatin known as heterochromatin, where genes are mostly silenced. Some genes are silenced as intended, as in the case of cell differentiation. For example, neuron cells express differently than liver cells. However, some silenced genes tend towards being reactivated as part of aging, where the cell is not operating at peak efficiency. Deleterious effects include activation of genes that cause inflammation, or general chaos that concludes in cell senescence.

Histone methylation can increase or decrease gene expression, depending on which and how many amino acid groups are methylated on the 8 histones of the nuclesome.

An example of histone methylation is H3K4me3, which denotes trimethylation of lysine location 4 on the histone H3 protein.

“When you think H3K4, think activation. Whether it’s methylated or acetylated, this site will turn on genes faster than you can say PRDM9. …Methylation of this fourth amino acid residue from the N-terminus of histone H3 is one of the most studied histone modifications, and with good reason: it’s tightly associated with the promoters of active genes. Like all lysine residues, H3K4 can be mono, di, or tri methylated, and each have slightly different distributions.” ¹²⁾ While acetylation loosens the grip on DNA, methylation can achieve activation by remodeling chromatin with the NURF complex. (Wysocka et al 2006)¹³⁾

Although H3K4me3 has been regarded as a transcription activator, newer results propose that “the impact of H3K4 methylation cannot be generalised but must be considered on a gene-by-gene basis taking into account both repressive and activating effects. (Cruz et al 2018)¹⁴⁾

Furthermore, Cruz et al showed that H3K4me3 occurrences along the chromatin has a predictable profile change with age, like sand dunes shifting in a uni-directional desert wind. The shifts increase or induce transcription at some promoters, while silencing others. Aging chromatin can also cause transcription to start from a non-promoter region, resulting in a mutated protein. 43% of yeast genes are differentially expressed after 48 hours of ageing.

There is much promise that supplementation of s-adenosyl methionine (SAMe) can help in maintaining chromatin methylation integrity. (Leonen 2018)¹⁵⁾

As mentioned earlier, mitochondria produce power for the cell. The citric acid cycle, or krebs cycle, is a process that occurs in the mitochondria for energy production. The process optimally produces 38 ATP, or adenosine triphosphate molecules, per cycle, which is the energy currency of the cell. When the phosphorylated ends of ATP are used up, AMP, or adenosine monophosphate, is left.

There is a sensor called AMPK, which senses the ratio between AMP and ATP in the cell. AMPK, or AMP-activated protein kinase, “stimulates energy generating processes such as glucose uptake and fatty acid oxidation and decreases energy consuming processes such as protein and lipid synthesis.” (Richter and Ruderman 2009)¹⁶⁾

“AMPK plays an important role to explain the therapeutic benefits of metformin, thiazolidinediones and exercise, which form the cornerstones of the clinical management of type 2 diabetes and associated metabolic disorders.” (Canto et al 2009)¹⁷⁾

Sirtuins are one of four classes of HDACs (Histone Deacetylases).

During the krebs cycle, NADH is produced, which fuels the electron transport chain within the mitochondria to produce a portion of the ATP, with NAD+ as a byproduct.

Sirtuins are enzymes which play a role in various gene expressions, which are dependent on NAD+. The seven sirtuins in mammals have a highly conserved version of the ancestral sirt2 found in c. elegans, which when overexpressed extended the life of the worms by 70%. Not only are the functions that sirtuins serve many and complex, so are the drivers that propel sirtuins to engage in their functions. However, all sirtuins are dependent on the levels of NAD+.

“Because of the NAD+ dependency of their activity, changes in NAD+ levels regulate the function of the whole sirtuin family. In fact, the sensing of NAD+ levels forms the basis for sirtuins to function as metabolic and nutritional sensors.” (Buler, Andersson, and Hakkola 2016)¹⁸⁾

The mode of action of sirtuins is mainly deacetylating lisine residues on various proteins (see table below, sourced from (Dang 2014)¹⁹⁾)

Sirtuins are involved in all of: ”(1) dietary interventions mimicking chronic dietary restriction, (2) inhibition of the mTOR–S6K pathway, (3) inhibition of the GH/IGF1 axis.“ (Grabowska 2017)²⁰⁾ Senescent cells have a decreased level of almost all sirtuins.

“The level of these enzymes decreases with age while their upregulation alleviates the symptoms of ageing/cellular senescence. Natural compounds present in the diet, classed as functional food/nutraceutics, could be an invaluable element of anti-ageing prophylactics or even intervention. Such compounds are nontoxic, easy to use and commonly available and could be included into a normal diet for long lasting supplementation.” (Grabowska 2017)²¹⁾

8 histones make up a nucleosome that DNA wraps twice around. The number of nucleosomes decreases with age, from humans to yeast. In yeast, overexpression of histones dramatically extends lifespan. (Feser et al 2010)²²⁾

In yeast, a 50% loss of histones appears to occur during cell replication. Histones protect DNA, and silence unwanted gene expression: “The loss of histones during aging led to transcriptional induction of all yeast genes. Genes that are normally repressed by promoter nucleosomes were most induced, accompanied by preferential nucleosome loss from their promoters. We also found elevated levels of DNA strand breaks, mitochondrial DNA transfer to the nuclear genome, large-scale chromosomal alterations, translocations, and retrotransposition during aging.” (Hu et al 2014)²³⁾

(UNDER CONSTRUCTION)

https://en.wikipedia.org/wiki/Mitochondrial_unfolded_protein_response
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3663447

Alternate review:
https://www.leafscience.org/hallmarks-of-aging-mitochondrial-dysfunction

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5391241

(UNDER CONSTRUCTION)