Fight Aging! Newsletter, December 30th 2019

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Contents

  • The Quest to Measure Human Biological Aging
  • Towards Small Molecule Therapies to Reverse T Cell Exhaustion
  • Reviewing What is Known of the Role of Transposable Element Activity in Aging
  • Berberine as an mTOR Inhibitor that Reduces Generation of Senescent Cells and Extends Life Span in Mice
  • Genetic Variants are not an Important Risk Factor in the Vast Majority of People and Age-Related Conditions
  • Why Doesn't the State of Having High Blood Cholesterol Cause Pain?
  • Age-Related Hyperglycemia as a Cause of Increased Cancer Incidence
  • CpG Site Density in the Genome Predicts Species Maximum Life Span
  • CD33 Influences Alzheimer's Risk via Regulation of Microglial Functions
  • More Insight into the Relationship Between Cell Size and Cell Senescence
  • Bioprinting Liver Organoids with Patient-Derived Cells
  • Refuting the Link Between Persistent Herpesvirus Infection and Alzheimer's Disease
  • More Visceral Fat and Less Muscle Mass Correlate with Lower Fluid Intelligence in Middle Age
  • Cynomolgus Macaques and Humans Exhibit Broadly Similar Age-Related Changes in the Gut Microbiome
  • Type 2 Diabetes as a Simple Condition of Excess Fat

The Quest to Measure Human Biological Aging
https://www.fightaging.org/archives/2019/12/the-quest-to-measure-human-biological-aging/

Today's open access review article is a discussion of the importance of being able to measure biological aging, easily and robustly. Initially, this is an approach to speed the development of rejuvenation therapies; at present one can only efficiently and quickly assess the results of a potential rejuvenation therapy in the context of its ability to reverse a specific age-related disease. There are scores of important age-related conditions to assess, and animal models of these conditions are usually significantly different from the human condition - different enough for a careful consideration of the details to be needed to determine whether or not the model is useful.

If one wants to assess the overall efficacy of a rejuvenation therapy rigorously, it remains the case that life span studies are the only recourse. At minimum, deliver the treatment to old mice and run the study for six months to a year to see how mortality differs between the treatment and control groups. This is painfully expensive, and just doesn't scale to a world in which the research and development community may want to assess hundreds to thousands of variants of potential rejuvenation therapies at any given time. What is desired here is a way to run a quick study in normal aged animals: take a baseline assessment of the state of aging, deliver the intervention, and then within a week or two redo the assessment to see what has changed.

At present a number of different approaches to the measurement of biological aging are under development to one degree or another. The epigenetic clock is one such approach, which looks for epigenetic reactions to the underlying damage of aging. In this case, the challenge is connecting the epigenetic alterations characteristic of aging back to the underlying processes of damage and dysfunction: it is far from clear that the present clocks measure all of aging, versus part of aging. Another approach would be to take the list of cell and tissue damage that causes aging and measure each portion of it. Until rejuvenation therapies based on repairing this damage are developed, however, it will remain unclear as to the relative contribution of each form of damage to the progression of aging. Further, few of these forms of damage can actually be measured in a practical, non-invasive fashion in human patients. There is much work yet needed here.

Measuring biological aging in humans: A quest

Substantial investment is necessary to develop an estimator of biological aging that is robust, precise, reliable, and sensitive to change. Thus, a fair question is whether such a titanic project is worth the effort and cost. The answer is YES, without hesitation. Developing an index of biological aging is perhaps the most critical milestone required to advance the field of aging research and, especially, to bring relieve from the burden of multimorbidity and disability in an expanding aging population. Ideally, these measures would be obtained by running tests using blood samples without performing a biopsy, preferably quickly and at low cost.

An index of biological aging could be used to empirically address the geroscience hypothesis: "Is biological aging is the cause of the global susceptibility to disease with aging." Data collected longitudinally - ideally in a life course epidemiological study - could then be used to test if individuals that accumulate coexisting diseases faster than in the general population also have accelerated biological aging. Similarly, these data could be used to test if individuals who are biologically "older," independent of chronological age, are at a higher risk of developing different medical or functional conditions that do not share physiological mechanisms. Once validated, the fundamental basis of biological aging can be used to probe deeper into questions related to the mechanisms of aging, such as the following: Are there genetic traits that are associated with faster or slower biological aging? Are there "hallmarks" that are better at capturing biological aging at different stages of life?

Developing a proxy measure of biological aging for humans still requires work but is a very dynamic and promising area of investigation with strong potential for translation. Some of the measures - namely mitochondrial function, DNA methylation, and, to a lesser extent, cellular senescence and autophagy - are ready to be implemented based on several epidemiological studies, although refinements are always possible. Measures of telomere length are hampered by noise and wide longitudinal variations that cannot be explained by health events and at this stage are not useful for measuring biological age. New methods are being developed, some of which are focused on detecting the DNA damage response (a typical marker of critical telomere shortening) may yield better results. Senescence has been studied successfully in T lymphocytes, skin, and intramuscular fat, and high-throughput methods will be available soon. In addition, specific patterns of circulating proteins may exist that indirectly estimate the burden of senescence. Similarly, measures of autophagy are routinely used in mammalian studies and should be applicable to humans.

Multiple lines of evidence suggest that the measures listed above are associated with the severity of multimorbidity but, except for the epigenetic clock, this association has not yet been clearly established. Logically, none of the measures described above represent an exhaustive measure of biological aging and, therefore, new aggregate measures are needed that leverage differences and complementarities of the various biomarkers. To accomplish these goals, the hallmarks of aging should be assessed in a group of individuals that is reasonably sized and enough dispersed across the lifespan to represent the variability of biological age in the general population. Initially, it will be important to evaluate the intercorrelation between these measures.

These questions have immense relevance for geriatric medicine. Despite the rising emphasis on prevention, most current medical care is dedicated to diagnosing and managing diseases that are already symptomatic, which does not address the underlying issues related to geriatric health conditions. By understanding the intrinsic mechanisms of biological aging, including damage and resilience, medical professional will be able to best orient and prescribe therapeutic choices.

Progress in research is not linear. Periods characterized by rates of incremental knowledge are interlaced with "eureka" moments as milestone discoveries suddenly open new possibilities that thrust research and knowledge to a higher level. Galileo's use of the telescope to explore the stars, Kary Mullis's description of polymerase chain reaction, and Edwin Hubble's demonstration that the universe is expanding are just few examples of these moments. The field of aging research is living one of those magical moments. Finding a reference metric for the rate of biological aging is key to understanding the molecular nature of the aging process. Defining and validating this metric in humans opens the door to a new kind of medicine that will overcome the limitation of current disease definitions, approaching health in a global perspective and bringing life course preventative measures to the center of attention.

Towards Small Molecule Therapies to Reverse T Cell Exhaustion
https://www.fightaging.org/archives/2019/12/towards-small-molecule-therapies-to-reverse-t-cell-exhaustion/

T cells of the adaptive immune system are a vital part of the defense against pathogens and cancers. T cells are not invulnerable, unfortunately. T cell exhaustion is a feature of cancers, persistent viral infections, and aging. Exhausted T cells are characterized by inhibition of replication, reduced secretion of immune signals, and sharply limited activity. The proximate cause is of this state is the expression of immune checkpoint proteins such as PD-1. The cancer research industry has achieved considerable success in the development of checkpoint inhibitors, monoclonal antibodies that bind to and inhibit immune checkpoint proteins. These therapies can effectively reverse T cell exhaustion in the context of cancer, allowing the immune system to more effectively attack tumor cells.

Are there other options? Today's open access paper reports on the development of a screening system to allow a search for small molecules capable of reversing T cell exhaustion. This is again achieved by interfering with the operation of immune checkpoints or their immediately downstream biochemistry. Small molecule therapies might be more appropriate than monoclonal antibodies for the reduction of T cell exhaustion in chronic viral infection or in older people in general, particularly given the relative costs of these two approaches.

Discovery of Small Molecules for the Reversal of T Cell Exhaustion

Immune surveillance for the recognition and removal of unwanted virus infected cells and the detection and attack of malignant cells resides primarily with the activity of cytotoxic T lymphocytes (CTLs). To counteract this response, viruses, and cancers reduce the function of CTLs, exhausting them. This is achieved, in part, by upregulation of inhibitory "checkpoint" receptors (IRs) on the surfaces of CTLs. The importance of this strategy in controlling T cell responses is illuminated by findings that neutralizing IRs such as PD-1 or CTLA-4 on exhausted T cells restores their effector responses. The use of such checkpoint inhibitory therapies has led to remarkable clinical benefits in cancer patients.

However, responses in many patients remain limited, in part, due to insufficient restoration of T cell function. Thus, the discovery of additional targets and pharmacologic drugs is required to overcome the limitations of current checkpoint blockade. Therapeutics with distinct properties could enhance the effectiveness of existing IR blockade agents or achieve responses in patients resistant to existing treatment modalities. Several recent reports examining the synergistic effects of antibody-based blockade strategies by targeting alternative IRs, cytokines, or cytokine signaling pathways have sparked numerous clinical trials. Discovery and utilization of low-molecular-weight therapeutics can complement, and in some cases replace, existing IR blockade biologics.

Functional exhaustion of virus-specific T cells was first described in mice infected with the clone 13 (CL13) variant of lymphocytic choriomeningitis virus (LCMV). CL13 causes a persistent viral infection resulting in varying degrees of suboptimal CD4 and CD8 T cell activity, characterized by reduced to absent cytotoxic capacity of anti-viral CD8 T cells, poor proliferative potential, decreased production of antiviral effector molecules such as interferon γ (IFN-γ) and tumor necrosis factor α (TNF-α), insufficient expression of several homeostatic cytokines, and sustained expression of IRs such as PD-1, LAG-3, and TIM-3 and the immunosuppressive cytokine interleukin-10 (IL-10). T cell exhaustion is progressive and thought to be driven by persistent antigen stimulation. The importance of immunosuppressive pathways that maintain T cell dysfunction was initially demonstrated by the resurrection of T cell activity following PD-1 or IL-10 receptor blockade during persistent LCMV infection.

Here, we report utilizing the in vivo LCMV-CL13 model to construct a platform for in vitro high-throughput screening (HTS) to detect small molecules that reverse T cell exhaustion. We identify 19 compounds from the ReFRAME drug-repurposing collection that restore cytokine production and enhance the proliferation of exhausted T cells. Analysis of our top hit, ingenol mebutate, a protein kinase C (PKC) inducing diterpene ester, reveals a role for this molecule in overriding the suppressive signaling cascade mediated by IR signaling on T cells. Collectively, these results demonstrate a disease-relevant methodology for identifying modulators of T cell function and reveal new targets for immunotherapy.

Reviewing What is Known of the Role of Transposable Element Activity in Aging
https://www.fightaging.org/archives/2019/12/reviewing-what-is-known-of-the-role-of-transposable-element-activity-in-aging/

Transposable elements make up a sizable portions of the genome, capable of copying themselves to other locations in the genome under the right circumstances. This activity is suppressed in youth, but increases in older individuals for reasons that are still being explored. Transposable element activity is thought to contribute to aging in a similar way to the effects of mutational damage to DNA, setting aside the risk of cancer, meaning a growing disarray in cellular metabolism due to altered genes and gene expression. When this occurs in stem cells or progenitor cells, this disarray might propagate to a sizable fraction of cells in a tissue.

It is still a little early to say to what degree transposable element activity is a problem, in comparison to the other contributing mechanisms of aging, and what the best approach to suppress it might be. Nonetheless, it is worth considering the recent research suggesting that the operation of DNA repair processes that address double-strand breaks in the nuclear genome causes epigenetic changes characteristic of aging. The LINE-1 retrotransposons have been shown to increase the pace at which double-strand breaks occur once they become active. Joining the dots, perhaps this is a plausible mechanism for cellular disarray. It is an interesting connection, but one that needs further exploration and validation, however.

The role of transposable elements activity in aging and their possible involvement in laminopathic diseases

Transposable elements (TEs) are mobile genetic elements able to change their position within a genome, often resulting in a duplication of their sequences. There are two main classes of these genetic elements: DNA transposons, which encode a transposase required for a cut-and-paste mechanism of transposition, and retrotransposons, which transpose by reverse transcription of an RNA intermediate. Mobilization of TEs may have deleterious effects on genomes, such as the induction of chromosome rearrangements and, when inserted in the coding region of a gene, the destruction or alteration of the normal gene functions. For this reason, TEs are normally repressed by specific silencing mechanisms guided by small non-coding RNAs (sncRNAs).

Beyond the deleterious effects, TEs have an important impact on genome-wide gene regulation. In fact, TEs and TE-derived sequences represent a consistent part of the genome of eukaryotic cells and comprise about 46% of the human genome. TE-derived sequences act as transcriptional regulatory regions in a substantial proportion of human genes, contributing to determining the regulation of the controlled genes. In fact, there is clear evidence that regulatory regions of TEs in mammalian cells have been domesticated to modulate the regulation of nearby genes. Transposition of TEs can deposit regulatory sequences across the genome, modifying the regulation of genes located nearby. Some of these events seem to have had evolutionary advantages.

The transposon theory of aging proposed that the increased activation of TEs in somatic tissues during the aging process leads to a shortening of the lifespan. Activation of TEs is a consequence of the loss of repressive structure that occurs gradually with aging in constitutive heterochromatin regions. Since TEs are highly enriched in these domains, loss of heterochromatin induces an increase in TE expression and a consequent increase in transposition rate. While there are different studies that confirm the upregulation in the expression of TEs during aging, it is not clear to which extent this activation is associated to production of de novo TE mutations in somatic tissues.

It is possible that the contribution of TEs to aging does not depend only on the production of de novo mutations. In fact, activation of LINE-1 retrotransposons leads to a high level of DNA double-strand breaks (DSB), while the predicted numbers of successful retrotransposition events appears lower. Since DNA damage is considered a cause of aging, the mechanism by which LINE-1 contributes to aging could depend on the significant degree of inefficiency in the LINE-1 integration process, which, however, produces a progressive increase of DSBs. Given these findings, LINE-1 element activation during the lifetime in somatic tissues has been considered a possible key factor in human aging.

Berberine as an mTOR Inhibitor that Reduces Generation of Senescent Cells and Extends Life Span in Mice
https://www.fightaging.org/archives/2019/12/berberine-as-an-mtor-inhibitor-that-reduces-generation-of-senescent-cells-and-extends-life-span-in-mice/

Today's open access paper is an interesting look at berberine as an mTOR inhibitor and its effects on cellular senescence in cell culture and animal models. This is particularly interesting in the context of recent work on rapamycin, showing low doses to reduce the burden of cellular senescence in aged skin. In both cases this appears to be the result of reducing the pace at which cells become senescent, allowing natural clearance mechanisms to catch up - though there is always the question of whether or not the various protein markers used to identify senescence are reduced because the number of senescent cells are reduced, or are reduced because the drug causes a lowering of expression of these proteins.

Is it a good idea to prevent cells from becoming senescent? Cellular senescence halts replication and encourages programmed cell death or destruction via the immune system. It is way to remove damaged and potentially damaged cells from tissues. If a method of preventing senescence gives cells a chance to repair themselves, then fine, but otherwise it starts to sound like a way to increase cancer risk - to have damaged cells remain active while damaged. To refute that proposition, one has to run life span studies, as the researchers did here. Clearly, in these mice, preventing entry into senescence is beneficial, since it increases life span. This may again be a matter of allowing natural clearance processes a chance to catch up and reduce the overall level of cellular senescence. Or it may be that the harmful inflammatory signals produced by senescent cells are, on balance, far worse that the raised cancer risk resulting from prevention of senescence.

Studies of this nature must lead us to think about the right dosing schedule for senolytic therapies capable of destroying senescent cells. If natural clearance of senescent cells is taking place in late life, and accumulation is a matter of too much creation versus a slowed pace of clearance, then senolytic treatments should be delivered every few months. If, on the other hand, accumulation is a matter of a small fraction of all senescent cells managing to linger for years or more, senolytic treatments can be much less frequent. At present there is all too little evidence, but the evidence that does exist suggests that the former scenario is more likely.

Berberine ameliorates cellular senescence and extends the lifespan of mice via regulating p16 and cyclin protein expression

Cellular senescence is one of the most important in vivo mechanisms related to aging. Senescent cells impair tissue function by irreparable cell damage resulting from acute stress or natural aging, consequently restricting the lifespan. Cellular senescence can be categorized into two groups. The replicative senescence, seen after approximately sixty rounds of cell division in cultures (the Hayflick limit), results from the progressive erosion of telomeres following each cell division. This progressive erosion leads to telomere dysfunction and irreversible cell-cycle arrest.

The second category is defined as premature cellular senescence. It is unrelated to telomere shortening but is related to persistent cellular stress. Thus, replicative stress caused by oxidative DNA damage, activation of oncogenes, and loss of tumor suppressor genes also results in premature senescence. Furthermore, premature senescence includes the irreversible impairment of tumor cell reproductive capability via chemotherapy or radiotherapy-induced apoptosis which is defined as a drug or radiation-induced senescence. The in vivo stress-induced premature senescence of normal cells is considered to be a critical mechanism affecting organismal aging and longevity.

Berberine (BBR), a natural alkaloid found in Coptis chinensis, has a long history of medicinal use. Furthermore, BBR possesses anti-cancer, anti-inflammatory, and anti-neurodegenerative properties. Although the biological properties of BBR are well-documented, there is little evidence of its role in anti-aging processes. It was previously observed that BBR inhibited mTOR/S6 signaling concurrent with the reduction in the level of endogenous oxidants and constitutive DNA damage response. Thus, it was hypothesized that BBR, with its potential anti-aging effects, could treat the senescence in aging cells.

This study presents the effects of berberine (BBR) on the aging process resulting in a promising extension of lifespan in model organisms. BBR extended the replicative lifespan, improved the morphology, and boosted rejuvenation markers of replicative senescence in human fetal lung diploid fibroblasts. BBR also rescued senescent cells with late population doubling (PD). Furthermore, the senescence-associated β-galactosidase (SA-β-gal)-positive cell rates of late PD cells grown in the BBR-containing medium were ~72% lower than those of control cells, and its morphology resembled that of young cells. Mechanistically, BBR improved cell growth and proliferation by promoting entry of cell cycles from the G0 or G1 phase to S/G2-M phase.

Most importantly, BBR extended the lifespan of chemotherapy-treated mice and naturally aged mice by ~52% and ~16.49%, respectively. The residual lifespan of the naturally aged mice was extended by 80%, from 85.5 days to 154 days. The oral administration of BBR in mice resulted in significantly improved health span, fur density, and behavioral activity. Therefore, BBR may be an ideal candidate for the development of an anti-aging medicine.

Genetic Variants are not an Important Risk Factor in the Vast Majority of People and Age-Related Conditions
https://www.fightaging.org/archives/2019/12/genetic-variants-are-not-an-important-risk-factor-in-the-vast-majority-of-people-and-age-related-conditions/

This is an age of genetics, in which the costs of obtaining and working with genetic data have dropped by orders of magnitude, while the capabilities of the tools and technologies have expanded to a similar degree. Give the scientific community a hammer, and a great many parts of the field start to look like a nail. Thus there are innumerable studies of genetics and longevity, genetics and specific age-related diseases, and so forth. There is considerable interest in trying to find out whether there is a genetic contribution to survival to extreme old age, and then using this information to develop therapies.

What the data tells us, however, is that we all age in pretty much the same way. The underlying processes of damage and reactions to damage are the same in everyone. The risk of age-related disease is not all that influenced by genetics for the vast majority of people and vast majority of conditions. Long-lived lineages of humans are a tiny, tiny fraction of the population, and may well exist for cultural rather than genetic reasons. Only a tiny number of genetic variants have been reliably correlated with longevity, and the effect sizes in each case are small, the variants adding only modestly to the odds of living longer.

What has by far the largest effect on variations in human aging? Firstly lifestyle, largely exercise and diet, and secondly environment, largely exposure to pathogens, particularly persistent viral infections. This will remain the case until the first rejuvenation therapies are widely adopted, at which point whether or not one uses them will become the largest contributing cause to variation in aging. Genetics is an enormously valuable branch of the sciences, but not as a direct path to human longevity.

Your DNA is not your destiny - or a good predictor of your health

In most cases, your genes have less than five per cent to do with your risk of developing a particular disease, according to new research. In the largest meta-analysis ever conducted, scientists have examined two decades of data from studies that examine the relationships between common gene mutations, also known as single nucleotide polymorphisms (SNPs), and different diseases and conditions. And the results show that the links between most human diseases and genetics are shaky at best. "Simply put, DNA is not your destiny, and SNPs are duds for disease prediction. The vast majority of diseases, including many cancers, diabetes, and Alzheimer's disease, have a genetic contribution of 5 to 10 per cent at best."

The study also highlights some notable exceptions, including Crohn's disease, celiac disease, and macular degeneration, which have a genetic contribution of approximately 40 to 50 per cent. "Despite these rare exceptions, it is becoming increasingly clear that the risks for getting most diseases arise from your metabolism, your environment, your lifestyle, or your exposure to various kinds of nutrients, chemicals, bacteria, or viruses."

Assessing the performance of genome-wide association studies for predicting disease risk

To date more than 3700 genome-wide association studies (GWAS) have been published that look at the genetic contributions of single nucleotide polymorphisms (SNPs) to human conditions or human phenotypes. Through these studies many highly significant SNPs have been identified for hundreds of diseases or medical conditions. However, the extent to which GWAS-identified SNPs or combinations of SNP biomarkers can predict disease risk is not well known. One of the most commonly used approaches to assess the performance of predictive biomarkers is to determine the area under the receiver-operator characteristic (ROC) curve (AUROC).

Our results indicate that the average AUROC for a typical GWAS-derived biomarker profile is low, just 0.55 with a standard deviation of 0.05. This is significantly lower than what we expected given that (the few) published AUROCs typically report a range between 0.62-0.67. The fact that published GWAS AUROCs tend to be high (~0.65) and unpublished GWAS AUROCs tend to be low (~0.55), suggests that one reason for the paucity of published GWAS AUROCs is that many AUROCs for SNP biomarker profiles are either uninterestingly low (less than 0.55), or not statistically different from those generated by a random predictor.

Welcome to the GWAS-ROCS Database Version 1.0

The GWAS-ROCS Database is a freely available electronic database containing the largest and most comprehensive set of SNP-derived AUROCs. All of the data is either directly from, or derived from, studies accessible through PubMed or GWAS Central - an open-access online repository of summary-level genome-wide association study (GWAS) data. The database currently houses 579 simulated populations (corresponding to 219 different conditions) and SNP data (odds ratio, risk allele frequency, and p-values) for 2886 unique SNPs. Each study simulation record (GR-Card) contains information detailing the original study as well as simulated population data (e.g. ROC curves, AUROCs, SNP-heritability scores) determined from careful population modelling to recreate individual-level GWAS data. All GWAS-ROCS data is downloadable and is intended for applications in genomics, biomarker discovery, and general education.

Why Doesn't the State of Having High Blood Cholesterol Cause Pain?
https://www.fightaging.org/archives/2019/12/why-doesnt-the-state-of-having-high-blood-cholesterol-cause-pain/

Progress in the sciences is as much a matter of finding novel questions to ask as it is a matter of answering existing questions. The novel question here is this: given that high blood cholesterol is harmful over the long term, accelerating the progression towards atherosclerosis, so why haven't we evolved to feel pain and discomfort from being in that state, leading to avoidance? The answer is mostly likely that issues that arise in later life, after reproduction is carried out, are not subject to selection pressure to anywhere near the degree needed to improve the situation for the individual. Evolution optimizes for early life success and reproduction.

To avoid any kind of potential harm to the body, to restore physiological functions when out of balance, and to satisfy the biochemical needs of the organism by giving itself signals that favour respective behaviour. Acknowledging this, one may ask why causal drivers of cardiovascular disease do not prompt the individual to behave in a way that diminishes these risk factors. Why does the insult to the vascular endothelium by smoking, high blood pressure, or high blood sugar not cause discomfort? Why does the vasculature of a person with familial hypercholesterolemia not hurt? Why does a person with high cholesterol not feel antipathy for fatty and high-caloric meals?

From an evolutionary perspective, the mentioned physiological functions preserve the integrity of the body with the ultimate goal to enable the organism to reproduce. Physical harms and unsatisfied physiological needs directly affect the probability of reproductive success and therefore, individuals displaying favourable behaviour in this regard are more likely to pass their genes on to the next generation. Any genetic trait with effects that become relevant only after reproduction does not exert pressure to be sustained. Such traits may even have been beneficial under the circumstances of feast-famine cycles under which they evolved. This explanation why detrimental genetic traits leading to hypercholesterolemia, diabetes mellitus, and obesity, occur with such high prevalence has been called "thrifty gene hypothesis".

Hypercholesterolemia affects one in two individuals in Western societies and is, relying on different lines of evidence, causal for the development of atherosclerotic cardiovascular disease. Genetic traits that favour high blood levels of cholesterol have likely been beneficial long ago to foster energy security and in consequence, lead to early reproduction. It is indisputable that cholesterol is an essential element of the human body, but with 93% of all cholesterol being intracellular and famine episodes being virtually absent today, do we than still need any cholesterol in our bloodstream? Very low levels of LDL cholesterol, due to mutations or aggressive medical treatment, do not appear to have any detrimental effects.

While the question why hypercholesterolemia does not hurt may primarily be of academic interest, the answer provided may be useful for patient care as well. It can explain why cholesterol levels referred to as "normal" by patients and physicians is still associated with subclinical atherosclerosis as precursor of established cardiovascular disease and should be a target of treatment. Since high cholesterol does not hurt, lipid lowering will not confer symptomatic benefit. Therefore, patient discussion - including the principles discussed here - is the key to medication adherence.

Age-Related Hyperglycemia as a Cause of Increased Cancer Incidence
https://www.fightaging.org/archives/2019/12/age-related-hyperglycemia-as-a-cause-of-increased-cancer-incidence/

Why is cancer an age-related condition? One can propose a range of mechanisms: the spread of stochastic DNA damage through cell populations; rising levels of chronic inflammation; ever more senescent cells turning out disruptive, pro-growth signals; the growing inability of the immune system to promptly destroy errant cells. The authors of this open access paper argue that the metabolic dysfunction of later life that leads to raised blood sugar, hyperglycemia, is also an important contributing factor to cancer risk. Most hyperglycemia is self-inflicted via obesity, but it can manifest in other ways as damage and systems failure accumulates in late life.

Aging can increase cancer incidence because of accumulated mutations that initiate cancer and via compromised body control of premalignant lesions development into cancer. Relative contributions of these two factors are debated. Recent evidence suggests that the latter is rate limiting. In particular, hyperglycemia caused by compromised body control of blood glucose may be a factor of selection of somatic mutation-bearing cells for the ability to use glucose for proliferation. High glucose utilization in aerobic glycolysis is a long known characteristic of cancer.

The new evidence adds to the concepts that have been being developed starting from mid-1970s to suggest that age-related shifts in glucose metabolism and lipid metabolism increase the risk of cancer and compromise prognoses for cancer patients and to propose antidiabetic biguanides, including metformin, for cancer prevention and as an adjuvant means of cancer treatment aimed at the metabolic rehabilitation of patients.

The new evidence is consistent with several effects of glucose contributing to aging and acting synergistically to enhance carcinogenesis. Glucose can affect (i) separate cells (via promoting somatic mutagenesis and epigenetic instability), (ii) cell populations (via being a factor of selection of phenotypic variants in cell populations for higher glucose consumption and, ultimately, for high aerobic glycolysis); (iii) cell microenvironment (via modification of extracellular matrix proteins), and (iv) the systemic levels (via shifting the endocrine regulation of metabolism toward increasing blood lipids and body fat, which compromise immunological surveillance and promote inflammation). Thus, maintenance of youthful metabolic characteristics must be important for cancer prevention and treatment.

CpG Site Density in the Genome Predicts Species Maximum Life Span
https://www.fightaging.org/archives/2019/12/cpg-site-density-in-the-genome-predicts-species-maximum-life-span/

Researchers investigating epigenetic modifications and their relationship to aging have found that the density of CpG sites, where DNA methylation occurs in order to modify the pace of production of specific proteins, correlates with maximum species life span. This is an interesting finding, but, as for the epigenetic clock used to assess aging in individuals, it will likely require the work of many research groups and many years to build a firm understanding as to why this correlation exists.

Ageing involves the decline of diverse biological functions and the dynamics of this process limit species maximum lifespan. Longevity of individuals is strongly linked to specific alleles in genetic model organisms. Ageing is also associated with several epigenetic changes involving DNA methylation (DNAm). DNAm of cytosine-phosphate-guanosine (CpG) sites, involves a covalent modification to cytosine to form 5-methylcytosine. This modification to DNA has the potential to regulate gene expression, including of genes critical for longevity, without altering the underlying sequence.

The observation that DNAm at promoter CpG sites can accumulate or decline predictably with age, over and above the more random process of epigenetic drift, has enabled the development of "clock like" biomarkers for age. Individual human age, for example, can be predicted with great accuracy in a range of tissues by an epigenetic clock. Similar epigenetic clocks have been created in a range of mammal and bird species.

Maximum lifespans differ greatly among species, even among fairly closely-related species. In vertebrates, species such as the pygmy goby (Eviota sigillata) live for only eight weeks, while the Greenland shark (Somniosus microcephalus) may live for more than 400 years. In mammals, the forest shrew (Myosorex varius) has one of the shortest reported lifespans at 2.1 years, whereas some bowhead whales (Balaena mysticeta) have been reported to be older than 200 years. Despite profound importance, lifespan is poorly characterised for most wild animals because it is difficult to estimate.

Maximum lifespan is believed to be under genetic control, but so far, no gene variants can account for differences in lifespan among species. Because ageing is characterised by changes in gene expression caused by DNAm, another potential controller of lifespan is genomic changes that accommodate DNAm's effects on regulation of gene expression. Specifically, clusters of high density CpG sites, also known as CpG islands, are highly conserved within promoter sequences and well known for regulating gene expression. CpG sites are also prone to mutation and their function in regulating gene expression may make them prime targets for evolutionary pressures to vary lifespans.

Here, we extend observations of the correlation between promoter CpG density and lifespan in mammals to produce a predictive model for lifespan in all vertebrates. We use reference genomes of animals with known lifespans to identify promoters that can be predictive of lifespan. We combined data from major databases including NCBI Genomes, the Eukaryotic Promoter Database (EPD), Animal Ageing and Longevity Database (AnAge) and TimeTree to build a predictive model that estimates lifespan. Our results show CpG density in selected promoters is highly predictive of lifespan across vertebrates. To our knowledge this is the first study which has built a genetic predictive model to estimate the lifespan of vertebrate species from genetic markers.

CD33 Influences Alzheimer's Risk via Regulation of Microglial Functions
https://www.fightaging.org/archives/2019/12/cd33-influences-alzheimers-risk-via-regulation-of-microglial-functions/

Researchers here explore CD33 as a possible target for the development of Alzheimer's disease treatments. The protein suppresses the ability of microglia in the brain to ingest and dispose of amyloid. This, in principle, will cause issues over the long term by promoting the presence of amyloid, leading to neural dysfunction and chronic inflammation in the brain. The work here is also interesting as an illustration of the complexities of trying to model the processes of Alzheimer's disease in mice, a species that doesn't normally suffer any of the relevant underlying mechanisms that produce the condition. Previous research proceeded on the basis that the mouse version of CD33 behaved in much the same way as the human version, which turns out not to be the case.

The strong genetic link between variants of CD33 and Alzheimer's disease (AD) susceptibility suggests that targeting the common risk allele of CD33, which preferentially encodes the longer human isoform of (hCD33M) containing its glycan-binding domain, could be a treatment strategy in neurodegenerative disease. To better understand if targeting CD33 in AD is a viable option, a better grasp is needed on the role CD33 plays in modulating the function of microglia. Our findings demonstrate that expression of the long isoform of hCD33 (hCD33M) alone is sufficient to repress phagocytosis in both monocytes and microglia. We have created transgenic mice expressing hCD33M, and these will be a valuable tool for future studies addressing the role of hCD33 in modulating plaque accumulation as well as pre-clinical testing of therapeutics aimed at targeting hCD33.

Divergent features between human CD33 (hCD33) and mouse CD33 (mCD33) include a unique transmembrane lysine in mCD33 and cytoplasmic tyrosine in hCD33. The functional consequences of these differences in restraining phagocytosis remains poorly understood. Using a new monoclonal antibody, we show that mCD33 is expressed at high levels on neutrophils and low levels on microglia. In mouse derived macrophages and monocytes, uptake of cargo - including aggregated amyloid - is not altered upon genetic ablation of mCD33. Alternatively, deletion of hCD33 in monocytic cell lines increased cargo uptake. Moreover, transgenic mice expressing hCD33 in the microglial cell lineage showed repressed cargo uptake in primary microglia. Therefore, mCD33 and hCD33 have divergent roles in regulating phagocytosis.

Accumulation of aggregated amyloid drives the formation of amyloid plaques and mouse models to study human genetic factors that modulate this process in vivo have been widely used. Our studies suggest that mCD33 may not be an appropriate surrogate for studying hCD33. We demonstrate that transgenic expression of hCD33M in the microglial cell lineage inhibits phagocytosis; these hCD33M transgenic mice should provide a valuable model to test the role of hCD33M in regulating plaque accumulation in vivo, which is currently being tested in ongoing studies in our laboratory. Indeed, establishing a good mouse model to study hCD33 is critical for both better understanding AD pathology and also testing therapeutics aimed at controlling microglial cell function by targeting hCD33M.

More Insight into the Relationship Between Cell Size and Cell Senescence
https://www.fightaging.org/archives/2019/12/more-insight-into-the-relationship-between-cell-size-and-cell-senescence/

Senescent cells accumulate with age and cause considerable disruption of metabolism and tissue function. This is an important contribution to aging, and there is thus funding and interest for continued research into senescent cell biochemistry. Senescent cells are very different from normal cells in many respects, but one of the more striking is that they are much larger. One group has used this to build a microfluidics platform capable of counting and sorting senescent cells, but we may well ask why exactly it is that senescent cells become large in comparison to normal cells. A hypothesis is offered in this popular science article.

Biologists have known since 1961 that normal human cells will only divide 40 to 60 times before ceasing to replicate - a constraint known as the Hayflick limit. Recent research shows that this limit may be defined by a cell's physical size. When Leonard Hayflick first described this senescence phenomenon, he pointed out that these senescent cells were actually huge. Researchers have shown that when cells below the Hayflick limit are induced to grow larger than they should be, they have all the characteristics of senescent cells.

But why do cells get so large, and why should that increased size cause a cell to senesce and ultimately stop dividing? The explanation is suggested to lie in how cells repair damage to the DNA coiled in their chromosomes. Natural DNA damage occurs constantly, and cells must periodically pause the cell cycle to fix it. However, other processes inside the cell - such as building proteins and other biomolecules - don't pause during DNA repair. As a result, every time the cell cycle stops, the cell gets a little larger. If a cell becomes too large, its own genes can't direct the production of enough protein to sustain the cell's function. Cellular functions decline and the cell becomes senescent.

One clue supporting this connection between size and senescence is that doubling the number of genes inside the cell - which doubles the amount of proteins it builds to sustain itself - reverses the senescence process. Furthermore, when using rapamycin to inhibit cells' ability to manufacture proteins (and thus get larger) while paused to repair DNA damage, the cells stay small and avoid senescence - they don't lose their replicative potential. "We've known for a very long time that DNA damage causes senescence, but nobody could explain it. I think we've come up with a proposal for why this is happening - cells get larger during the time they arrest in the cell cycle to repair the damage, and when they are large they lose their functionality. This appears to be universally true from yeast to humans."

Bioprinting Liver Organoids with Patient-Derived Cells
https://www.fightaging.org/archives/2019/12/bioprinting-liver-organoids-with-patient-derived-cells/

Researchers here report on the use of 3-D printing techniques to generate small, functional liver organoids from patient-derived cells. A cell sample is reprogrammed into induced pluripotent stem cells, and these are then differentiated into liver cell clusters to be used in the printing process. These organoids lack a vasculature, and thus cannot be made larger than a few millimeters in size. Given the progress made by Lygenesis and other groups towards the practical use of liver organoids even without vasculature, however, by implantation into lymph nodes, or into the liver itself, patients may well benefit considerably in the near future.

Using human blood cells, researchers have succeeded in obtaining hepatic organoids ("mini-livers") that perform all of the liver's typical functions, such as producing vital proteins, storing vitamins, and secreting bile, among many others. The innovation permits the production of hepatic tissue in the laboratory in only 90 days and may in the future become an alternative to organ transplantation. This study combined bioengineering techniques, such as cell reprogramming and the cultivation of pluripotent stem cells, with 3D bioprinting. Thanks to this strategy, the tissue produced by the bioprinter maintained hepatic functions for longer than reported by other groups in previous studies.

"More stages have yet to be achieved until we obtain a complete organ, but we're on the right track to highly promising results. In the very near future, instead of waiting for an organ transplant, it may be possible to take cells from the patient and reprogram them to make a new liver in the laboratory. Another important advantage is zero probability of rejection, given that the cells come from the patient." The innovative part of the study resided in how the cells were included in the bioink used to produce tissue in the 3D printer. Instead of printing individualized cells, researchers developed a method of grouping them before printing. These clumps of cells, or spheroids, are what constitute the tissue and maintain its functionality much longer.

The researchers thereby avoided a problem faced by most human tissue bioprinting techniques, namely, the gradual loss of contact among cells and hence loss of tissue functionality. Spheroid formation in this study already occurred in the differentiation process, when pluripotent cells were transformed into hepatic tissue cells (hepatocytes, vascular cells, and mesenchymal cells). Researchers started the differentiation process with the cells already grouped together. They were cultured in agitation, and groups formed spontaneously.

Refuting the Link Between Persistent Herpesvirus Infection and Alzheimer's Disease
https://www.fightaging.org/archives/2019/12/refuting-the-link-between-persistent-herpesvirus-infection-and-alzheimers-disease/

There is a reasonable mechanism by which persistent viral infections might raise the risk of Alzheimer's disease: amyloid-β is an antimicrobial peptide, a part of the innate immune system. The presence of viral particles will contribute to greater production of amyloid-β, which will accelerate the pace at which amyloid-β might aggregate in older individuals due to an imbalance between production and clearance. The aggregates then cause the usual progression to neural inflammation, damage, and cognitive decline. Does the epidemiological data support a role for persistent herpes viruses in Alzheimer's risk, however? Previous studies suggested yes, but here researchers dismantle and refute one of those studies, while suggesting that people need to be more careful when using statistics. This sequence of events happens more often than you might think in the research community.

Like all types of dementia, Alzheimer's disease is characterized by massive death of brain cells, the neurons. Identifying the reason why neurons begin and continue to die in the brains of Alzheimer's disease patients is an active area of research. One theory that has gained traction in the past year is that certain microbial infections, such as those caused by viruses, can trigger Alzheimer's disease. A 2018 study reported increased levels of human herpesvirus in the postmortem brain tissues of more than 1,000 patients with Alzheimer's disease when compared to the brain tissues of healthy-aging subjects or those suffering from a different neurodegenerative condition.

Surprisingly, when researchers reanalyzed the data sets from the 2018 study using the identical statistical methods with rigorous filtering, as well as four commonly used statistical tools, they were unable to produce the same results. The team was motivated to reanalyze the data from the previous study because they observed that while the p-values (a statistical parameter that predicts the probability of obtaining the observed results of a test, assuming that other conditions are correct) were highly significant, they were being ascribed to data in which the differences were not visually appreciable. Moreover, the p-values did not fit with simple logistic regression - a statistical analysis that predicts the outcome of the data as one of two defined states. In fact, after several types of rigorous statistical tests, they found no link between the abundance of herpes viral DNA or RNA and likelihood of Alzheimer's disease in this cohort.

"As high-throughput 'omics' technologies, which include those for genomics, proteomics, metabolomics and others, become affordable and easily available, there is a rising trend toward 'big data' in basic biomedical research. In these situations, given the massive amounts of data that have to be mined and extracted in a short time, researchers may be tempted to rely solely on p-values to interpret results and arrive at conclusions. Our study highlights one of the potential pitfalls of over-reliance on p-values. While p-values are a very valuable statistical parameter, they cannot be used as a stand-alone measure of statistical correlation - data sets from high-throughput procedures still need to be carefully plotted to visualize the spread of the data. Data sets also have to be used in conjunction with accurately calculated p-values to make gene-disease associations that are statistically correct and biologically meaningful."

More Visceral Fat and Less Muscle Mass Correlate with Lower Fluid Intelligence in Middle Age
https://www.fightaging.org/archives/2019/12/more-visceral-fat-and-less-muscle-mass-correlate-with-lower-fluid-intelligence-in-middle-age/

Fluid intelligence is described as the ability to solve novel reasoning problems; high fluid intelligence tends to imply a greater capacity to learn, ability to comprehend, and so forth. Fluid intelligence declines with age, but researchers here suggest that has more to do with the effects of visceral fat tissue and loss of muscle mass than it does with an inexorable aging process in the brain - at least into middle age, if not later in life. Both visceral fat and skeletal muscle are metabolically active tissues, though more is understood about the harms caused by visceral fat than about the protective effects that are lost as muscle declines with age. It is reasonable to think, based on weight of evidence, that chronic inflammation and other forms of immune dysfunction with age are strongly influenced by visceral fat, and that this in turn has an effect on brain function. All of the common neurodegenerative conditions of late life have a strong inflammatory component to their progression.

Researches looked at data from more than 4,000 middle-aged to older UK Biobank participants, both men and women. The researchers examined direct measurements of lean muscle mass, abdominal fat, and subcutaneous fat, and how they were related to changes in fluid intelligence over six years. The researches discovered that people mostly in their 40s and 50s who had higher amounts of fat in their mid-section had worse fluid intelligence as they got older. Greater muscle mass, by contrast, appeared to be a protective factor. These relationships stayed the same even after taking into account chronological age, level of education, and socioeconomic status. "Chronological age doesn't seem to be a factor in fluid intelligence decreasing over time. It appears to be biological age, which here is the amount of fat and muscle."

Generally, people begin to gain fat and lose lean muscle once they hit middle age, a trend that continues as they get older. To overcome this, implementing exercise routines to maintain lean muscle becomes more important. Exercising, especially resistance training, is essential for middle-aged women, who naturally tend to have less muscle mass than men.

The study also looked at whether or not changes in immune system activity could explain links between fat or muscle and fluid intelligence. Previous studies have shown that people with a higher body mass index (BMI) have more immune system activity in their blood, which activates the immune system in the brain and causes problems with cognition. BMI only takes into account total body mass, so it has not been clear whether fat, muscle, or both jump-start the immune system. In this study, in women, the entire link between more abdominal fat and worse fluid intelligence was explained by changes in two types of white blood cells: lymphocytes and eosinophils. In men, a completely different type of white blood cell, basophils, explained roughly half of the fat and fluid intelligence link. While muscle mass was protective, the immune system did not seem to play a role.

Cynomolgus Macaques and Humans Exhibit Broadly Similar Age-Related Changes in the Gut Microbiome
https://www.fightaging.org/archives/2019/12/cynomolgus-macaques-and-humans-exhibit-broadly-similar-age-related-changes-in-the-gut-microbiome/

The relative sizes of gut microbial populations are known to change significantly with age; harmful bacteria become more numerous while beneficial bacteria become less numerous. This results in greater chronic inflammation and a lowered production of beneficial metabolites. Numerous causes are proposed for this shift in the microbiome, from dietary changes characteristic of aging to declining immune function, but it is far from clear as to the relative contribution of each such mechanism. In the years ahead we might expect to see strategies emerge to reverse age-related changes in the microbiome, such as application of fecal microbiota transplantation to providing old people with young microbial populations, or the delivery of beneficial bacterial populations in pill form.

Previous clinical and rodent studies have suggested that age may affect the composition of the gut microbiota. Here, monkeys were used to investigate this issue and this animal model has the following advantages: (i) the microbial composition of monkeys is highly similar to that of humans, which makes it easier to translate these findings into human research; (ii) it can effectively avoid the influences of confounding factors such as living environment and genetic background; (iii) nonhuman primates exhibit similar key life span metrics as humans. Here, we characterized the composition and function of the gut microbiota at three representative age phases, which is a new development in this field.

Our results showed that the diversity of the gut microbiota in cynomolgus macaques was reduced with age, which was consistent with previous human studies. Moreover, we found that the microbial composition of the three groups was significantly different. Firmicutes and Bacteroidetes were the dominant phyla in both humans and cynomolgus macaques. Similar to human studies, we found that, compared with the young and adult groups, the old group showed a slight increase in Firmicutes, whereas Bacteroidetes gradually decreased after youth.

With increased age, the relative abundances of Veillonellaceae and Coriobacteriaceae were significantly increased, and Ruminococcaceae and Rikenellaceae were significantly decreased at the family level. There is evidence to confirm that the family Veillonellaceae is associated with age-related diseases such as atherosclerosis and stroke. Ruminococcaceae play a vital role in the maintenance of gut health through degrading cellulose and hemicellulose components of plant material by CAZymes and transporters. These compounds are fermented and converted into short-chain fatty acids (mainly acetate, butyrate, and propionate), which are absorbed by the host and are important for metabolic and immunological homeostasis. Our finding showed that the relative abundance of Ruminococcaceae was negatively correlated with age. Consistent with our findings, previous studies showed that Ruminococcaceae, one of the core microbiota, becomes less abundant in older people, whereas some taxa associated with unhealthy aging emerge. These findings suggested that Ruminococcaceae may have a positive effect on the aging process.

Type 2 Diabetes as a Simple Condition of Excess Fat
https://www.fightaging.org/archives/2019/12/type-2-diabetes-as-a-simple-condition-of-excess-fat/

Research of recent years has shown that the triggering mechanism for type 2 diabetes is specifically excess fat in the pancreas. The only way to place that fat into the pancreas, in the normal course of affairs, is to become very overweight - to overload the body with fat to the point that it cannot find places to safely store it. Losing this excess fat through a low calorie diet, and then maintaining a lower weight going forward, is a cure for type 2 diabetes, as demonstrated in clinical trials.

For the first time, scientists have been able to observe people developing type 2 diabetes - and confirmed that fat over-spills from the liver into the pancreas, triggering the chronic condition. The study involved a group of people who previously had type 2 diabetes but had lost weight and successfully reversed the condition as part of the DiRECT trial. The majority remained non-diabetic for the rest of the two year study, however, a small group went on to re-gain the weight and re-developed type 2 diabetes while monitored by the study organizers.

"We saw that when a person accumulates too much fat, which should be stored under the skin, then it has to go elsewhere in the body. The amount that can be stored under the skin varies from person to person, indicating a 'personal fat threshold' above which fat can cause mischief. When fat cannot be safely stored under the skin, it is then stored inside the liver, and over-spills to the rest of the body including the pancreas. This 'clogs up' the pancreas, switching off the genes which direct how insulin should effectively be produced, and this causes type 2 diabetes."

"This means we can now see Type 2 diabetes as a simple condition where the individual has accumulated more fat than they can cope with. Importantly this means that through diet and persistence, patients are able to lose the fat and potentially reverse their diabetes. The sooner this is done after diagnosis, the more likely it is that remission can be achieved."

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