Fight Aging!

Fight Aging! publishes news and commentary relevant to the goal of ending all age-related disease, to be achieved by bringing the mechanisms of aging under the control of modern medicine. This weekly newsletter is sent to thousands of interested subscribers. To subscribe or unsubscribe from the newsletter, please visit: https://www.fightaging.org/newsletter/

Longevity Industry Consulting Services

Reason, the founder of Fight Aging! and Repair Biotechnologies, offers strategic consulting services to investors, entrepreneurs, and others interested in the longevity industry and its complexities. To find out more: https://www.fightaging.org/services/

Contents

• An Overview of Early Work on the mTOR Inhibitor Rapamycin
• Longer Genes May Be More Disrupted than Shorter Genes by Random DNA Damage Occuring with Age
• Changes in Synaptic Ultrastructure Connected to Age-Related Impairment of Working Memory
• Age-Related Changes in Nuclear DNA Structure Make Transcription Mechanisms Faster and More Error-Prone
• Senescent Cells Induce Dedifferentiation in Salamander Regeneration
• ATF4 Knockout in Mice Greatly Slows Age-Related Loss of Strength and Endurance
• An Interview with Stephanie Planque of Covalent Bioscience
• More Details on Cyclarity's Approach to Clearing 7-Ketocholesterol
• Reviewing the Aging of the Gut Microbiome
• A Mechanism for Fisetin to Reduce Stress-Induced Cellular Senescence
• There is Still Room to Improve Upon Epigenetic Clocks
• Investigating Mechanisms By Which Some Gut Microbes May Shorten Fly Life Span
• Theorizing that the APOEε4 Variant Increases Alzheimer's Risk Through Increased Microglial Inflammation
• Detection of Small Amounts of Misfolded α-Synuclein Identifies Early Parkinson's Disease
• Targeting a Mechanism of Hyperphosphorylation in Alzheimer's Disease Pathology

An Overview of Early Work on the mTOR Inhibitor Rapamycin
https://www.fightaging.org/archives/2023/04/an-overview-of-early-work-on-the-mtor-inhibitor-rapamycin/

The path to understanding that pharmacological inhibition of mTOR replicates some of the calorie restriction response to cause a slowing of aging started with studies of rapamycin. The primary mechanism of interest is upregulation of autophagy, a cellular housekeeping mechanism that is involved in a range of interventions that slow aging in short-lived species. Other mechanisms may well turn out to be involved, as altering metabolism is a complex business and still incompletely understood.

The various mTOR inhibitors are collectively one of the most studied, and arguably best of the existing approaches to alter metabolism in order to modestly slow aging in mammals. This isn't rejuvenation, and isn't anywhere near as good as the effects of first generation senolytics when it comes to rapidly reversing aspects of aging in old animals. Rapamycin and other mTOR inhibitors are quite robust in their effects in comparison to many of the other alleged calorie restriction mimetics, however, so there is that.

Rapamycin, the only drug that has been consistently demonstrated to increase mammalian longevity. An update.

Prior to 2009 the consensus of scholars was that aging could not be treated or if it could be it must be a youth factor (e.g., growth hormone). Numerous advertised non-scientific approaches absconded with people's funds, mostly confused people, and were counterproductive for the field. However, there were two scientific settings in which aging could be reproducibly delayed. Unfortunately, neither was optimal for use in people. They were restrictions of diet and/or growth factors by genetic means. Since people do not like restricting anything, especially food, progress toward a deeper understanding of aging and potential ways to delay its effects was slow.

In recognition of this bottleneck, the National Institute of Aging established the Interventions Testing Program (ITP) to identify compounds that could be tested for aging effects under rigorous and standard conditions. To date, the ITP website indicates they have tested or in the process of testing 64 different compounds, some at varied doses and in combination. Twenty publications from the ITP have reported increases in lifespan from ten compounds. Importantly, the ITP also reports compounds that do not extend lifespan.

Here we focus of the ITP 2009 test of what was then an unlikely candidate drug called rapamycin. Results showing increased median and maximum lifespan in advanced aged males and females in this paper reset the paradigm for aging studies. It suggested that pharmacological agents can prevent, delay, and/or reduce the severity of age-caused morbidities. We will first briefly remind readers about the biology of the cell systems affected by rapamycin, better known as mTOR. Next, we will review the results of several studies on the effects chronic rapamycin has on lifespan in both sexes including our recollection of the first study. Following that, we will relate selected examples of the effects chronic rapamycin has on age-caused diseases.

We conclude with our view of what rapamycin effects are telling us about aging and how it might be working. We confess at the outset that we have only a faint picture of rapamycin's function as an anti-aging agent and suggest that it will be as complicated and mysterious as the studies to determine how restriction of food and growth factors work, which after half a century still have a way to go.

Longer Genes May Be More Disrupted than Shorter Genes by Random DNA Damage Occuring with Age
https://www.fightaging.org/archives/2023/04/longer-genes-may-be-more-disrupted-than-shorter-genes-by-random-dna-damage-occuring-with-age/

Random mutational damage to nuclear DNA occurs constantly. While near all of it is restored by the highly efficient suite of DNA repair mechanisms present in the cell, some is not. This damage accumulates over time. Fortunately, near all of it occurs in DNA that is unused in that cell type, or occurs in genes that are not all that important, or occurs in somatic cells that have few replications remaining before hitting the Hayflick limit. In other words, most DNA damage isn't all that important, and even where it sticks, it will be cleared from the body via the normal processes of replacement of cells in a tissue.

How does DNA damage contribute to aging? Firstly, cancer risk: an unlikely combination of mutations occurring in any cell can give rise to a cancerous cell capable of unfettered replication. It is a risk throughout life, but that risk grows as the immune system ages and as the aged, ever more inflammatory tissue environment becomes more hospitable to the growth of a nascent cancer. Beyond cancer, it is likely that damage to stem cells is the primary problem, as lingering mutations in stem cells can spread throughout tissues to form patterns of overlapping mutational damage called somatic mosaicism. A minor loss of function in one cell is not a disaster. A minor loss of function in half of an organ may be a meaningful contribution to degenerative aging.

Is DNA damage really random in its effects on genes, however? Today's open access paper is one of a number to point out that longer genes are more vulnerable, and that an examination of changes in gene expression shows a greater loss of expression of longer DNA sequences than shorter DNA sequences. It is interesting to speculate on the degree to which this shapes the details of changes in cell behavior observed in aging, as compared to the contributions of the many other issues resulting from forms of damage. It is hard to do much more than speculate, however. Metabolism is ferociously complex, and the best way forward to answer any question is to repair a specific form of damage and see what happens as a result. Repair random mutational damage on a cell by cell basis is not a near term prospect, however, given the present state of genetic engineering.

It is worth noting that a different group of researchers has suggested that a reduction in the expression of longer DNA sequences with advancing age is the result of age-related changes in regulation of transcription, not DNA damage. It will be interesting to see how this debate over mechanisms progresses as more data emerges.

Age or lifestyle-induced accumulation of genotoxicity is associated with a length-dependent decrease in gene expression

DNA damage has long been proposed as a primary molecular driver of aging. Aging has also been associated with a series of transcriptional changes, most of which are highly tissue- and cell type-specific. Even though the search for a global aging signature has been the goal of much research, meta-analyses have shown that very few genes are consistently upregulated or downregulated with aging across different tissues. It appears that, at the mRNA level, aging signatures are not defined by the overexpression of particular sets of genes, but rather an overall decay in transcription.

Genetic material is constantly challenged throughout the lifespan of the organism, both by endogenous and environmental genotoxins. Some of this damage happens in the form of transcription-blocking lesions (TBLs), which impede transcriptional elongation. Accumulation of TBLs provokes a genome-wide shutdown of transcription, which also affects undamaged genes through poorly understood mechanism. Assuming a constant TBL incidence, meaning that any base pair in the genome has a similar probability of suffering damage that results in a lesion, a greater accumulation of TBLs is to be expected in longer genes. In fact, a gene length-dependent accumulation of other forms of genetic damage, like somatic mutations, has already been reported in conditions like Alzheimer's disease. Hence, TBLs, just like somatic mutations are expected to accumulate with aging, and their accumulation should be dependent on gene length. However, unlike somatic mutations, TBLs have a strong and direct impact on mRNA production, and their gene length-dependent effects are likely to be measurable from RNA sequencing data of aged tissues.

So far, a potential relationship between age-related transcriptional changes and gene length has received relatively little attention. Here, we aimed to extend these early observations, which were based on bulk microarray and RNA sequencing data to the existing aging datasets based on single cell RNA sequencing technology. We also extended our gene length analyses to mouse and human datasets of lifestyle-induced genotoxic exposure (UV, smoke) and progeroid syndromes (Cockayne syndrome and trichothiodystrophy).

We found a pervasive age-associated length-dependent underexpression of genes across species, tissues, and cell types. Furthermore, we observed length-dependent underexpression associated with UV-radiation and smoke exposure, and in progeroid diseases, Cockayne syndrome, and trichothiodystrophy. Finally, we studied published gene sets showing global age-related changes. Genes underexpressed with aging were significantly longer than overexpressed genes. These data highlight a previously undetected hallmark of aging.

Changes in Synaptic Ultrastructure Connected to Age-Related Impairment of Working Memory
https://www.fightaging.org/archives/2023/04/changes-in-synaptic-ultrastructure-connected-to-age-related-impairment-of-working-memory/

In today's open access paper, researchers report the discovery of differences in the synaptic ultrastructure of aging primates, differences that are connected to loss of memory function. The working hypothesis is that faltering mitochondrial activity inhibits correct formation of synapses, and that this issue is one of the important factors to distinguish individuals that go on to develop worse memory performance in later life.

Every cell contains hundreds of mitochondria, descendants of ancient symbiotic bacteria. Mitochondria are responsible for generating the chemical energy store molecules, adenosine triphosphate, that power cellular processes. It is well known that this activity declines with age, perhaps largely due to failing quality control of damaged mitochondria. Autophagy targeted to mitochondria, known as mitophagy, recycles worn and damaged mitochondria, but is shown to become less effective with age. This occurs for a variety of proximate causes that include changes to mitochondria themselves, as well as failures in parts of the complex autophagy mechanisms.

In energy-hungry tissues like the brain and muscles, loss of mitochondrial activity likely produces a sizable contribution to age-related dysfunction. Many different cellular processes will be affected, and the example in today's paper is but one of these. Restoration of mitochondrial function in older individuals is an important goal for the research community, but so far the range of available interventions have struggled to outperform the effects of exercise and calorie restriction. This includes mTOR inhibition, mitochondrially targeted antioxidants, NAD+ precursor supplements, and so forth. One might hope that the next generation of interventions, including transplantation of functional mitochondria, will produce more impressive outcomes.

Mitochondria power-supply failure may cause age-related cognitive impairment

Brains are like puzzles, requiring many nested and codependent pieces to function well. The brain is divided into areas, each containing many millions of neurons connected across thousands of synapses. These synapses, which enable communication between neurons, depend on even smaller structures: message-sending boutons (swollen bulbs at the branch-like tips of neurons), message-receiving dendrites (complementary branch-like structures for receiving bouton messages), and power-generating mitochondria. To create a cohesive brain, all these pieces must be accounted for.

Prior studies had found that brains lose synapses as they age, and the researchers saw this pattern in their non-human primate model, too. But when they looked at the synapses that remained, they found evidence of a breakdown in coordination between the size of boutons and the mitochondria they contained. A fundamental neuroscientific principle, the ultrastructural size principle, explains that whenever one part of the synaptic complex changes in size, so too must all the other parts. The synapse, the mitochondria, the boutons - all these parts must scale in accordance with one another. The team found that adherence to the ultrastructural size principle was essential for avoiding working memory impairment with age. By viewing violation of the ultrastructural size principle and mitochondria-related failures as the key to age-related cognitive impairment, the study ushers in a new era for aging research.

Violation of the ultrastructural size principle in the dorsolateral prefrontal cortex underlies working memory impairment in the aged common marmoset (Callithrix jacchus)

Here, we tested the hypothesis that changes to synaptic ultrastructure that affect synaptic efficacy stratify marmosets that age with cognitive impairment from those that age without cognitive impairment. We utilized electron microscopy to visualize synapses in the marmoset dorsolateral prefrontal cortex (dlPFC) and measured the sizes of boutons, presynaptic mitochondria, and synapses. We found that coordinated scaling of the sizes of synapses and mitochondria with their associated boutons is essential for intact working memory performance in aged marmosets. Further, lack of synaptic scaling, due to a remarkable failure of synaptic mitochondria to scale with presynaptic boutons, selectively underlies age-related working memory impairment.

We posit that this decoupling results in mismatched energy supply and demand, leading to impaired synaptic transmission. We also found that aged marmosets have fewer synapses in dlPFC than young, though the severity of synapse loss did not predict whether aging occurred with or without cognitive impairment. This work identifies a novel mechanism of synapse dysfunction that stratifies marmosets that age with cognitive impairment from those that age without cognitive impairment. The process by which synaptic scaling is regulated is yet unknown and warrants future investigation.

Age-Related Changes in Nuclear DNA Structure Make Transcription Mechanisms Faster and More Error-Prone
https://www.fightaging.org/archives/2023/04/age-related-changes-in-nuclear-dna-structure-make-transcription-mechanisms-faster-and-more-error-prone/

Some recent work on length-dependent issues in transcription of genes to RNA observed in aging have touched on the role of RNA polymerase II (Pol II), a protein that performs the initial work of moving along a DNA sequence in the genome, reading that sequence in order to assemble the precursor to a corresponding messenger RNA molecule. Do age-related changes in the maintenance of nuclear DNA structure and the activity of Pol II make it harder for longer genes to undergo accurate transcription? Today's open access paper is focused on fidelity of transcription in the context of Pol II behavior, but the work has relevance to those other discussions regarding a selective disadvantage applied to the transcription of longer gene sequences in later life.

The structural organization of nuclear DNA is exceedingly complex and dynamic, ever-changing as the result of a rapid interplay between histones, epigenetic structural additions, and other molecules to expose different regions to transcriptional machinery such as Pol II. At a high level, one might think of the genome as being wrapped around histones, with portions becoming unwrapped for transcription as needed. With age, a great deal changes in the epigenetic decorations placed upon DNA, and thus also in the arrangement of packaged DNA. It is not unreasonable to think that this has a range of effects on cell and tissue function.

A cell is state machine built upon a feedback loop: gene expression produces protein machinery that react to the environment to cause epigenetic changes that alter gene expression. Historically, we might have viewed epigenetic changes in aging as an issue that occurs far downstream of molecular damage and environmental change in tissues that causes aging, but recent discoveries have suggested that much of that epigenetic change characteristic of aging might result from depletion of specific resources following cycles of DNA repair, and thus be a direct consequence of stochastic damage to DNA. Much remains to be determined in certainty; the best approach to establishing the relevance of any specific mechanism involved in aging is to fix it in isolation of other mechanisms and observe the result.

Ageing studies in five animals suggests how to reverse decline

Researchers analysed genome-wide transcription changes in five organisms: nematode worms, fruit flies, mice, rats, and humans, at different adult ages. The researchers measured how ageing changed the speed at which the enzyme that drives transcription, RNA polymerase II (Pol II), moved along the DNA strand as it made the RNA copy. They found that, on average, Pol II became faster with age, but less precise and more error-prone across all five groups.

Previous research had shown that restricting diet and inhibiting insulin signalling can delay ageing and extend lifespan in many animals, so the researchers then investigated whether these measures had any effect on the speed of Pol II. In worms, mice and fruit flies that carried mutations in insulin signalling genes, Pol II moved at a slower pace. The enzyme also travelled more slowly in mice on a low-calorie diet. But the ultimate question was whether changes in Pol II speed affected lifespan. Researchers tracked the survival of fruit flies and worms that carried a mutation that slowed Pol II down. These animals lived 10% to 20% longer than their non-mutant counterparts. When the researchers used gene editing to reverse the mutations in worms, the animals' lifespans shortened.

The researchers wondered whether Pol II's acceleration could be explained by structural changes in how DNA is packed inside cells. To minimize the space that they take up, the vast threads of genetic information are tightly wound around proteins called histones into bundles called nucleosomes. By analysing human lung cells and umbilical vein cells, the researchers found that ageing cells contained fewer nucleosomes, smoothing the path for Pol II to travel faster. When the team boosted the expression of histones in the cells, Pol II moved at a slower pace. In fruit flies, the elevated histone levels seemed to increase their lifespans.

Ageing-associated changes in transcriptional elongation influence longevity

Physiological homeostasis becomes compromised during ageing, as a result of impairment of cellular processes, including transcription and RNA splicing. However, the molecular mechanisms leading to the loss of transcriptional fidelity are so far elusive, as are ways of preventing it. Here we profiled and analysed genome-wide, ageing-related changes in transcriptional processes across different organisms: nematodes, fruitflies, mice, rats and humans. The average transcriptional elongation speed (RNA polymerase II speed) increased with age in all five species. Along with these changes in elongation speed, we observed changes in splicing, including a reduction of unspliced transcripts and the formation of more circular RNAs.

Two lifespan-extending interventions, dietary restriction and lowered insulin-IGF signalling, both reversed most of these ageing-related changes. Genetic variants in RNA polymerase II that reduced its speed in worms and flies increased their lifespan. Similarly, reducing the speed of RNA polymerase II by overexpressing histone components, to counter age-associated changes in nucleosome positioning, also extended lifespan in flies and the division potential of human cells. Our findings uncover fundamental molecular mechanisms underlying animal ageing and lifespan-extending interventions, and point to possible preventive measures.

Senescent Cells Induce Dedifferentiation in Salamander Regeneration
https://www.fightaging.org/archives/2023/04/senescent-cells-induce-dedifferentiation-in-salamander-regeneration/

Regeneration from injury is an intricate dance of many different cell types: stem cells, somatic cells, cells that become senescent, and innate immune cells such as macrophages. This is true of every higher species, but what is the meaningful difference between species capable of regenerating entire limbs and internal organs, such as salamanders, and species that scar and exhibit only partial regeneration of lost tissue, such as near all mammals? In recent years, researchers have discovered that senescent cells and macrophages behave differently in injured tissues in species capable of proficient regeneration. Clearance of senescent cells is unusually efficient in salamanders, for example.

A characteristic of proficient tissue regeneration is a recapitulation of embryonic development, in which cells dedifferentiate to form a blastema in order to rebuild the structure of lost tissue. In today's open access paper, researchers find that salamander senescent cells produce signaling that encourages this dedifferentiation in muscle tissue during limb regeneration. Similar research in zebrafish, another highly regenerative species, has shown that senescent cells are necessary for regeneration of retinal tissues. While the senescence-associated secretory phenotype (SASP) produced by senescent cells is clearly different from species to species, identifying specific signal differences that may be involved in proficient regeneration, as here, is very much a work in progress.

Benefits of "Zombie" Cells: Senescent Cells Aid Regeneration in Salamanders

Senescent cells are cells that have permanently stopped dividing in response to cellular stress but have not died. As organisms age, the number of senescent cells in the body increases. This accumulation is currently considered one of the hallmarks of aging and has been linked to a variety of diseases, including cancer. A growing body of evidence suggests that senescent cells may also have beneficial effects, such as wound healing or preventing tissue scarring.

Salamanders have unique regeneration abilities and are able to re-grow many organs of their bodies, including lost limbs. To check if the presence of senescent cells influences the limb regeneration process, researchers found a way to modulate the number of senescent cells in the wound. The team observed that the presence of senescent cells enhanced the regeneration process. "When more senescent cells were present in the wound, the animals developed a larger regeneration bud, or - as we call it - blastema. This is a collection of cells that are going to form all the needed tissues in the new limb. The larger the blastema, the more cells are there to regrow the limb and the quicker the regeneration process. The presence of senescent cells seemed to 'fuel' the regeneration process."

"Our results show that senescent cells use cell-cell communication to influence the regeneration process. They secrete molecules that signal to mature muscle fibers to dedifferentiate into muscle progenitor cells. These cells can multiply themselves as well as differentiate into new muscle cells, thereby enhancing the regeneration process. This signaling appears to be an important part of promoting regeneration."

Senescent cells enhance newt limb regeneration by promoting muscle dedifferentiation

Salamanders are able to regenerate their entire limbs throughout lifespan, through a process that involves significant modulation of cellular plasticity. Limb regeneration is accompanied by the endogenous induction of cellular senescence, a state of irreversible cell cycle arrest associated with profound non-cell-autonomous consequences. While traditionally associated with detrimental physiological effects, here, we show that senescent cells can enhance newt limb regeneration.

Through a lineage tracing approach, we demonstrate that exogenously derived senescent cells promote dedifferentiation of mature muscle tissue to generate regenerative progenitors. In a paradigm of newt myotube dedifferentiation, we uncover that senescent cells promote myotube cell cycle re-entry and reversal of muscle identity via secreted factors. Transcriptomic profiling and loss of function approaches identify the FGF-ERK signalling axis as a critical mediator of senescence-induced muscle dedifferentiation. While chronic senescence constrains muscle regeneration in physiological mammalian contexts, we thus highlight a beneficial role for cellular senescence as an important modulator of dedifferentiation, a key mechanism for regeneration of complex structures.

ATF4 Knockout in Mice Greatly Slows Age-Related Loss of Strength and Endurance
https://www.fightaging.org/archives/2023/04/atf4-knockout-in-mice-greatly-slows-age-related-loss-of-strength-and-endurance/

In this study, researchers show that mice lacking a functional ATF4 gene show little to no loss of grip strength and treadmill performance into late life; it is quite an impressive effect size. Assessments of muscle biochemistry do show age-related declines, but to a lesser degree than the controls. How ATF4 knockout functions to produce this outcome is an interesting question. The researchers point out a range of possible downstream and upstream targets that have been implicated in the regulation of muscle growth, but it will clearly require further work to identify the important mechanisms involved.

Aging slowly erodes skeletal muscle strength and mass, eventually leading to profound functional deficits and muscle atrophy. The molecular mechanisms of skeletal muscle aging are not well understood. To better understand mechanisms of muscle aging, we investigated the potential role of ATF4, a transcription regulatory protein that can rapidly promote skeletal muscle atrophy in young animals deprived of adequate nutrition or activity.

To test the hypothesis that ATF4 may be involved in skeletal muscle aging, we studied fed and active muscle-specific ATF4 knockout mice (ATF4 mKO mice) at 6 months of age, when wild-type mice have achieved peak muscle mass and function, and at 22 months of age, when wild-type mice have begun to manifest age-related muscle atrophy and weakness. We found that 6-month-old ATF4 mKO mice develop normally and are phenotypically indistinguishable from 6-month-old littermate control mice. However, as ATF4 mKO mice become older, they exhibit significant protection from age-related declines in strength, muscle quality, exercise capacity, and muscle mass.

Furthermore, ATF4 mKO muscles are protected from some of the transcriptional changes characteristic of normal muscle aging (repression of certain anabolic mRNAs and induction of certain senescence-associated mRNAs), and ATF4 mKO muscles exhibit altered turnover of several proteins with important roles in skeletal muscle structure and metabolism. Collectively, these data suggest ATF4 as an essential mediator of skeletal muscle aging and provide new insight into a degenerative process that impairs the health and quality of life of many older adults.

An Interview with Stephanie Planque of Covalent Bioscience
https://www.fightaging.org/archives/2023/04/an-interview-with-stephanie-planque-of-covalent-bioscience/

Covalent Bioscience develops catalytic antibodies, a way to bind and neutralize target molecules in the body without consuming the antibody molecule itself. A given dose of catalytic antibody can thus remove many times more target molecules than is the case for standard monoclonal antibodies. It offers the potential for highly efficient removal of age-related amyloids present outside cells, perhaps the most interesting of the many possible use cases, such as those related to suppression of specific signal molecules. Like most biotech companies, the backstory behind the science emphasizes the point that progression of any given technology from academia to industry is slow indeed.

Covalent Bioscience was incorporated in 2010 by Dr Sudhir Paul and Dr Richard Massey based on catalytic antibody technology and several exciting potential products for unmet medical needs. The technology and potential products were developed in Dr. Sudhir Paul's group at the University of Texas (UT). Dr Richard Massey and Dr Sudhir Paul have worked together on the field of catalytic antibody (or catabody) when Dr Massey was in Igen in the 80s. I have worked with Dr. Paul since 1999 and am one of the co-founders of Covalent Bioscience. We, the founders of Covalent Bioscience, share the same conviction that our platform technology holds the potential to generate superior immunotherapeutic drugs and vaccines.

Today, Covalent Bioscience has grown to a preclinical stage company holding significant assets. Our broad technology platform can be applied to generate novel lead products for unmet needs across multiple areas of medicine. We have three promising lead products for diseases that proved very difficult to treat and prevent by conventional means. Two of them are catabodies for treating age-associated diseases such as Alzheimer's disease and transthyretin amyloidosis. The products are expected to remove toxic aggregates that cause diseases in a more efficient and safe manner than conventional antibodies.

In 2018, Dr Paul and I moved full time to Covalent Bioscience. Our lab is located at the skirt of the Houston Medical Center, biggest medical center in the world. In 2020, Covalent Bioscience received from The University of Texas the commercial rights to all inventions and research materials/tools Paul's team generated there. With our current funding, we are generating new catabodies and working in collaboration with a pharma company to advance one of our lead products closer to human trials.

More Details on Cyclarity's Approach to Clearing 7-Ketocholesterol
https://www.fightaging.org/archives/2023/04/more-details-on-cyclaritys-approach-to-clearing-7-ketocholesterol/

This recent article from the SENS Research Foundation discusses calcium chelation and, separately, the tailored cyclodextrin molecules developed by Cyclarity to sequester 7-ketocholesterol. This altered form of cholesterol is toxic to cells, and may provide a significant contribution to a range of age-related conditions, including atherosclerosis. Cyclarity will be conducting initial human trials in the near future. Since the best way to determine exactly how important 7-ketocholesterol is in the context of atherosclerosis in humans is to remove it, it will be interesting to see how this goes. It is vital to progress that more programs of this nature make it to human trials, rather than becoming bogged down in academic questions over ways to determine the likely degree of efficacy in advance of clinical development.

Cyclarity's UDP-003 is a small molecule LysoSENS therapy that directly removes damaged cholesterol products that turn macrophages into foam cells and thus drive atherosclerosis. Researchers set out to design a molecular precision tool that would remove 7-ketocholesterol (7KC) selectively while leaving normal physiological cholesterol untouched. Using a combination of experimentation with existing cyclodextrins, trial-and-error virtual experiments in existing molecular modeling software, and eventually a new VR molecular modeling and design system, Cyclarity constructed a novel cyclodextrin dimer in virtual space and tested it in silico against native and oxidized cholesterol before testing it in actual lab conditions - and then back again to the virtual system in an iterative optimization cycle.

This dimer is comprised of two different cyclodextrins, one of them "scoop-like" and the other a "gripper" complex, linked together in a configuration where the two can cooperate to create a binding cavity. It's a bit like a reusable coffee pod or a shaker cup for protein shakes, with a chamber to take in the desired material and then a sealable cap to hold the contents in place. This dual structure allows UDP-003 to first capture 7KC and then surround it, holding on to it with extremely high affinity. Trapped in the UDP-003 core, 7KC can't interact or react with anything else in the body, allowing UDP-003 to passively carry it out of the cell, through the circulation, and harmlessly out of the body via excretion.

In experimental systems, UDP-003 sucks very high amounts of 7KC from cultured cells and blood cells, as well as from surgically captured atherosclerotic plaque, with no corresponding effect on free unmodified cholesterol in blood. A useful safety test is to see if a cyclodextrin will extract cholesterol out of the membranes of red blood cells, causing them to lyse; on such tests, UDP-003 has extremely little hemolytic activity.

In 2021, the UK's Medicines and Healthcare products Regulatory Agency (MHRA - their equivalent of FDA) awarded Cyclarity an Innovation Passport under its Innovative Licensing and Access Pathway (ILAP), which is a new program designed to help shepherd truly innovative therapies more quickly through the regulatory process by giving awardees early and ongoing contact and feedback with the regulators. Thanks to this and a solid scientific foundation, UDP-003 trials are coming up fast in the UK. As of this writing (late winter of 2023), Cyclarity is finishing up its animal safety data and getting ready to produce enough UPD-003 at pharmaceutical grade to run their first human trial. While only a safety trial, it will be a critical first-in-human test of the new molecule.

Reviewing the Aging of the Gut Microbiome
https://www.fightaging.org/archives/2023/04/reviewing-the-aging-of-the-gut-microbiome/

Researchers here take a high level tour of what is known of age-related changes in the gut microbiome and how they influence health. Accumulating evidence shows a loss of beneficial populations that generate useful metabolites such as butyrate, accompanied by an increase in harmful populations that can provoke chronic inflammation. This is a likely a meaningful contribution to the onset and development age-related conditions, making it a priority to develop ways to reset the balance of populations in the gut microbiome. The best of the available approaches, given the evidence to date, is fecal microbiota transplantation from a young donor. This has been shown to rejuvenation the aging microbiome, improve health, and even extend life span in short-lived laboratory species.

The trillions of microorganisms found in and on the human body (the microbiota) offer tremendous potential in understanding aging. The microbiome (the aggregate genetic content of the microbiota) exceeds the human genome by multiple orders of magnitude. Microorganisms colonize numerous sites in and on the body, with the greatest extent of colonization occurring within the gastrointestinal (GI) tract. Extensive and rigorous prior research has emphasized the key role that the gut microbiota has in host health and disease, including contributions to diseases associated with aging such as cancer, Parkinson's disease, obesity, and type 2 diabetes. Yet, despite remarkable progress in understanding the cellular and molecular mechanisms through which the microbiome contributes to individual diseases linked to aging, the net effects of the microbiome for the aging process or the potential for manipulating the microbiome to promote healthy aging remain unclear.

The overall association between the human microbiome and age is strong enough that it is possible to predict biological age with striking precision with the microbiome. An initial proof-of-concept was demonstrated in early life, in which a "microbiota maturity index" established in healthy individuals was delayed in the context of malnutrition. More recently, machine learning tools have enabled the accurate prediction of age in adults from distal gut metagenomic data with a mean absolute error of 6 to 8 years. The composition of the microbiota found in other body habitats, including the skin and oral cavity, is also linked to age.

In animal studies, the microbiome can decrease life span in older animals. In C. elegans, GI accumulation of Escherichia coli contributes to age-related death. Removal of germ-free D. melanogaster from sterile conditions reduces life span in adults. More recently, the detrimental effects of the microbiome in aging animals has been studied using the African turquoise killifish. Middle-aged (9.5-week-old) killifish treated with antibiotics outlived untreated fish, suggesting that the microbiota impairs life span in older killifish. Remarkably, inoculation with the GI microbiota of 6-week-old killifish significantly increased the life span of middle-aged killifish groups.

These findings are also relevant to mammals. Work in two mouse models of progeria (a human premature aging syndrome) supports the potential for microbiome-based interventions to extend life span. The gut microbiota was altered in prematurely aging mice, including a significant decrease in Akkermansia muciniphila in a model of the most common human progeria syndrome. As in killifish, fecal microbiota transplantation (FMT) from wild-type mice significantly increased the life span of transgenic prematurely aging recipient mice. Even more excitingly, the Verrucomicrobium A. muciniphila, a common member of the human gut microbiota, was sufficient to extend life span in the mice. These results provide a major step towards identifying the cellular and molecular mechanisms responsible for microbiota-dependent changes in life span as well as an important step towards the potential translation of these results to humans.

A Mechanism for Fisetin to Reduce Stress-Induced Cellular Senescence
https://www.fightaging.org/archives/2023/04/a-mechanism-for-fisetin-to-reduce-stress-induced-cellular-senescence/

Senescent cells accumulate with age, largely due to cells reaching the Hayflick limit, but a range of cell stresses can also induce senescence. Senescent cells are rapidly cleared by the immune system in youth, but the balance between creation and destruction shifts with advancing age. The immune system becomes less capable, but it is also likely that the aged environment inflicts greater stress that leads to more cells becoming senescent.

Clearance of senescent cells via senolytic compounds that provoke these cells into self-destruction is presently a well funded and promising area of development. Fisetin is one such senolytic, interesting for being a cheap, safe, and widely used plant-derived supplement, but only animal data has so far been published on its ability to rapidly clear senescent cells. As noted in this paper, it may be that fisetin can to some degree also prevent cells from becoming senescent in response to stress, which might slow the accumulation of senescent cells over time. As is always the case, it is worth remembering that just because a mechanism is demonstrated to exist in cell cultures doesn't mean that it does provide a meaningfully large contribution to the balance of creation and destruction of senescent cells in living animals, however. That remains to be shown.

Reactive oxygen species (ROS) are a key risk factor of cellular senescence and age-related diseases, and protein kinase C (PKC) has been shown to activate NADPH oxidases (NOXs), which generate ROS. Although PKC activation induces oxidative stress, leading to the cellular dysfunction in various cell types, the correlation between PKC and senescence has not been reported in vascular smooth muscle cell (VSMC). Several studies have indicated cellular senescence is accompanied by phosphatase and tensin homolog (PTEN) loss and that an interaction exists between PTEN and PKC. Therefore, we aimed to determine whether PTEN and PKC are associated with VSMC senescence and to investigate the mechanism involved.

We found hydrogen peroxide (H2O2) decreased PTEN expression and increased PKCδ phosphorylation. Moreover, H2O2 upregulated the NOX1 subunits, p22phox and p47phox, and induced VSMC senescence via p53-p21 signaling pathway. We identified PKCδ activation contributed to VSMC senescence through activation of NOX1 and ROS production. However, fisetin inhibited cellular senescence induced by the PTEN-PKCδ-NOX1-ROS signaling pathway, and this anti-aging effect was attributed to reduced ROS production caused by suppressing NOX1 activation. These results suggest that the PTEN-PCKδ signaling pathway is directly related to senescence via NOX1 activation and that the downregulation of PKCδ by flavonoids such as fisetin provides a potential means of treating age-associated diseases.

There is Still Room to Improve Upon Epigenetic Clocks
https://www.fightaging.org/archives/2023/04/there-is-still-room-to-improve-upon-epigenetic-clocks/

Researchers here demonstrate that there is still room to improve the accuracy of epigenetic clocks based on patterns of DNA methylation. It could be argued that more effort should go towards generating a sufficient understanding of DNA methylation to allow the use of existing clocks to assess potential rejuvenation therapies, however. The long-term promise of epigenetic clocks is to provide a way to rapidly determine whether or not a given intervention is producing a meaningful reversal of aging, a replacement for time-consuming, expensive life span studies. Because researchers do not at present understand how underlying processes of aging are reflected in specific DNA methylation changes, it is impossible to take clock data at face value for any given intervention that targets only one aspect of aging. A clock may be insensitive to that mechanism of aging or it may give it too much weight. There is no way to know without undertaking life span studies to calibrate the clock against the intervention, defeating the point of the exercise.

"First generation" epigenetic ageing clocks, including those by Horvath and Hannum, were trained on chronological age (cAge), with near-perfect clocks expected to arise as sample sizes grow. However, cAge clocks hold limited capability for tracking and quantifying age-related health status, also termed biological age (bAge). To address this, "second generation" clocks have been trained on other age-related measures, including a phenotypic biomarker of morbidity (PhenoAge), rate of ageing (DunedinPACE), and time to all-cause mortality (GrimAge). Regressing an epigenetic clock predictor (whether trained on cAge or bAge) on chronological age within a cohort gives rise to an "age acceleration" residual with positive values corresponding to faster biological ageing.

Here, we sought to improve the prediction of both cAge and bAge. We first present large-scale epigenome-wide association studies (EWAS) of cAge (for both linear and quadratic CpG effects) and time to all-cause mortality as a proxy for bAge. A predictor of cAge is then generated using DNA methylation data from 11 cohorts, including samples from more than 18,000 participants of the Generation Scotland study. Through data linkage to death records in Generation Scotland, we develop a bAge predictor of time to all-cause mortality, which we compare against GrimAge, in four external cohorts. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival. These analyses highlight the potential for large DNA methylation resources to generate increasingly accurate predictors of (i) cAge, with potential forensic utility, and (ii) bAge, with potential implications for risk prediction and clinical trials.

Investigating Mechanisms By Which Some Gut Microbes May Shorten Fly Life Span
https://www.fightaging.org/archives/2023/04/investigating-mechanisms-by-which-some-gut-microbes-may-shorten-fly-life-span/

The lifespan of flies is especially sensitive to intestinal function, making them perhaps an interesting model in which to study mechanisms by which changes in the gut microbiome can affect health and longevity. It is clear that the gut microbiome changes with age, and different microbial populations can affect health in different ways. At the high level, it is thought that much of the harm done in later life is mediated by increased chronic inflammation, a reaction to harmful species or the metabolites that they produce. At the detail level, a lot of work remains to be accomplished when it comes to mapping the biochemistry underlying the way in which the presence of specific microbes can provoke a maladaptive response. In the work here, the issue appears a little more than just an immune response, extending to stem cell function and other determinants of metabolism.

Commensal microbes in animals have a profound impact on tissue homeostasis, stress resistance, and ageing. We previously showed in Drosophila melanogaster that Acetobacter persici is a member of the gut microbiota that promotes ageing and shortens fly lifespan. However, the molecular mechanism by which this specific bacterial species changes lifespan and physiology remains unclear. The difficulty in studying longevity using gnotobiotic flies is the high risk of contamination during ageing. To overcome this technical challenge, we used a bacteria-conditioned diet enriched with bacterial products and cell wall components. Here, we demonstrate that an A. persici-conditioned diet shortens lifespan and increases intestinal stem cell (ISC)/a> proliferation. Feeding adult flies a diet conditioned with A. persici, but not with Lactiplantibacillus plantarum, can decrease lifespan but increase resistance to paraquat or oral infection of Pseudomonas entomophila, indicating that the bacterium alters the trade-off between lifespan and host defence.

A transcriptomic analysis using fly intestine revealed that A. persici preferably induces antimicrobial peptides (AMPs), while L. plantarum upregulates amidase peptidoglycan recognition proteins (PGRPs). The specific induction of these genes by peptidoglycans from two bacterial species is due to the stimulation of the receptor PGRP-LC in the anterior midgut for AMPs or PGRP-LE from the posterior midgut for amidase PGRPs. Heat-killed A. persici also shortens lifespan and increases ISC proliferation via PGRP-LC, but it is not sufficient to alter the stress resistance. Our study emphasizes the significance of peptidoglycan specificity in determining the gut bacterial impact on healthspan. It also unveils the postbiotic effect of specific gut bacterial species, which turns flies into a "live fast, die young" lifestyle.

Theorizing that the APOEε4 Variant Increases Alzheimer's Risk Through Increased Microglial Inflammation
https://www.fightaging.org/archives/2023/04/theorizing-that-the-apoe%ce%b54-variant-increases-alzheimers-risk-through-increased-microglial-inflammation/

It is well established that the ε4 variant of APOE increases the risk of Alzheimer's disease, but there is no firm consensus as to why this is the case. Theories abound. Researchers here suggest that the mechanism of interest is increased neuroinflammation, as APOEε4 increases the tendency for the innate immune cells known as microglia to become activated and inflammatory in the aging brain. There has been an increased focus on chronic inflammation in Alzheimer's disease in recent years, particularly given the continued failure to produce meaningful patient benefits via clearance of amyloid-β, with some researchers going so far as to suggest it is the primary driving mechanism in the onset and progression of the condition.

Alzheimer's disease (AD) is a multifactorial disorder neuropathologically characterized by amyloid-β (Aβ) plaques and tau neurofibrillary tangles. Among the multiple pathogenic processes involved in AD etiology, neuroinflammation, commonly associated with microglial reactivity, has been increasingly recognized. Microglial activation plays a key role in the accumulation of AD hallmark proteinopathies, rather than being merely an epiphenomenon of their deposition. Specifically, recent observations from animal and human studies suggest that microglial activation precedes and may drive tau spread over the neocortex, from the medial temporal to association and primary sensory structures. Such microglial activation is synaptotoxic, affects brain connectivity, and predicts clinical decline. Aβ pathology can trigger microglial activation in AD, but Aβ plaques and activated microglia only partially overlap topographically in the human brain, and microglial activation may occur before demonstrable Aβ deposition.

Using complementary positron emission tomography (PET) radiotracers for the topographical quantification of microglial activation, Aβ, and tau accumulation across the brain, we investigated the association between the APOEε4 genotype, microglial activation, Aβ, and tau in a cohort of individuals across the aging and AD continuum. We hypothesized that APOEε4 is associated with microglial activation independently of AD hallmark proteinopathies. We then tested whether microglial activation mediates the effects of APOEε4 on tau accumulation, neurodegeneration, and clinical impairment.

We found that APOEε4 carriers presented an increased microglial activation relative to noncarriers in regions within the medial temporal cortex accounting for Aβ and tau deposition. Furthermore, microglial activation mediated the Aβ-independent effects of APOEε4 on tau accumulation, which was further associated with neurodegeneration and clinical impairment. The physiological distribution of APOE mRNA expression predicted the patterns of APOEε4-related microglial activation in our population, suggesting that APOE gene expression may regulate the local vulnerability to neuroinflammation. Our results support that the APOEε4 genotype exerts Aβ-independent effects on AD pathogenesis by activating microglia in brain regions associated with early tau deposition.

Detection of Small Amounts of Misfolded α-Synuclein Identifies Early Parkinson's Disease
https://www.fightaging.org/archives/2023/04/detection-of-small-amounts-of-misfolded-%ce%b1-synuclein-identifies-early-parkinsons-disease/

Parkinson's disease is characterized by misfolding and aggregation of α-synuclein, a pathology that spreads from where it initially starts, frequently in the intestinal nervous system, spreading between nerve cells. Researchers here report on a technique to identify the presence of small amounts of misfolded α-synuclein, demonstrating that it allows for early detection of the condition. Near every disease is easier to treat or at least slow down in its earlier stages, and early detection may well be an essential part of efforts to prevent the development of common age-related neurodegenerative conditions, such as Parkinson's disease.

Parkinson's disease is characterized by deposits of a protein known as alpha-synuclein (aSyn) in the nervous system. This protein can become corrupted and start to change shape in a process called misfolding. These misfolded proteins will start to clump together and poison the surrounding healthy nerve cells that are responsible for brain function, particularly for motor skills.

Protein Misfolding Cyclic Amplification (PMCA) - also termed seed amplification assay (SAA) technology - is under development at Amprion Inc., a biotech company focusing on the commercial utilization of SAA for early diagnosis of Parkinson's, Alzheimer's, and other neurodegenerative diseases. Researchers at Amprion studied 1,123 participants who were enrolled at 33 facilities globally between July 2010 and July 2019, representing the largest analysis so far of aSyn-SAA for the biochemical diagnosis of Parkinson's disease. Of these, 545 had Parkinson's disease, 163 were healthy people with no evidence of Parkinson's, 54 had evidence of the disease on brain scans, 51 were in the early stages of the disease, and 310 had genetic mutations that are known to cause Parkinson's but hadn't yet done so.

Using aSyn-SAA as a test in early Parkinson's detected the disease 87% of the time. Among participants who did not have Parkinson's, the test showed the absence of the disease 96% of the time. Interestingly, 30% of participants with the LRRK2 gene mutation - which causes a disease that looks like Parkinson's - do not have misfolded aSyn, but instead appear to have a different biological disease. In a group of patients who had lost their sense of smell, which is another sign of Parkinson's, the disease was detected 98.6% of the time. Significantly, 86% of prodromal, or pre-symptomatic, cases of Parkinson's disease were positive for aSyn-SAA years before clinical symptoms of the disease appeared, opening the door for an early diagnosis before substantial damage in the brain.

Currently, misfolded aSyn can only be detected by taking a spinal tap, which is an invasive and painful procedure. However, researchers are optimizing the aSyn-SAA technology to be utilized to detect the protein in blood, a skin biopsy, or a swab of the nose.

Targeting a Mechanism of Hyperphosphorylation in Alzheimer's Disease Pathology
https://www.fightaging.org/archives/2023/04/targeting-a-mechanism-of-hyperphosphorylation-in-alzheimers-disease-pathology/

Hyperphosphorylation of tau protein produces aggregation and neurofibrillary tangles in later stage Alzheimer's disease. Researchers here use a peptide to inhibit one of the mechanisms by which increased phosphorylation occurs in neurons in older individuals. The approach produces promising results in a mouse model of Alzheimer's disease, but - as is usually the case - one has to wonder as to whether or not this interaction of model and treatment in mice is relevant to the human condition. Old mice do not naturally develop any pathology resembling Alzheimer's disease, so all of the models are by their nature very artificial, and embody assumptions about which forms of pathology in the aging brain are most important. The outcome of this state of affairs is that many approaches to have worked well in mouse models went on to fail to achieve meaningful results in human patients, at great cost in time and funding.

Researchers have treated mice with a peptide that blocks the hyperactive version of an enzyme called CDK5, finding dramatic reductions in neurodegeneration and DNA damage in the brain. These mice also showed improvements in their ability to perform tasks such as learning to navigate a water maze. The CDK5 gene encodes a type of enzyme known as a cyclin-dependent kinase. Most of the other cyclin-dependent kinases are involved in controlling cell division, but CDK5 is not. Instead, it plays important roles in the development of the central nervous system, and also helps to regulate synaptic function.

CDK5 is activated by a smaller protein that it interacts with, known as P35. When P35 binds to CDK5, the enzyme's structure changes, allowing it to phosphorylate - add a phosphate molecule to - its targets. However, in Alzheimer's and other neurodegenerative diseases, P35 is cleaved into a smaller protein called P25, which can also bind to CDK5 but has a longer half-life than P35. When bound to P25, CDK5 becomes more active in cells. P25 also allows CDK5 to phosphorylate molecules other than its usual targets, including the Tau protein. Hyperphosphorylated Tau proteins form the neurofibrillary tangles that are one of the characteristic features of Alzheimer's disease.

Researchers have shown that transgenic mice engineered to express P25 develop severe neurodegeneration. In humans, P25 has been linked to several diseases, including not only Alzheimer's but also Parkinson's disease and frontotemporal dementia. Pharmaceutical companies have tried to target P25 with small-molecule drugs, but these drugs tend to cause side effects because they also interfere with other cyclin-dependent kinases, so none of them have been tested in patients. This team decided to take a different approach to targeting P25, by using a peptide instead of a small molecule. They designed their peptide with a sequence identical to that of a segment of CDK5 known as the T loop, which is a structure critical to the binding of CDK5 to P25. In tests in neurons grown in a lab dish, the researchers found that treatment with the peptide led to a moderate reduction in CDK5 activity. Those tests also showed that the peptide does not inhibit the normal CDK5-P35 complex, nor does it affect other cyclin-dependent kinases.

When the researchers tested the peptide in a mouse model of Alzheimer's disease that has hyperactive CDK5, they saw a myriad of beneficial effects, including reductions in DNA damage, neural inflammation, and neuron loss. These effects were much more pronounced in the mouse studies than in tests in cultured cells.