Fight Aging!

Drainage of cerebrospinal fluid from the brain into the body is reduced with age. The known pathways become impaired. Firstly, drainage holes in the cribriform plate behind the nose ossify and close up. Secondly the glymphatic system that carries away fluid from the brain loses lymphatic vessel density and vessel function. The outcome of reduced fluid flow leaving the brain is that metabolic wastes build up, causing inappropriate changes in cell behavior, including an increase in inflammatory signaling produced by the innate immune cells called microglia. Neurodegenerative conditions are characterized by chronic inflammation in the brain, disruptive to tissue structure and function.

As a companion to yesterday's paper on VEGF-C gene therapy to restore glymphatic drainage of cerebrospinal fluid in aged mice, today I'll point out a study that assesses glymphatic fluid flow in aged humans. The researchers correlate reduced flow with both loss of cognitive function and structural changes in the brain characteristic of aging. A relatively recently developed imaging technique known as Diffusion Tensor Image Analysis Along the Perivascular Space (DTI-ALPS) was employed. This uses MRI to obtain an assessment of how much water is flowing out of the brain via lymphatic vessels and perivascular spaces in a region where a number of vessels are conveniently lined up in parallel. The technique doesn't actually measure flow, but rather measures the direction and extent of local diffusion of water molecules in many small volumes. If there is flow, one would expect a very unbalanced "diffusion", with a lot of movement in the direction of the flow. So far the technique appears to be producing good results.

Glymphatic function decline as a mediator of core memory-related brain structures atrophy in aging

This study aimed to elucidate the role of the glymphatic system - a crucial pathway for clearing waste in the brain - in the aging process and its contribution to cognitive decline. We specifically focused on the diffusion tensor imaging analysis along the perivascular space (ALPS) index as a noninvasive biomarker of glymphatic function. Data were drawn from the Alzheimers Disease Neuroimaging Initiative (ADNI) database and a separate validation cohort to analyze the ALPS index in cognitively normal older adults. The relationships among the ALPS index, brain morphometry, and memory performance were examined.

As a biomarker of glymphatic function, the ALPS index appeared to decline with age in both cohorts. According to the brain morphology analysis, the ALPS index was positively correlated with the thickness of the left entorhinal cortex (r = 0.258), and it played a mediating role between aging and left entorhinal cortex thinning. The independent cohort further validated the correlation between the ALPS index and the left entorhinal cortex thickness (r = 0.414). Additionally, in both the primary and validation cohorts, the ALPS index played a significant mediating role in the relationship between age and durable or delayed memory decline.

In conclusion, this study highlights the ALPS index as a promising biomarker for glymphatic function and links it to atrophy of the core memory brain regions during aging. Furthermore, these results suggest that targeting glymphatic dysfunction could represent a novel therapeutic approach to mitigate age-related memory decline.

To my eyes, what one should take away from the study noted here is that adopting any form of healthier diet is beneficial over the long term. Another important item to consider is just how few people make it to age 70 without developing a major chronic medical condition. Thirdly, that the reasonable best case outcome for adjusting diet is to move the odds of avoiding chronic disease at age 70 from less than 10% to something more like 20%. Stepping back to consider the bigger picture, these are not good odds whether or not one's diet is healthy. These numbers are exactly why we need to spend less time focused on ever more detailed diet optimization and more time focused on assisting the development of potential rejuvenation therapies that address the underlying causes of aging.

As the global population ages, it is critical to identify diets that, beyond preventing noncommunicable diseases, optimally promote healthy aging. Here, using longitudinal questionnaire data from the Nurses' Health Study (1986-2016) and the Health Professionals Follow-Up Study (1986-2016), we examined the association of long-term adherence to eight dietary patterns and ultraprocessed food consumption with healthy aging, as assessed according to measures of cognitive, physical and mental health, as well as living to 70 years of age free of chronic diseases.

After up to 30 years of follow-up, 9,771 (9.3%) of 105,015 participants (66% women, mean age = 53 ± 8 years) achieved healthy aging. For each dietary pattern, higher adherence was associated with greater odds of healthy aging and its domains. The odds ratios for the highest quintile versus the lowest ranged from 1.45 (healthful plant-based diet) to 1.86 (Alternative Healthy Eating Index). When the age threshold for healthy aging was shifted to 75 years, the Alternative Healthy Eating Index diet showed the strongest association with healthy aging, with an odds ratio of 2.24.

Higher intakes of fruits, vegetables, whole grains, unsaturated fats, nuts, legumes, and low-fat dairy products were linked to greater odds of healthy aging, whereas higher intakes of trans fats, sodium, sugary beverages, and red or processed meats (or both) were inversely associated. Our findings suggest that dietary patterns rich in plant-based foods, with moderate inclusion of healthy animal-based foods, may enhance overall healthy aging, guiding future dietary guidelines.

Link: https://doi.org/10.1038/s41591-025-03570-5

The epidemiological evidence for exposure to microplastic and nanoplastic particles to be harmful and contribute to age-related disease is sparse at this time, with nowhere near as sizable a weight of compelling evidence as exists for the analogous topic of particulate air pollution. This may be a matter of time, however; give it another two decades and the fields might look quite similar. Or they might not! It is too early to say. There is a lot of hype and excitement around the topic, so it seems likely that the necessary large human studies to establish and quantify any meaningful contribution to age-related disease will be conducted in the years to come. Meanwhile, the first few smaller studies suggesting that such a contribution exists are attracting a fair amount of attention.

Microplastics - defined as fragments of plastic between 1 nanometer and 5 millimeters across - are released as larger pieces of plastic break down. They come from many different sources, such as food and beverage packaging, consumer products and building materials. People can be exposed to microplastics in the water they drink, the food they eat and the air they breathe.

The study examines associations between the concentration of microplastics in bodies of water and the prevalence of various health conditions in communities along the East, West and Gulf Coasts, as well as some lakeshores, in the United States between 2015-2019. While inland areas also contain microplastics pollution, researchers focused on lakes and coastlines because microplastics concentrations are better documented in these areas. They used a dataset covering 555 census tracts from the National Centers for Environmental Information that classified microplastics concentration in seafloor sediments as low (zero to 200 particles per square meter) to very high (over 40,000 particles per square meter).

The researchers assessed rates of high blood pressure, diabetes, stroke, and cancer in the same census tracts in 2019 using data from the U.S. Centers for Disease Control and Prevention. They also used a machine learning model to predict the prevalence of these conditions based on patterns in the data and to compare the associations observed with microplastics concentration to linkages with 154 other social and environmental factors such as median household income, employment rate, and particulate matter air pollution in the same areas.

The results revealed that microplastics concentration was positively correlated with high blood pressure, diabetes, and stroke, while cancer was not consistently linked with microplastics pollution. The results also suggested a dose relationship, in which higher concentrations of microplastic pollution are associated with a higher prevalence of disease. However, researchers said that evidence of an association does not necessarily mean that microplastics are causing these health problems. More studies are required to determine whether there is a causal relationship or if this pollution is occurring alongside another factor that leads to health issues, they said.

Link: https://www.acc.org/About-ACC/Press-Releases/2025/03/25/10/19/New-Evidence-Links-Microplastics-with-Chronic-Disease

Cerebrospinal fluid is produced constantly, circulates through the brain, and drains into the body. This flow carries metabolic waste from the brain, and researchers are coming to view the age-related impairment of cerebrospinal fluid drainage as an important contribution to loss of cognitive function and the development of neurodegenerative conditions in later life. Several pathways for drainage have been identified, each of which is known to lose function with advancing age.

Firstly, cerebrospinal fluid drains through holes in the cribriform plate behind the nose. This pathway ossifies and closes up with age or injury. Studies conducted by Leucadia Therapeutics have added a weight of evidence to the importance of impairment of this fluid drainage path to the development of Alzheimer's disease, which begins in a part of the brain specifically served by cribriform plate drainage. Secondly, the glymphatic system drains cerebrospinal fluid into lymphatic vessels. The meninges, the layered membrane surrounding the brain and spinal cord, is lined with lymphatic vessels and fluid passes into them from the brain. This system of vessels suffers atrophy and dysfunction with age, just like the rest of the lymphatic system. Analogies can be made to the decline of the vasculature for blood flow throughout the body; the density of small capillary vessels declines with age as the processes of maintenance and creation of new vessels become dysfunctional.

In today's open access paper, researchers show that this analogy holds for the approach of provoking increased vessel creation as a way to address the age-related loss of small vessels. It has been demonstrated that upregulation of VEGF via gene therapy improves angiogenesis in older mice. It also improves late-life health, likely in part by removing some of the loss of capillary density. For lymphatic vessels, the analogous signaling protein to promote generation of new vessels is VEGF-C. Here, researchers demonstrate that delivering VEGF-C as a gene therapy to the the meninges can restore cerebrospinal fluid drainage in old mice, and also improve measures of brain function. They show that inflammatory signaling in the brain is reduced once drainage is improved, lending support to the view that the whole problem of reduced drainage is that an increase in metabolic waste in the brain provokes a maladaptive inflammatory response from microglia, innate immune cells of the central nervous system.

Meningeal lymphatics-microglia axis regulates synaptic physiology

Meningeal lymphatic vessels, located in the dura mater of the meninges, drain cerebrospinal fluid (CSF) together with its content of central nervous system (CNS)-derived waste primarily into deep cervical lymph nodes. Since the discovery of meningeal lymphatic vessels, accumulating evidence from mouse models and humans has linked their dysfunction to various neurodegenerative conditions. Ablation of meningeal lymphatics by chemical, genetic, or surgical means exacerbates behavioral outcomes in mouse models of Alzheimer's disease, traumatic brain injury, and chronic stress. Conversely, enhancing the function of meningeal lymphatics ameliorates cognitive deficits in mouse models of Alzheimer's disease, aging, and craniosynostosis.

Here, we show that prolonged impairment of meningeal lymphatics alters the balance of cortical excitatory and inhibitory synaptic inputs, accompanied by deficits in memory tasks. These synaptic and behavioral alterations induced by lymphatic dysfunction are mediated by microglia, leading to increased expression of the interleukin 6 gene (Il6). IL-6 drives inhibitory synapse phenotypes. Restoring meningeal lymphatic function in aged mice via intracisternal injection of adeno-associated virus encoding VEGF-C reverses age-associated synaptic and behavioral alterations. Our findings suggest that dysfunctional meningeal lymphatics adversely impact cortical circuitry through an IL-6-dependent mechanism and identify a potential target for treating aging-associated cognitive decline.

There are now scores of published aging clocks built on various omics databases containing data for people at different ages. Many measurable aspects of metabolism and cell biochemistry change with age in sufficiently similar ways across the population to build clocks that reflect biological age, the burden of damage and dysfunction that causes mortality. Prior to the development of modern machine learning techniques, assembling such a clock would have been prohibitively difficult and expensive, but machine learning makes it straightforward enough for any small research group to create a new clock in a relatively short period of time. Thus there are now a great many aging clocks.

At this point the focus should shift to validation of clocks, as the whole point of having a measure of biological age is to be able to use it to rapidly assess the quality of potential rejuvenation therapies. At present no clock can be treated as entirely trustworthy; they do have quirks, and it remains unclear as to how underlying processes of damage, such as accumulation of senescent cells, produce changes in specific clock parameters. Without knowing these relationships, a clock might overestimate or underestimate the effects of a specific therapy on aging.

Metabolites that mark aging are not fully known. We analyze 408 plasma metabolites in Long Life Family Study participants to characterize markers of age, aging, extreme longevity, and mortality. We identify 308 metabolites associated with age, 258 metabolites that change over time, 230 metabolites associated with extreme longevity, and 152 metabolites associated with mortality risk. We replicate many associations in independent studies.

By summarizing the results into 19 signatures, we differentiate between metabolites that may mark aging-associated compensatory mechanisms from metabolites that mark cumulative damage of aging and from metabolites that characterize extreme longevity. We generate and validate a metabolomic clock that predicts biological age. Network analysis of the age-associated metabolites reveals a critical role of essential fatty acids to connect lipids with other metabolic processes. These results characterize many metabolites involved in aging and point to nutrition as a source of intervention for healthy aging therapeutics.

Link: https://doi.org/10.1016/j.celrep.2024.114913

Many dysfunctions and conditions of aging correlate with one another. For closer correlations, the question is whether this relationship exists because (a) one condition contributes meaningfully to the progression of the other, or (b) both conditions are similar in terms of which forms of underlying age-related cell and tissue damage contribute to their onset and progression. Or both! Here, researchers link the severity of sarcopenia, the age-related loss of muscle mass and strength, with arterial stiffness and hypertension. They review the existing hypotheses for causation in this relationship, noting that mechanisms exist to explain either direction of causation.

This cross-sectional study aimed to determine whether sarcopenia is related to arterial stiffness or hypertension in older adults without underweight and obesity. A total of 2,237 male and female adults in the Korea National Health and Nutritional Examination Survey who were ≥60 years and did not have underweight and obesity (body mass index of 18.5 to 25.0 kg/m2) were involved. Arterial stiffness and systolic and diastolic blood pressure showed an increasing trend from normal to moderate-to-severe sarcopenia. Subjects with moderate or severe sarcopenia were 3.545 or 8.903 times more likely to be in the highest tertile of arterial stiffness, and those with moderate or severe sarcopenia were 2.106 or 11.725 times more likely to be hypertensive.

While the exact mechanisms are not fully understood, several potential explanations for the relationship between sarcopenia, arterial stiffness or hypertension have been proposed. Reduced muscle mass and intramuscular fat infiltration cause a decrease in insulin-responsive target tissue, resulting in insulin resistance; consequently, arterial stiffness increases, which indicates the onset of hypertension. The results of the present study supported this potential mechanism in that insulin resistance, evaluated using the triglyceride-glucose index, showed a significant increasing trend from normal to moderate-to-severe sarcopenia. Additionally, chronic inflammation may be a potential explanation for the relationships of sarcopenia with arterial stiffness and hypertension. This potential mechanism was also supported by the finding in the present study that white blood cell counts showed a significant increasing trend from normal to moderate-to-severe sarcopenia.

Furthermore, individuals with sarcopenia commonly exhibit functional impairment or physical disability, which induces a reduction in muscle contraction-derived anti-inflammatory markers called myokines. Since decreased myokine levels are an independent predictor of increased risk of sarcopenia and arterial issues, myokine deficiency in sarcopenia is more likely to increase the risk of arterial stiffness or hypertension. Unfortunately, the present study does not provide objective data on myokine deficiency in sarcopenia patients. However, given that sarcopenia is a common cause of functional impairment or physical disability, decreased myokine secretion in sarcopenia patients is reasonable.

Finally, increased arterial stiffness may induce pulse pressure amplification in arteries. It may stimulate hypertrophy, remodeling or rarefaction in the microcirculation, which makes blood vessels unresponsive to the demand for changing blood flow, thereby leading to increased oxidative stress in muscles. Oxidative stress damages muscle components, such as reducing the number and function of satellite cells, and may induce muscle mass reduction. Depending on all of these factors, sarcopenia may be a trigger of arterial stiffness or hypertension, and arterial stiffness or hypertension may worsen sarcopenia.

Link: https://doi.org/10.3389/fpubh.2024.1469196

The history of attempts to treat Alzheimer's disease is littered with costly failures. One can blame the complexity of both the brain and the condition, which resists attempts to pick apart its contributing mechanisms. One can blame the fact that Alzheimer's is a condition that only naturally occurs in humans (and perhaps dolphins and chimpanzees, with limited evidence in both cases). Access to the biochemistry of the living brain in humans in the ways needed for Alzheimer's research is essentially impossible for ethical and practical reasons. Equally, any practical animal model of Alzheimer's disease, such as the many mouse models, is artificial and embodies certain assumptions about which pathology and processes are most important. Treatments that address the artificially created pathology in the model tend to be successful in that model. Then they fail in humans, after great expense, demonstrating that some of the assumptions were incorrect.

Today's open access review paper is a concise tour of the major categories of drug development. It does omit a range of therapies targeting pathological neurofibrillary tangles made of hyperphosphorylated tau protein, a feature of late stage Alzheimer's disease, and a number of more recent approaches such as clearance of senescent cells as a way to reduce inflammation and tissue dysfunction. Overall it is a cautionary tale for anyone who might be feeling enthused about any of these other approaches to the condition. At some point, the right mechanism will be targeted, but which one is it? The classic problem for every age-related condition is that there is no shortage of contributing mechanisms to consider, but without having already developed a therapy that can address one mechanism in isolation, it is next to impossible to determine whether that one mechanism is important and a good target.

Therapeutic agents for Alzheimer's disease: a critical appraisal

Alzheimer's disease (AD), the most common cause of dementia, is a progressive neurodegenerative disorder, characterized by the degeneration of cholinergic neurons in the nucleus basalis, and the presence of extracellular plaques of beta amyloid (Aβ) and intracellular neurofibrillary tangles composed of phosphorylated tau. AD presents with an impairment in early episodic memory, followed by a gradual and progressive deterioration in cognition and behavior.

The characteristic features of the familial form (FAD) were originally described by Alois Alzheimer in 1906. In FAD, Aβ-containing plaques appear at least 20 years before any signs of memory impairment. While prevention of Aβ formation could provide a treatment option for FAD if started early enough, it represents only about 1% of subjects with AD. The rest have the sporadic form of AD (SAD), with an age of onset of more than 65 years. Their brains also have Aβ-containing plaques, but so do those of healthy, older people with no overt signs of dementia. Since no correlation was found between the number of Aβ plaques and the degree of cognitive impairment in individuals with SAD, the original hypothesis was changed and soluble oligomers of Aβ proposed as the cause of neurodegeneration.

During the last decade, the pharmaceutical industry has concentrated its efforts to affect the processes leading to neurodegeneration by developing drugs to decrease Aβ. Mutations in genes and precursors of Aβ are found in the familial form of the disease. This led to the evaluation of seven monoclonal antibodies against Aβ in subjects with AD, two of which were approved for use by the FDA. They caused only a small improvement in cognitive function, probably because they were given to those with much more prevalent sporadic forms of dementia. They also have potentially serious adverse effects.

γ-secretase is a multi-subunit protease that was identified as responsible for the generation of Aβ, and thus considered a prime therapeutic target in AD. This led to the development of γ-secretase inhibitors like semagacestat to inhibit the formation of Aβ. However, a phase 3 trial in patients with mild to moderate AD was prematurely stopped because the drug actually worsened several measures of cognitive function. Like other γ-secretase inhibitors, avagacestat and tarenflurbil, semagacestat caused serious adverse effects, including cancer, skin related disorders, hypersensitivity reactions, increase in infections, and renal failure. β-secretase inhibitors also prevent formation of Aβ from amyloid precursor protein and their adverse effects are less serious than those of γ-secretase inhibitors. However, verubecestat, atabecestat, and lanabecestat all worsened cognitive function in subjects with mild-moderate AD.

Oxidative stress and elevated pro-inflammatory cytokines are present in all subjects with AD and are well correlated with the degree of memory impairment. Drugs that affect these processes include TNFα blocking antibodies and MAPK p38 inhibitors that reduce cognitive impairment when given for other inflammatory conditions. However, their adverse effects and inability to penetrate the brain preclude their use for dementia. Rosiglitazone is used to treat diabetes, a risk factor for AD, but failed in a clinical trial because it was given to subjects that already had dementia. Ladostigil reduces oxidative stress and suppresses the release of pro-inflammatory cytokines from activated microglia without blocking their effects. Chronic oral administration to aging rats prevented the decline in memory and suppressed overexpression of genes adversely affecting synaptic function in relevant brain regions. In a phase 2 trial, ladostigil reduced the decline in short-term memory and in whole brain and hippocampal volumes in human subjects with mild cognitive impairment and had no more adverse effects than placebo.

The innate immune cells known as macrophages can be found in tissues throughout the body, where they perform many functions. Macrophages do not just find and destroy pathogens and potentially problematic cells, they also help to coordinate regeneration from injury. They can take on pro-inflammatory or anti-inflammatory states depending on circumstances. Researchers are interested in finding ways to reduce inflammation and promote greater regeneration by manipulating macrophage state and activities, and here the focus is on macrophages resident in the heart, an organ that exhibits relatively little regenerative capacity following injury.

Macrophages are essential factors of the body's innate immune system and mononuclear phagocyte system and are widely present in the structure of the tissues, including the heart. Cardiac macrophages play an integral physiological role to regulate the physiological and pathological processes of the cardiovascular system. Resident macrophages are heterogeneous and plastic, and multiple subsets with different phenotypes and functions are present in the same tissue and are involved in different pathophysiological processes. There is increasing evidence suggesting that cardiac-resident macrophage populations play a critical role in regulating heart development, electrical conduction, and ventricular remodelling processes.

The mechanisms used by cardiac macrophages to influence cardiovascular disease (CVD) vary and include both direct and indirect interactions with other cardiac cells. In particular, the identification of specific targets for cardiac resident macrophages to regulate CVD would be crucial. Due to the development of various exogenous (using delivery of toxic substances, blocking antibodies and small interfering RNAs) and genetic methods (transgenic methods) to broadly and specifically target these macrophage populations, this has provided us with the opportunity to understand the function of various cardiac and pericardial macrophages. Relatively few studies have addressed therapies targeting cardiac resident macrophages in patients with CVD although mechanistic knowledge about cardiac resident macrophages and their contribution to cardiovascular risk have accumulated in recent years.

Link: https://doi.org/10.1136/heartjnl-2024-324333

Advanced glycation endproducts (AGEs) are an undesirable form of metabolic waste. The formation of long-lived AGEs that cross-link molecules in the extracellular matrix can change the physical properties of tissue, such as by contributing to the stiffening of blood vessel walls that occurs with age. Further, most varieties of AGE, while being only short-lived, can interact with cell receptors to provoke a maladaptive inflammatory response, thereby contributing to the chronic inflammation of aging. Inflammation, in turn, alters cell behavior for the worse throughout the body. Here, researchers provide an overview of how AGEs contribute to the age-related loss of muscle mass that leads to sarcopenia.

By binding with receptor for advanced glycation end products (RAGEs), AGEs can activate a series of intracellular signalling pathways in skeletal muscle cells related to the elevated levels of inflammation and oxidative stress, as well as impaired insulin/insulin-like growth factor-1 (IGF-1) signalling and mitochondrial biogenesis, which lead to reduced protein synthesis, increased protein degradation, intracellular lipid accumulation, changes in muscle fibre type composition and muscle energy metabolism, and a higher rate of apoptosis, finally resulting in muscle atrophy and impaired regeneration abilities.

Through directly targeted glycosylation, AGEs can damage the biological properties and functions of proteins which include the functional and structural proteins of skeletal muscle as well as collagens in the extracellular matrix, resulting in muscle dysfunction such as impaired force production and increased stiffness. Furthermore, AGEs can also indirectly affect skeletal muscle by contributing to neuromuscular junction lesion and vascular disorders.

Link: https://doi.org/10.1302/2046-3758.143.BJR-2024-0252.R1

Entropy is one of those slippery concepts wherein the same word has been adopted by different scientific disciplines to mean subtly different things. I'd recommend a recent article that attempts to explain for the layperson how these this different meanings arose, and that they overlap at the concept of measuring our ignorance of the state of a system, our inability to predict the state of that system. Here we'll talk about entropy as a measure of the randomness of a distribution; the more random the distribution, the less our ability to predict its specifics. The distribution of interest for today is the methylation state (methylated or not methylated) at one or more CpG sites on the genome, across many genome copies in many cells.

DNA structure determines whether or not a given gene sequence is exposed to transcription machinery and RNA is produced. One of the mechanisms determining the shape of DNA is whether or not methyl groups are added at specific locations called CpG sites, named because a a cytosine nucleotide (C) is followed by a guanine nucleotide (G) with the two linked by a phosphate group (p). This DNA methylation is the basis for epigenetic clocks that assess chronological and biological age, because the methylation status of some CpG sites is characteristic of the damage and dysfunction of aging. While whether or not a CpG site is methylated is a binary outcome, this data is measured across the many, many cells and genomes in a given blood or tissue sample. Current epigenetic clocks take the average of all of those 1s and 0s as the input of that specific CpG site to the clock algorithm.

In today's open access paper, researchers start instead by considering the entropy of the distribution of methylation status at a CpG site across the many measured genomes. For this purpose, entropy is a measure of how noisy or random the data is. The researchers then show that one can construct an epigenetic clock from the entropy values per CpG site that performs as well as clocks built using average values of methylation state. This suggests that aging is not just resulting in a move of some CpG sites towards one status, but also an increase in noise in DNA methylation, a move in both directions, an increase in randomness. Age-related noise in gene transcription is already a topic for discussion in the field, so why not age-related epigenetic noise as well?

DNA methylation entropy is a biomarker for aging

To measure age associated changes in DNA methylation, we collected buccal swabs from 100 individuals ranging from 7.2 to 84 years old. The DNA methylation profiles were generated using targeted bisulfite sequencing. Our target panel contained approximately 3000 regions that were selected to cover age associated CpG sites that were identified in multiple epigenetic clocks. Each probe is 120 base pairs, and therefore captures a region of DNA that is slightly larger than the probe length. We obtained an average coverage of 293 reads per sample across these regions.

We first calculated the mean methylation of each CpG site in each of the 3000 loci across the 100 samples, and then averaged these levels over a region. We also computed the Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM). This approach computes the read level methylation of a region after reads are dichotomized into methylated or unmethylated based on the presence of one or more methylcytosines. We also computed the methylation entropy for each locus using four CpG sites within each region, using the Shannon entropy formula. With four CpG sites, there are 16 possible methylation states, and we computed the probability of each state as well as the entropy of the four CpG sites.

We next generated scatter plots that compared the values of the three metrics across loci. Age-related changes in mean methylation and CHALM were strongly correlated. By contrast, the scatter plots of entropy versus mean methylation or CHALM resulted in more complex patterns with both positive and negative trends. This demonstrates that methylation entropy is measuring different properties of a locus compared to mean methylation and CHALM, and that loci can become both more or less disordered with age, independently of whether the methylation is increasing or decreasing with age.

We next asked whether we could compare the use of these three metrics to construct epigenetic clocks that predict the age of each individual. Selecting only four CpG sites per region to calculate entropy was sufficient to achieve chronological age estimates that were correlated with the actual age. The mean average error was 5.199 years, which was lower than the other mean-based methods that incorporated many more CpG sites. This suggests that the entropy of a locus is potentially a more useful biomarker of aging than the methylation level of individual sites. Though the 3000 loci analyzed may or may not be representative of the whole genome, this suggests that the entropy of an organism's methylation profile is informative of its epigenetic age.

Non-coding RNA sequences in the genome undergo transcription to produce an RNA molecule, but that RNA is not translated into a protein. Nonetheless, non-coding RNAs collectively form just as complex an interacting environment as proteins, important to the function of the cell. Non-coding RNAs remain poorly explored, as much of the work on cell biology to date has focused on proteins. It is unclear if the present catalog of non-coding RNAs is complete, and many of the known entries have unknown functions. Here, the argument is made for non-coding RNAs to collectively be an important determinant of species life span, based on the differences observed between short-lived and long-lived species.

Lifespan is a complex process that interacts with multifactors, yet it is fundamentally an evolutionary process in which genetic factors evolve to cope with lifespan evolution. Thus, it is essential to uncover the genetic factors that contribute to lifespan variations among different species. Current studies have focused on protein-coding genes in the search for longevity determinants, but the results from these studies have not provided sufficient evidence to explain the evolutionary lifespan disparity, even between a small group of species or individuals. The genetic factors contributing to large-scale lifespan gaps between species remain elusive.

When species genomes evolve, they usually acquire more noncoding RNAs (ncRNAs) than proteins. For example, the human genome contains a larger number of ncRNAs than its mouse counterpart, whereas most proteins remain similar. Importantly, these ncRNAs are actively transcribed with their own functional system and they endogenously execute fundamental functions, including lifespan extensions. Therefore, it is reasonable to hypothesize that ncRNAs play a key role in the evolution of the lifespan of an organism.

The present study analyzed multiple large datasets and revealed that ncRNAs indeed work as the primary evolutionary drivers extending animal lifespans and serve as crucial determinants of reproductive systems. Longevity and reproduction are two most important traits of any organism evolution, suggesting that ncRNAs work as the fundamental drivers driving the long evolutionary process and they carry crucial functions in the organism's genome.

Link: https://doi.org/10.1016/j.gmg.2024.100034

Researchers here outline how it is possible to use what is known of gene regulatory networks in order to design better approaches to slow aging. Proteins interact with one another, and feedback loops involving interactions and changes in expression among many proteins determine each aspect of cell behavior. The key realization is that in such a complex system, one has to think about these networks rather than any one individual protein in order to maximize the chance of producing a useful approach to altering cell behavior.

Earlier aging studies focused on individual genes or pathways in isolation and measured lifespan as a static endpoint. As a result, how aging-related genes interact with one another and how these gene regulatory networks (GRNs) operate dynamically to drive aging remain significant unanswered challenges. GRNs consist of nodes, that symbolize genes or regulatory elements, and edges, that depict the interactions or regulatory connections between these nodes. Highly connected nodes at the center of a GRN are the major orchestrators of the response of a cell to stimuli.

The dynamics of these nodes can often be explained by focusing on a few key local interactions, namely subgraphs. Network motifs are recurrent sub-GRNs, typically including up to four nodes, that have characterized behaviors. Network motifs can be as simple as positive autoregulation which ensures the sustained activity of a node. By contrast, mutual inhibition between two nodes can lead to two distinct cell fates where the system stabilizes in one of two states based on initial conditions. The negative feedback loop is a motif that is especially crucial for ensuring homeostasis, and is activated by deviations from a set point that trigger mechanisms to counteract those changes. These motifs are observed in many GRNs and are reinforced by redundant and compensatory pathways to increase the resilience of the system to perturbations.

Decoding the emergent behavior of aging-related GRNs sets the stage for rational design of new interventional strategies to mitigate age-related diseases and promote healthy longevity. However, the intricate nature of aging-related processes cannot be fully understood through traditional reductionist methods. Instead, systems-level approaches designed to analyze the nonlinear dynamics of gene circuits are required. In addition, such network-based approaches can be naturally integrated with synthetic biology to reveal the design principles of prolongevity strategies.

Link: https://doi.org/10.1016/j.tcb.2025.02.006

Mitochondria are the power plants of the cell, producing the chemical energy store molecule adenosine triphosphate (ATP) to power cellular biochemistry. Mitochondrial function declines with age, in part due to damage to mitochondria DNA and in part due to changes in nuclear gene expression that affect proteins needed by mitochondria. This is considered an important contribution to age-related degeneration, particularly in tissues such as muscle and brain that have high energy needs.

Cells will take up mitochondria from their surroundings and make use of them. Studies in mice have indicated that transplantation of mitochondria harvested from cell cultures can produce lasting benefits. The processes of aging that diminish mitochondrial function take a while to operate, and youthful mitochondria can improve function for an extended period of time. The challenge here is that mice are small and people are large; reliable production of the large numbers of mitochondria needed is the primary hurdle preventing clinical use of this approach in old people.

A number of companies are working on the mitochondrial manufacturing challenge, including cellvie and Mitrix Bio. In today's open access paper, an academic group describes a potential approach to the problem, though this is aimed at local injection into cartilage. The goal of whole-body infusions of replacement mitochondria might require another two orders of magnitude of increased scale, and it remains to be seen if this approach will work at that level.

Organelle-tuning condition robustly fabricates energetic mitochondria for cartilage regeneration

Mitochondria are vital organelles whose impairment leads to numerous metabolic disorders. Mitochondrial transplantation serves as a promising clinical therapy. However, its widespread application is hindered by the limited availability of healthy mitochondria, with the dose required reaching up to 10^9 mitochondria per injection/patient. This necessitates sustainable and tractable approaches for producing high-quality human mitochondria.

In this study, we demonstrated a highly efficient mitochondria-producing strategy by manipulating mitobiogenesis and tuning organelle balance in human mesenchymal stem cells (MSCs). Utilizing an optimized culture medium (mito-condition) developed from our established formula, we achieved an 854-fold increase in mitochondria production compared to normal MSC culture within 15 days. These mitochondria were not only significantly expanded but also exhibited superior function both before and after isolation, with ATP production levels reaching 5.71 times that of normal mitochondria.

Mechanistically, we revealed activation of the AMPK pathway and the establishment of a novel cellular state ideal for mitochondrial fabrication, characterized by enhanced proliferation and mitobiogenesis while suppressing other energy-consuming activities. Furthermore, the in vivo function of these mitochondria was validated in the mitotherapy in a mouse osteoarthritis model, resulting in significant cartilage regeneration over a 12-week period. Overall, this study presented a new strategy for the off-the-shelf fabrication of human mitochondria and provided insights into the molecular mechanisms governing organelle synthesis.

The age-related dysfunction of the brain is a deep, complicated, and incompletely understood field of study. Even if aging is driven by relatively simple processes of damage, the brain is a very complex organ, and thus the outcome of even simple dysfunctions will be a very complex web of further interacting consequences. Thus there are any number of papers similar to the one noted here, in which researchers focus on one specific protein and what is known of its interactions in the brain. As a rule, discoveries regarding disease-specific mechanisms are usually broadly true, but it is rarely clear (or even easily understood) as to how much these mechanisms contribute to the overall burden of pathology, whether they are in fact useful targets to pursue for the development of therapies, or just minor components of the disease as a whole.

CD2AP is expressed throughout the body. Since the identification of the association between CD2AP and Alzheimer's disease (AD), the function of CD2AP in the brain has been attracting more and more attention. The mRNA data from the Allen Brain Atlas suggest that although CD2AP may be expressed at low levels in neurons, it is relatively enriched in highly plastic brain regions such as the hippocampus, cortex, and cerebellum. In addition, high expression of CD2AP was observed in dendritic endosomes of primary cultured mouse neurons and the absence of CD2AP in neurons was shown to cause synaptic damage. Moreover, we recently discovered that CD2AP was expressed at higher levels in microglia compared to neurons in mice and that CD2AP could regulate microglial activation in response to amyloid-β toxicity.

CD2AP is intricately involved in intracellular protein transport and degradation, vesicle trafficking, cell signaling, and cytoskeleton remodeling. As a risk factor for AD, abnormalities in CD2AP in the nervous system may contribute to the pathogenesis of AD through various mechanisms, including influencing the transport and processing of amyloid precursor protein (APP) and thus amyloid-β generation, participating in Tau-mediated neurotoxicity, disrupting synaptic function and vesicle release, modulating microglial activation, and compromising the integrity of the blood-brain barrier. However, the specific molecular mechanisms by which CD2AP participates in these processes have yet to be fully elucidated.

Link: https://www.doi.org/10.61373/bm025i.0026

Researchers here find that age-related changes in the gut microbiome are quite different by sex, and are influenced by the host's mitochondrial haplotype as well. It is now well known that changes occur in the gut microbiome with age, and these changes contribute to age-related degeneration via reduced production of beneficial metabolites and increased inflammation - but there may well be a great deal of variation from individual to individual. The work noted here was conducted in rats, so it remains to be seen as to whether matters are much the same in humans.

We evaluated the impact of sex and mitochondrial-haplotype on the age-related changes in the fecal gut microbiome of the genetically heterogeneous rodent model, the OKC-HETB/W rat. The age-related changes in the microbiome differed markedly between male and female rats. Five microbial species changed significantly with age in male rats compared to nine microbial species in female rats. Only three of these microbes changed with age in both male and female rats. The mitochondrial-haplotype of the rats also affected how aging altered the microbiome.

Interestingly, most of the microbial species that changed significantly with age were mitochondrial-haplotype and sex specific, i.e., changing in one sex and not the other. We also discovered that sex and mitochondrial-haplotype significantly affected the age-related variations in content of fecal short-chain fatty acids and plasma metabolites that influence or are regulated by the microbiome, e.g., tryptophan derived metabolites and bile acids. This study demonstrates that the host's sex plays a significant role in how the gut microbiome evolves with age, even within a genetically diverse background. Importantly, this is the first study to show that the mitochondrial-haplotype of a host impacts the age-related changes in the microbiome.

Link: https://doi.org/10.18632/aging.206211