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“DNA Methylation Clocks for Dogs and Humans”, Horvath et al 2022

“DNA methylation clocks for dogs and humans”⁠, Steve Horvath, Ake T. Lu, Amin Haghani, Joseph A. Zoller, Caesar Z. Li, Andrea R. Lim, Robert T. Brooke et al (2022-05-17; ):

Epigenetic estimators of age (known as “clocks”) allow one to identify interventions that slow or reverse aging. Previous epigenetic clocks only applied to one species at a time.

Here, we describe epigenetic clocks that apply to both dogs and humans.

These clocks, which measure methylation levels in highly conserved stretches of the DNA, promise to increase the likelihood that interventions that reverse epigenetic age in one species will have the same effect in the other.


DNA methylation profiles have been used to develop biomarkers of aging known as epigenetic clocks, which predict chronological age with remarkable accuracy and show promise for inferring health status as an indicator of biological age. Epigenetic clocks were first built to monitor human aging, but their underlying principles appear to be evolutionarily conserved⁠, as they have now been successfully developed for many mammalian species.

Here, we describe reliable and highly accurate epigenetic clocks shown to apply to 93 domestic dog breeds. The methylation profiles were generated using the mammalian methylation array, which utilizes DNA sequences that are conserved across all mammalian species. Canine epigenetic clocks were constructed to estimate age and also average time to death.

We also present 2 highly accurate human-dog dual species epigenetic clocks (r = 0.97), which may facilitate the ready translation from canine to human use (or vice versa) of antiaging treatments being developed for longevity and preventive medicine. Finally, epigenome-wide association studies here reveal individual methylation sites that may underlie the inverse relationship between breed weight and lifespan.

Overall, we describe robust biomarkers to measure aging and, potentially, health status in canines.

“Clock Work: Deconstructing the Epigenetic Clock Signals in Aging, Disease, and Reprogramming”, Levine et al 2022

“Clock Work: Deconstructing the Epigenetic Clock Signals in Aging, Disease, and Reprogramming”⁠, Morgan Levine, Albert Tzongyang Higgins-Chen, Kyra Thrush, Christopher J. Minteer, Peter Niimi (2022-02-15; similar):

Epigenetic clocks have come to be regarded as powerful tools for estimating aging. However, a major drawback in their application is our lack of mechanistic understanding. We hypothesize that uncovering the underlying biology is difficult due to the fact that epigenetic clocks are multifactorial composites: They are comprised of disparate parts, each with their own causal mechanism and functional consequences. Thus, only by deconstructing epigenetic clock signals will it be possible to glean biological insight. Here we clustered 5,717 clock CpGs into twelve distinct modules using multi-tissue and in-vitro datasets. We show that epigenetic clocks are comprised of different proportions of modules, which may explain their discordance when simultaneously applied in a given study. We also observe that epigenetic reprogramming does not reset the entire clock and instead the observed rejuvenation is driven by a subset of modules. Overall, two modules stand-out in terms of their unique features. The first is one of the most responsive to epigenetic reprogramming; is the strongest predictor of all-cause mortality; and shows increases with in vitro passaging up until senescence burden begins to emerge. The light-second module is moderately responsive to reprogramming; is very accelerated in tumor vs. normal tissues; and tracks with passaging in vitro even as population doublings decelerate. Overall, we show that clock deconstruction can identify unique DNAm alterations and facilitate our mechanistic understanding of epigenetic clocks.

“An Open Science Study of Ageing in Companion Dogs”, Creevy et al 2022

2022-creevy.pdf: “An open science study of ageing in companion dogs”⁠, Kate E. Creevy, Joshua M. Akey, Matt Kaeberlein, Daniel E. L. Promislow, Brian G. Barnett, Brooke Benton et al (2022-02-02; ; similar):

The Dog Aging Project (DAP) is a long-term longitudinal study of ageing in tens of thousands [>30k] of companion dogs.

The domestic dog is among the most variable mammal species in terms of morphology, behaviour, risk of age-related disease and life expectancy. Given that dogs share the human environment and have a sophisticated healthcare system but are much shorter-lived than people, they offer an unique opportunity to identify the genetic, environmental and lifestyle factors associated with healthy lifespan.

To take advantage of this opportunity, the Dog Aging Project will collect extensive survey data, environmental information, electronic veterinary medical records, genome-wide sequence information, clinicopathology and molecular phenotypes derived from blood cells, plasma and faecal samples.

Here, we describe the specific goals and design of the Dog Aging Project and discuss the potential for this open-data, community science study to greatly enhance understanding of ageing in a genetically variable, socially relevant species living in a complex environment.

  1. Objectives—science of ageing

    • Define normative ageing in dogs as a function of breed, size and sex
    • Identify genetic and environmental determinants of age-specific morbidity and mortality in companion dogs
    • Develop panels of prognostic and predictive biomarkers
    • Increase the duration of healthy lifespan in dogs
  2. Objectives—open science

    • Create an open-data resource for comprehensive study of the genetic and environmental determinants of healthy ageing in companion dogs
    • Provide researchers with access to biospecimens through the DAP Biobank⁠, together with the detailed longitudinal data associated with each biospecimen
    • Build and maintain a research infrastructure that allows for addition of new studies within the DAP framework
    • Study and promote ethical approaches for research in companion animals

…The DAP has 4 primary scientific aims. These include (1) characterizing ageing in companion dogs on 3 separate axes: multimorbidity, frailty and inflammaging; (2) using low-coverage whole-genome sequencing with imputation on at least 10,000 dogs to analyse the genetic architecture of age-related traits in dogs; (3) collecting metabolome, epigenome and microbiome profiles to develop biomarkers of ageing in dogs [epigenetic clock] and to better understand the mechanisms by which genetic, environmental and lifestyle variation influence ageing; and (4) carrying out a randomized, double-masked, placebo-controlled study to determine the effects of rapamycin on lifespan and healthspan in large-breed, middle-aged dogs.

“Heterochronic Parabiosis Reprograms the Mouse Brain Transcriptome by Shifting Aging Signatures in Multiple Cell Types”, Ximerakis et al 2022

“Heterochronic parabiosis reprograms the mouse brain transcriptome by shifting aging signatures in multiple cell types”⁠, Methodios Ximerakis, Kristina M. Holton, Richard M. Giadone, Ceren Ozek, Monika Saxena, Samara Santiago et al (2022-01-28; similar):

Aging is a complex process involving transcriptomic changes associated with deterioration across multiple tissues and organs, including the brain. Recent studies using heterochronic parabiosis have shown that various aspects of aging-associated decline are modifiable or even reversible. To better understand how this occurs, we performed single-cell transcriptomic profiling of young and old mouse brains following parabiosis. For each cell type, we catalogued alterations in gene expression, molecular pathways, transcriptional networks, ligand-receptor interactions, and senescence status. Our analyses identified gene signatures demonstrating that heterochronic parabiosis regulates several hallmarks of aging in a cell-type-specific manner. Brain endothelial cells were found to be especially malleable to this intervention, exhibiting dynamic transcriptional changes that affect vascular structure and function. These findings suggest novel strategies for slowing deterioration and driving regeneration in the aging brain through approaches that do not rely on disease-specific mechanisms or actions of individual circulating factors.

“Multi-omic Rejuvenation of Naturally Aged Tissues by a Single Cycle of Transient Reprogramming”, Chondronasiou et al 2022

“Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming”⁠, Dafni Chondronasiou, Diljeet Gill, Lluc Mosteiro, Rocio G. Urdinguio, Antonio Berenguer, Monica Aguilera et al (2022-01-21; similar):

The expression of the pluripotency factors OCT4, SOX2, KLF4 and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, cycles of brief OSKM expression do not change cell identity but can reverse markers of aging in cells and extend longevity in progeroid mice. However, little is known about the mechanisms involved.

Here, we have studied changes in the DNA methylome, transcriptome and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites altered with aging were also restored to young levels upon transient reprogramming.

These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic and metabolomic changes towards a younger configuration in multiple tissues and in the serum.

“Mendelian Randomization of Genetically Independent Aging Phenotypes Identifies LPA and VCAM1 As Biological Targets for Human Aging”, Timmers et al 2022

“Mendelian randomization of genetically independent aging phenotypes identifies LPA and VCAM1 as biological targets for human aging”⁠, Paul R. H. J. Timmers, Evgeny S. Tiys, Saori Sakaue, Masato Akiyama, Tuomo T. J. Kiiskinen, Wei Zhou et al (2022-01-20; ; similar):

Length and quality of life are important to us all, yet identification of promising drug targets for human aging using genetics has had limited success.

In the present study, we combine 6 European-ancestry genome-wide association studies of human aging traits—healthspan, father and mother lifespan, exceptional longevity, frailty index and self-rated health—in a principal component framework that maximizes their shared genetic architecture. The first principal component (aging-GIP1) captures both length of life and indices of mental and physical wellbeing.

We identify 27 genomic regions associated with aging-GIP1, and provide additional, independent evidence for an effect on human aging for loci near HTT and MAML3 using a study of Finnish and Japanese survival. Using proteome-wide, 2-sample, Mendelian randomization and colocalization, we provide robust evidence for a detrimental effect of blood levels of apolipoprotein(a) and vascular cell adhesion molecule 1 on aging-GIP1.

Together, our results demonstrate that combining multiple aging traits using genetic principal components enhances the power to detect biological targets for human aging.

“Rare Genetic Variants Correlate With Better Processing Speed”, Song et al 2022

“Rare Genetic Variants Correlate with Better Processing Speed”⁠, Zeyuan Song, Anastasia Gurinovich, Marianne Nygaard, Jonas Mengel-From, Stacy Andersen, Stephanie Cosentino et al (2022-01-12; ; similar):

We conducted a genome-wide association study (GWAS) of Digit Symbol Substitution Test (DSST) scores administered in 4207 family members of the Long Life Family Study (LLFS). Genotype data were imputed to the HRC panel of 64,940 haplotypes resulting in ~15M genetic variants with quality score > 0.7. The results were replicated using genetic data imputed to the 1000 Genomes phase 3 reference panel from two Danish twin cohorts: the study of Middle Aged Danish Twins and the Longitudinal Study of Aging Danish Twins. The GWAS in LLFS discovered 20 rare genetic variants (minor allele frequency (MAF) < 1.0%) that reached genome-wide statistical-significance (p-value < 5×10−8). Among these, 18 variants had large protective effects on the processing speed, including rs7623455, rs9821776, rs9821587, rs78704059 on chromosome 3, which were replicated in the combined Danish twin cohort. These SNPs are located in/​near two genes, THRB and RARB, that belonged to thyroid hormone receptors family that may influence speed of metabolism and cognitive aging. The gene-level tests in LLFS confirmed that these two genes are associated with processing speed.

“An Epigenetic Aging Analysis of Randomized Metformin and Weight Loss Interventions in Overweight Postmenopausal Breast Cancer Survivors”, Nwanaji-Enwerem et al 2021

“An epigenetic aging analysis of randomized metformin and weight loss interventions in overweight postmenopausal breast cancer survivors”⁠, Jamaji C. Nwanaji-Enwerem, Felicia Fei-Lei Chung, Lars Van der Laan, Alexei Novoloaca, Cyrille Cuenin et al (2021-12-17; similar):

Metformin and weight loss relationships with epigenetic age measures—biological aging biomarkers—remain understudied.

We performed a post-hoc analysis of a randomized controlled trial (NCT01302379) among overweight/​obese breast cancer survivors (n = 192) assigned to metformin⁠, placebo, weight loss with metformin⁠, or weight loss with placebo interventions for 6 months.

Epigenetic age [Hannum, Horvath, SkinBloodClock, PhenoAge, DNAm TL, MiAge] was correlated with chronological age (r = 0.20–0.86; p < 0.005). However, no statistically-significant epigenetic aging associations were observed by intervention arms.

Consistent with published reports in non-cancer patients, 6 months of metformin therapy may be inadequate to observe expected epigenetic age deceleration. Longer duration studies are needed to better characterize these relationships.

[Keywords: RCT, DNA methylation age, biomarkers, GrimAge, PhenoAge]

…In unadjusted intent-to-treat models, when compared to placebo, no treatment arm demonstrated any statistically-significant differences or notable trends for any EA marker (Table 1). The results remained null even when intent-to-treat models included adjustments for leukocyte composition and number of days from randomization to the end of the study. Unadjusted and adjusted sensitivity analyses that focused on examining differences between high intervention adherence women and those in the placebo group also did not demonstrate any notable trends for any EA marker. Although weight loss—compared to placebo—was associated with EA in high adherence models, the association was in the opposite direction as expected and would not persist after multiple testing adjustment.

“Longevity, Cellular Senescence and the Gut Microbiome: Lessons to Be Learned from Crocodiles”, Siddiqui et al 2021

“Longevity, cellular senescence and the gut microbiome: lessons to be learned from crocodiles”⁠, Ruqaiyyah Siddiqui, Sutherland Maciver, Adel Elmoselhi, Nelson Cruz Soares, Naveed Ahmed Khan (2021-12-13; ; similar):

Crocodiles are flourishing large-bodied ectotherms in a world dominated by endotherms. They survived the Cretaceous extinction event, that eradicated the dinosaurs who are thought to be their ancestral hosts. Crocodiles reside in polluted environments; and often inhabit water which contains heavy metals; frequent exposure to radiation; feed on rotten meat and considered as one of the hardy species that has successfully survived on this planet for millions of years. Another capability that crocodiles possess is their longevity. Crocodiles live much longer than similar-sized land mammals, sometimes living up to 100 years. But how do they withstand such harsh conditions that are detrimental to Homo sapiens?

Given the importance of gut microbiome on its’ host physiology, we postulate that the crocodile gut microbiome and/​or its’ metabolites produce substances contributing to their “hardiness” and longevity. Thus, we accomplished literature search in PubMed⁠, Web of Science and Google Scholar and herein, we discuss the composition of the crocodile gut microbiome, longevity and cellular senescence in crocodiles, their resistance to infectious diseases and cancer, and our current knowledge of the genome and epigenome of these remarkable species. Furthermore, preliminary studies that demonstrate the remarkable properties of crocodile gut microbial flora are discussed.

Given the profound role of the gut microbiome in the health of its’ host, it is likely that the crocodile gut microbiome and its’ metabolites may be contributing to their extended life expectancy and elucidating the underlying mechanisms and properties of these metabolites may hold clues to developing new treatments for age-related diseases for the benefit of Homo sapiens.

[Keywords: crocodiles, gut microbiome, longevity, novel metabolites, senescence, anti-cancer, infectious diseases, drug discovery]

“Profiling Epigenetic Age in Single Cells”, Trapp et al 2021

2021-trapp.pdf: “Profiling epigenetic age in single cells”⁠, Alexandre Trapp, Csaba Kerepesi, Vadim N. Gladyshev (2021-12-09; similar):

[Twitter] DNA methylation dynamics have emerged as a promising biomarker of mammalian aging, with multivariate machine learning models (‘epigenetic clocks’) enabling measurement of biological age in bulk tissue samples. However, intrinsically sparse and binarized methylation profiles of individual cells have so far precluded the assessment of aging in single-cell epigenomics data⁠.

Here we introduce scAge⁠, a statistical framework for epigenetic age profiling at single-cell resolution, and validate our approach in mice. Our method recapitulates the chronological age of tissues while uncovering heterogeneity among cells.

We show accurate tracking of the aging process in hepatocytes, demonstrate attenuated epigenetic aging in muscle stem cells and track age dynamics in embryonic stem cells. We also use scAge to reveal, at the single-cell level, a natural and stratified rejuvenation event occurring during early mouse embryogenesis⁠. We provide our framework as a resource to enable exploration of epigenetic aging trajectories at single-cell resolution.

“Rejuvant®, a Potential Life-extending Compound Formulation With Alpha-ketoglutarate and Vitamins, Conferred an Average 8 Year Reduction in Biological Aging, After an Average of 7 Months of Use, in the TruAge DNA Methylation Test”, Demidenko1 et al 2021

“Rejuvant®, a potential life-extending compound formulation with alpha-ketoglutarate and vitamins, conferred an average 8 year reduction in biological aging, after an average of 7 months of use, in the TruAge DNA methylation test”⁠, Oleksandr Demidenko1, Diogo Barardo, Valery Budovskii, Robb Finnemore, Francis R. Palmer III, Brian K. Kennedy et al (2021-11-30; similar):

The search continues for possible interventions that delay and/​or reverse biological aging, resulting in extended healthspan and lifespan. Interventions delaying aging in animal models are well established; however, most lack validation in humans. The length of human lifespan makes it impractical to perform survival analysis⁠. Instead, aging biomarkers, such as DNA methylation (DNAm) clocks⁠, have been developed to monitor biological age.

Herein we report a retrospective analysis of DNA methylation [TruAge] age in 42 individuals taking Rejuvant®, an alpha-ketoglutarate-based formulation (sustained release CaAKG), for an average period of 7 months. DNAm testing was performed at baseline and by the end of treatment with Rejuvant® supplementation.

Remarkably, individuals showed an average decrease in biological aging of 8 years (p = 6.538 × 10−12). Furthermore, the supplementation with Rejuvant® is robust to individual differences, as indicated by the fact that a large majority of participants decreased their biological age. Moreover, we found that Rejuvant® is of additional benefit to chronologically and biologically older individuals.

While continued testing, particularly in a placebo-controlled design, is required, the nearly 8-year reversal in the biological age of individuals taking Rejuvant® for 4 to 10 months is noteworthy, making the natural product cocktail an intriguing candidate to affect human aging.

“Metformin Treatment of Diverse Caenorhabditis Species Reveals the Importance of Genetic Background in Longevity and Healthspan Extension Outcomes”, Onken et al 2021

“Metformin treatment of diverse Caenorhabditis species reveals the importance of genetic background in longevity and healthspan extension outcomes”⁠, Brian Onken, Christine A. Sedore, Anna L. Coleman-Hulbert, David Hall, Erik Johnson, Eleanor Grace Jones et al (2021-11-27; similar):

Metformin⁠, the most commonly prescribed anti-diabetes medication, has multiple reported health benefits, including lowering the risks of cardiovascular disease and cancer, improving cognitive function with age, extending survival in diabetic patients, and, in several animal models, promoting youthful physiology and lifespan. Due to its longevity and health effects, metformin is now the focus of the first proposed clinical trial of an anti-aging drug—the Targeting Aging with Metformin (TAME) program.

Genetic variation will likely influence outcomes when studying metformin health effects in human populations. To test for metformin impact in diverse genetic backgrounds, we measured lifespan and healthspan effects of metformin treatment in 3 Caenorhabditis species representing genetic variability greater than that between mice and humans.

We show that metformin increases median survival in 3 C. elegans strains, but not in C. briggsae and C. tropicalis strains. In C. briggsae, metformin either has no impact on survival or decreases lifespan. In C. tropicalis, metformin decreases median survival in a dose-dependent manner. We show that metformin prolongs the period of youthful vigor in all C. elegans strains and in 2 C. briggsae strains, but that metformin has a negative impact on the locomotion of C. tropicalis strains.

Our data demonstrate that metformin can be a robust promoter of healthy aging across different genetic backgrounds, but that genetic variation can determine whether metformin has positive, neutral, or negative lifespan/​healthspan impact. These results underscore the importance of tailoring treatment to individuals when testing for metformin health benefits in diverse human populations.

“Multi-omic Rejuvenation and Lifespan Extension upon Exposure to Youthful Circulation”, Zhang et al 2021

“Multi-omic rejuvenation and lifespan extension upon exposure to youthful circulation”⁠, Bohan Zhang, David E. Lee, Alexandre Trapp, Alexander Tyshkovskiy, Ake T. Lu, Akshay Bareja, Csaba Kerepesi et al (2021-11-12; similar):

Heterochronic parabiosis (HPB) is known for its functional rejuvenation effects across several mouse tissues. However, its impact on the biological age of organisms and their long-term health remains unknown. Here, we performed extended (3-month) HPB, followed by a 2-month detachment period of anastomosed pairs. Old detached mice exhibited improved physiological parameters and lived longer than control isochronic mice. HPB drastically reduced the biological age of blood and liver based on epigenetic analyses across several clock models on two independent platforms; remarkably, this rejuvenation effect persisted even after 2 months of detachment. Transcriptomic and epigenomic profiles of anastomosed mice showed an intermediate phenotype between old and young, suggesting a comprehensive multi-omic rejuvenation effect. In addition, old HPB mice showed transcriptome changes opposite to aging, but akin to several lifespan-extending interventions. Altogether, we reveal that long-term HPB can decrease the biological age of mice, in part through long-lasting epigenetic and transcriptome remodeling, culminating in the extension of lifespan and healthspan.

“Nutritional Reprogramming of Mouse Liver Proteome Is Dampened by Metformin, Resveratrol, and Rapamycin”, Couteur et al 2021

2021-lecouteur.pdf: “Nutritional reprogramming of mouse liver proteome is dampened by metformin, resveratrol, and rapamycin”⁠, David G. Le Couteur, Samantha M. Solon-Biet, Benjamin L. Parker, Tamara Pulpitel, Amanda E. Brandon, Nicholas J. Hunt et al (2021-11-11; similar):

In Brief: In a study of the hepatic proteome⁠, Le Couteur et al 2021 show that dietary energy and macronutrients influence fundamental cellular machinery, including the spliceosome and mitochondria. Metformin, rapamycin, and resveratrol broadly dampened the proteomic responses to diet rather than acting on specific nutrient sensing pathways. The impact of diet was substantially more important than that of drugs.


Nutrient sensing pathways influence metabolic health and aging, offering the possibility that diet might be used therapeutically, alone or with drugs targeting these pathways.

We used the Geometric Framework for Nutrition to study interactive and comparative effects of diet and drugs on the hepatic proteome in mice across 40 dietary treatments differing in macronutrient ratios, energy density, and drug treatment (metformin, rapamycin, resveratrol).

There was a strong negative correlation between dietary energy and the spliceosome and a strong positive correlation between dietary protein and mitochondria, generating oxidative stress at high protein intake. Metformin, rapamycin, and resveratrol had lesser effects than and dampened responses to diet. Rapamycin and metformin reduced mitochondrial responses to dietary protein while the effects of carbohydrates and fat were downregulated by resveratrol.

Dietary composition has a powerful impact on the hepatic proteome, not just on metabolic pathways but fundamental processes such as mitochondrial function and RNA splicing.

[Keywords: Nutrition, Geometric Framework, macronutrients, proteome, liver, mitochondria, spliceosome, metformin, rapamycin, resveratrol, caloric restriction]

“Coevolution of Brain Size and Longevity in Parrots”, Smeele et al 2021

“Coevolution of brain size and longevity in parrots”⁠, Simeon Q. Smeele, Dalia A. Conde, Annette Baudisch, Simon Bruslund, Andrew Iwaniuk, Johanna Staerk, Timothy F. Wright et al (2021-10-28; ⁠, ; similar):

Parrots are well-known for their exceptionally long lives and cognitive complexity. While previous studies have demonstrated a correlation between longevity and brain size in a variety of taxa, little research has been devoted to understanding this link in parrots.

Here we employed a large-scale comparative analysis that investigated the influence of brain size and life history variables on patterns of longevity. Specifically, we addressed two hypotheses for evolutionary drivers of longevity: the Cognitive Buffer Hypothesis, which proposes that increased cognitive abilities enable longer life spans, and the Expensive Brain Hypothesis, which holds that the increase in life span is caused by prolonged developmental time of and increased parental investment in, large brained offspring.

We estimated life expectancy from detailed zoo records for 133,818 individuals across 244 parrot species. Using Bayesian structural equation models, we found a consistent correlation between relative brain size and life expectancy in parrots. This correlation was best explained by a direct effect of relative brain size. Notably, we found no effects of developmental time, clutch size, or age at first reproduction.

Our results provide support for the Cognitive Buffer Hypothesis, and demonstrate a principled Bayesian approach that addresses data uncertainty and imputation of missing values.

“Ultra-cheap and Scalable Epigenetic Age Predictions With TIME-Seq”, Griffin et al 2021

“Ultra-cheap and scalable epigenetic age predictions with TIME-Seq”⁠, Patrick T. Griffin, Alice E. Kane, Alexandre Trapp, Jien Li, Maeve S. McNamara, Margarita V. Meer, Michael R. MacArthur et al (2021-10-28; similar):

Epigenetic “clocks” based on DNA methylation (DNAme) are the most robust and widely employed aging biomarker. They have been built for numerous species and reflect gold-standard interventions that extend lifespan. However, conventional methods for measuring epigenetic clocks are expensive and low-throughput. Here, we describe Tagmentation-based Indexing for Methylation Sequencing (TIME-Seq) for ultra-cheap and scalable targeted methylation sequencing of epigenetic clocks and other DNAme biomarkers. Using TIME-Seq, we built and validated inexpensive epigenetic clocks based on genomic and ribosomal DNAme in hundreds of mice and human samples. We also discover it is possible to accurately predict age from extremely low-cost shallow sequencing (eg. 10,000 reads) of TIME-Seq libraries using scAge, a probabilistic age-prediction algorithm originally applied to single cells. Together, these methods reduce the cost of DNAme biomarker analysis by more than two orders of magnitude, thereby expanding and democratizing their use in aging research, clinical trials, and disease diagnosis.

“Effect of Metformin and Lifestyle Interventions on Mortality in the Diabetes Prevention Program and Diabetes Prevention Program Outcomes Study”, Lee et al 2021

2021-lee.pdf: “Effect of Metformin and Lifestyle Interventions on Mortality in the Diabetes Prevention Program and Diabetes Prevention Program Outcomes Study”⁠, Christine G. Lee, Brandy Heckman-Stoddard, Dana Dabelea, Kishore M. Gadde, David Ehrmann, Leslie Ford et al (2021-10-25; similar):

Objective: To determine whether metformin or lifestyle modification can lower rates of all-cause and cause-specific mortality in the Diabetes Prevention Program and Diabetes Prevention Program Outcomes Study.

Research Design & Methods: From 1996 to 1999, 3,234 adults at high risk for type 2 diabetes were randomized to an intensive lifestyle intervention, masked metformin, or placebo. Placebo and lifestyle interventions stopped in 2001, and a modified lifestyle program was offered to everyone, but unmasked study metformin continued in those originally randomized. Causes of deaths through 31 December 2018 were adjudicated by blinded reviews. All-cause and cause-specific mortality hazard ratios (HRs) were estimated from Cox proportional hazards regression models and Fine-Gray subdistribution hazard competing risks model, respectively.

Results: Over a median of 21 years (interquartile range 20–21), 453 participants died. Cancer was the leading cause of death (n = 170), followed by cardiovascular disease (n = 131). Compared with placebo, metformin did not influence mortality from all causes (HR 0.99 [95% CI 0.79, 1.25]), cancer (HR 1.04 [95% CI 0.72, 1.52]), or cardiovascular disease (HR 1.08 [95% CI 0.70, 1.66]). Similarly, lifestyle modification did not impact all-cause (HR 1.02 [95% CI 0.81, 1.28]), cancer (HR 1.07 [95% CI 0.74, 1.55]), or cardiovascular disease (HR 1.18 [95% CI 0.77, 1.81]) mortality. Analyses adjusted for diabetes status and duration, BMI⁠, cumulative glycemic exposure, and cardiovascular risks yielded results similar to those for all-cause mortality.

Conclusions: Cancer was the leading cause of mortality among adults at high risk for type 2 diabetes⁠. Although metformin and lifestyle modification prevented diabetes, neither strategy reduced all-cause, cancer, or cardiovascular mortality rates.

“Many Chronological Aging Clocks Can Be Found throughout the Epigenome: Implications for Quantifying Biological Aging”, Porter et al 2021

“Many chronological aging clocks can be found throughout the epigenome: Implications for quantifying biological aging”⁠, Hunter L. Porter, Chase A. Brown, Xiavan Roopnarinesingh, Cory B. Giles, Constantin Georgescu, Willard M. Freeman et al (2021-10-16; similar):

Epigenetic alterations are a hallmark of aging and age-related diseases. Computational models using DNA methylation data can create “epigenetic clocks” which are proposed to reflect “biological” aging. Thus, it is important to understand the relationship between predictive clock sites and aging biology.

To do this, we examined over 450,000 methylation sites from 9,699 samples.

We found ~20% of the measured genomic cytosines can be used to make many different epigenetic clocks whose age prediction performance surpasses that of telomere length. Of these predictive sites, the average methylation change over a lifetime was small (~1.5%) and these sites were under-represented in canonical regions of epigenetic regulation. There was only a weak association between “accelerated” epigenetic aging and disease. We also compare tissue-specific and pan-tissue clock performance. This is critical to applying clocks both to new sample sets in basic research, as well as understanding if clinically available tissues will be feasible samples to evaluate “epigenetic aging” in unavailable tissues (eg. brain).

Despite the reproducible and accurate age predictions from DNA methylation data, these findings suggest they may have limited utility as currently designed in understanding the molecular biology of aging and may not be suitable as surrogate endpoints in studies of anti-aging interventions. Purpose-built clocks for specific tissues age ranges or phenotypes may perform better for their specific purpose. However, if purpose-built clocks are necessary for meaningful predictions, then the utility of clocks and their application in the field needs to be considered in that context.

“Polygenic Basis and Biomedical Consequences of Telomere Length Variation”, Codd et al 2021

“Polygenic basis and biomedical consequences of telomere length variation”⁠, Veryan Codd, Qingning Wang, Elias Allara, Crispin Musicha, Stephen Kaptoge, Svetlana Stoma, Tao Jiang et al (2021-10-05; ; similar):

Telomeres⁠, the end fragments of chromosomes, play key roles in cellular proliferation and senescence.

Here we characterize the genetic architecture of naturally occurring variation in leukocyte telomere length (LTL) and identify causal links between LTL and biomedical phenotypes in 472,174 well-characterized UK Biobank participants.

We identified 197 independent sentinel variants associated with LTL at 138 genomic loci (108 new). Genetically determined differences in LTL were associated with multiple biological traits, ranging from height to bone marrow function, as well as several diseases spanning neoplastic, vascular and inflammatory pathologies. Finally, we estimated that, at the age of 40 years, people with an LTL >1 s.d. shorter than the population mean had a 2.5-year-lower life expectancy compared with the group with ≥1 s.d. longer LDL.

Overall, we furnish new insights into the genetic regulation of LTL, reveal wide-ranging influences of LTL on physiological traits, diseases and longevity, and provide a powerful resource available to the global research community.

“Escape of Hair Follicle Stem Cells Causes Stem Cell Exhaustion during Aging”, Zhang et al 2021

2021-zhang.pdf: “Escape of hair follicle stem cells causes stem cell exhaustion during aging”⁠, Chi Zhang, Dongmei Wang, Jingjing Wang, Li Wang, Wenli Qiu, Tsutomu Kume, Robin Dowell, Rui Yi (2021-10-04; ; similar):

Stem cell (SC) exhaustion is a hallmark of aging. However, the process of SC depletion during aging has not been observed in live animals, and the underlying mechanism contributing to tissue deterioration remains obscure.

We find that, in aged mice, epithelial cells escape from the hair follicle (HF) SC compartment to the dermis, contributing to HF miniaturization. Single-cell RNA-seq and assay for transposase-accessible chromatin using sequencing (ATAC-seq) reveal reduced expression of cell adhesion and extracellular matrix genes in aged HF-SCs, many of which are regulated by Foxc1 and Nfatc1⁠. Deletion of Foxc1 and Nfatc1 recapitulates HF miniaturization and causes hair loss⁠. Live imaging captures individual epithelial cells migrating away from the SC compartment and HF disintegration.

This study illuminates a hitherto unknown activity of epithelial cells escaping from their niche as a mechanism underlying SC reduction and tissue degeneration. Identification of homeless epithelial cells in aged tissues provides a new perspective for understanding aging-associated diseases.

[A good use case for epigenetic reprogramming?]

[“Losing Your Hair? You Might Blame the Great Stem Cell Escape: By observing mouse hair follicles, scientists discovered an unexpected mechanism of aging. ‘If I didn’t see it with my own eyes I wouldn’t believe it’, one said”:

“…Dr. Yi, like most scientists, had assumed that with age the stem cells died in a process known as stem cell exhaustion. He expected that the death of a hair follicle’s stem cells meant that the hair would turn white and, when enough stem cells were lost, the strand of hair would die. But this hypothesis had not been fully tested. Together with a graduate student, Chi Zhang, Dr. Yi decided that to understand the aging process in hair, he needed to watch individual strands of hair as they grew and aged.

Ordinarily, researchers who study aging take chunks of tissue from animals of different ages and examine the changes. There are 2 drawbacks to this approach, Dr. Yi said. First, the tissue is already dead. And it is not clear what led to the changes that are observed or what will come after them.

He decided his team would use a different method. They watched the growth of individual hair follicles in the ears of mice using a long wavelength laser that can penetrate deep into tissue. They labeled hair follicles with a green fluorescent protein, anesthetized the animals so they did not move, put their ear under the microscope and went back again and again to watch what was happening to the same hair follicle. What they saw was a surprise: When the animals started to grow old and gray and lose their hair, their stem cells started to escape their little homes in the bulge. The cells changed their shapes from round to amoeba-like and squeezed out of tiny holes in the follicle. Then they recovered their normal shapes and darted away. Sometimes, the escaping stem cells leapt long distances, in cellular terms, from the niche where they lived. The stem cells then vanished, perhaps consumed by the immune system.

“If I did not see it for myself I would not have believed it”, Dr. Yi said. “It’s almost crazy in my mind.”

But why? Dr. Yi and his colleagues’ next step was to ask if genes are controlling the process. They discovered 2—FOXC1 and NFATC1—that were less active in older hair follicle cells. Their role was to imprison stem cells in the bulge. So the researchers bred mice that lacked those genes to see if they were the master controllers. By the time the mice were 4 to 5 months old, they started losing hair. By age 16 months, when the animals were middle-aged, they looked ancient: They had lost a lot of hair and the sparse strands remaining were gray.

Now the researchers want to save the hair stem cells in aging mice.

This story of the discovery of a completely unexpected natural process makes Dr. Chuong wonder what remains to be learned about living creatures. “Nature has endless surprises waiting for us”, he said. “You can see fantastic things.”“]

“Increased Somatic Mutation Burdens in Normal Human Cells due to Defective DNA Polymerases”, Robinson et al 2021

“Increased somatic mutation burdens in normal human cells due to defective DNA polymerases”⁠, Philip S. Robinson, Tim H. H. Coorens, Claire Palles, Emily Mitchell, Federico Abascal, Sigurgeir Olafsson et al (2021-09-30; ; similar):

Mutation accumulation in somatic cells contributes to cancer development and is proposed as a cause of aging. DNA polymerases Pol ε and Pol δ replicate DNA during cell division. However, in some cancers, defective proofreading due to acquired POLE⁠/​POLD1 exonuclease domain mutations causes markedly elevated somatic mutation burdens with distinctive mutational signatures. Germline POLE/​POLD1 mutations cause familial cancer predisposition.

Here, we sequenced normal tissue and tumor DNA from individuals with germline POLE/​POLD1 mutations. Increased mutation burdens with characteristic mutational signatures were found in normal adult somatic cell types, during early embryogenesis and in sperm. Thus human physiology can tolerate ubiquitously elevated mutation burdens.

Except for increased cancer risk, individuals with germline POLE/​POLD1 mutations do not exhibit overt features of premature aging.

These results do not support a model in which all features of aging are attributable to widespread cell malfunction directly resulting from somatic mutation burdens accrued during life.

“Human Mortality at Extreme Age”, Belzile et al 2021

“Human mortality at extreme age”⁠, Léo R. Belzile, Anthony C. Davison, Holger Rootzén, Dmitrii Zholud (2021-09-29; ; similar):

We use a combination of extreme value statistics⁠, survival analysis and computer-intensive methods to analyse the mortality of Italian and French semi-supercentenarians.

After accounting for the effects of the sampling frame, extreme-value modelling leads to the conclusion that constant force of mortality beyond 108 years describes the data well and there is no evidence of differences between countries and cohorts. These findings are consistent with use of a Gompertz model and with previous analysis of the International Database on Longevity and suggest that any physical upper bound for the human lifespan is so large that it is unlikely to be approached.

Power calculations make it implausible that there is an upper bound below 130 years. There is no evidence of differences in survival between women and men after age 108 in the Italian data and the International Database on Longevity, but survival is lower for men in the French data.

“Lithium Can Mildly Increase Health during Ageing but Not Lifespan in Mice”, Nespital et al 2021

“Lithium can mildly increase health during ageing but not lifespan in mice”⁠, Tobias Nespital, Brit Neuhaus, Andrea Mesaros, André Pahl, Linda Partridge (2021-09-21; ; similar):

Lithium is a nutritional trace element, used clinically as an anti-depressant. Preclinically, lithium has neuroprotective effects in invertebrates and mice, and it can also extend lifespan in fission yeast, C. elegans and Drosophila. An inverse correlation of human mortality with the concentration of lithium in tap water suggests a possible, evolutionarily conserved mechanism mediating longevity.

Here, we assessed the effects of lithium treatment on lifespan and ageing parameters in mice. Lithium has a narrow therapeutic dose range, and overdosing can severely affect organ health.

Within the tolerable dosing range, we saw some mildly positive effects of lithium on health span but not on lifespan.

“Extending Human Healthspan and Longevity: a Symposium Report”, DeVito et al 2021

2021-devito.pdf: “Extending human healthspan and longevity: a symposium report”⁠, Loren M. DeVito, Nir Barzilai, Ana Maria Cuervo, Laura J. Niedernhofer, Sofiya Milman, Morgan Levine et al (2021-09-08; similar):

For many years, it was believed that the aging process was inevitable and that age-related diseases could not be prevented or reversed. The geroscience hypothesis, however, posits that aging is, in fact, malleable and, by targeting the hallmarks of biological aging, it is indeed possible to alleviate age-related diseases and dysfunction and extend longevity. This field of geroscience thus aims to prevent the development of multiple disorders with age, thereby extending healthspan, with the reduction of morbidity toward the end of life. Experts in the field have made remarkable advancements in understanding the mechanisms underlying biological aging and identified ways to target aging pathways using both novel agents and repurposed therapies. While geroscience researchers currently face substantial barriers in bringing therapies through clinical development, proof-of-concept studies, as well as early-stage clinical trials, are underway to assess the feasibility of drug evaluation and lay a regulatory foundation for future FDA approvals in the future.

[Keywords: biological aging, healthspan, hallmarks of aging, geroscience, longevity]

…On May 19, 2021, experts in geroscience met virtually at the New York Academy of Sciences’ symposium, “Extending Human HealthSpan and Longevity”, organized by Stephanie Lederman, Glenda Greenwald, Orla Smith, Nir Barzilai, James L. Kirkland, and Judith Campisi, to discuss the molecular mechanisms that contribute to longevity and how those insights show that disease emergence can be prevented or reversed by repurposing or developing novel therapies that target these processes. This report summarizes the speakers’ presentations at the one-day symposium.

“Counteracting Age-related VEGF Signaling Insufficiency Promotes Healthy Aging and Extends Life Span”, Grunewald et al 2021

2021-grunewald.pdf: “Counteracting age-related VEGF signaling insufficiency promotes healthy aging and extends life span”⁠, M. Grunewald, S. Kumar, H. Sharife, E. Volinsky, A. Gileles-Hillel, T. Licht, A. Permyakova, L. Hinden et al (2021-07-30; similar):

More VEGF, more life span and health span: Advanced aging is celebrated but its ill effects of deterioration at the cell, tissue, and organ levels are not. Grunewald et al provide evidence for the vascular theory of aging, which reports that an age-related decrease of vascular function is a driver of organismal aging at large (see the Perspective by Augustin & Kipnis). Vascular endothelial growth factor (VEGF) signaling insufficiency underlies this vascular insufficiency in aged mice. A modest compensatory increase in circulatory VEGF was sufficient to preserve a young-like vascular homeostasis, alleviate multiple adverse age-related processes, and ameliorate a host of age-associated pathologies in mice.


Aging is an established risk factor for vascular diseases, but vascular aging itself may contribute to the progressive deterioration of organ function.

Here, we show in aged mice that vascular endothelial growth factor (VEGF) signaling insufficiency, which is caused by increased production of decoy receptors, may drive physiological aging across multiple organ systems. Increasing VEGF signaling prevented age-associated capillary loss, improved organ perfusion and function, and extended life span. Healthier aging was evidenced by favorable metabolism and body composition and amelioration of aging-associated pathologies including hepatic steatosis, sarcopenia, osteoporosis, “inflammaging” (age-related multi-organ chronic inflammation), and increased tumor burden.

These results indicate that VEGF signaling insufficiency affects organ aging in mice and suggest that modulating this pathway may result in increased mammalian life span and improved overall health.


Introduction: All body cells rely on blood vessels (BVs) for the provision of oxygen and other blood-borne substances and, in certain settings, also for the provision of endothelial-derived paracrine factors. Like other organ systems, the vascular system undergoes aging, which leads to progressive functional deterioration. Given the centrality of BVs to organ homeostasis, it has been hypothesized that vascular aging is an upstream, founding factor in organismal aging, but experimental support for this proposition is limited. Vascular aging involves both large and small vessels, with the latter marked by capillary rarefaction, i.e., age-related failure to maintain adequate microvascular density (MVD). A key homeostatic mechanism preventing MVD reduction relies on the angiogenic activity of vascular endothelial growth factor (VEGF), which by virtue of its hypoxic inducibility, constantly acts to replenish lost vessels and match vascular supply to the tissue needs. The reason(s) that VEGF fails to do so during aging is unknown.

Rationale: Compromised vascular function is expected to perturb organ homeostasis in ways conducive for the development of age-related frailties and diseases. Accordingly, counteracting critical facets of vascular aging might be an useful approach for their alleviation. The presumption that insufficient vascular supply in aging is underlined by VEGF signaling insufficiency, primarily (but not exclusively) because of its indispensable role in preventing capillary loss, led us to investigate whether securing a young-like level of VEGF signaling might rectify capillary loss and its sequelae. On the premise that deteriorated vascular function is an upstream driver of multi-organ malfunctioning, it is envisioned that its rectification might confer comprehensive geroprotection.

Results: Although VEGF production is not substantially reduced during mouse aging, longitudinal monitoring revealed that VEGF signaling was greatly reduced in multiple key organs. This was associated with increased production of soluble VEGFR1 (sVEGFR1) generated through an age-related shift in alternative splicing of VEGFR1 mRNA and its activity as a VEGF trap. A modest increase of circulatory VEGF using a transgenic VEGF gain-of-function system or adeno-associated virus (AAV)–assisted VEGF transduction maintained a more youthful level of VEGF signaling and provided protection from age-related capillary loss, compromised perfusion, and reduced tissue oxygenation. Aging hallmarks such as mitochondrial dysfunction, compromised metabolic flexibility, endothelial cell senescence, and inflammaging were alleviated in VEGF-treated mice. Conversely, VEGF loss of function by conditional induction of transgenic sFlt1 in endothelial cells accelerated the development of these adverse age-related phenotypes. VEGF-treated mice lived longer and had an extended health span, as reflected by reduced abdominal fat accumulation, reduced liver steatosis, reduced muscle loss (sarcopenia) associated with better preservation of muscle-generating force, reduced bone loss (osteoporosis), reduced kyphosis, and reduced burden of spontaneous tumors.

Conclusion: The study provides compelling evidence for the proposition that vascular aging is a hierarchically high driver of overall organismal aging. It places VEGF signaling insufficiency at center stage to multi-organ aging and suggests that its undoing might confer comprehensive geroprotection.

“The Economic Value of Targeting Aging”, Scott et al 2021

“The economic value of targeting aging”⁠, Andrew J. Scott, Martin Ellison, David A. Sinclair (2021-07-05; backlinks; similar):

Developments in life expectancy and the growing emphasis on biological and ‘healthy’ aging raise a number of important questions for health scientists and economists alike. Is it preferable to make lives healthier by compressing morbidity, or longer by extending life? What are the gains from targeting aging itself compared to efforts to eradicate specific diseases? Here we analyze existing data to evaluate the economic value of increases in life expectancy, improvements in health and treatments that target aging.

We show that a compression of morbidity that improves health is more valuable than further increases in life expectancy, and that targeting aging offers potentially larger economic gains than eradicating individual diseases. We show that a slowdown in aging that increases life expectancy by 1 year is worth US$38 trillion, and by 10 years, US$367 trillion.

Ultimately, the more progress that is made in improving how we age, the greater the value of further improvements.

Figure 2: willingness-to-pay (WTP) by year of life for metformin treatment started at age 75. The value for each year (by age) of improvements in the incidence of various diseases under simulated impact of metformin. Sum of separate effects, the total of each individual effect; Total effect, the overall value for each year of health improvements attributed to metformin. Solid lines represent WTP for each of the 5 comorbidities separately.

…The economic value of gains from targeting aging are large because delaying aging produces complementarities between health and longevity, affect a large number of diseases due to the rising prevalence of age-related comorbidities, and create synergies arising from competing risks. Crucially, delaying aging leads to a virtuous circle in which slowing aging begets demand for further slowing in aging. This virtuous circle arises because society’s gains from delaying aging rise with the average age of society, increase with the quality of life in old age, and depend on the number of older people. This provides a distinctive dynamic to targeting aging compared to treatments aimed at specific diseases, in which gains diminish once successful treatments are discovered.

“An Aged Immune System Drives Senescence and Ageing of Solid Organs”, Yousefzadeh et al 2021

2021-yousefzadeh.pdf: “An aged immune system drives senescence and ageing of solid organs”⁠, Matthew J. Yousefzadeh, Rafael R. Flores, Yi Zhu, Zoe C. Schmiechen, Robert W. Brooks, Christy E. Trussoni et al (2021-05-12; similar):

Ageing of the immune system, or immunosenescence, contributes to the morbidity and mortality of the elderly. To define the contribution of immune system ageing to organism ageing, here we selectively deleted Ercc1, which encodes a crucial DNA repair protein, in mouse hematopoietic cells to increase the burden of endogenous DNA damage and thereby senescence in the immune system only. We show that Vav-iCre+/​−;Ercc1−/​fl mice were healthy into adulthood, then displayed premature onset of immunosenescence characterized by attrition and senescence of specific immune cell populations and impaired immune function, similar to changes that occur during ageing in wild-type mice. Notably, non-lymphoid organs also showed increased senescence and damage, which suggests that senescent, aged immune cells can promote systemic ageing. The transplantation of splenocytes from Vav-iCre+/​−;Ercc1−/​fl or aged wild-type mice into young mice induced senescence in trans, whereas the transplantation of young immune cells attenuated senescence. The treatment of Vav-iCre+/​−;Ercc1−/​fl mice with rapamycin reduced markers of senescence in immune cells and improved immune function. These data demonstrate that an aged, senescent immune system has a causal role in driving systemic ageing and therefore represents a key therapeutic target to extend healthy ageing.

“Carbohydrate Restriction for Diabetes: Rediscovering Centuries-old Wisdom”, Lennerz et al 2021

2021-lennerz.pdf: “Carbohydrate restriction for diabetes: rediscovering centuries-old wisdom”⁠, Belinda S. Lennerz, Andrew P. Koutnik, Svetlana Azova, Joseph I. Wolfsdorf, David S. Ludwig (2021-01-04; similar):

Carbohydrate restriction, used since the 1700s to prolong survival in people with diabetes, fell out of favor after the discovery of insulin. Despite costly pharmacological and technological developments in the last few decades, current therapies do not achieve optimal outcomes, and most people with diabetes remain at high risk for microvascular and macrovascular complications. Recently, low-carbohydrate diets have regained popularity, with preliminary evidence of benefit for body weight, postprandial hyperglycemia, hyperinsulinemia, and other cardiometabolic risk factors in type 2 diabetes and, with more limited data, in type 1 diabetes. High-quality, long-term trials are needed to assess safety concerns and determine whether this old dietary approach might help people with diabetes attain clinical targets more effectively, and at a lower cost, than conventional treatment.

“Reprogramming to Recover Youthful Epigenetic Information and Restore Vision”, Lu et al 2020

2020-lu.pdf: “Reprogramming to recover youthful epigenetic information and restore vision”⁠, Yuancheng Lu, Benedikt Brommer, Xiao Tian, Anitha Krishnan, Margarita Meer, Chen Wang, Daniel L. Vera et al (2020-12-02; ; backlinks; similar):

Ageing is a degenerative process that leads to tissue dysfunction and death. A proposed cause of ageing is the accumulation of epigenetic noise that disrupts gene expression patterns, leading to decreases in tissue function and regenerative capacity. Changes to DNA methylation patterns over time form the basis of ageing clocks, but whether older individuals retain the information needed to restore these patterns—and, if so, whether this could improve tissue function—is not known.

Over time, the central nervous system (CNS) loses function and regenerative capacity. Using the eye as a model CNS tissue, here we show that ectopic expression of Oct4 (also known as Pou5f1), Sox2 and Klf4 genes (OSK) in mouse retinal ganglion cells restores youthful DNA methylation patterns and transcriptomes, promotes axon regeneration after injury, and reverses vision loss in a mouse model of glaucoma and in aged mice. The beneficial effects of OSK-induced reprogramming in axon regeneration and vision require the DNA demethylases TET1 and TET2.

These data indicate that mammalian tissues retain a record of youthful epigenetic information—encoded in part by DNA methylation—that can be accessed to improve tissue function and promote regeneration in vivo.

“Effect of Vitamin D Supplementation, Omega–3 Fatty Acid Supplementation, or a Strength-Training Exercise Program on Clinical Outcomes in Older Adults: The DO-HEALTH Randomized Clinical Trial”, Bischoff-Ferrari et al 2020

2020-bischoffferrari.pdf: “Effect of Vitamin D Supplementation, Omega–3 Fatty Acid Supplementation, or a Strength-Training Exercise Program on Clinical Outcomes in Older Adults: The DO-HEALTH Randomized Clinical Trial”⁠, Heike A. Bischoff-Ferrari, Bruno Vellas, René Rizzoli, Reto W. Kressig, José A. P. da Silva, Michael Blauth et al (2020-11-10; ; similar):

Key Points:

Question: Do vitamin D, omega-3, and a strength-training exercise program alone or in combination prevent 6 health outcomes among relatively healthy adults aged 70 years or older?

Findings: In this randomized trial that included 2157 adults aged 70 years or older, 3-year treatment with vitamin D3 (2000 IU/​d), with omega-3 fatty acids (1 g/​d), or with a strength-training exercise program did not result in statistically-significant differences in improvement in systolic or diastolic blood pressure, nonvertebral fractures, physical performance, infection rate, or cognition.

Meaning: These findings do not support the use of vitamin D, omega-3, or a strength-training exercise program for these clinical outcomes among relatively healthy older adults. Abstract

Importance: The benefits of vitamin D, omega-3 fatty acids, and exercise in disease prevention remain unclear.

Objective: To test whether vitamin D, omega-3s, and a strength-training exercise program, alone or in combination, improved 6 health outcomes among older adults.

Design, Setting, and Participants: Double-blind, placebo-controlled, 2 × 2 × 2 factorial randomized clinical trial among 2157 adults aged 70 years or older who had no major health events in the 5 years prior to enrollment and had sufficient mobility and good cognitive status. Patients were recruited between December 2012 and November 2014, and final follow-up was in November 2017.

Interventions: Participants were randomized to 3 years of intervention in 1 of the following 8 groups: 2000 IU/​d of vitamin D3, 1 g/​d of omega-3s, and a strength-training exercise program (n = 264); vitamin D3 and omega-3s (n = 265); vitamin D3 and exercise (n = 275); vitamin D3 alone (n = 272); omega-3s and exercise (n = 275); omega-3s alone (n = 269); exercise alone (n = 267); or placebo (n = 270).

Main Outcomes and Measures: The 6 primary outcomes were change in systolic and diastolic blood pressure (BP), Short Physical Performance Battery (SPPB), Montreal Cognitive Assessment (MoCA), and incidence rates (IRs) of nonvertebral fractures and infections over 3 years. Based on multiple comparisons of 6 primary end points, 99% confidence intervals are presented and p < 0.01 was required for statistical-significance.

Results: Among 2157 randomized participants (mean age, 74.9 years; 61.7% women), 1900 (88%) completed the study. Median follow-up was 2.99 years. Overall, there were no statistically-significant benefits of any intervention individually or in combination for the 6 end points at 3 years. For instance, the differences in mean change in systolic BP with vitamin D vs no vitamin D and with omega-3s vs no omega-3s were both −0.8 (99% CI, –2.1 to 0.5) mm Hg, with p < 0.13 and p < 0.11, respectively; the difference in mean change in diastolic BP with omega-3s vs no omega-3s was –0.5 (99% CI, –1.2 to 0.2) mm Hg; p = 0.06); and the difference in mean change in IR of infections with omega-3s vs no omega-3s was –0.13 (99% CI, –0.23 to –0.03), with an IR ratio of 0.89 (99% CI, 0.78–1.01; p = 0.02). No effects were found on the outcomes of SPPB, MoCA, and incidence of nonvertebral fractures). A total of 25 deaths were reported, with similar numbers in all treatment groups.

Table 1: Summary results.

Conclusions and Relevance: Among adults without major comorbidities aged 70 years or older, treatment with vitamin D3, omega-3s, or a strength-training exercise program did not result in statistically-significant differences in improvement in systolic or diastolic blood pressure, nonvertebral fractures, physical performance, infection rates, or cognitive function. These findings do not support the effectiveness of these 3 interventions for these clinical outcomes.

Trial Registration: ClinicalTrials.gov Identifier: NCT01745263

“Surprisingly Long Survival of Premature Conclusions about Naked Mole-rat Biology”, Braude et al 2020

2020-braude.pdf: “Surprisingly long survival of premature conclusions about naked mole-rat biology”⁠, Stan Braude, Susanne Holtze, Sabine Begall, Julia Brenmoehl, Hynek Burda, Philip Dammann, Delphine del Marmol et al (2020-10-30; similar):

Naked mole-rats express many unusual traits for such a small rodent. Their morphology, social behaviour, physiology, and ageing have been well studied over the past half-century. Many early findings and speculations about this subterranean species persist in the literature, although some have been repeatedly questioned or refuted. While the popularity of this species as a natural-history curiosity, and oversimplified story-telling in science journalism, might have fuelled the perpetuation of such misconceptions, an accurate understanding of their biology is especially important for this new biomedical model organism. We review 28 of these persistent myths about naked mole-rat sensory abilities, ecophysiology, social behaviour, development and ageing, and where possible we explain how these misunderstandings came about.

  • Ecophysiology and environment:

    • naked mole-rats are hairless
    • naked mole-rats are strictly subterranean and never go above ground
    • naked mole-rats have unusually long burrows
    • naked mole-rats are the only poikilothermic mammals
    • naked mole-rats have uniquely low thyroid hormone levels
    • naked mole-rat burrows are hypoxic and hypercapnic
  • Sensory ecology

    • Naked mole-rats are blind
    • naked mole-rats have degenerated hearing
    • naked mole-rats are the most vocal rodents because they live in large groups
    • naked mole-rats feel no pain
  • Social behaviour and reproduction:

    • naked mole-rats are the only eusocial mammals
    • colonies have castes of breeders and non-breeders, involving frequent workers, infrequent workers, non-workers, and dispersers
    • colonies have up to three male breeders (pashas)
    • colonies have a single queen
    • not all females can become queens
    • queens suppress workers with pheromones
    • queens shove workers to get them to work
    • naked mole-rats never leave their natal colonies
    • naked mole-rats are inbred
  • Development, longevity, ageing and senescence:

    • the GH/​IGF axis is impaired in naked mole-rats
    • naked mole-rats are long-lived because they have low oxidative stress and damage
    • naked mole-rat cells do not display cellular senescence
    • naked mole-rats are immune to disease
    • naked mole-rats do not get tumours or cancer
    • naked mole-rats have extremely large hyaluronan
    • naked mole-rat cells have early contact inhibition that prevents cancer
    • naked mole-rats are non-ageing
  • Taxonomy:

    • naked mole-rats are the single member of a taxonomic family

“C60 in Olive Oil Causes Light-dependent Toxicity and Does Not Extend Lifespan in Mice”, Grohn et al 2020

2020-grohn.pdf: “C60 in olive oil causes light-dependent toxicity and does not extend lifespan in mice”⁠, Kristopher J. Grohn, Brandon S. Moyer, Danique C. Wortel, Cheyanne M. Fisher, Ellie Lumen, Anthony H. Bianchi et al (2020-10-29; ; backlinks; similar):

C60 is a potent antioxidant that has been reported to substantially extend the lifespan of rodents when formulated in olive oil (C60-OO) or extra virgin olive oil (C60-EVOO). Despite there being no regulated form of C60-OO, people have begun obtaining it from online sources and dosing it to themselves or their pets, presumably with the assumption of safety and efficacy. In this study, we obtain C60-OO from a sample of online vendors, and find marked discrepancies in appearance, impurity profile, concentration, and activity relative to pristine C60-OO formulated in-house. We additionally find that pristine C60-OO causes no acute toxicity in a rodent model but does form toxic species that can cause statistically-significant morbidity and mortality in mice in under 2 weeks when exposed to light levels consistent with ambient light. Intraperitoneal injections of C60-OO did not affect the lifespan of CB6F1 female mice. Finally, we conduct a lifespan and health span study in males and females C57BL/​6 J mice comparing oral treatment with pristine C60-EVOO and EVOO alone versus untreated controls. We failed to observe statistically-significant lifespan and health span benefits of C60-EVOO or EVOO supplementation compared to untreated controls, both starting the treatment in adult or old age. Our results call into question the biological benefit of C60-OO in aging.

“Reversal of Epigenetic Age With Diet and Lifestyle in a Pilot Randomized Clinical Trial”, Fitzgerald et al 2020

“Reversal of Epigenetic Age with Diet and Lifestyle in a Pilot Randomized Clinical Trial”⁠, Kara Fitzgerald, Romilly Hodges, Douglas Hanes, Emily Stack, David Cheishvili, Moshe Szyf, Janine Henkel et al (2020-07-14; ; backlinks; similar):

Manipulations to set back biological age and extend lifespan in animal models are well established, and translation to humans has begun. The length of human life makes it impractical to evaluate results by plotting mortality curves, so surrogate markers of age have been suggested and, at present, the best established surrogates are DNA methylation clocks. Herein we report on a randomized, controlled clinical trial designed to be a first step in evaluating the effect of a diet and lifestyle intervention on biological age. Compared to participants in the control group (n = 20), participants in the treatment group tested an average 3.23 years younger at the end of the eight-week program according to the Horvath DNAmAge clock (p = 0.018). Those in the treatment group (n = 18) tested an average 1.96 years younger at the end of the program compared to the same individuals at the beginning with a strong trend towards statistical-significance (p = 0.066 for within group change). This is the first such trial to demonstrate a potential reversal of biological age. In this study, the intervention was confined to diet and lifestyle changes previously identified as safe to use. The prescribed program included multiple components with documented mechanistic activity on epigenetic pathways, including moderate exercise, breathing exercises for stress, and a diet rich in methyl donor nutrients and polyphenols.

“Epigenetic Clocks: A Review”, Luis 2020

“Epigenetic clocks: A review”⁠, José Luis (2020-06-16; backlinks; similar):

It has recently been found possible to estimate age, mortality risk, or general health by looking merely at the epigenome. The models used to do so are referred to as epigenetic (or methylation) clocks⁠.

Epigenetic clocks are increasingly becoming a popular choice for scientists in the field of aging research to measure the putative efficacy of anti-aging interventions. They may make it possible to get results before full Kaplan-Meier curves are available, and they could serve, at least seemingly, as a replacement for a host of other biomarkers. I recommend reading the introductory sections of “The Longevity FAQ” as well as those about epigenetics before reading this post as it gives some more context.

Conclusion

Even with a small number of the CpGs of the epigenome measured, it has been possible to construct clocks that accurately track age and health. We still don’t know exactly why the clocks work, just that they do. There is some interesting evidence pointing out to at least part of the pattern seem in the aged epigenome being causal, not just a reflection of the overall condition of the tissue or organism, so we may soon see the epigenome becoming a target for novel drugs. If you want to continue reading about this, Bell et. al 2019’s review (from where I extract the table below) and Raj & Horvath 2020 are the best starting points.

“The Burden of Rare Protein-truncating Genetic Variants on Human Lifespan”, Liu et al 2020

“The burden of rare protein-truncating genetic variants on human lifespan”⁠, Jimmy Z. Liu, Chia-Yen Chen, Ellen A. Tsai, Christopher D. Whelan, David Sexton, Sally John, Heiko Runz et al (2020-06-03; ):

Genetic predisposition is believed to contribute substantially to the age at which we die. Genome-wide association studies (GWAS) have implicated more than 20 genetic loci to phenotypes related to human lifespan1. However, little is known about how lifespan is impacted by gene loss-of-function. Through whole-exome sequencing of 238,239 UK Biobank participants, we assessed the relevance of protein-truncating variant (PTV) gene burden on individual and parental survival. We identified exome-wide (p < 2.5e-6) statistically-significant associations between BRCA2, BRCA1, TET2, PPM1D, LDLR, EML2 and DEDD2 PTV-burden with human lifespan. Gene and gene-set PTV-burden phenome-wide association studies (PheWAS) further highlighted the roles of these genes in cancer and cardiovascular disease as relevant for overall survival. The overlap between PTV-burden and prior GWAS results was modest, underscoring the value of sequencing in well-powered cohorts to complement GWAS for identifying loci associated with complex traits and disease.

“Reversal of Aging via in Vivo Epigenetic Reprogramming”, Lu 2020b

2020-lu-2.pdf: “Reversal of Aging via in Vivo Epigenetic Reprogramming”⁠, Yuancheng Lu (2020-05-12; ; similar):

Aging is a degenerative process leading to tissue dysfunction and death. A proposed cause of aging is the accumulation of epigenetic noise, which disrupts youthful gene expression patterns that are required for cells to function optimally and recover from damage. Changes to DNA methylation patterns over time form the basis of ‘aging clocks’, but whether old individuals retain information to reset the clocks and, if so, whether it would improve tissue function is not known. Of all the tissues in the body, the central nervous system (CNS) is one of the first to lose regenerative capacity. Using the eye as a model tissue, we show that expression of Oct4, Sox2, and Klf4 genes (OSK) in mice resets youthful gene expression patterns and the DNA methylation age of retinal ganglion cells, promotes axon regeneration after optic nerve crush injury, and restores vision in a mouse model of glaucoma and in normal aged mice. This process, which we call the reversal of information loss via epigenetic reprogramming or REVIVER, requires non-global, active DNA demethylation by TET enzymes and the downstream enzyme TDG, indicating that alterations in DNA methylation patterns may not simply indicate age, but participate in aging. Thus, old tissues retain a faithful record of youthful epigenetic information that can be accessed for functional age reversal.

[Paper version of thesis: “Reprogramming to recover youthful epigenetic information and restore vision [in mice]”⁠, Lu et al 2020.]

“Current Perspectives on the Cellular and Molecular Features of Epigenetic Ageing”, Raj & Horvath 2020

2020-raj.pdf: “Current perspectives on the cellular and molecular features of epigenetic ageing”⁠, Kenneth Raj, Steve Horvath (2020-04-10; backlinks; similar):

It has been noted for quite some time that DNA methylation levels decline with age. The importance of this change remained unknown until it became possible to measure methylation status of specific sites on the DNA.

It was observed that while the methylation of some sites does indeed decrease with age, that of others increase or remain unchanged. The application of machine learning methods to these quantitative changes in multiple sites, allowed the generation of a highly accurate estimator of age, called the epigenetic clock. The application of this clock on large human epidemiological data sets revealed that discordance between the predicted (epigenetic age) and chronological age is associated with many age-related pathologies, particularly when the former is greater than the latter. The epigenetic clock clearly captures to some degree, biological features that accompany the ageing process.

Despite the ever-increasing scope of pathologies that are found to be associated with accelerated epigenetic ageing, the basic principles that underlie the ticking of the clock remain elusive. Here, we describe the known molecular and cellular attributes of the clock and consider their properties, and proffer opinions as to how they may be connected and what might be the underlying mechanism. Emerging from these considerations is the inescapable view that epigenetic ageing begins from very early moments after the embryonic stem cell stage and continues un-interrupted through the entire life-course.

This appears to be a consequence of processes that are necessary for the development of the organism from conception and to maintain it thereafter through homeostasis. Hence, while the speed of ageing can, and is affected by external factors, the essence of the ageing process itself is an integral part of, and the consequence of the development of life.

Impact statement: The field of epigenetic ageing is relatively new, and the speed of its expansion presents a challenge in keeping abreast with new discoveries and their implications. Several reviews have already addressed the great number of pathologies, health conditions, life-style, and external stressors that are associated with changes to the rate of epigenetic ageing. While these associations highlight and affirm the ability of epigenetic clock to capture biologically meaningful changes associated with age, they do not inform us about the underlying mechanisms.

In this very early period since the development of the clock, there have been rather limited experimental research that are aimed at uncovering the mechanism. Hence, the perspective that we proffer is derived from available but nevertheless limited lines of evidence that together provide a seemingly coherent narrative that can be tested. This, we believe would be helpful towards uncovering the workings of the epigenetic clock.

“Cryonics for All?”, Thau 2020

2020-thau.pdf: “Cryonics for all?”⁠, Tena Thau (2020-01-31; ⁠, ; backlinks)

“Vitamin D Supplementation for Prevention of Mortality in Adults”, G et al 2019b

2014-bjelakovic-2.pdf: “Vitamin D supplementation for prevention of mortality in adults”⁠, Bjelakovic G, Gluud LL, Nikolova D, Whitfield K, Wetterslev J, Simonetti RG, Bjelakovic M, Gluud C. (2019-12-17; backlinks)

“The Genetics of Human Ageing”, Melzer et al 2019

2019-melzer.pdf: “The genetics of human ageing”⁠, David Melzer, Luke C. Pilling, Luigi Ferrucci (2019-11-05)

“Erosion of the Epigenetic Landscape and Loss of Cellular Identity As a Cause of Aging in Mammals”, Yang et al 2019

“Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals”⁠, Jae-Hyun Yang, Patrick T. Griffin, Daniel L. Vera, John K. Apostolides, Motoshi Hayano, Margarita V. Meer et al (2019-10-19; similar):

All living things experience entropy⁠, manifested as a loss of inherited genetic and epigenetic information over time. As budding yeast cells age, epigenetic changes result in a loss of cell identity and sterility, both hallmarks of yeast aging. In mammals, epigenetic information is also lost over time, but what causes it to be lost and whether it is a cause or a consequence of aging is not known. Here we show that the transient induction of genomic instability, in the form of a low number of non-mutagenic DNA breaks, accelerates many of the chromatin and tissue changes seen during aging, including the erosion of the epigenetic landscape, a loss of cellular identity, advancement of the DNA methylation clock and cellular senescence. These data support a model in which a loss of epigenetic information is a cause of aging in mammals.

One Sentence Summary

The act of repairing DNA breaks induces chromatin reorganization and a loss of cell identity that may contribute to mammalian aging

“Effect of Lower Versus Higher Red Meat Intake on Cardiometabolic and Cancer Outcomes: A Systematic Review of Randomized Trials”, Zeraatkar et al 2019

2019-zeraatkar.pdf: “Effect of Lower Versus Higher Red Meat Intake on Cardiometabolic and Cancer Outcomes: A Systematic Review of Randomized Trials”⁠, Dena Zeraatkar, Bradley C. Johnston, Jessica Bartoszko, Kevin Cheung, Malgorzata M. Bala, Claudia Valli et al (2019-10-01; ; backlinks; similar):

Background: Few randomized trials have evaluated the effect of reducing red meat intake on clinically important outcomes.

Purpose: To summarize the effect of lower versus higher red meat intake on the incidence of cardiometabolic and cancer outcomes in adults.

Data Sources: Embase⁠, CENTRAL, CINAHL, Web of Science⁠, and ProQuest from inception to July 2018 and MEDLINE from inception to April 2019, without language restrictions.

Study Selection: Randomized trials (published in any language) comparing diets lower in red meat with diets higher in red meat that differed by a gradient of at least 1 serving per week for 6 months or more.

Data Extraction: Teams of 2 reviewers independently extracted data and assessed the risk of bias and the certainty of the evidence.

Data Synthesis: Of 12 eligible trials, a single trial enrolling 48 835 women provided the most credible, though still low-certainty, evidence that diets lower in red meat may have little or no effect on all-cause mortality (hazard ratio [HR], 0.99 [95% CI, 0.95 to 1.03]), cardiovascular mortality (HR, 0.98 [CI, 0.91 to 1.06]), and cardiovascular disease (HR, 0.99 [CI, 0.94 to 1.05]). That trial also provided low-certainty to very-low-certainty evidence that diets lower in red meat may have little or no effect on total cancer mortality (HR, 0.95 [CI, 0.89 to 1.01]) and the incidence of cancer, including colorectal cancer (HR, 1.04 [CI, 0.90 to 1.20]) and breast cancer (HR, 0.97 [0.90 to 1.04]).

Limitations: There were few trials, most addressing only surrogate outcomes, with heterogeneous comparators and small gradients in red meat consumption between lower versus higher intake groups.

Conclusion: Low-certainty to very-low-certainty evidence suggests that diets restricted in red meat may have little or no effect on major cardiometabolic outcomes and cancer mortality and incidence.

“Exercise Conditioned Plasma Dampens Inflammation via Clusterin and Boosts Memory”, Miguel et al 2019

“Exercise conditioned plasma dampens inflammation via clusterin and boosts memory”⁠, Zurine De Miguel, Michael J. Betley, Drew Willoughby, Benoit Lehallier, Niclas Olsson, Liana Bonanno et al (2019-09-19; ; similar):

Physical exercise seems universally beneficial to human and animal health, slowing cognitive aging and neurodegeneration. Cognitive benefits are tied to increased plasticity and reduced inflammation within the hippocampus, yet little is known about the factors and mechanisms mediating these effects. We discovered “runner” plasma, collected from voluntarily running mice, infused into sedentary mice recapitulates the cellular and functional benefits of exercise on the brain. Importantly, runner plasma reduces baseline neuroinflammatory gene expression and prominently suppresses experimentally induced brain inflammation. Plasma proteomic analysis shows a striking increase in complement cascade inhibitors including clusterin, which is necessary for the anti-inflammatory effects of runner plasma. Cognitively impaired patients participating in structured exercise for 6 months showed higher plasma clusterin levels, which correlated positively with improvements in endurance and aerobic capacity. These findings demonstrate the existence of anti-inflammatory “exercise factors” that are transferable, benefit the brain, and are present in humans engaging in exercise.

“TRIIM: Reversal of Epigenetic Aging and Immunosenescent Trends in Humans”, Fahy et al 2019

2019-fahy.pdf: “TRIIM: Reversal of epigenetic aging and immunosenescent trends in humans”⁠, Gregory M. Fahy, Robert T. Brooke, James P. Watson, Zinaida Good, Shreyas S. Vasanawala, Holden Maecker et al (2019-09-08; backlinks; similar):

Epigenetic “clocks” can now surpass chronological age in accuracy for estimating biological age. Here, we use four such age estimators to show that epigenetic aging can be reversed in humans. Using a protocol intended to regenerate the thymus, we observed protective immunological changes, improved risk indices for many age-related diseases, and a mean epigenetic age ~1.5 years less than baseline after 1 year of treatment (−2.5-year change compared to no treatment at the end of the study). The rate of epigenetic aging reversal relative to chronological age accelerated from −1.6 year/​year from 0–9 month to −6.5 year/​year from 9–12 month. The GrimAge predictor of human morbidity and mortality showed a 2-year decrease in epigenetic vs. chronological age that persisted six months after discontinuing treatment. This is to our knowledge the first report of an increase, based on an epigenetic age estimator, in predicted human lifespan by means of a currently accessible aging intervention.

“A Prospective Analysis of Genetic Variants Associated With Human Lifespan”, Wright et al 2019

“A Prospective Analysis of Genetic Variants Associated with Human Lifespan”⁠, Kevin M. Wright, Kristin A. Rand, Amir Kermany, Keith Noto, Don Curtis, Daniel Garrigan, Dmitri Slinkov et al (2019-09; ; similar):

We present a massive investigation into the genetic basis of human lifespan. Beginning with a genome-wide association (GWAS) study using a de-identified snapshot of the unique AncestryDNA database—more than 300,000 genotyped individuals linked to pedigrees of over 400,000,000 people—we mapped six genome-wide statistically-significant loci associated with parental lifespan. We compared these results to a GWA analysis of the traditional lifespan proxy trait, age, and found only one locus, APOE, to be associated with both age and lifespan. By combining the AncestryDNA results with those of an independent UK Biobank dataset, we conducted a meta-analysis of more than 650,000 individuals and identified fifteen parental lifespan-associated loci. Beyond just those statistically-significant loci, our genome-wide set of polymorphisms accounts for up to 8% of the variance in human lifespan; this value represents a large fraction of the heritability estimated from phenotypic correlations between relatives.

“Restoration of Brain Circulation and Cellular Functions Hours Post-mortem”, Vrselja et al 2019

2019-vrselja.pdf: “Restoration of brain circulation and cellular functions hours post-mortem”⁠, Zvonimir Vrselja, Stefano G. Daniele, John Silbereis, Francesca Talpo, Yury M. Morozov, André M. M. Sousa et al (2019-05-17; similar):

The brains of humans and other mammals are highly vulnerable to interruptions in blood flow and decreases in oxygen levels. Here we describe the restoration and maintenance of microcirculation and molecular and cellular functions of the intact pig brain under ex vivo normothermic conditions up to four hours post-mortem. We have developed an extracorporeal pulsatile-perfusion system and a haemoglobin-based, acellular, non-coagulative, echogenic, and cytoprotective perfusate that promotes recovery from anoxia, reduces reperfusion injury, prevents oedema, and metabolically supports the energy requirements of the brain. With this system, we observed preservation of cytoarchitecture; attenuation of cell death; and restoration of vascular dilatory and glial inflammatory responses, spontaneous synaptic activity, and active cerebral metabolism in the absence of global electrocorticographic activity. These findings demonstrate that under appropriate conditions the isolated, intact large mammalian brain possesses an underappreciated capacity for restoration of microcirculation and molecular and cellular activity after a prolonged post-mortem interval.

“Genetically Heterogeneous Mice Exhibit a Female Survival Advantage That Is Age-specific and Site-specific: Results from a Large Multi-site Study”, Cheng et al 2019

“Genetically heterogeneous mice exhibit a female survival advantage that is age-specific and site-specific: Results from a large multi-site study”⁠, Catherine J. Cheng, Jonathan A. L. Gelfond, Randy Strong, James F. Nelson (2019-02-23; ; backlinks; similar):

[See also Lucanic et al 2017 on C. elegans] The female survival advantage is a robust characteristic of human longevity. However, underlying mechanisms are not understood, and rodent models exhibiting a female advantage are lacking. Here, we report that the genetically heterogeneous (UM-HET3) mice used by the National Institute on Aging Interventions Testing Program (ITP) are such a model.

Analysis of age-specific survival of 3,690 control ITP mice revealed a female survival advantage paralleling that of humans. As in humans, the female advantage in mice was greatest in early adulthood, peaking around 350 days of age and diminishing progressively thereafter. This persistent finding was observed at 3 geographically distinct sites and in 6 separate cohorts over a 10-year period.

Because males weigh more than females and bodyweight is often inversely related to lifespan, we examined sex differences in the relationship between bodyweight and survival. Although present in both sexes, the inverse relationship between bodyweight and longevity was much stronger in males, indicating that male mortality is more influenced by bodyweight than is female mortality.

In addition, male survival varied more across site and cohort than female survival, suggesting greater resistance of females to environmental modulators of survival. Notably, at 24 months the relationship between bodyweight and longevity shifted from negative to positive in both sexes, similar to the human condition in advanced age.

These results indicate that the UM-HET3 mouse models the human female survival advantage and provide evidence for greater resilience of females to modulators of survival.

“What Do We Need to Know to Treat Degenerative Aging As a Medical Condition to Extend Healthy Lifespan?”, Stambler 2019

2019-stambler.pdf: “What Do We Need to Know to Treat Degenerative Aging as a Medical Condition to Extend Healthy Lifespan?”⁠, Ilia Stambler (2019-01-01)

“A Longitudinal Big Data Approach for Precision Health”, Rose et al 2019

2019-rose.pdf: “A longitudinal big data approach for precision health”⁠, Sophia Miryam Schüssler-Fiorenza Rose, Kévin Contrepois, Kegan J. Moneghetti, Wenyu Zhou, Tejaswini Mishra et al (2019-01-01)

“An Evolutionary Perspective on Why Food Overconsumption Impairs Cognition”, Mattson 2019

2019-mattson.pdf: “An Evolutionary Perspective on Why Food Overconsumption Impairs Cognition”⁠, Mark P. Mattson (2019-01-01)

“Turning Back Time With Emerging Rejuvenation Strategies”, Mahmoudi et al 2019

2019-mahmoudi.pdf: “Turning back time with emerging rejuvenation strategies”⁠, Salah Mahmoudi, Lucy Xu, Anne Brunet (2019-01-01)

“Relaxed Selection Limits Lifespan by Increasing Mutation Load”, Cui et al 2019

2019-cui.pdf: “Relaxed Selection Limits Lifespan by Increasing Mutation Load”⁠, Rongfeng Cui, Tania Medeiros, David Willemsen, Leonardo N. M. Iasi, Glen E. Collier, Martin Graef, Martin Reichard et al (2019-01-01)

“Genomic Underpinnings of Lifespan Allow Prediction and Reveal Basis in Modern Risks”, Timmers et al 2018

“Genomic underpinnings of lifespan allow prediction and reveal basis in modern risks”⁠, Paul RHJ Timmers, Ninon Mounier, Kristi Läll, Krista Fischer, Zheng Ning, Xiao Feng, Andrew Bretherick et al (2018-07-06; ; backlinks; similar):

We use a multi-stage genome-wide association of 1 million parental lifespans of genotyped subjects and data on mortality risk factors to validate previously unreplicated findings near CDKN2B-AS1, ATXN2/​BRAP, FURIN/​FES, ZW10, PSORS1C3, and 13q21.31, and identify and replicate novel findings near GADD45G, KCNK3, LDLR, POM121C, ZC3HC1, and ABO. We also validate previous findings near 5q33.3/​EBF1 and FOXO3, whilst finding contradictory evidence at other loci. Gene set and tissue-specific analyses show that expression in fetal brain cells and adult dorsolateral prefrontal cortex is enriched for lifespan variation, as are gene pathways involving lipid proteins and homeostasis, vesicle-mediated transport, and synaptic function. Individual genetic variants that increase dementia, cardiovascular disease, and lung cancer –but not other cancers-explain the most variance, possibly reflecting modern susceptibilities, whilst cancer may act through many rare variants, or the environment. Resultant polygenic scores predict a mean lifespan difference of around five years of life across the deciles.

“Anti-aging Food That Improves Markers of Health in Senior Dogs by Modulating Gut Microbiota and Metabolite Profiles”, Gebreselassie et al 2018

“Anti-aging food that improves markers of health in senior dogs by modulating gut microbiota and metabolite profiles”⁠, Eden Ephraim Gebreselassie, Matthew I. Jackson, Maha Yerramilli, Dennis E. Jewell (2018-05-16; ⁠, ; similar):

Dysbiosis is one of the major changes in aging that leads to an accumulation of toxic microbial metabolites. The aim of this study was to evaluate the effect of a test food containing components of citrus, carrot, spinach and tomato on gut microbiota and age-related metabolites in senior dogs.

The study was conducted on 36 dogs between 8 and 13 years of age. All dogs were maintained on a control food (control 1), which used corn as major source of fiber. After 30 days, the dogs were divided into two groups of 18 dogs. One of the groups received the test food for 30 days while the other group received the control 2 food, containing multiple whole grains as the test food but without the above added sources of fiber present in the test food. After a washout period on the control 1 food for 30 days, a cross-over was performed so that the test or the control 2 food was fed for 30 days to those dogs which had not yet been fed that food.

Samples from feces and blood were collected after each 30 days period to analyze changes in gut microbial composition and metabolites. The consumption of the test food led to increased proportions of Adlercreutzia, Oscillospira, Phascolarcobacteria, Faecalibacterium and Ruminococcus, Christensenellaceae, Ruminococcaceae, Cyanobacteria and Acidobacteria and decreased proportions of Megamonas, Salmonella, Enterobacteriaceae and Fusobacterium. Pets had higher levels of glycerol and fatty acids and lower levels of pyrraline and mucin amino acids in feces. The test food also reduced circulating levels of pyrraline, symmetric dimethylarginine and phenolic uremic toxins, including the microbial brain toxin, 4-ethylphenyl sulfate. Christensenellaceae abundance was strongly associated with the observed health benefits.

Fermentable fibers from fruits and vegetables enhance health in senior dogs by modulating the gut bacteria and metabolites involved in aging, kidney, brain and gut health.

“Early Time-Restricted Feeding Improves Insulin Sensitivity, Blood Pressure, and Oxidative Stress Even without Weight Loss in Men With Prediabetes”, Sutton et al 2018

2018-sutton.pdf: “Early Time-Restricted Feeding Improves Insulin Sensitivity, Blood Pressure, and Oxidative Stress Even without Weight Loss in Men with Prediabetes”⁠, Elizabeth F. Sutton⁠, Robbie Beyl, Kate S. Early, William T. Cefalu, Eric Ravussin, Courtney M. Peterson et al (2018-01-01)

“Autophagy and the Cell Biology of Age-related Disease”, Leidal et al 2018

2018-leidal.pdf: “Autophagy and the cell biology of age-related disease”⁠, Andrew M. Leidal, Beth Levine, Jayanta Debnath (2018-01-01)

“Effect of Low-Fat vs Low-Carbohydrate Diet on 12-Month Weight Loss in Overweight Adults and the Association With Genotype Pattern or Insulin SecretionThe DIETFITS Randomized Clinical Trial”, Association 2018

2018-gardner.pdf: “Effect of Low-Fat vs Low-Carbohydrate Diet on 12-Month Weight Loss in Overweight Adults and the Association With Genotype Pattern or Insulin SecretionThe DIETFITS Randomized Clinical Trial”⁠, American Medical Association (2018-01-01)

“Selection for Long and Short Sleep Duration in Drosophila Melanogaster Reveals the Complex Genetic Network Underlying Natural Variation in Sleep”, Harbison et al 2017

“Selection for long and short sleep duration in Drosophila melanogaster reveals the complex genetic network underlying natural variation in sleep”⁠, Susan T. Harbison, Yazmin L. Serrano Negron, Nancy F. Hansen, Amanda S. Lobell (2017-11-01; ⁠, ; backlinks):

[available as the Sleep Inbred Panel] Why do some individuals need more sleep than others? Forward mutagenesis screens in flies using engineered mutations have established a clear genetic component to sleep duration, revealing mutants that convey very long or short sleep. Whether such extreme long or short sleep could exist in natural populations was unknown.

We applied artificial selection for high and low night sleep duration to an outbred population of Drosophila melanogaster for 13 generations.

At the end of the selection procedure, night sleep duration diverged by 9.97 hours in the long and short sleeper populations, and 24-hour sleep was reduced to 3.3 hours in the short sleepers. Neither long nor short sleeper lifespan differed appreciably from controls, suggesting little physiological consequences to being an extreme long or short sleeper.

Whole genome sequence data from seven generations of selection revealed several hundred thousand changes in allele frequencies at polymorphic loci across the genome. Combining the data from long and short sleeper populations across generations in a logistic regression implicated 126 polymorphisms in 80 candidate genes, and we confirmed three of these genes and a larger genomic region with mutant and chromosomal deficiency tests, respectively. Many of these genes could be connected in a single network based on previously known physical and genetic interactions. Candidate genes have known roles in several classic, highly conserved developmental and signaling pathways—EGFR, Wnt, Hippo, and MAPK.

The involvement of highly pleiotropic pathway genes suggests that sleep duration in natural populations can be influenced by a wide variety of biological processes, which may be why the purpose of sleep has been so elusive.


One of the biggest mysteries in biology is the need to sleep. Sleep duration has an underlying genetic basis, suggesting that very long and short sleep times could be bred for experimentally. How far can sleep duration be driven up or down? Here we achieved extremely long and short night sleep duration by subjecting a wild-derived population of Drosophila melanogaster to an experimental breeding program. At the end of the breeding program, long sleepers averaged 9.97 hours more nightly sleep than short sleepers. We analyzed whole-genome sequences from seven generations of the experimental breeding to identify allele frequencies that diverged between long and short sleepers, and verified genes and genomic regions with mutation and deficiency testing. These alleles map to classic developmental and signaling pathways, implicating many diverse processes that potentially affect sleep duration.

…Sleep was measured in 100 virgin males and 100 virgin females of each population each generation. The 25% most extreme long (short) sleepers were chosen as parents for the next generation of the long (short) sleeping populations. Control populations were maintained by choosing 25% of the males and females at random to be parents for the next generation. Night sleep duration, defined as sleep during the lights-off period, ranges from 0 to 12 hours (720 minutes).

Unselected control populations averaged 495.9 ± 11.71 (replicate 1) and 364.9 ± 11.99 (replicate 2) minutes of night sleep at generation 13 and were not statistically-significantly different from night sleep in the outbred population prior to selection (Figure 1A; S3 Table).

…Flies responded rapidly and dramatically to 13 generations of artificial selection (Figure 1A; p = 0.0002; S1 and S2 Tables). Night sleep in the short-sleeping populations was reduced to 111.9 ± 10.74 minutes (replicate 1) and 54.8 ± 5.66 minutes (replicate 2) by generation 13. In contrast, night sleep in the long-sleeping populations was increased to 685.0 ± 3.35 (replicate 1) and 678.5 ± 3.46 minutes (replicate 2) in the same generation. Night sleep differed by 598.4 minutes (9.97 hours) on average between long sleepers and short sleepers. The phenotypic response was moderately asymmetrical in the direction of decreased night sleep (p = 0.0344; Figure 1A).

Figure 1: Phenotypic response to artificial selection for night sleep duration. (A), combined-sex average night sleep duration ± SE is plotted for each generation of selection; (B), combined-sex night sleep coefficient of environmental variation (CVE) is plotted for each generation of selection; (C) & (D), combined-sex cumulative selection differential (ΣS) versus combined-sex cumulative response (ΣR) for (C) long sleep and (D) short sleep populations; (E), combined-sex cumulative differential (ΣD) versus combined-sex cumulative response (ΣR) for the control populations. Light blue and dark blue triangles indicate Replicate 1 and Replicate 2 populations selected for long sleep; Light red and dark red squares indicate Replicate 1 and Replicate 2 populations selected for short sleep; and light gray and black circles indicate Replicate 1 and Replicate 2 control populations.

…The estimated realized heritabilities h2, which indicate the degree to which the animals responded to the selection procedure, were relatively high for long-sleepers;65, 68–70 h2 = 0.310 ± 0.022 and h2 = 0.238 ± 0.032 (all p < 0.0001) for replicates 1 and 2, respectively (Figure 1C). For short sleepers, the realized heritabilities were h2 = 0.179 ± 0.026 and h2 = 0.215 ± 0.017 (all p < 0.0001) (Figure 1D). In addition, the regression of the control after 13 generations of breeding with random parents was not statistically-significant, {-0.108 ± 0.312 (p = 0.7368) and −0.271 ± 0.206 (p = 0.2161) for replicates 1 and 2 (Figure 1E)}, suggesting that inbreeding depression did not impact these populations.67 Thus, the outbred population, which was derived from DGRP lines with the largest mean differences in night sleep duration responded rapidly to artificial selection for long or short night sleep. This heritable response indicates that these populations will be informative for identifying genes and pathways involved in night sleep duration.

Response of life history traits to selection for long or short night sleep duration: Sleep is crucial for life, yet its relationship to important life history and fitness traits is not well understood. Several previous mutagenesis screens have noted reduced lifespan in mutants with short sleep duration,44, 45, 49, 51, 77, 78 though there are exceptions.51, 79 We measured lifespan in all 6 selection populations; in contrast to the reduced lifespan seen in short-sleeping mutants, we found no statistically-significant differences in lifespan for either sex in any of the selection populations (Figure 4A; S5 Table).

If we assume that sleep is associated with fitness, an asymmetrical response to selection would indicate reduced fitness in the direction of the greater response to selection.67 Thus, we would predict that short-sleeping flies would be less fit than long-sleeping ones. To investigate this possibility, we measured egg-to-adult viability as a proxy for fitness. We found no differences among selection populations (Figure 4B; S5 Table). However, we noted a propensity for flies to die during sleep monitoring in the latter generations of the experiment (Figure 4C). Over the course of the entire experiment there were no statistically-significant differences among populations in the numbers of flies surviving, but there were statistically-significant differences in survival at generations 3 (p = 0.0429), 9 (p = 0.0352) and 10 (p = 0.0455). Short-sleeping females were the most vulnerable, though flies of all populations were less likely to survive the sleep monitoring. Thus, any physiological consequences of being an extreme long or short sleeper did not manifest themselves in either lifespan or egg-to-adult viability, but the reduced survival of short sleepers during the later generations of selection suggests that they might be more susceptible to stress.

Figure 4: The response of life history traits to selection for long or short night sleep duration. (A), percentage flies surviving versus lifespan; (B), number of flies surviving to the adult stage versus generation of selection; (C), percentage of males and females surviving sleep assay. Light blue and dark blue triangles indicate Replicate 1 and Replicate 2 populations selected for long sleep; Light red and dark red squares indicate Replicate 1 and Replicate 2 populations selected for short sleep; and light gray and black circles indicate Replicate 1 and Replicate 2 control populations.

“Metformin Reduces All-cause Mortality and Diseases of Ageing Independent of Its Effect on Diabetes Control: A Systematic Review and Meta-analysis”, Campbell et al 2017

2017-campbell.pdf: “Metformin reduces all-cause mortality and diseases of ageing independent of its effect on diabetes control: A systematic review and meta-analysis”⁠, Jared M. Campbell, Susan M. Bellman, Matthew D. Stephenson, Karolina Lisy (2017-11-01; backlinks; similar):

  • Diabetics on metformin have lower morality than non-diabetics and other diabetics.
  • Diabetics on metformin have less cancer than non-diabetics and other diabetics.
  • Diabetics on metformin have less cardiovascular disease than other diabetics.
  • Metformin appears to extend health and life spans independent of its effect on diabetes.
  • Metformin may be able to extend health and lifespans in the general population.

This systematic review investigated whether the insulin sensitizer metformin has a geroprotective effect in humans.

Pubmed and Embase were searched along with databases of unpublished studies. Eligible research investigated the effect of metformin on all-cause mortality or diseases of ageing relative to non-diabetic populations or diabetics receiving other therapies with adjustment for disease control achieved. Overall, 260 full-texts were reviewed and 53 met the inclusion criteria.

Diabetics taking metformin had statistically-significantly lower all-cause mortality than non-diabetics (hazard ratio (HR) = 0.93, 95% CI 0.88–0.99), as did diabetics taking metformin compared to diabetics receiving non-metformin therapies (HR = 0.72, 95% CI 0.65–0.80), insulin (HR = 0.68, 95% CI 0.63–0.75) or sulphonylurea (HR = 0.80, 95% CI 0.66–0.97). Metformin users also had reduced cancer compared to non-diabetics (rate ratio = 0.94, 95% CI 0.92–0.97) and cardiovascular disease (CVD) compared to diabetics receiving non-metformin therapies (HR = 0.76, 95% CI 0.66–0.87) or insulin (HR = 0.78, 95% CI 0.73–0.83).

Differences in baseline characteristics were observed which had the potential to bias findings, although statistical adjustments were made.

The apparent reductions in all-cause mortality and diseases of ageing associated with metformin use suggest that metformin could be extending life and healthspans by acting as a geroprotective agent.

[Keywords: metformin, ageing, insulin sensitizer, lifespan, longevity, geroprotection]

“Genome-wide Meta-analysis Associates HLA-DQA1/DRB1 and LPA and Lifestyle Factors With Human Longevity”, Joshi et al 2017

“Genome-wide meta-analysis associates HLA-DQA1/DRB1 and LPA and lifestyle factors with human longevity”⁠, Peter K. Joshi, Nicola Pirastu, Katherine A. Kentistou, Krista Fischer, Edith Hofer, Katharina E. Schraut et al (2017-10-13; ⁠, ⁠, ⁠, ; backlinks; similar):

Genomic analysis of longevity offers the potential to illuminate the biology of human aging. Here, using genome-wide association meta-analysis of 606,059 parents’ survival, we discover two regions associated with longevity (HLA-DQA1/​DRB1 and LPA). We also validate previous suggestions that APOE, CHRNA3/​5, CDKN2A/​B, SH2B3 and FOXO3A influence longevity. Next we show that giving up smoking, educational attainment, openness to new experience and high-density lipoprotein (HDL) cholesterol levels are most positively genetically correlated with lifespan while susceptibility to coronary artery disease (CAD), cigarettes smoked per day, lung cancer, insulin resistance and body fat are most negatively correlated. We suggest that the effect of education on lifespan is principally mediated through smoking while the effect of obesity appears to act via CAD. Using instrumental variables, we suggest that an increase of one body mass index unit reduces lifespan by 7 months while 1 year of education adds 11 months to expected lifespan.

“A Long Journey to Reproducible Results: Replicating Our Work Took Four Years and 100,000 Worms but Brought Surprising Discoveries”, Lithgow et al 2017

“A long journey to reproducible results: Replicating our work took four years and 100,000 worms but brought surprising discoveries”⁠, Gordon J. Lithgow, Monica Driscoll, Patrick Phillips (2017-08-22; ⁠, ; backlinks; similar):

About 15 years ago, one of us (G.J.L.) got an uncomfortable phone call from a colleague and collaborator. After nearly a year of frustrating experiments, this colleague was about to publish a paper1 chronicling his team’s inability to reproduce the results of our high-profile paper2 in a mainstream journal. Our study was the first to show clearly that a drug-like molecule could extend an animal’s lifespan. We had found over and over again that the treatment lengthened the life of a roundworm by as much as 67%. Numerous phone calls and e-mails failed to identify why this apparently simple experiment produced different results between the labs. Then another lab failed to replicate our study. Despite more experiments and additional publications, we couldn’t work out why the labs were getting different lifespan results. To this day, we still don’t know. A few years later, the same scenario played out with different compounds in other labs…In another, now-famous example, two cancer labs spent more than a year trying to understand inconsistencies6. It took scientists working side by side on the same tumour biopsy to reveal that small differences in how they isolated cells—vigorous stirring versus prolonged gentle rocking—produced different results. Subtle tinkering has long been important in getting biology experiments to work. Before researchers purchased kits of reagents for common experiments, it wasn’t unheard of for a team to cart distilled water from one institution when it moved to another. Lab members would spend months tweaking conditions until experiments with the new institution’s water worked as well as before. Sources of variation include the quality and purity of reagents, daily fluctuations in microenvironment and the idiosyncratic techniques of investigators7. With so many ways of getting it wrong, perhaps we should be surprised at how often experimental findings are reproducible.

…Nonetheless, scores of publications continued to appear with claims about compounds that slow ageing. There was little effort at replication. In 2013, the three of us were charged with that unglamorous task…Our first task, to develop a protocol, seemed straightforward.

But subtle disparities were endless. In one particularly painful teleconference, we spent an hour debating the proper procedure for picking up worms and placing them on new agar plates. Some batches of worms lived a full day longer with gentler technicians. Because a worm’s lifespan is only about 20 days, this is a big deal. Hundreds of e-mails and many teleconferences later, we converged on a technique but still had a stupendous three-day difference in lifespan between labs. The problem, it turned out, was notation—one lab determined age on the basis of when an egg hatched, others on when it was laid. We decided to buy shared batches of reagents from the start. Coordination was a nightmare; we arranged with suppliers to give us the same lot numbers and elected to change lots at the same time. We grew worms and their food from a common stock and had strict rules for handling. We established protocols that included precise positions of flasks in autoclave runs. We purchased worm incubators at the same time, from the same vendor. We also needed to cope with a large amount of data going from each lab to a single database. We wrote an iPad app so that measurements were entered directly into the system and not jotted on paper to be entered later. The app prompted us to include full descriptors for each plate of worms, and ensured that data and metadata for each experiment were proofread (the strain names MY16 and my16 are not the same). This simple technology removed small recording errors that could disproportionately affect statistical analyses.

Once this system was in place, variability between labs decreased. After more than a year of pilot experiments and discussion of methods in excruciating detail, we almost completely eliminated systematic differences in worm survival across our labs (see ‘Worm wonders’)…Even in a single lab performing apparently identical experiments, we could not eliminate run-to-run differences.

…We have found one compound that lengthens lifespan across all strains and species. Most do so in only two or three strains, and often show detrimental effects in others.

“Identifying Genetic Variants That Affect Viability in Large Cohorts”, Mostafavi et al 2017

“Identifying genetic variants that affect viability in large cohorts”⁠, Hakhamanesh Mostafavi, Tomaz Berisa, Felix R. Day, John R. B. Perry, Molly Przeworski, Joseph K. Pickrell et al (2017-08-03; ; similar):

A number of open questions in human evolutionary genetics would become tractable if we were able to directly measure evolutionary fitness. As a step towards this goal, we developed a method to examine whether individual genetic variants, or sets of genetic variants, currently influence viability. The approach consists in testing whether the frequency of an allele varies across ages, accounting for variation in ancestry. We applied it to the Genetic Epidemiology Research on Adult Health and Aging (GERA) cohort and to the parents of participants in the UK Biobank. Across the genome, we found only a few common variants with large effects on age-specific mortality: tagging the APOE ε4 allele and near CHRNA3. These results suggest that when large, even late-onset effects are kept at low frequency by purifying selection⁠. Testing viability effects of sets of genetic variants that jointly influence 1 of 42 traits, we detected a number of strong signals. In participants of the UK Biobank of British ancestry, we found that variants that delay puberty timing are associated with a longer parental life span (P~6.2 × 10−6 for fathers and P~2.0 × 10−3 for mothers), consistent with epidemiological studies. Similarly, variants associated with later age at first birth are associated with a longer maternal life span (P~1.4 × 10−3). Signals are also observed for variants influencing cholesterol levels, risk of coronary artery disease (CAD), body mass index, as well as risk of asthma. These signals exhibit consistent effects in the GERA cohort and among participants of the UK Biobank of non-British ancestry. We also found marked differences between males and females, most notably at the CHRNA3 locus, and variants associated with risk of CAD and cholesterol levels. Beyond our findings, the analysis serves as a proof of principle for how upcoming biomedical data sets can be used to learn about selection effects in contemporary humans.

Author summary:

Our global understanding of adaptation in humans is limited to indirect statistical inferences from patterns of genetic variation, which are sensitive to past selection pressures. We introduced a method that allowed us to directly observe ongoing selection in humans by identifying genetic variants that affect survival to a given age (ie. viability selection). We applied our approach to the GERA cohort and parents of the UK Biobank participants. We found viability effects of variants near the APOE and CHRNA3 genes, which are associated with the risk of Alzheimer disease and smoking behavior, respectively. We also tested for the joint effect of sets of genetic variants that influence quantitative traits. We uncovered an association between longer life span and genetic variants that delay puberty timing and age at first birth. We also detected detrimental effects of higher genetically predicted cholesterol levels, body mass index, risk of coronary artery disease (CAD), and risk of asthma on survival. Some of the observed effects differ between males and females, most notably those at the CHRNA3 gene and variants associated with risk of CAD and cholesterol levels. Beyond this application, our analysis shows how large biomedical data sets can be used to study natural selection in humans.

“Safe Landing Strategies During a Fall: Systematic Review and Meta-Analysis”, Moon & Sosnoff 2017

2016-moon.pdf: “Safe Landing Strategies During a Fall: Systematic Review and Meta-Analysis”⁠, Yaejin Moon, Jacob J. Sosnoff (2017-04-01; similar):

Objectives: To systematically synthesize information on safe landing strategies for a fall, and quantitatively examine the effects of the strategies to reduce the risk of injury from a fall.

Data Sources: PubMed, Web of Science⁠, Cumulative Index to Nursing and Allied Health Literature, and Cochrane Library.

Study Selection: Databases were searched using the combinations of keywords of “falls”, “strategy”, “impact”, and “load.” Randomized controlled trials, cohort studies, pre-post studies, and cross-sectional studies were included.

Data Extraction: Fall strategies were extracted and categorized by falling direction. Measurements of impact loads that reflect the risk of injuries were extracted (eg. impact velocity, impact force, fall duration, impact angle). Hedges’ g was used as effect size to quantify the effect of a protective landing strategy to reduce the impact load.

Data Synthesis: A total of 7 landing strategies (squatting, elbow flexion, forward rotation, martial arts rolling, martial arts slapping, relaxed muscle, stepping) in 13 studies were examined. In general, all strategies, except for the martial arts slapping technique, statistically-significantly reduced impact load (g values = 0.73–2.70). Squatting was an efficient strategy to reduce impact in backward falling (g = 1.77), while elbow flexion with outstretched arms was effective in forward falling (g = 0.82). Also, in sideways falling strategies, martial arts rolling (g = 2.70) and forward rotation (g = 0.82) were the most efficient strategies to reduce impact load.

Conclusions: The results showed that landing strategies have a statistically-significant effect on reducing impact load during a fall and might be effective to reduce the impact load of falling. The current study also highlighted limitations of the previous studies that focused on a young population and self-initiated falls. Further investigation with elderly individuals and unexpected falls is necessary to verify the effectiveness and suitability of the strategies for at-risk populations in real-life falls.

[Keywords: accidental falls, movement, wounds and injuries]

“Dietary Restriction and AMPK Increase Lifespan via Mitochondrial Network and Peroxisome Remodeling”, Weir et al 2017

2017-weir.pdf: “Dietary Restriction and AMPK Increase Lifespan via Mitochondrial Network and Peroxisome Remodeling”⁠, Heather J. Weir, Pallas Yao, Frank K. Huynh, Caroline C. Escoubas, Renata L. Goncalves, Kristopher Burkewitz et al (2017-01-01)

“2,4-Dinitrophenol, the Inferno Drug: a Netnographic Study of User Experiences in the Quest for Leanness”, McVeigh et al 2017

2017-mcveigh.pdf: “2,4-Dinitrophenol, the inferno drug: a netnographic study of user experiences in the quest for leanness”⁠, Jim McVeigh, Jennifer Germain, Marie Claire Van Hout (2017; similar):

Background: Despite not being licensed for human consumption, the Internet has triggered renewed, widespread interest and availability of 2,4-Dinitrophenol (DNP). DNP, a cellular metabolic poison, causes thermogenesis resulting in fat burning and weight loss. Whilst extensively available for purchase online, research on user experiences of DNP is limited.

Methods: A netnographic approach was used to describe user experiences of DNP via online public websites. Public websites discussing DNP were identified and a purposeful sample selected. Discussion threads were downloaded and a textual qualitative analysis conducted. Four themes containing 71 categories were generated.

Results: There exists a plethora of communal folk pharmacological advice and recommendations for DNP manufacture and use, together with associated harms and outcomes. The efficacy and untoward effects of DNP were described and discussed alongside the notion that DNP should only be used by experienced bodybuilders. Dosage and regimes for optimal use were also described.

Conclusion: This unique study provides a rich examination of the knowledge, attitudes, and motivations of DNP users, illustrating the important role of online public websites in sharing information. Further understanding of DNP users and the online communities in which they reside is warranted to facilitate engagement and formulate appropriate and effective policy responses.

[Keywords: 2,4-Dinitrophenol, DNP, fat burn, Internet]

“Nutritional Ecology and the Evolution of Aging”, Raubenheimer et al 2016

2016-raubenheimer.pdf: “Nutritional ecology and the evolution of aging”⁠, David Raubenheimer, Stephen J. Simpson, David G. Le Couteur, Samantha M. Solon-Biet, Sean C. P. Coogan et al (2016-12-15; backlinks; similar):

  • Much aging research concerns a nutrition-related model, dietary restriction, yet the role of nutrition is poorly understood
  • It is widely assumed that energy intake is the causal link between dietary restriction and lifespan
  • Nutritional ecology predicts that specific macronutrient blends (balance), rather than energy, should link diet to lifespan
  • The effects of energy and nutrient balance on lifespan can be partitioned using the Geometric Framework for nutrition
  • This more detailed, ecologically-inspired view can help to reconcile mechanistic and evolutionary theories of aging

Considerable progress has been made in understanding both evolutionary and mechanistic aspects of biological aging, although the 2 areas remain poorly integrated. We suggest that a greater emphasis on ecology can help to remedy this, by focusing on the interface between biological mechanisms and the environments in which they evolved by natural selection⁠.

Among the most salient aspects of the environment relevant to aging is nutrition, and yet in the bulk of aging research nutrition is coarsely represented as dietary restriction or caloric restriction⁠, without consideration for how specific components of diet, beyond “energy” (the undifferentiated mix of macronutrients), are driving the observed effects. More recently, it has become clear that specific nutrients (notably amino acids) and interactions among nutrients (ie. nutritional balance) play important roles in the biology of aging. We show how a method developed in nutritional ecology, called the Geometric Framework for nutrition, can help to understand the nutritional interactions of animals with their environments, by explicitly distinguishing the roles of calories, individual nutrients and nutrient balance. Central to these models are the active regulatory responses that animals use to mediate between variation in the nutritional environment and fitness-related consequences such as lifespan and reproduction.

These homeostatic responses provide a guide for researchers that can help to link the biological mechanisms with evolutionary processes in the context of a multi-dimensional nutritional environment.

[Keywords: aging, evolution, Geometric Framework, healthspan, lifespan, longevity]

“Transient Rapamycin Treatment Can Increase Lifespan and Healthspan in Middle-aged Mice”, Bitto et al 2016

“Transient rapamycin treatment can increase lifespan and healthspan in middle-aged mice”⁠, Alessandro Bitto, Takashi K. Ito, Victor V. Pineda, Nicolas J. LeTexier, Heather Z. Huang, Elissa Sutlief et al (2016-08-23; ; backlinks; similar):

The FDA approved drug rapamycin increases lifespan in rodents and delays age-related dysfunction in rodents and humans. Nevertheless, important questions remain regarding the optimal dose, duration, and mechanisms of action in the context of healthy aging.

Here we show that 3 months of rapamycin treatment is sufficient to increase life expectancy by up to 60% and improve measures of healthspan in middle-aged mice. This transient treatment is also associated with a remodeling of the microbiome⁠, including dramatically increased prevalence of segmented filamentous bacteria in the small intestine. We also define a dose in female mice that does not extend lifespan, but is associated with a striking shift in cancer prevalence toward aggressive hematopoietic cancers and away from non-hematopoietic malignancies.

These data suggest that a short-term rapamycin treatment late in life has persistent effects that can robustly delay aging, influence cancer prevalence, and modulate the microbiome.

“Metformin As a Tool to Target Aging”, Barzilai et al 2016

2016-barzilai.pdf: “Metformin as a Tool to Target Aging”⁠, Nir Barzilai, Jill P. Crandall, Stephen B. Kritchevsky, Mark A. Espeland (2016-01-01; backlinks)

“Performance of Informative Priors Skeptical of Large Treatment Effects in Clinical Trials: A Simulation Study”, Pedroza et al 2015

2015-pedroza.pdf: “Performance of informative priors skeptical of large treatment effects in clinical trials: A simulation study”⁠, Claudia Pedroza, Weilu Han, Van Thi Thanh Truong, Charles Green, Jon E. Tyson (2015-12-13; ; backlinks; similar):

One of the main advantages of Bayesian analyses of clinical trials is their ability to formally incorporate skepticism about large treatment effects through the use of informative priors⁠. We conducted a simulation study to assess the performance of informative normal, Student-t, and beta distributions in estimating relative risk (RR) or odds ratio (OR) for binary outcomes. Simulation scenarios varied the prior standard deviation (SD; level of skepticism of large treatment effects), outcome rate in the control group, true treatment effect, and sample size. We compared the priors with regards to bias, mean squared error (MSE), and coverage of 95% credible intervals. Simulation results show that the prior SD influenced the posterior to a greater degree than the particular distributional form of the prior. For RR, priors with a 95% interval of 0.50–2.0 performed well in terms of bias, MSE, and coverage under most scenarios. For OR, priors with a wider 95% interval of 0.23–4.35 had good performance. We recommend the use of informative priors that exclude implausibly large treatment effects in analyses of clinical trials, particularly for major outcomes such as mortality.

[Keywords: Bayesian analysis, informative priors, large treatment effects, binary data, clinical trial, robust priors]

“Why Correlation Usually ≠ Causation”, Branwen 2014

Causality: “Why Correlation Usually ≠ Causation”⁠, Gwern Branwen (2014-06-24; ⁠, ⁠, ⁠, ⁠, ⁠, ; backlinks; similar):

Correlations are oft interpreted as evidence for causation; this is oft falsified; do causal graphs explain why this is so common, because the number of possible indirect paths greatly exceeds the direct paths necessary for useful manipulation?

It is widely understood that statistical correlation between two variables ≠ causation. Despite this admonition, people are overconfident in claiming correlations to support favored causal interpretations and are surprised by the results of randomized experiments, suggesting that they are biased & systematically underestimate the prevalence of confounds / common-causation. I speculate that in realistic causal networks or DAGs, the number of possible correlations grows faster than the number of possible causal relationships. So confounds really are that common, and since people do not think in realistic DAGs but toy models, the imbalance also explains overconfidence.

“Vitamin D and Vitamin D Analogues for Preventing Fractures in Post‐menopausal Women and Older Men”, Avenell et al 2014

2014-avenell.pdf: “Vitamin D and vitamin D analogues for preventing fractures in post‐menopausal women and older men”⁠, Alison Avenell, Jenson CS Mak, Dianne O’Connell (2014-04-14; backlinks; similar):

Background: Vitamin D and related compounds have been used to prevent osteoporotic fractures in older people. This is the third update of a Cochrane review first published in 1996.

Objectives: To determine the effects of vitamin D or related compounds, with or without calcium, for preventing fractures in post-menopausal women and older men.

Search methods: We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialised Register (to December 2012), the Cochrane Central Register of Controlled Trials (2012, Issue 12), MEDLINE (1966 to November Week 3 2012), Embase (1980 to 2012 Week 50), CINAHL (1982 to December 2012), BIOSIS (1985 to 2013-01-03), Current Controlled Trials (December 2012) and reference lists of articles.

Selection criteria: Randomised or quasi-randomised trials that compared vitamin D or related compounds, alone or with calcium, against placebo, no intervention or calcium alone, and that reported fracture outcomes in older people. The primary outcome was hip fracture. Data collection and analysis

Two authors independently assessed trial risk of selection bias and aspects of methodological quality, and extracted data. Data were pooled, where possible, using the fixed-effect model, or the random-effects model when heterogeneity between studies appeared substantial. Main results

We included 53 trials with a total of 91,791 participants. Thirty-one trials, with sample sizes ranging from 70 to 36,282 participants, examined vitamin D (including 25-hydroxy vitamin D) with or without calcium in the prevention of fractures in community, nursing home or hospital inpatient populations. Twelve of these 31 trials had participants with a mean or median age of 80 years or over.

Another group of 22 smaller trials examined calcitriol or alfacalcidol (1-alphahydroxyvitamin D3), mostly with participants who had established osteoporosis. These trials were carried out in the setting of institutional referral clinics or hospitals.

In the assessment of risk of bias for random sequence generation, 21 trials (40%) were deemed to be at low risk, 28 trials (53%) at unclear risk and four trials at high risk (8%). For allocation concealment, 22 trials were at low risk (42%), 29 trials were at unclear risk (55%) and two trials were at high risk (4%).

There is high quality evidence that vitamin D alone, in the formats and doses tested, is unlikely to be effective in preventing hip fracture (11 trials, 27,693 participants; risk ratio (RR) 1.12, 95% confidence intervals (CI) 0.98 to 1.29) or any new fracture (15 trials, 28,271 participants; RR 1.03, 95% CI 0.96 to 1.11).

There is high quality evidence that vitamin D plus calcium results in a small reduction in hip fracture risk (nine trials, 49,853 participants; RR 0.84, 95% confidence interval (CI) 0.74 to 0.96; P value 0.01). In low-risk populations (residents in the community: with an estimated eight hip fractures per 1000 per year), this equates to one fewer hip fracture per 1000 older adults per year (95% CI 0 to 2). In high risk populations (residents in institutions: with an estimated 54 hip fractures per 1000 per year), this equates to nine fewer hip fractures per 1000 older adults per year (95% CI 2 to 14).

There is high quality evidence that vitamin D plus calcium is associated with a statistically-significant reduction in incidence of new non-vertebral fractures. However, there is only moderate quality evidence of an absence of a statistically-significant preventive effect on clinical vertebral fractures. There is high quality evidence that vitamin D plus calcium reduces the risk of any type of fracture (10 trials, 49,976 participants; RR 0.95, 95% CI 0.90 to 0.99).

In terms of the results for adverse effects: mortality was not adversely affected by either vitamin D or vitamin D plus calcium supplementation (29 trials, 71,032 participants, RR 0.97, 95% CI 0.93 to 1.01). Hypercalcaemia, which was usually mild (2.6 to 2.8 mmol/​L), was more common in people receiving vitamin D or an analogue, with or without calcium (21 trials, 17,124 participants, RR 2.28, 95% CI 1.57 to 3.31), especially for calcitriol (four trials, 988 participants, RR 4.41, 95% CI 2.14 to 9.09), than in people receiving placebo or control. There was also a small increased risk of gastrointestinal symptoms (15 trials, 47,761 participants, RR 1.04, 95% CI 1.00 to 1.08), especially for calcium plus vitamin D (four trials, 40,524 participants, RR 1.05, 95% CI 1.01 to 1.09), and a statistically-significant increase in renal disease (11 trials, 46,548 participants, RR 1.16, 95% CI 1.02 to 1.33). Other systematic reviews have found an increased association of myocardial infarction with supplemental calcium; and evidence of increased myocardial infarction and stroke, but decreased cancer, with supplemental calcium plus vitamin D, without an overall effect on mortality.

Authors’ conclusions: Vitamin D alone is unlikely to prevent fractures in the doses and formulations tested so far in older people. Supplements of vitamin D and calcium may prevent hip or any type of fracture. There was a small but statistically-significant increase in gastrointestinal symptoms and renal disease associated with vitamin D and calcium. This review found that there was no increased risk of death from taking calcium and vitamin D.

“Vitamin D Status and Ill Health: a Systematic Review”, Autier et al 2014

2014-autier.pdf: “Vitamin D status and ill health: a systematic review”⁠, Philippe Autier, Mathieu Boniol, Cécile Pizot, Patrick Mullie (2014-01-01; ; backlinks)

“Vitamin D Supplementation for Prevention of Cancer in Adults (Review)”, G et al 2014

2014-bjelakovic.pdf: “Vitamin D supplementation for prevention of cancer in adults (Review)”⁠, Bjelakovic G, Gluud LL, Nikolova D, Whitfield K, Krstic G, Wetterslev J, Gluud C (2014-01-01; backlinks)

“Who By Very Slow Decay”, Alexander 2013

“Who By Very Slow Decay”⁠, Scott Alexander (2013-07-17; ; backlinks; similar):

[Essay by psychiatrist about care of the dying in American healthcare: people die agonizing, slow, expensive deaths, prolonged by modern healthcare, deprived of all dignity and joy by disease and decay. There is little noble about it.]

You will become bedridden, unable to walk or even to turn yourself over. You will become completely dependent on nurse assistants to intermittently shift your position to avoid pressure ulcers. When they inevitably slip up, your skin develops huge incurable sores that can sometimes erode all the way to the bone, and which are perpetually infected with foul-smelling bacteria. Your limbs will become practically vestigial organs, like the appendix, and when your vascular disease gets too bad, one or more will be amputated, sacrifices to save the host. Urinary and fecal continence disappear somewhere in the process, so you’re either connected to catheters or else spend a while every day lying in a puddle of your own wastes until the nurses can help you out…

Somewhere in the process your mind very quietly and without fanfare gives up the ghost. It starts with forgetting a couple of little things, and progresses…They don’t remember their own names, they don’t know where they are or what they’re doing there, and they think it’s the 1930s or the 1950s or don’t even have a concept of years at all. When you’re alert and oriented “x0”, the world becomes this terrifying place where you are stuck in some kind of bed and can’t move and people are sticking you with very large needles and forcing tubes down your throat and you have no idea why or what’s going on.

So of course you start screaming and trying to attack people and trying to pull the tubes and IV lines out. Every morning when I come in to work I have to check the nurses’ notes for what happened the previous night, and every morning a couple of my patients have tried to pull all of their tubes and lines out. If it’s especially bad they try to attack the staff, and although the extremely elderly are really bad at attacking people this is nevertheless Unacceptable Behavior and they have to be restrained ie tied down to the bed. A presumably more humane alternative sometimes used instead or in addition is to just drug you up on all of those old-timey psychiatric medications that actual psychiatrists don’t use anymore because of their bad reputation…Nevertheless, this is the way many of my patients die. Old, limbless, bedridden, ulcerated, in a puddle of waste, gasping for breath, loopy on morphine, hopelessly demented, in a sterile hospital room with someone from a volunteer program who just met them sitting by their bed.

…I work in a Catholic hospital. People here say the phrase “culture of life” a lot, as in “we need to cultivate a culture of life.” They say it almost as often as they say “patient-centered”. At my hospital orientation, a whole bunch of nuns and executives and people like that got up and told us how we had to do our part to “cultivate a culture of life.”

And now every time I hear that phrase I want to scream. 21st century American hospitals do not need to “cultivate a culture of life”. We have enough life. We have life up the wazoo. We have more life than we know what to do with. We have life far beyond the point where it becomes a sick caricature of itself. We prolong life until it becomes a sickness, an abomination, a miserable and pathetic flight from death that saps out and mocks everything that made life desirable in the first place. 21st century American hospitals need to cultivate a culture of life the same way that Newcastle needs to cultivate a culture of coal, the same way a man who is burning to death needs to cultivate a culture of fire.

And so every time I hear that phrase I want to scream, or if I cannot scream, to find some book of hospital poetry that really is a book of hospital poetry and shove it at them, make them read it until they understand. There is no such book, so I hope it will be acceptable if I just rip off of Wilfred Owen directly:

If in some smothering dreams you too could pace
Behind the gurney that we flung him in,
And watch the white eyes writhing in his face,
His hanging face, like a devil’s sack of sin;
If you could hear, at every jolt, the blood
Come gargling from the froth-corrupted lungs,
Obscene with cancer, bitter with the cud
Of vile, incurable sores on innocent tongues
My friend, you would not so pontificate
To reasoners beset by moral strife
The old lie: we must try to cultivate
A culture of life.

“Reappraisal of Metformin Efficacy in the Treatment of Type 2 Diabetes: a Meta-analysis of Randomised Controlled Trials”, Boussageon et al 2012

“Reappraisal of metformin efficacy in the treatment of type 2 diabetes: a meta-analysis of randomised controlled trials”⁠, Rémy Boussageon, Irène Supper, Theodora Bejan-Angoulvant, Nadir Kellou, Michel Cucherat, Jean-Pierre Boissel et al (2012; similar):

Background: The UK Prospective Diabetes Study showed that metformin decreases mortality compared to diet alone in overweight patients with type 2 diabetes mellitus. Since then, it has been the first-line treatment in overweight patients with type 2 diabetes. However, metformin-sulphonylurea bitherapy may increase mortality.

Methods and Findings: This meta-analysis of randomised controlled trials evaluated metformin efficacy (in studies of metformin versus diet alone, versus placebo, and versus no treatment; metformin as an add-on therapy; and metformin withdrawal) against cardiovascular morbidity or mortality in patients with type 2 diabetes. We searched MEDLINE⁠, Embase⁠, and the Cochrane database. Primary end points were all-cause mortality and cardiovascular death. Secondary end points included all myocardial infarctions, all strokes, congestive heart failure, peripheral vascular disease, leg amputations, and microvascular complications. Thirteen randomised controlled trials (13,110 patients) were retrieved; 9,560 patients were given metformin, and 3,550 patients were given conventional treatment or placebo. Metformin did not significantly affect the primary outcomes all-cause mortality, risk ratio (RR) = 0.99 (95% CI: 0.75 to 1.31), and cardiovascular mortality, RR = 1.05 (95% CI: 0.67 to 1.64). The secondary outcomes were also unaffected by metformin treatment: all myocardial infarctions, RR = 0.90 (95% CI: 0.74 to 1.09); all strokes, RR = 0.76 (95% CI: 0.51 to 1.14); heart failure, RR = 1.03 (95% CI: 0.67 to 1.59); peripheral vascular disease, RR = 0.90 (95% CI: 0.46 to 1.78); leg amputations, RR = 1.04 (95% CI: 0.44 to 2.44); and microvascular complications, RR = 0.83 (95% CI: 0.59 to 1.17). For all-cause mortality and cardiovascular mortality, there was significant heterogeneity when including the UK Prospective Diabetes Study subgroups (I2 = 41% and 59%). There was significant interaction with sulphonylurea as a concomitant treatment for myocardial infarction (p = 0.10 and 0.02, respectively).

Conclusions: Although metformin is considered the gold standard, its benefit/​risk ratio remains uncertain. We cannot exclude a 25% reduction or a 31% increase in all-cause mortality. We cannot exclude a 33% reduction or a 64% increase in cardiovascular mortality. Further studies are needed to clarify this situation.

“Vitamin D and Cardiovascular Outcomes: A Systematic Review and Meta-Analysis”, Elamin et al 2011

2011-elamin.pdf: “Vitamin D and Cardiovascular Outcomes: A Systematic Review and Meta-Analysis”⁠, Mohamed B. Elamin, Nisrin O. Abu Elnour, Khalid B. Elamin, Mitra M. Fatourechi, Aziz A. Alkatib, Jaime P. Almandoz et al (2011-07-01; backlinks; similar):

Context: Several studies found association between vitamin D levels and hypertension, coronary artery calcification, and heart disease.

Objective: The aim of this study was to summarize the evidence on the effect of vitamin D on cardiovascular outcomes.

Design and Methods: We searched electronic databases from inception through August 2010 for randomized trials. Reviewers working in duplicate and independently extracted study characteristics, quality, and the outcomes of interest. Random-effects meta-analysis was used to pool the relative risks (RR) and the weighted mean differences across trials.

Results: We found 51 eligible trials with moderate quality. Vitamin D was associated with nonsignificant effects on the patient-important outcomes of death [RR, 0.96; 95% confidence interval (CI), 0.93, 1.00; p = 0.08], myocardial infarction (RR, 1.02; 95% CI, 0.93, 1.13; p = 0.64), and stroke (RR, 1.05; 95% CI, 0.88, 1.25; p = 0.59). These analyses were associated with minimal heterogeneity. There were no statistically-significant changes in the surrogate outcomes of lipid fractions, glucose, or diastolic or systolic blood pressure. The latter analyses were associated with statistically-significant heterogeneity, and the pooled estimates were trivial in absolute terms.

Conclusions: Trial data available to date are unable to demonstrate a statistically-significant reduction in mortality and cardiovascular risk associated with vitamin D. The quality of the available evidence is low to moderate at best.

“Metformin As a Geroprotector”, Bulterijs 2011

2011-bulterijs.pdf: “Metformin As a Geroprotector”⁠, Sven Bulterijs (2011-01-01; backlinks)

“The Replication Crisis: Flaws in Mainstream Science”, Branwen 2010

Replication: “The Replication Crisis: Flaws in Mainstream Science”⁠, Gwern Branwen (2010-10-27; ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ⁠, ; backlinks; similar):

2013 discussion of how systemic biases in science, particularly medicine and psychology, have resulted in a research literature filled with false positives and exaggerated effects, called ‘the Replication Crisis’.

Long-standing problems in standard scientific methodology have exploded as the “Replication Crisis”: the discovery that many results in fields as diverse as psychology, economics, medicine, biology, and sociology are in fact false or quantitatively highly inaccurately measured. I cover here a handful of the issues and publications on this large, important, and rapidly developing topic up to about 2013, at which point the Replication Crisis became too large a topic to cover more than cursorily. (A compilation of some additional links are provided for post-2013 developments.)

The crisis is caused by methods & publishing procedures which interpret random noise as important results, far too small datasets, selective analysis by an analyst trying to reach expected/​desired results, publication bias, poor implementation of existing best-practices, nontrivial levels of research fraud, software errors, philosophical beliefs among researchers that false positives are acceptable, neglect of known confounding like genetics, and skewed incentives (financial & professional) to publish ‘hot’ results.

Thus, any individual piece of research typically establishes little. Scientific validation comes not from small p-values, but from discovering a regular feature of the world which disinterested third parties can discover with straightforward research done independently on new data with new procedures—replication.

“Association of Circulating Visfatin Concentrations With Insulin Resistance and Low-grade Inflammation After Dietary Energy Restriction in Spanish Obese Non-diabetic Women: Role of Body Composition Changes”, Agueda et al 2010

2012-agueda.pdf: “Association of circulating visfatin concentrations with insulin resistance and low-grade inflammation after dietary energy restriction in Spanish obese non-diabetic women: Role of body composition changes”⁠, M. Agueda, A. Lasa, E. Simon, R. Ares, E. Larrarte, I. Labayen (2010-10-15; similar):

Background and Aims: To assess the influence of body composition changes on circulating serum visfatin after following 12 weeks of energy restricted diet intervention. We also examined the possible role of visfatin in glucose metabolism and in obesity-associated low-grade inflammation.

Methods and Results: A total of 78 obese (BMI 34.0 ± 2.8 kg/​m2) women aged 36.7±7 y volunteered to participate in the study. We measured by DXA body fat mass (FM) and lean mass (LM). Fasting serum visfatin, glucose, insulin, adiponectin, leptin, IL-1β, IL-6, IL-8, TNF-α and CRP concentrations were analyzed before and after the intervention and HOMA and QUIKI indexes were calculated. Mean weight loss 7.7 ± 3.0 kg and HOMA decreased in 24 ± 35%. Serum visfatin concentration change was negatively associated with LM difference (p < 0.05), whereas no statistically-significant relationship was observed with FM changes after energy restricted diet intervention. Changes in circulating serum visfatin levels were statistically-significantly and inversely associated with HOMA-IR (p < 0.01) and positively with QUICKI index (p < 0.02) after energy restricted diet intervention, regardless of achieved body weight loss. We did not find any statistically-significant association between changes in visfatin levels and IL-1β, IL-6, IL-8, TNF-α and CRP levels after dietary intervention (all p > 0.2).

Conclusion: Circulating visfatin concentration is associated with sensitivity improvement achieved after energy restricted diet intervention induced weight loss. Furthermore, LM changes could be an influencing factor on visfatin concentrations and consequently, on the improvement of insulin sensitivity after weight loss in obese non-diabetic women. Our findings did not provide any evidence for a role of visfatin increase on low-grade inflammation after weight loss.

[Keywords: visfatin, weight loss, obesity, insulin resistance, inflammation]

“Extraskeletal Effects of Vitamin D in Older Adults: Cardiovascular Disease, Mortality, Mood, and Cognition”, MPH & MHS 2010

2010-barnard.pdf: “Extraskeletal effects of vitamin D in older adults: Cardiovascular disease, mortality, mood, and cognition”⁠, Karen Barnard MBBCh MPH, Cathleen Colón-Emeric MHS (2010-01-01; ; backlinks)

“Effects of Calcium and Vitamin D Supplementation on Hip Bone Mineral Density and Calcium-Related Analytes in Elderly Ambulatory Australian Women: A Five-Year Randomized Controlled Trial”, Zhu et al 2008

2008-zhu.pdf: “Effects of Calcium and Vitamin D Supplementation on Hip Bone Mineral Density and Calcium-Related Analytes in Elderly Ambulatory Australian Women: A Five-Year Randomized Controlled Trial”⁠, Kun Zhu, Amanda Devine, Ian M. Dick, Scott G. Wilson, Richard L. Prince (2008-03-01; backlinks; similar):

Context: Effects of long-term calcium, with or without vitamin D, on hip bone mineral density (BMD) and bone turnover in sunny climates have not been reported.

Objective: The aim was to evaluate the effect of vitamin D added to calcium supplementation on hip dual-energy x-ray absorptiometry BMD and calcium-related analytes.

Design, Setting, and Participants: The study was a 5-yr randomized, controlled, double-blind trial of 120 community-dwelling women aged 70–80 yr.

Intervention: The interventions were 1200 mg/​d calcium with placebo vitamin D (Ca group) or with 1000 IU/​d vitamin D2 (CaD group), or double placebo (control).

Main Outcome Measures: Hip BMD, plasma 25-hydroxyvitamin D, biomarkers of bone turnover, PTH, and intestinal calcium absorption were measured.

Results: Hip BMD was preserved in CaD (−0.17%) and Ca (0.19%) groups but not controls (−1.27%) at yr 1 and maintained in the CaD group only at yr 3 and 5. The beneficial effects were mainly in those with baseline 25-hydroxyvitamin D levels below the median (68 nmol/​liter). At yr 1, compared with controls, the Ca and CaD groups had 6.8 and 11.3% lower plasma alkaline phosphatase, respectively (p ≤ 0.02), and 28.7 and 34.5% lower urinary deoxypyridinoline to creatinine ratio, respectively (p ≤ 0.05). At 5 yr, this suppression was maintained only in the CaD group. CaD reduced PTH at 3 and 5 yr cf. controls (27.8 and 31.3%, p ≤ 0.005) in those with baseline PTH levels above the median (3.6 pmol/​liter). Therapy did not affect intestinal calcium absorption at high carrier loads.

Conclusions: Addition of vitamin D to calcium has long-term beneficial effects on bone density in elderly women living in a sunny climate, probably mediated by a long-term reduction in bone turnover rate.

“Understanding the Odd Science of Aging”, Kirkwood 2005

“Understanding the Odd Science of Aging”⁠, Thomas B. L. Kirkwood (2005-02-25; ; backlinks; similar):

Evolutionary considerations suggest aging is caused not by active gene programming but by evolved limitations in somatic maintenance, resulting in a build-up of damage. Ecological factors such as hazard rates and food availability influence the trade-offs between investing in growth, reproduction, and somatic survival, explaining why species evolved different life spans and why aging rate can sometimes be altered, for example, by dietary restriction.

To understand the cell and molecular basis of aging is to unravel the multiplicity of mechanisms causing damage to accumulate and the complex array of systems working to keep damage at bay.

  • Why Does Aging Occur?

  • Is Aging Programmed?

  • Evolutionary Genetics

  • Evolutionary Physiology

  • How Aging Is Caused

  • Molecular Mechanisms of Aging

    • Somatic Mutation Theory
    • Telomere Loss Theory
    • Mitochondrial Theory
    • Altered Proteins Theory and Waste Accumulation Theory
    • Network Theories of Aging
  • Cellular Aging

  • Modifying the Rate of Aging

  • Plasticity in the Natural Regulation of Aging Rate

  • Pushing the Boundaries of Our Understanding of Aging

  • Semelparous Organisms

  • Extrinsic Mortality and Life Span

  • Nonaging Species

  • Aging in Unicellular Organisms

  • Conclusions

“A Randomized, Controlled Trial of Quadriceps Resistance Exercise and Vitamin D in Frail Older People: The Frailty Interventions Trial in Elderly Subjects (FITNESS)”, Latham et al 2003

2003-latham.pdf: “A Randomized, Controlled Trial of Quadriceps Resistance Exercise and Vitamin D in Frail Older People: The Frailty Interventions Trial in Elderly Subjects (FITNESS)”⁠, Nancy K. Latham, Craig S. Anderson, Arier Lee, Derrick A. Bennett, Anne Moseley, Ian D. Cameron, For The Fitness Collaborative Group et al (2003-02-20; ; backlinks; similar):

Objectives: To determine the effectiveness of vitamin D and home-based quadriceps resistance exercise on reducing falls and improving the physical health of frail older people after hospital discharge.

Design: Multicenter, randomized, controlled trial with a factorial design.

Setting: Five hospitals in Auckland, New Zealand, and Sydney, Australia.

Participants: Two hundred forty-three frail older people.

Interventions: Patients were randomized to receive a single dose of vitamin D (calciferol, 300,000 IU) or placebo tablets and 10 weeks of high-intensity home-based quadriceps resistance exercise or frequency-matched visits.

Measurements: The primary endpoints were physical health according to the short-form health survey at 3 months and falls over 6 months. Physical performance and self-rated function were secondary endpoints. Assessments took place in the participants’ homes at 3 and 6 months after randomization and were performed by blinded assessors.

Results: There was no effect of either intervention on physical health or falls, but patients in the exercise group were at increased risk of musculoskeletal injury (risk ratio = 3.6, 95% confidence interval = 1.5–8.0). Vitamin D supplementation did not improve physical performance, even in those who were vitamin D deficient (<12 ng/​mL) at baseline.

Conclusion: Neither vitamin D supplementation nor a home-based program of high-intensity quadriceps resistance exercise improved rehabilitation outcomes in frail older people after hospitalization. There was no effect of vitamin D on physical performance, and the exercises increased the risk of musculoskeletal injury. These findings do not support the routine use of these interventions at these dosages in the rehabilitation of frail older people.

“The Reserve-capacity Hypothesis: Evolutionary Origins and Modern Implications of the Trade-off between Tumor-suppression and Tissue-repair”, Weinstein & Ciszek 2002

2002-weinstein.pdf: “The reserve-capacity hypothesis: evolutionary origins and modern implications of the trade-off between tumor-suppression and tissue-repair”⁠, Bret S. Weinstein, Deborah Ciszek (2002-05; similar):

Antagonistic pleiotropy, the evolutionary theory of senescence, posits that age related somatic decline is the inevitable late-life by-product of adaptations that increase fitness in early life. That concept, coupled with recent findings in oncology and gerontology, provides the foundation for an integrative theory of vertebrate senescence that reconciles aspects of the ‘accumulated damage’ ‘metabolic rate’, and ‘oxidative stress’ models. We hypothesize that (1) in vertebrates, a telomeric fail-safe inhibits tumor formation by limiting cellular proliferation. (2) The same system results in the progressive degradation of tissue function with age. (3) These patterns are manifestations of an evolved antagonistic pleiotropy in which extrinsic causes of mortality favor a species-optimal balance between tumor suppression and tissue repair. (4) With that trade-off as a fundamental constraint, selection adjusts telomere lengths—longer telomeres increasing the capacity for repair, shorter telomeres increasing tumor resistance. (5) In environments where extrinsically induced mortality is frequent, selection against senescence is comparatively weak as few individuals live long enough to suffer a substantial phenotypic decline. The weaker the selection against senescence, the further the optimal balance point moves toward shorter telomeres and increased tumor suppression. The stronger the selection against senescence, the farther the optimal balance point moves toward longer telomeres, increasing the capacity for tissue repair, slowing senescence and elevating tumor risks. (6) In iteroparous organisms selection tends to co-ordinate rates of senescence between tissues, such that no one organ generally limits life-span. A subsidiary hypothesis argues that senescent decline is the combined effect of (1) uncompensated cellular attrition and (2) increasing histological entropy. Entropy increases due to a loss of the intra-tissue positional information that normally regulates cell fate and function. Informational loss is subject to positive feedback, producing the ever-accelerating pattern of senescence characteristic of iteroparous vertebrates. Though telomere erosion begins early in development, the onset of senescence should, on average, be deferred to the species-typical age of first reproduction, the balance point at which selection on this trade-off should allow exhaustion of replicative capacity to overtake some cell lines. We observe that captive-rodent breeding protocols, designed to increase reproductive output, simultaneously exert strong selection against reproductive senescence and virtually eliminate selection that would otherwise favor tumor suppression. This appears to have greatly elongated the telomeres of laboratory mice. With their telomeric failsafe effectively disabled, these animals are unreliable models of normal senescence and tumor formation. Safety tests employing these animals likely overestimate cancer risks and underestimate tissue damage and consequent accelerated senescence.

“Book Review: _Validation of Exceptional Longevity: by Bernard Jeune and James W. Vaupel”, Gavrilov & Gavrilova 2000

2000-gavrilov.pdf: “Book review: _Validation of Exceptional Longevity: by Bernard Jeune and James W. Vaupel”⁠, Leonid A. Gavrilov, Natalia S. Gavrilova (2000-01-01)

“Prevention of Femoral and Lumbar Bone Loss With Hormone Replacement Therapy and Vitamin D3 in Early Postmenopausal Women: A Population-Based 5–Year Randomized Trial”, Komulainen et al 1999

1999-komulainen.pdf: “Prevention of Femoral and Lumbar Bone Loss with Hormone Replacement Therapy and Vitamin D3 in Early Postmenopausal Women: A Population-Based 5–Year Randomized Trial”⁠, Marja Komulainen, Heikki Kröger, Marjo T. Tuppurainen, Anna-Mari Heikkinen, Esko Alhava, Risto Honkanen et al (1999-02-01; backlinks; similar):

The long term effects of hormone replacement therapy (HRT) and vitamin D3 (Vit D) on bone mineral density (BMD) were studied. A total of 464 nonosteoporotic early postmenopausal women from the Kuopio Osteoporosis Study (n = 13,100) were randomized to 4 groups: (1) HRT (sequential combination of 2 mg estradiol valerate and 1 mg cyproterone acetate), (2) Vit D3 (300 and 100 IU/​day during the fifth year), (3) HRT and Vit D combined, and (4) placebo. Lumbar (L2–L4) and femoral neck BMD were determined by dual x-ray absorptiometry (DXA) at baseline and after 2.5 and 5 yr of treatment.

Intention to treat analysis (n = 464) showed that after 5 yr, lumbar BMD remained unchanged in the HRT and HRT plus Vit D groups[+ 0.2% (p = 0.658) and +0.9% (p = 0.117), respectively], whereas lumbar BMD decreased by 4.6% in the Vit D group and by 4.5% in the placebo group (p < 0.001 in both). The loss of femoral neck BMD was less in the HRT (−1.4%; p = 0.005) and HRT plus Vit D (−1.3%; p = 0.003) groups than in the Vit D and placebo groups (−4.3%; p < 0.001 in both). Among those 370 women who complied with the 5-yr treatment, the effect was more pronounced: lumbar BMD had increased by 1.5% in the HRT (p = 0.009) and by 1.8% in the HRT plus Vit D group (p = 0.005), with a plateau after 2.5 yr, whereas lumbar BMD had decreased in both the Vit D and placebo groups (4.6% and 4.7%; p < 0.001, respectively). Femoral neck BMD decreased again less in the HRT (−0.4%) and HRT plus Vit D (−0.6%) groups than in the Vit D and placebo groups (−4.4% in both).

This study confirms the positive long term effect of HRT on BMD also seen in intention to treat analysis. The data suggest that low dose vitamin D3 supplementation does not prevent bone loss in healthy, nonosteoporotic, early postmenopausal women, and it confers no benefit additional to that of HRT alone.

“A C. Elegans Mutant That Lives Twice As Long As Wild Type”, Kenyon et al 1993

1993-kenyon.pdf: “A C. elegans mutant that lives twice as long as wild type”⁠, Cynthia Kenyon, Jean Chang, Erin Gensch, Adam Rudner, Ramon Tabtiang (1993-12-02; similar):

We have found that mutations in the gene daf-2 can cause fertile, active, adult Caenorhabditis elegans hermaphrodites to live more than twice as long as wild type.

This lifespan extension, the largest yet reported in any organism, requires the activity of a second gene, daf-16⁠. Both genes also regulate formation of the dauer larva⁠, a developmentally arrested larval form that is induced by crowding and starvation and is very long-lived.

Our findings raise the possibility that the longevity of the dauer is not simply a consequence of its arrested growth, but instead results from a regulated lifespan extension mechanism that can be uncoupled from other aspects of dauer formation. daf-2 and daf-16 provide entry points into understanding how lifespan can be extended.

Miscellaneous