Biology subjects

Mitchell, S. J.

Publications and source records attributed to Mitchell, S. J..

18 recordsLinked to original sources

bioRxiv2026

Pharmacologic AMPK Activation Extends Lifespan in C. elegans and Improves Aspects of Healthspan in Mice

Dysregulated energy metabolism is a hallmark of aging. Many interventions that extend lifespan converge on the conserved master regulator of energy metabolism, AMP-activated kinase (AMPK), and direct genetic activation of AMPK extends lifespan in multiple species. Here, we test the ability of a specific and potent pharmacologic AMPK activator, MK-8722, to extend lifespan in C. elegans and improve healthspan in aged mice. Treatment with MK-8722 from adulthood significantly extended lifespan in an AMPK-dependent manner in both wildtype and Cockayne syndrome model csb-1 mutant C. elegans, without impairing motility or reproductive capacity. Mice treated with MK-8722 from 18 until 24 months of age had significantly reduced body fat accumulation, blocked age-associated declines in fasting blood glucose and enhanced circadian rhythmicity in respiratory quotient, suggesting an improved overall metabolic state. Hepatic RNA sequencing revealed a decrease in inflammation-related pathways and an increase in sterol metabolic pathways, which was consistent with significantly increased levels of multiple sterol-derived metabolites, including lithocholic acid, a proposed mediator of the benefits of caloric restriction. Our results support pharmacologic AMPK activation as a promising gerotherapeutic strategy.

physiology↗

bioRxiv2026

Mapping the mammalian dark metabolome by in vivo isotope tracing

Despite decades of biochemical study, a comprehensive map of the mammalian metabolome remains elusive. Mass spectrometry-based metabolomics detects thousands of small molecule-associated signals in mammalian tissues, but it is currently unclear how many of these reflect products of endogenous metabolism. Here, we leverage systematic in vivo isotope tracing to infer the biosynthetic origins of unidentified metabolites. We administered 26 different isotopically labelled nutrients to mice, measured circulating and tissue metabolite labelling by mass spectrometry, and developed a statistical framework to infer the number of carbon atoms incorporated from each of these precursors into more than 4,000 putative metabolites. We show this information can be harnessed for biosynthesis-aware structure elucidation using a multimodal AI model that co-embeds isotopic labelling patterns with chemical structures. This approach revealed several previously unrecognized families of mammalian metabolites, including cysteine-derived alkylthiazolidines, dithioacetal mercapturic acid derivatives, short-chain N-acyltaurines, acylglycyltaurines, and N-oxidized taurines. It further uncovered a family of mevalonate-derived isoprenoid metabolites that includes 2,3-dihydrofarnesoic acid, which is markedly depleted in both mouse and human aging. Age-related depletion of these isoprenoids is driven by impaired coenzyme A synthesis. Our work establishes the biosynthetic precursors for thousands of unidentified metabolites and reveals multiple previously unrecognized branches of mammalian metabolism.

biochemistry↗

bioRxiv2026

ATG-18 drives longevity in an HLH-30-dependent manner

Enhancing autophagy increases lifespan and healthspan in animal models, yet the precise molecular mechanisms underlying these effects are not fully understood. Here we show that overexpression of the essential autophagic gene atg-18 extends the lifespan of C. elegans. We describe a previously unknown, pleiotropic mechanism by which atg-18 impacts lysosomes and extends lifespan through the transcription factor hlh-30, the master regulator of lysosomal biogenesis. We show that, under stress conditions, HLH-30 requires atg-18 for nuclear translocation. Furthermore, atg-18 overexpression broadly improves health and stress resilience yet paradoxically increases early-life susceptibility to lethal heat stress. In contrast, enhances heat-stress survival a loss-of-function of function mutation in atg-18 enhances heat-stress survival, uncovering a temporal-specific effect of atg-18. These finding suggest an ATG-18--HLH-30 autophagy--lysosome pathway that plays a key role in lifespan and healthspan. Bulleted main discoveriesO_LIATG-18 overexpression increases C. elegans lifespan and plays an important role in resilience against starvation and heat stress. C_LIO_LIATG-18 is required for nuclear translocation of HLH-30 C_LIO_LIHLH-30 is required for ATG-18--mediated lifespan extension C_LIO_LIATG-18 positively regulates lysosomal biogenesis, suggesting a novel role as a molecular coordinator between autophagy and the lysosomal network. C_LI

molecular biology↗

bioRxiv2025

Genetic Modulation of Lifespan: Dynamic Effects, Sex Differences, and Body Weight Trade-offs

The dynamics of lifespan are shaped by DNA variants that exert effects at different ages. We have mapped genetic loci that modulate age-specific mortality using an actuarial approach. We started with an initial population of 6,438 pubescent siblings and ended with a survivorship of 559 mice that lived to at least 1100 days. Twenty-nine Vita loci dynamically modulate the mean lifespan of survivorships with strong age- and sex-specific effects. Fourteen have relatively steady effects on mortality while other loci act forcefully only early or late in life and with polarities of effects that invert. A distinct set of 19 Soma loci shape the negative correlation between weights of young adults with their life expectancies--much more strongly so in males than females. Another set of 11 Soma loci shape the positive correlation between weights at older ages with life expectancies. The Vita and Soma loci share 289 age-dependent epistatic interactions (LODs [≥]3.8) but fewer than 4% are common to both sexes. We provide two examples of how to move from maps toward potential mechanisms. Our findings provide an empirical bridge between evolutionary theories on aging and genetic and molecular causes. These loci and their interactions are key to begin to understand the impact of interventions that may extend healthy lifespan in mice and even in humans.

genetics↗

bioRxiv2025

Lack of consistent effect of dietary fiber on immune checkpoint blockade efficacy across diverse murine tumor models

Immune checkpoint blockade (ICB) has transformed cancer treatment, but success rates remain low in most cancers. Recent research suggest that dietary fiber enhances ICB response in melanoma patients and murine preclinical models through microbiome-dependent mechanisms. Yet, the robustness of this effect across cancer types and dietary contexts remains unclear. Specifically, prior literature compared grain-based chow (high fiber) to low-fiber purified diet, but these diets differ also on other dimensions including phytochemicals. Here we investigated, in mice fed grain-based chow or purified diets with differing quantities of isolated fibers (cellulose and inulin), metabolite levels and ICB activity in multiple tumor models. The blood and fecal metabolome were relatively similar between mice fed high- and low-fiber purified diets, but differed massively between mice fed purified diets or chow, identifying the factor as diet type, independent of fiber. Tumor growth studies in three implantable and two spontaneous genetically engineered tumor models revealed that fiber has a weaker impact on ICB (anti-PD-1) efficacy than previously reported. In some models, dietary modulation impacted ICB activity, but not in a consistent direction across models. In none of the models did we observe the pattern expected if fiber controlled ICB efficacy: strong efficacy in both chow and high-fiber purified diet but low efficacy in low-fiber purified diet. Thus, dietary fiber appears to have limited or inconsistent effect on ICB efficacy in mouse models, and other dietary factors that correlate with fiber intake may underlie the clinical correlations between fiber consumption and immunotherapy outcomes.

cancer biology↗

bioRxiv2024

Sulfur Amino Acid Restriction Enhances Exercise Capacity in Mice by Boosting Fat Oxidation

Dietary restriction of the sulfur-containing amino acids methionine and cysteine (SAAR) improves body composition, enhances insulin sensitivity, and extends lifespan; benefits seen also with endurance exercise. Yet, the impact of SAAR on skeletal muscle remains largely unexplored. Here we demonstrate that one week of SAAR in sedentary, young, male mice increases endurance exercise capacity. Indirect calorimetry showed that SAAR increased lipid oxidation at rest and delayed the onset of carbohydrate utilization during exercise. Transcriptomic analysis revealed increased expression of genes involved in fatty acid catabolism especially in glycolytic muscle following SAAR. These findings were functionally supported by increased fatty acid circulatory turnover flux and muscle {beta}-oxidation. Reducing lipid uptake from circulation through endothelial cell (EC)-specific CD36 deletion attenuated the running phenotype. Mechanistically, VEGF-signaling inhibition prevented exercise increases following SAAR, without affecting angiogenesis, implicating noncanonical VEGF signaling and EC CD36-dependent fatty acid transport in regulating exercise capacity by influencing muscle substrate availability.

physiology↗

bioRxiv2024

Long-term NMN treatment increases lifespan and healthspan in mice in a sex dependent manner

Nicotinamide adenine dinucleotide (NAD) is essential for many enzymatic reactions, including those involved in energy metabolism, DNA repair and the activity of sirtuins, a family of defensive deacylases. During aging, levels of NAD+ can decrease by up to 50% in some tissues, the repletion of which provides a range of health benefits in both mice and humans. Whether or not the NAD+ precursor nicotinamide mononucleotide (NMN) extends lifespan in mammals is not known. Here we investigate the effect of long-term administration of NMN on the health, cancer burden, frailty and lifespan of male and female mice. Without increasing tumor counts or severity in any tissue, NMN treatment of males and females increased activity, maintained more youthful gene expression patterns, and reduced overall frailty. Reduced frailty with NMN treatment was associated with increases in levels of Anerotruncus colihominis, a gut bacterium associated with lower inflammation in mice and increased longevity in humans. NMN slowed the accumulation of adipose tissue later in life and improved metabolic health in male but not female mice, while in females but not males, NMN increased median lifespan by 8.5%, possible due to sex-specific effects of NMN on NAD+ metabolism. Together, these data show that chronic NMN treatment delays frailty, alters the microbiome, improves male metabolic health, and increases female mouse lifespan, without increasing cancer burden. These results highlight the potential of NAD+ boosters for treating age-related conditions and the importance of using both sexes for interventional lifespan studies.

pharmacology and toxicology↗

bioRxiv2024

Long-term fasting remodels gut microbial metabolism and host metabolism

Long-term fasting has become a promising research subject for its potential of treating and preventing metabolic diseases. However, little is known about its impact on the functional capacity of the gut microbiome and the combined effect on the serum metabolome. Here, we demonstrate extensive remodelling of the gut microbial ecosystem in humans (n=92) after an average of 9.8 days of fasting ([~]250 kcal / day). Fasting transiently affected the relative abundance of the majority of bacterial species (306 decreased and 210 increased out of 772). Species changes could largely be explained by their genomic repertoire of carbohydrate-active enzymes (CAZymes), which were investigated here for the first time. Fasting induced extensive abundance changes in CAZyme families, depleting families with dietary fibre substrates and increasing families with host-derived glycan substrates. Likewise, we observed extensive changes in the serum metabolome, with 382 out of 721 metabolites significantly affected (246 increased and 136 decreased). In-depth metagenome-metabolome co-variation analysis suggested Oscillibacter species to be key producers of indole-3-propionic acid, a crucial metabolite for cardiometabolic health. Together, our results provide an unprecedented view on the impact of long-term fasting on gut microbiome composition and function.

microbiology↗

bioRxiv2024

Impaired glycolysis in aged endothelial cells is associated with reduced neovascularisation upon tissue ischemia

The vascular system experiences an age-associated decline in tissue perfusion and response to ischemic diseases. The factors driving this age-associated neovascularization decline remain unclear. While old endothelial cells (ECs) adopt a pro-angiogenic gene expression profile, we observed a stark reduction in the proliferative capacity of old ECs, while migratory capabilities remain intact. This is paralleled by a drastic decline in glycolytic capacity and ATP production, which likely act as limiting factors to neovascularization. These findings may provide new strategies to restore EC function in aging, thereby improving organ resilience and extending health- and lifespan.

molecular biology↗

bioRxiv2023

Short-term Pre-operative Methionine Restriction Induces Browning of Perivascular Adipose Tissue and Improves Vein Graft Remodeling in Mice

Short-term preoperative methionine restriction (MetR) shows promise as a translatable strategy to modulate the bodys response to surgical injury. Its application, however, to improve post-interventional vascular remodeling remains underexplored. Here, we find that MetR protects from arterial intimal hyperplasia in a focal stenosis model and adverse vascular remodeling after vein graft surgery. RNA sequencing reveals that MetR enhances the brown adipose tissue phenotype in arterial perivascular adipose tissue (PVAT) and induces it in venous PVAT. Specifically, PPAR- was highly upregulated in PVAT-adipocytes. Furthermore, MetR dampens the post-operative pro-inflammatory response to surgery in PVAT-macrophages in vivo and in vitro. This study shows for the first time that the detrimental effects of dysfunctional PVAT on vascular remodeling can be reversed by MetR, and identifies pathways involved in browning of PVAT. Furthermore, we demonstrate the potential of short-term pre-operative MetR as a simple intervention to ameliorate vascular remodeling after vascular surgery. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/565269v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@112f51aorg.highwire.dtl.DTLVardef@1998bd8org.highwire.dtl.DTLVardef@1ac5046org.highwire.dtl.DTLVardef@1ca4c87_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2023

Voltage-dependent volume regulation controls epithelial cell extrusion and morphology

Epithelial cells work collectively to provide a protective barrier, yet also turn over rapidly by cell death and division. If the number of dying cells does not match those dividing, the barrier would vanish, or tumors can form. Mechanical forces and the stretch-activated ion channel (SAC) Piezo1 link both processes; stretch promotes cell division and crowding triggers cell death by initiating live cell extrusion1,2. However, it was not clear how particular cells within a crowded region are selected for extrusion. Here, we show that individual cells transiently shrink via water loss before they extrude. Artificially inducing cell shrinkage by increasing extracellular osmolarity is sufficient to induce cell extrusion. Pre-extrusion cell shrinkage requires the voltage-gated potassium channels Kv1.1 and Kv1.2 and the chloride channel SWELL1, upstream of Piezo1. Activation of these voltage-gated channels requires the mechano-sensitive Epithelial Sodium Channel, ENaC, acting as the earliest crowd-sensing step. Imaging with a voltage dye indicated that epithelial cells lose membrane potential as they become crowded and smaller, yet those selected for extrusion are markedly more depolarized than their neighbours. Loss of any of these channels in crowded conditions causes epithelial buckling, highlighting an important role for voltage and water regulation in controlling epithelial shape as well as extrusion. Thus, ENaC causes cells with similar membrane potentials to slowly shrink with compression but those with reduced membrane potentials to be eliminated by extrusion, suggesting a chief driver of cell death stems from insufficient energy to maintain cell membrane potential.

cell biology↗

bioRxiv2022

Cystathionine gamma lyase overexpression enhances neovascularization through NAD-dependent mechanisms

ObjectiveHydrogen sulfide (H2S) is a proangiogenic gas produced primarily by the transsulfuration enzyme cystathionine-gamma-lyase (CGL). CGL-dependant H2S production is required for neovasculariation in models of peripheral arterial disease. However, the benefits of increasing endogenous CGL and its mechanism of action have yet to be elucidated. Methods10 weeks old male whole-body CGL overexpressing mice (CGLTg) and wild type littermates (C57BL/6J) were subjected to the hindlimb ischemia model. Functional recovery was assessed through treadmill exercise endurance testing, while ischemic leg perfusion recovery was measured by laser Doppler perfusion imaging and tissue immunohistochemistry. To examine angiogenic potential, aortic ring sprouting assay and post-natal mouse retinal vasculature development studies were performed. Lastly, comparative metabolomics, NAD+/NADH analysis, and quantitative real-time PCR were performed on WT and CGLTg gastrocnemius muscles. ResultsThe restoration of blood flow upon femoral ligation occurred more rapidly in CGLTg mice. CGLTg mice were able to run further and for longer compared to WT mice. In ischemic gastrocnemius, capillary density was increased in mice overexpressing CGL. Endothelial cell sprouting was increased in aorta isolated from CGLTg mice, especially when cultured in VEGF-only media. Metabolomics analysis demonstrated an increased presence of niacinamide, a precursor of nicotinamide adenine dinucleotide (NAD+/ NADH) in the muscle of CGLTg mice. Finally, CGL overexpression and NMN supplementation improved endothelial cell migration in vitro. ConclusionsTaken together, our results demonstrate that CGL overexpression improves the neovascularization of skeletal muscle upon hindlimb ischemia. These effects are mediated by changes in the NAD pathway, which improves endothelial cell migration.

physiology↗

bioRxiv2022

Ketones facilitate transcriptional resolution of secondary DNA structures in premature aging

There is currently no established intervention for Cockayne syndrome, a disease characterized by progressive early onset neurodegeneration with features of premature aging. Here, we tested if acetyl-CoA precursors, citrate and beta-hydroxybutyrate, could reduce features of Cockayne syndrome in three model systems. We identified the gene Helicase 89B as a homologue of CSB in drosophila and found that the ketone beta-hydroxybutyrate rescued features of premature aging in Hel89B deficient flies. In mammals, loss of the citrate carrier Indy exacerbated the phenotype of Csbm/m mice which was rescued by a ketogenic diet. The rescue effect appeared to be mediated through ketone stimulated histone acetylation and facilitation of transcriptional readthrough of secondary DNA structures. These findings link a ketogenic diet with transcriptional resolution of secondary structures and DNA repair.

physiology↗

bioRxiv2021

Short-term Ketogenic Diet Induces a Molecular Response that is Distinct from Dietary Protein Restriction

There is increasing interest in utilizing short-term dietary interventions in the contexts of cancer, surgical stress and metabolic disease. These short-term diets may be more feasible than extended interventions and may be designed to complement existing therapies. In particular, the high-fat, low-carbohydrate ketogenic diet (KD), traditionally used to treat epilepsy, has gained popularity as a potential strategy for weight loss and improved metabolic health. In mice, long-term KD improves insulin sensitivity and extends lifespan and healthspan. Dietary protein restriction (PR) causes increased energy expenditure, weight loss and improved glucose homeostasis. Since KD is inherently a low-protein diet (10% of calories from protein vs. 20% in control diet), here we evaluated the potential for mechanistic overlap between PR and KD via activation of a PR response. Mice were fed control, protein-free, or one of four ketogenic diets with varying protein content for 8 days. PF and KD diets both decreased body weight, fat mass, and liver weights, and reduced fasting glucose and insulin levels, compared to mice fed the control diet. However, PF and KD differed with respect to insulin tolerance and hepatic insulin sensitivity, which were increased in PF-fed mice and impaired in KD-fed mice relative to controls. Furthermore, contrary to the PF-fed mice, mice fed ketogenic diets containing at least 5% protein did not increase hepatic Fgf21 or brown adipose Ucp1 expression. Interestingly, mice fed KD lacking protein demonstrated greater elevations in hepatic Fgf21 than mice fed a low-fat PF diet. To further elucidate potential mechanistic differences between PF and KD diets and the interplay between dietary protein and carbohydrate restriction, we conducted RNA-seq analysis on livers from mice fed each of the six diets and identified distinct gene sets which respond to dietary protein content, dietary fat content, and ketogenesis. We conclude that KD with 10% of energy from protein does not induce a protein restriction response, and that the overlapping metabolic benefits of KD and PF diets occur via distinct underlying mechanisms.

physiology↗

bioRxiv2021

Ultra-cheap and scalable epigenetic age predictions with TIME-Seq

Epigenetic "clocks" based on DNA methylation (DNAme) have emerged as the most robust and widely employed aging biomarkers, but conventional methods for applying them are expensive and laborious. Here, we develop Tagmentation-based Indexing for Methylation Sequencing (TIME-Seq), a highly multiplexed and scalable method for low-cost epigenetic clocks. Using TIME-Seq, we applied multi-tissue and tissue-specific epigenetic clocks to over 1,600 mouse DNA samples. We also discovered a novel approach for age prediction from shallow sequencing (e.g., 10,000 reads) by adapting scAge for bulk measurements. In benchmarking experiments, TIME-Seq performed favorably against prevailing methods and could quantify the effects of interventions thought to accelerate, slow, and reverse aging in mice. Finally, we built and validated a highly accurate human blood clock from 1,056 demographically representative individuals. Our methods increase the scalability and reduce the cost of epigenetic age predictions by more than 100-fold, enabling accurate aging biomarkers to be applied in more large-scale animal and human studies.

genomics↗

bioRxiv2021

Gut Microbiota predicts Healthy Late-life Aging in Male Mice

Calorie restriction (CR) extends lifespan and retards age-related chronic diseases in most species. There is growing evidence that the gut microbiota has a pivotal role in host health and age-related pathological conditions. Yet, it is still unclear how CR and the gut microbiota are related to healthy aging. Here we report findings from a small longitudinal study of male C57BL/6 mice maintained on either ad libitum or mild (15%) CR diets from 21 months of age and tracked until natural death. We demonstrate that CR results in a significant reduction in frailty index (FI), a well-established indicator of aging. We observed significant alterations in bacterial load, diversity, and compositional patterns of the mouse gut microbiota during the aging process. Interrogating the FI-related microbial features using machine learning techniques, we show that gut microbial signatures from 21-month-old mice can predict the healthy aging of 30-month-old mice with reasonable accuracy. This study deepens our understanding of the links between CR, gut microbiota, and frailty in the aging process of mice.

microbiology↗

bioRxiv2019

Age and life expectancy clocks based on machine learning analysis of mouse frailty

The identification of genes and interventions that slow or reverse aging is hampered by the lack of non-invasive metrics that can predict life expectancy of pre-clinical models. Frailty Indices (FIs) in mice are composite measures of health that are cost-effective and non-invasive, but whether they can accurately predict health and lifespan is not known. Here, mouse FIs were scored longitudinally until death and machine learning was employed to develop two clocks. A random forest regression was trained on FI components for chronological age to generate the FRIGHT (Frailty Inferred Geriatric Health Timeline) clock, a strong predictor of chronological age. A second model was trained on remaining lifespan to generate the AFRAID (Analysis of Frailty and Death) clock, which accurately predicts life expectancy and the efficacy of a lifespan-extending intervention up to a year in advance. Adoption of these clocks should accelerate the identification of novel longevity genes and aging interventions.

physiology↗

bioRxiv2019

DNA Break-Induced Epigenetic Drift as a Cause of Mammalian Aging

There are numerous hallmarks of aging in mammals, but no unifying cause has been identified. In budding yeast, aging is associated with a loss of epigenetic information that occurs in response to genome instability, particularly DNA double-strand breaks (DSBs). Mammals also undergo predictable epigenetic changes with age, including alterations to DNA methylation patterns that serve as epigenetic \"age\" clocks, but what drives these changes is not known. Using a transgenic mouse system called \"ICE\" (for inducible changes to the epigenome), we show that a tissues response to non-mutagenic DSBs reorganizes the epigenome and accelerates physiological, cognitive, and molecular changes normally seen in older mice, including advancement of the epigenetic clock. These findings implicate DSB-induced epigenetic drift as a conserved cause of aging from yeast to mammals.\n\nOne Sentence SummaryDNA breaks induce epigenomic changes that accelerate the aging clock in mammals

molecular biology↗