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Soucy A, Potts C, Kaija A, Harrington A, McGilvrey M, Sutphin GL, Korstanje R, Tero B, Seeker J, Pinz I, Vary C, Ryzhova L, Liaw L. Effects of a Global Rab27a Null Mutation on Murine PVAT and Cardiovascular Function. Arterioscler Thromb Vasc Biol 2024. [PMID: 38660803 DOI: 10.1161/atvbaha.124.320969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 04/04/2024] [Indexed: 04/26/2024]
Abstract
BACKGROUND RAB27A, a modulator of secretion, is expressed within vessels and perivascular adipose tissue. We hypothesized that loss of RAB27A would alter cardiovascular function. METHODS Body weight of Rab27aash mice was measured from 2 to 18 months of age, along with glucose resorption at 6 and 12 months of age and glucose sensitivity at 18 months of age. Body weight and cellular and molecular features of perivascular adipose tissue and aortic tissue were examined in a novel C57BL/6J Rab27a null strain. Analyses included morphometric quantification and proteomic analyses. Wire myography measured vasoreactivity, and echocardiography measured cardiac function. Comparisons across ages and genotypes were evaluated via 2-way ANOVA with multiple comparison testing. Significance for myography was determined via 4-parameter nonlinear regression testing. RESULTS Genome-wide association data linked rare human RAB27A variants with body mass index and glucose handling. Changes in glucose tolerance were observed in Rab27aash male mice at 18 months of age. In WT (wild-type) and Rab27a null male mice, body weight, adipocyte lipid area, and aortic area increased with age. In female mice, only body weight increased with age, independent of RAB27A presence. Protein signatures from male Rab27a null mice suggested greater associations with cardiovascular and metabolic phenotypes compared with female tissues. Wire myography results showed Rab27a null males exhibited increased vasoconstriction and reduced vasodilation at 8 weeks of age. Rab27a null females exhibited increased vasoconstriction and vasodilation at 20 weeks of age. Consistent with these vascular changes, male Rab27a null mice experienced age-related cardiomyopathy, with severe differences observed by 21 weeks of age. CONCLUSIONS Global RAB27A loss impacted perivascular adipose tissue and thoracic aorta proteomic signatures, altered vasocontractile responses, and decreased left ventricular ejection fraction in mice.
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Affiliation(s)
- Ashley Soucy
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono (A.S., M.M.G., R.K., I.P., C.V., L.L.)
| | - Christian Potts
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
| | - Abigail Kaija
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
| | - Anne Harrington
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
| | - Marissa McGilvrey
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
| | - George L Sutphin
- The Jackson Laboratory, Bar Harbor, ME (G.L.S., R.K.)
- Now with Department of Molecular and Cellular Biology, University of Arizona, Tucson (G.L.S.)
| | - Ron Korstanje
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono (A.S., M.M.G., R.K., I.P., C.V., L.L.)
- The Jackson Laboratory, Bar Harbor, ME (G.L.S., R.K.)
| | - Benjamin Tero
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
| | - Jacob Seeker
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
| | - Ilka Pinz
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono (A.S., M.M.G., R.K., I.P., C.V., L.L.)
| | - Calvin Vary
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono (A.S., M.M.G., R.K., I.P., C.V., L.L.)
| | - Larisa Ryzhova
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
| | - Lucy Liaw
- MaineHealth Institute for Research, MaineHealth, Scarborough, ME (A.S., C.P., A.K., A.H., M.M., B.T., J.S., I.P., C.V., L.R., L.L.)
- Graduate School of Biomedical Science and Engineering, University of Maine, Orono (A.S., M.M.G., R.K., I.P., C.V., L.L.)
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Hull B, Irby IM, Miller KM, Anderson A, Gardea EA, Sutphin GL. Experimental variables that impact outcomes in Caenorhabditis elegans aging stress response. bioRxiv 2024:2024.01.09.574889. [PMID: 38260451 PMCID: PMC10802420 DOI: 10.1101/2024.01.09.574889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cellular stress is a fundamental component of age-associated disease. Cells encounter various forms of stress - oxidative stress, protein misfolding, DNA damage, etc. - and respond by activating specific, well-defined stress response pathways. As we age, the burden of stress and resulting damage increases while our cells' ability to deal with the consequences becomes diminished due to dysregulation of cellular stress response pathways. Many interventions that extend lifespan activate one or more stress response pathways or allow cells to maintain normal stress response later in life. The nematode Caenorhabditis elegans is a commonly used model for both aging and stress response research. As such, stress response experiments are regularly conducted as part of studies focused on mechanisms of aging in C. elegans. However, experimental design across experiments in the field are highly variable, including stressor dose, age at exposure, culture type (liquid vs. solid), bacterial strain used as a food source, and environmental temperature. These differences can result in different experimental outcomes, making comparison of results between studies challenging. Here we evaluate several experimental variables that are variable in the published literature and find that each can meaningfully alter experimental outcomes for multiple stressors. Our goal is to raise awareness of the issue of experimental variability within the field and suggest a standardized experimental design to serve as a set of guidelines for future experiments. By adopting these guidelines as a starting point, and explicitly noting differences in specific experiments, we aim to promote rigor and reproducibility, ultimately fostering more interpretable and translatable outcomes in geroscience research.
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Espejo LS, DeNicola D, Chang LM, Hofschneider V, Haskins AE, Balsa J, Freitas SS, Antenor A, Hamming S, Hull B, Castro-Portuguez R, Dang H, Sutphin GL. The Emerging Role of 3-Hydroxyanthranilic Acid on C. elegans Aging Immune Function. bioRxiv 2024:2024.01.07.574394. [PMID: 38260592 PMCID: PMC10802494 DOI: 10.1101/2024.01.07.574394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
3-hydroxyanthranilic acid (3HAA) is considered to be a fleeting metabolic intermediate along tryptophan catabolism through the kynurenine pathway. 3HAA and the rest of the kynurenine pathway have been linked to immune response in mammals yet whether it is detrimental or advantageous is a point of contention. Recently we have shown that accumulation of this metabolite, either through supplementation or prevention of its degradation, extends healthy lifespan in C. elegans and mice, while the mechanism remained unknown. Utilizing C. elegans as a model we investigate how 3HAA and haao-1 inhibition impact the host and the potential pathogens. What we find is that 3HAA improves host immune function with aging and serves as an antimicrobial against gram-negative bacteria. Regulation of 3HAA's antimicrobial activity is accomplished via tissue separation. 3HAA is synthesized in the C. elegans hypodermal tissue, localized to the site of pathogen interaction within the gut granules, and degraded in the neuronal cells. This tissue separation creates a new possible function for 3HAA that may give insight to a larger evolutionarily conserved function within the immune response.
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Affiliation(s)
- Luis S Espejo
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Destiny DeNicola
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Leah M Chang
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Anne E Haskins
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Jonah Balsa
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Samuel S Freitas
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Angelo Antenor
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Sage Hamming
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Bradford Hull
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Hope Dang
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - George L Sutphin
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
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Dang H, Castro-Portuguez R, Espejo L, Backer G, Freitas S, Spence E, Meyers J, Shuck K, Gardea EA, Chang LM, Balsa J, Thorns N, Corban C, Liu T, Bean S, Sheehan S, Korstanje R, Sutphin GL. On the benefits of the tryptophan metabolite 3-hydroxyanthranilic acid in Caenorhabditis elegans and mouse aging. Nat Commun 2023; 14:8338. [PMID: 38097593 PMCID: PMC10721613 DOI: 10.1038/s41467-023-43527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Tryptophan metabolism through the kynurenine pathway influences molecular processes critical to healthy aging including immune signaling, redox homeostasis, and energy production. Aberrant kynurenine metabolism occurs during normal aging and is implicated in many age-associated pathologies including chronic inflammation, atherosclerosis, neurodegeneration, and cancer. We and others previously identified three kynurenine pathway genes-tdo-2, kynu-1, and acsd-1-for which decreasing expression extends lifespan in invertebrates. Here we report that knockdown of haao-1, a fourth gene encoding the enzyme 3-hydroxyanthranilic acid (3HAA) dioxygenase (HAAO), extends lifespan by ~30% and delays age-associated health decline in Caenorhabditis elegans. Lifespan extension is mediated by increased physiological levels of the HAAO substrate 3HAA. 3HAA increases oxidative stress resistance and activates the Nrf2/SKN-1 oxidative stress response. In pilot studies, female Haao knockout mice or aging wild type male mice fed 3HAA supplemented diet were also long-lived. HAAO and 3HAA represent potential therapeutic targets for aging and age-associated disease.
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Affiliation(s)
- Hope Dang
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Luis Espejo
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Samuel Freitas
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Erica Spence
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Jeremy Meyers
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Karissa Shuck
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Emily A Gardea
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Leah M Chang
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Jonah Balsa
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | - Niall Thorns
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Teresa Liu
- The Jackson Laboratory, Bar Harbor, ME, USA
| | | | | | | | - George L Sutphin
- Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA.
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Gardea EA, DeNicola D, Freitas S, Peterson W, Dang H, Shuck K, Fang-Yen C, Sutphin GL. Long-Term Culture and Monitoring of Isolated Caenorhabditis elegans on Solid Media in Multi-Well Devices. J Vis Exp 2022. [PMID: 36571410 PMCID: PMC10368520 DOI: 10.3791/64681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The nematode Caenorhabditis elegans is among the most common model systems used in aging research owing to its simple and inexpensive culture techniques, rapid reproduction cycle (~3 days), short lifespan (~3 weeks), and numerous available tools for genetic manipulation and molecular analysis. The most common approach for conducting aging studies in C. elegans, including survival analysis, involves culturing populations of tens to hundreds of animals together on solid nematode growth media (NGM) in Petri plates. While this approach gathers data on a population of animals, most protocols do not track individual animals over time. Presented here is an optimized protocol for the long-term culturing of individual animals on microfabricated polydimethylsiloxane (PDMS) devices called WorMotels. Each device allows up to 240 animals to be cultured in small wells containing NGM, with each well isolated by a copper sulfate-containing moat that prevents the animals from fleeing. Building on the original WorMotel description, this paper provides a detailed protocol for molding, preparing, and populating each device, with descriptions of common technical complications and advice for troubleshooting. Within this protocol are techniques for the consistent loading of small-volume NGM, the consistent drying of both the NGM and bacterial food, options for delivering pharmacological interventions, instructions for and practical limitations to reusing PDMS devices, and tips for minimizing desiccation, even in low-humidity environments. This technique allows the longitudinal monitoring of various physiological parameters, including stimulated activity, unstimulated activity, body size, movement geometry, healthspan, and survival, in an environment similar to the standard technique for group culture on solid media in Petri plates. This method is compatible with high-throughput data collection when used in conjunction with automated microscopy and analysis software. Finally, the limitations of this technique are discussed, as well as a comparison of this approach to a recently developed method that uses microtrays to culture isolated nematodes on solid media.
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Affiliation(s)
- Emily A Gardea
- Department of Molecular & Cellular Biology, University of Arizona
| | - Destiny DeNicola
- Department of Molecular & Cellular Biology, University of Arizona
| | - Samuel Freitas
- Department of Molecular & Cellular Biology, University of Arizona
| | - Will Peterson
- Department of Molecular & Cellular Biology, University of Arizona
| | - Hope Dang
- Department of Molecular & Cellular Biology, University of Arizona
| | - Karissa Shuck
- Department of Molecular & Cellular Biology, University of Arizona
| | - Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania
| | - George L Sutphin
- Department of Molecular & Cellular Biology, University of Arizona;
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Espejo L, Hull B, Chang LM, DeNicola D, Freitas S, Silbar V, Haskins A, Turner EA, Sutphin GL. Long-Term Culture of Individual Caenorhabditis elegans on Solid Media for Longitudinal Fluorescence Monitoring and Aversive Interventions. J Vis Exp 2022:10.3791/64682. [PMID: 36533827 PMCID: PMC10368144 DOI: 10.3791/64682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023] Open
Abstract
Caenorhabditis elegans are widely used to study aging biology. The standard practice in C. elegans aging studies is to culture groups of worms on solid nematode growth media (NGM), allowing the efficient collection of population-level data for survival and other physiological phenotypes, and periodic sampling of subpopulations for fluorescent biomarker quantification. Limitations to this approach are the inability to (1) follow individual worms over time to develop age trajectories for phenotypes of interest and (2) monitor fluorescent biomarkers directly in the context of the culture environment. Alternative culture approaches use liquid culture or microfluidics to monitor individual animals over time, in some cases including fluorescence quantification, with the tradeoff that the culture environment is contextually distinct from solid NGM. The WorMotel is a previously described microfabricated multi-well device for culturing isolated worms on solid NGM. Each worm is maintained in a well containing solid NGM surrounded by a moat filled with copper sulfate, a contact repellent for C. elegans, allowing longitudinal monitoring of individual animals. We find copper sulfate insufficient to prevent worms from fleeing when subjected to aversive interventions common in aging research, including dietary restriction, pathogenic bacteria, and chemical agents that induce cellular stress. The multi-well devices are also molded from polydimethylsiloxane, which produces high background artifacts in fluorescence imaging. This protocol describes a new approach for culturing isolated roundworms on solid NGM using commercially available polystyrene microtrays, originally designed for human leukocyte antigen (HLA) typing, allowing the measurement of survival, physiological phenotypes, and fluorescence across the lifespan. A palmitic acid barrier prevents worms from fleeing, even in the presence of aversive conditions. Each plate can culture up to 96 animals and easily adapts to a variety of conditions, including dietary restriction, RNAi, and chemical additives, and is compatible with automated systems for collecting lifespan and activity data.
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Affiliation(s)
- Luis Espejo
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - Bradford Hull
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - Leah M Chang
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - Destiny DeNicola
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - Samuel Freitas
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - Vanessa Silbar
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - Anne Haskins
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - Emily A Turner
- Department of Molecular & Cellular Biology, University of Arizona, Tucson
| | - George L Sutphin
- Department of Molecular & Cellular Biology, University of Arizona, Tucson;
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Castro-Portuguez R, Freitas S, Sutphin GL. Abstract LB-241: Kynurenine metabolism as a biomarker and therapeutic target in hepatocellular carcinoma (HCC). Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Hepatocellular carcinoma (HCC) is the most prevalent cancer in the liver, the 5th more common cause of deaths by cancer in the US, and the 3th worldwide. Tumor heterogeneity, few targeted therapies, and late detection make the overall prognosis of patients unsatisfactory and demonstrate the need for better early-detection biomarkers. Liver, by its nature, is the major site of amino acid processing and highly regulated by metabolic signaling. In particular, the majority of ingested tryptophan is processed in the liver through the kynurenine pathway, the endpoint of which is de novo NAD+ biosynthesis. Cumulative evidence shows that dysregulation tryptophan-kynurenine metabolism may promote tumor reprogramming and carcinogenesis. In this work, we provide new insight on how kynurenine pathway can be used as biomarker for patient prognosis.
Methods: Using a publicly available gene expression dataset from liver hepatocellular carcinoma (LIHC) samples available through The Cancer Genome Atlas (TCGA), we employ Principal Component Analysis (PCA) to show that expression of kynurenine pathway gene in cancer cells can be used to cluster patients with particular clinical profiles and predict prognosis. Hierarchical clustering and dimensionality reduction demonstrate the segregation of cluster patients based on gene-pattern expression profiles. Kaplan-Meier survival curves were used to determine patient overall survival and Wilcoxon Signed Rank test to prove statistical significance.
Results: Principal Component 1 (PC1) explains 14.5% gene variance among the patients while PC2 explain 9.2% of variance. Clustering genes by expression across patients, IDO, IDO2, AADAT, KMO, CCBL1, CCBL2, KYNU and ACMSD form one cluster, HAAO and AFMID form a second, and QPRT and TDO2 fall outside of clear cluster boundaries. Hierarchical k-means clustering of the patients based on the kynurenine gene-expression profiled segregated patients into four clusters. Heatmap representation of z-score values reveal that each cluster represents tumors with elevated expression of a specific gene or pair of genes: TDO, HAAO/AFMID, QPRT, and KYNU. Other kynurenine pathway genes appear to have stable expression among the population of HCC patients. Dimensionality reduction using t-Distributed Stochastic Neighbor Embedding (t-SNE) identified the same distribution as hierarchical clustering. One of the outcomes that was clearly determined by this segregation among HCC patients was overall survival. Using the total number of patients from the dataset (n = 371), patients with high QPRT expression had poor prognosis with increased median mortality, with no effect in the maximum survival. There is a significant decrease in the survival between patients in cluster 3 (with high QPRT expression) and those in cluster 2 (with high HAAO/AFMID expression) (HR = 1.2, [95% CI 0.5-1.8] P = 0.0181, Gehan-Breslow-Wilcoxon Test). Furthermore, patients with high vs low QPRT expression have significantly different survival rates (HR = 1.4, [95% CI 0.9-2.2] P = 0.0344, Gehan-Breslow-Wilcoxon Test).
Conclusions: Kynurenine metabolism can be used to determine patient prognosis among HCC patients. In ongoing work, we are testing the hypothesis that inhibition of QPRT with phthalic acid will sensitize HepG2 to cisplatin-induced apoptosis, to validate our prediction model.
Citation Format: Raul Castro-Portuguez, Samuel Freitas, George L. Sutphin. Kynurenine metabolism as a biomarker and therapeutic target in hepatocellular carcinoma (HCC) [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-241.
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Castro-Portuguez R, Sutphin GL. Kynurenine pathway, NAD + synthesis, and mitochondrial function: Targeting tryptophan metabolism to promote longevity and healthspan. Exp Gerontol 2020; 132:110841. [PMID: 31954874 DOI: 10.1016/j.exger.2020.110841] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 12/12/2022]
Abstract
Aging is characterized by a progressive decline in the normal physiological functions of an organism, ultimately leading to mortality. Nicotinamide adenine dinucleotide (NAD+) is an essential cofactor that plays a critical role in mitochondrial energy production as well as many enzymatic redox reactions. Age-associated decline in NAD+ is implicated as a driving factor in several categories of age-associated disease, including metabolic and neurodegenerative disease, as well as deficiency in the mechanisms of cellular defense against oxidative stress. The kynurenine metabolic pathway is the sole de novo NAD+ biosynthetic pathway, generating NAD+ from ingested tryptophan. Altered kynurenine pathway activity is associated with both aging and a variety of age-associated diseases. Kynurenine pathway interventions can extend lifespan in both fruit flies and nematodes, and altered NAD+ metabolism represents one potential mediating mechanism. Recent studies demonstrate that supplementation with NAD+ or NAD+-precursors increase longevity and promote healthy aging in fruit flies, nematodes, and mice. NAD+ levels and the intrinsic relationship to mitochondrial function have been widely studied in the context of aging. Mitochondrial function and dynamics have both been implicated in longevity determination in a range of organisms from yeast to humans, at least in part due to their intimate link to regulating an organism's cellular energy economy and capacity to resist oxidative stress. Recent findings support the idea that complex communication between the mitochondria and the nucleus orchestrates a series of events and stress responses involving mitophagy, mitochondrial number, mitochondrial unfolded protein response (UPRmt), and mitochondria fission and fusion events. In this review, we discuss how mitochondrial morphological changes and dynamics operate during aging, and how altered metabolism of tryptophan to NAD+ through the kynurenine pathway interacts with these processes.
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Affiliation(s)
- Raul Castro-Portuguez
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, 85721, AZ, USA
| | - George L Sutphin
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, 85721, AZ, USA; Department of Molecular and Cellular Biology, University of Arizona, Tucson, 85721, AZ, USA.
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Mendenhall A, Sutphin GL. INTERVENING IN THE LONGEVITY NETWORK. Innov Aging 2019. [PMCID: PMC6846208 DOI: 10.1093/geroni/igz038.2293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This session will focus on interventions to delay biological aging with the goal of in increasing lifespan and healthspan.
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Sutphin GL, Sutphin GL. TARGETING TRYPTOPHAN-KYNURENINE METABOLISM TO EXTEND LIFESPAN AND TREAT AGE-ASSOCIATED DISEASE. Innov Aging 2019. [PMCID: PMC6846846 DOI: 10.1093/geroni/igz038.2294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The kynurenine pathway, the major route for tryptophan catabolism, becomes dysregulated with age and in many age-associated pathologies in humans. Interventions targeting kynurenine metabolism are being pursued for neurodegeneration, cardiovascular disease, and chronic kidney disease. By manipulating kynurenine pathway enzymes and metabolites, we have extended lifespan up to 40% in Caenorhabditis elegans. Our most promising single target is the metabolite 3-hydroxyanthranilic acid dioxygenase (3HAA). Elevating physiological 3HAA by directly supplementing 3HAA or inhibiting the enzyme 3HAA dioxygenase (HAAO) extends worm lifespan by ~30% while reducing oxidative stress by directly degrading hydrogen peroxide. In rodents, anti-inflammatory activity of 3HAA improves outcomes in models of cardiovascular disease, asthma, and autoimmune encephalomyelitis. We are now beginning to validate our C. elegans work in mice and investigating a mechanistic model in which 3HAA acts to extend healthy lifespan by slowing age-associated accumulation of oxidative damage and repressing chronic inflammation.
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Sutphin GL. A new defense in the battle of the sexes. eLife 2019; 8:50140. [PMID: 31418689 PMCID: PMC6697443 DOI: 10.7554/elife.50140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 08/09/2019] [Indexed: 11/13/2022] Open
Abstract
Young Caenorhabditis elegans hermaphrodites use their own sperm to protect against the negative consequences of mating.
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Affiliation(s)
- George L Sutphin
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, United States
- BIO5 Institute, University of Arizona, Tucson, United States
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12
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Bubier JA, Sutphin GL, Reynolds TJ, Korstanje R, Fuksman-Kumpa A, Baker EJ, Langston MA, Chesler EJ. Integration of heterogeneous functional genomics data in gerontology research to find genes and pathway underlying aging across species. PLoS One 2019; 14:e0214523. [PMID: 30978202 PMCID: PMC6461221 DOI: 10.1371/journal.pone.0214523] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 03/15/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the biological mechanisms behind aging, lifespan and healthspan is becoming increasingly important as the proportion of the world's population over the age of 65 grows, along with the cost and complexity of their care. BigData oriented approaches and analysis methods enable current and future bio-gerontologists to synthesize, distill and interpret vast, heterogeneous data from functional genomics studies of aging. GeneWeaver is an analysis system for integration of data that allows investigators to store, search, and analyze immense amounts of data including user-submitted experimental data, data from primary publications, and data in other databases. Aging related genome-wide gene sets from primary publications were curated into this system in concert with data from other model-organism and aging-specific databases, and applied to several questions in genrontology using. For example, we identified Cd63 as a frequently represented gene among aging-related genome-wide results. To evaluate the role of Cd63 in aging, we performed RNAi knockdown of the C. elegans ortholog, tsp-7, demonstrating that this manipulation is capable of extending lifespan. The tools in GeneWeaver enable aging researchers to make new discoveries into the associations between the genes, normal biological processes, and diseases that affect aging, healthspan, and lifespan.
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Affiliation(s)
- Jason A. Bubier
- The Jackson Laboratory, Bar Harbor ME, United States of America
| | - George L. Sutphin
- The University of Arizona, Molecular and Cellular Biology, United States of America
| | | | - Ron Korstanje
- The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, ME, United States of America
| | | | | | | | - Elissa J. Chesler
- The Jackson Laboratory, Bar Harbor ME, United States of America
- The Jackson Laboratory Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, ME, United States of America
- * E-mail:
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13
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Miller H, Fletcher M, Primitivo M, Leonard A, Sutphin GL, Rintala N, Kaeberlein M, Leiser SF. Genetic interaction with temperature is an important determinant of nematode longevity. Aging Cell 2017; 16:1425-1429. [PMID: 28940623 PMCID: PMC5676069 DOI: 10.1111/acel.12658] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2017] [Indexed: 11/29/2022] Open
Abstract
As in other poikilotherms, longevity in C. elegans varies inversely with temperature; worms are longer-lived at lower temperatures. While this observation may seem intuitive based on thermodynamics, the molecular and genetic basis for this phenomenon is not well understood. Several recent reports have argued that lifespan changes across temperatures are genetically controlled by temperature-specific gene regulation. Here, we provide data that both corroborate those studies and suggest that temperature-specific longevity is more the rule than the exception. By measuring the lifespans of worms with single modifications reported to be important for longevity at 15, 20, or 25 °C, we find that the effect of each modification on lifespan is highly dependent on temperature. Our results suggest that genetics play a major role in temperature-associated longevity and are consistent with the hypothesis that while aging in C. elegans is slowed by decreasing temperature, the major cause(s) of death may also be modified, leading to different genes and pathways becoming more or less important at different temperatures. These differential mechanisms of age-related death are not unlike what is observed in humans, where environmental conditions lead to development of different diseases of aging.
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Affiliation(s)
- Hillary Miller
- Cellular and Molecular Biology Program University of Michigan Ann Arbor MI 48109 USA
| | - Marissa Fletcher
- Department of Pathology University of Washington Seattle WA 98195 USA
| | - Melissa Primitivo
- Department of Pathology University of Washington Seattle WA 98195 USA
| | - Alison Leonard
- Department of Pathology University of Washington Seattle WA 98195 USA
| | - George L. Sutphin
- Department of Pathology University of Washington Seattle WA 98195 USA
| | - Nicholas Rintala
- Department of Pathology University of Washington Seattle WA 98195 USA
| | - Matt Kaeberlein
- Department of Pathology University of Washington Seattle WA 98195 USA
| | - Scott F. Leiser
- Cellular and Molecular Biology Program University of Michigan Ann Arbor MI 48109 USA
- Molecular & Integrative Physiology Department University of Michigan Ann Arbor MI 48109 USA
- Department of Internal Medicine University of Michigan Ann Arbor MI 48109 USA
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14
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Sutphin GL, Backer G, Sheehan S, Bean S, Corban C, Liu T, Peters MJ, van Meurs JBJ, Murabito JM, Johnson AD, Korstanje R. Caenorhabditis elegans orthologs of human genes differentially expressed with age are enriched for determinants of longevity. Aging Cell 2017; 16:672-682. [PMID: 28401650 PMCID: PMC5506438 DOI: 10.1111/acel.12595] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2017] [Indexed: 12/21/2022] Open
Abstract
We report a systematic RNAi longevity screen of 82 Caenorhabditis elegans genes selected based on orthology to human genes differentially expressed with age. We find substantial enrichment in genes for which knockdown increased lifespan. This enrichment is markedly higher than published genomewide longevity screens in C. elegans and similar to screens that preselected candidates based on longevity‐correlated metrics (e.g., stress resistance). Of the 50 genes that affected lifespan, 46 were previously unreported. The five genes with the greatest impact on lifespan (>20% extension) encode the enzyme kynureninase (kynu‐1), a neuronal leucine‐rich repeat protein (iglr‐1), a tetraspanin (tsp‐3), a regulator of calcineurin (rcan‐1), and a voltage‐gated calcium channel subunit (unc‐36). Knockdown of each gene extended healthspan without impairing reproduction. kynu‐1(RNAi) alone delayed pathology in C. elegans models of Alzheimer's disease and Huntington's disease. Each gene displayed a distinct pattern of interaction with known aging pathways. In the context of published work, kynu‐1, tsp‐3, and rcan‐1 are of particular interest for immediate follow‐up. kynu‐1 is an understudied member of the kynurenine metabolic pathway with a mechanistically distinct impact on lifespan. Our data suggest that tsp‐3 is a novel modulator of hypoxic signaling and rcan‐1 is a context‐specific calcineurin regulator. Our results validate C. elegans as a comparative tool for prioritizing human candidate aging genes, confirm age‐associated gene expression data as valuable source of novel longevity determinants, and prioritize select genes for mechanistic follow‐up.
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Affiliation(s)
| | - Grant Backer
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Susan Sheehan
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Shannon Bean
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Caroline Corban
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Teresa Liu
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
| | - Marjolein J. Peters
- Department of Internal Medicine; Erasmus Medical Center; Postbus 2040 3000 CA Rotterdam The Netherlands
| | - Joyce B. J. van Meurs
- Department of Internal Medicine; Erasmus Medical Center; Postbus 2040 3000 CA Rotterdam The Netherlands
| | - Joanne M. Murabito
- Section of General Internal Medicine; Boston University School of Medicine; 801 Massachusetts Ave, Crosstown Center Boston MA 02118 USA
- The National Heart, Lung, and Blood Institute's Framingham Heart Study; 73 Mt. Wayte Ave, Suite 2 Framingham MA 01702-5827 USA
| | - Andrew D. Johnson
- The National Heart, Lung, and Blood Institute's Framingham Heart Study; 73 Mt. Wayte Ave, Suite 2 Framingham MA 01702-5827 USA
- Population Sciences Branch; National Heart, Lung, and Blood Institute; Building 31, Room 5A52, 31 Center Drive MSC 2486 Bethesda MD 20892 USA
| | - Ron Korstanje
- The Jackson Laboratory; 600 Main Street Bar Harbor ME 04609 USA
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15
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Leiser SF, Jafari G, Primitivo M, Sutphin GL, Dong J, Leonard A, Fletcher M, Kaeberlein M. Age-associated vulval integrity is an important marker of nematode healthspan. Age (Dordr) 2016; 38:419-431. [PMID: 27566309 PMCID: PMC5266215 DOI: 10.1007/s11357-016-9936-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 07/13/2016] [Indexed: 06/06/2023]
Abstract
Improving healthspan, defined as the period where organisms live without frailty and/or disease, is a major goal of biomedical research. While healthspan measures in people are relatively easy to identify, developing robust markers of healthspan in model organisms has proven challenging. Studies using the nematode Caenorhabditis elegans have provided vital information on the basic mechanisms of aging; however, worm health is difficult to define, and the impact of interventions that increase lifespan on worm healthspan has been controversial. Here, we describe a marker of population healthspan in C. elegans that we term age-associated vulval integrity defects, or Avid, frequently described elsewhere as rupture or exploding. We connect the presence of this phenotype with temperature, reproduction, diet, and longevity. Our results show that Avid occurs in post-reproductive worms under common laboratory conditions at a frequency that correlates negatively with temperature; Avid is rare in worms kept at 25 °C and more frequent in worms kept at 15 °C. We describe the kinetics of Avid, link the phenotype to oocyte production, and describe how Avid involves the ejection of worm proteins and/or internal organ(s) from the vulva. Finally, we find that Avid is preventable by removing worms from food, suggesting that Avid results from the intake, digestion, and/or absorption of food. Our results show that Avid is a significant cause of death in worm populations maintained under laboratory conditions and that its prevention often correlates with worm longevity. We propose that Avid is a powerful marker of worm healthspan whose underlying molecular mechanisms may be conserved.
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Affiliation(s)
- Scott F Leiser
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA.
| | - Gholamali Jafari
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Melissa Primitivo
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Jingyi Dong
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Alison Leonard
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Marissa Fletcher
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, 98195, USA.
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16
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Sutphin GL, Mahoney JM, Sheppard K, Walton DO, Korstanje R. WORMHOLE: Novel Least Diverged Ortholog Prediction through Machine Learning. PLoS Comput Biol 2016; 12:e1005182. [PMID: 27812085 PMCID: PMC5094675 DOI: 10.1371/journal.pcbi.1005182] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/05/2016] [Indexed: 01/01/2023] Open
Abstract
The rapid advancement of technology in genomics and targeted genetic manipulation has made comparative biology an increasingly prominent strategy to model human disease processes. Predicting orthology relationships between species is a vital component of comparative biology. Dozens of strategies for predicting orthologs have been developed using combinations of gene and protein sequence, phylogenetic history, and functional interaction with progressively increasing accuracy. A relatively new class of orthology prediction strategies combines aspects of multiple methods into meta-tools, resulting in improved prediction performance. Here we present WORMHOLE, a novel ortholog prediction meta-tool that applies machine learning to integrate 17 distinct ortholog prediction algorithms to identify novel least diverged orthologs (LDOs) between 6 eukaryotic species-humans, mice, zebrafish, fruit flies, nematodes, and budding yeast. Machine learning allows WORMHOLE to intelligently incorporate predictions from a wide-spectrum of strategies in order to form aggregate predictions of LDOs with high confidence. In this study we demonstrate the performance of WORMHOLE across each combination of query and target species. We show that WORMHOLE is particularly adept at improving LDO prediction performance between distantly related species, expanding the pool of LDOs while maintaining low evolutionary distance and a high level of functional relatedness between genes in LDO pairs. We present extensive validation, including cross-validated prediction of PANTHER LDOs and evaluation of evolutionary divergence and functional similarity, and discuss future applications of machine learning in ortholog prediction. A WORMHOLE web tool has been developed and is available at http://wormhole.jax.org/.
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Affiliation(s)
| | - J. Matthew Mahoney
- Department of Neurological Sciences, University of Vermont College of Medicine, Burlington, VT, United States of America
| | - Keith Sheppard
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - David O. Walton
- The Jackson Laboratory, Bar Harbor, ME, United States of America
| | - Ron Korstanje
- The Jackson Laboratory, Bar Harbor, ME, United States of America
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17
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McCormick MA, Delaney JR, Tsuchiya M, Tsuchiyama S, Shemorry A, Sim S, Chou ACZ, Ahmed U, Carr D, Murakami CJ, Schleit J, Sutphin GL, Wasko BM, Bennett CF, Wang AM, Olsen B, Beyer RP, Bammler TK, Prunkard D, Johnson SC, Pennypacker JK, An E, Anies A, Castanza AS, Choi E, Dang N, Enerio S, Fletcher M, Fox L, Goswami S, Higgins SA, Holmberg MA, Hu D, Hui J, Jelic M, Jeong KS, Johnston E, Kerr EO, Kim J, Kim D, Kirkland K, Klum S, Kotireddy S, Liao E, Lim M, Lin MS, Lo WC, Lockshon D, Miller HA, Moller RM, Muller B, Oakes J, Pak DN, Peng ZJ, Pham KM, Pollard TG, Pradeep P, Pruett D, Rai D, Robison B, Rodriguez AA, Ros B, Sage M, Singh MK, Smith ED, Snead K, Solanky A, Spector BL, Steffen KK, Tchao BN, Ting MK, Vander Wende H, Wang D, Welton KL, Westman EA, Brem RB, Liu XG, Suh Y, Zhou Z, Kaeberlein M, Kennedy BK. A Comprehensive Analysis of Replicative Lifespan in 4,698 Single-Gene Deletion Strains Uncovers Conserved Mechanisms of Aging. Cell Metab 2015; 22:895-906. [PMID: 26456335 PMCID: PMC4862740 DOI: 10.1016/j.cmet.2015.09.008] [Citation(s) in RCA: 165] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 07/31/2015] [Accepted: 09/08/2015] [Indexed: 02/05/2023]
Abstract
Many genes that affect replicative lifespan (RLS) in the budding yeast Saccharomyces cerevisiae also affect aging in other organisms such as C. elegans and M. musculus. We performed a systematic analysis of yeast RLS in a set of 4,698 viable single-gene deletion strains. Multiple functional gene clusters were identified, and full genome-to-genome comparison demonstrated a significant conservation in longevity pathways between yeast and C. elegans. Among the mechanisms of aging identified, deletion of tRNA exporter LOS1 robustly extended lifespan. Dietary restriction (DR) and inhibition of mechanistic Target of Rapamycin (mTOR) exclude Los1 from the nucleus in a Rad53-dependent manner. Moreover, lifespan extension from deletion of LOS1 is nonadditive with DR or mTOR inhibition, and results in Gcn4 transcription factor activation. Thus, the DNA damage response and mTOR converge on Los1-mediated nuclear tRNA export to regulate Gcn4 activity and aging.
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Affiliation(s)
- Mark A McCormick
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Joe R Delaney
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Mitsuhiro Tsuchiya
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Scott Tsuchiyama
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Anna Shemorry
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Sylvia Sim
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Umema Ahmed
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Daniel Carr
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Christopher F Bennett
- Department of Pathology, University of Washington, Seattle, WA 98195, USA; Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Adrienne M Wang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Brady Olsen
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Richard P Beyer
- Department of Occupational and Environmental Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Theodor K Bammler
- Department of Occupational and Environmental Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Donna Prunkard
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Simon C Johnson
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Elroy An
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Arieanna Anies
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Anthony S Castanza
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Eunice Choi
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Nick Dang
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Shiena Enerio
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Marissa Fletcher
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lindsay Fox
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sarani Goswami
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Sean A Higgins
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Molly A Holmberg
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Di Hu
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Jessica Hui
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Monika Jelic
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Ki-Soo Jeong
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Elijah Johnston
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Emily O Kerr
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jin Kim
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Diana Kim
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Katie Kirkland
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Shannon Klum
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Soumya Kotireddy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Eric Liao
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Michael Lim
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Michael S Lin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Winston C Lo
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Dan Lockshon
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Hillary A Miller
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Richard M Moller
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Brian Muller
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Jonathan Oakes
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Diana N Pak
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Zhao Jun Peng
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Kim M Pham
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Tom G Pollard
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Prarthana Pradeep
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Dillon Pruett
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Dilreet Rai
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Brett Robison
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Ariana A Rodriguez
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Bopharoth Ros
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Michael Sage
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Manpreet K Singh
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Erica D Smith
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Katie Snead
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Amrita Solanky
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Benjamin L Spector
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Kristan K Steffen
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Bie Nga Tchao
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Marc K Ting
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Helen Vander Wende
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Dennis Wang
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - K Linnea Welton
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Eric A Westman
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Rachel B Brem
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA
| | - Xin-Guang Liu
- Aging Research Institute, Guangdong Medical College, Dongguan 523808, Guangdong, P.R. China
| | - Yousin Suh
- Aging Research Institute, Guangdong Medical College, Dongguan 523808, Guangdong, P.R. China; Department of Genetics, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Zhongjun Zhou
- Department of Biochemistry, University of Hong Kong, Hong Kong
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.
| | - Brian K Kennedy
- Buck Institute for Research on Aging, 8001 Redwood Boulevard, Novato, CA 94945, USA; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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18
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Chandler-Brown D, Choi H, Park S, Ocampo BR, Chen S, Le A, Sutphin GL, Shamieh LS, Smith ED, Kaeberlein M. Sorbitol treatment extends lifespan and induces the osmotic stress response in Caenorhabditis elegans. Front Genet 2015; 6:316. [PMID: 26579191 PMCID: PMC4621483 DOI: 10.3389/fgene.2015.00316] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 10/05/2015] [Indexed: 12/21/2022] Open
Abstract
The response to osmotic stress is a highly conserved process for adapting to changing environmental conditions. Prior studies have shown that hyperosmolarity by addition of sorbitol to the growth medium is sufficient to increase both chronological and replicative lifespan in the budding yeast, Saccharomyces cerevisiae. Here we report a similar phenomenon in the nematode Caenorhabditis elegans. Addition of sorbitol to the nematode growth medium induces an adaptive osmotic response and increases C. elegans lifespan by about 35%. Lifespan extension from 5% sorbitol behaves similarly to dietary restriction in a variety of genetic backgrounds, increasing lifespan additively with mutation of daf-2(e1370) and independently of daf-16(mu86), sir-2.1(ok434), aak-2(ok524), and hif-1(ia04). Dietary restriction by bacterial deprivation or mutation of eat-2(ad1113) fails to further extend lifespan in the presence of 5% sorbitol. Two mutants with constitutive activation of the osmotic response, osm-5(p813) and osm-7(n1515), were found to be long-lived, and lifespan extension from sorbitol required the glycerol biosynthetic enzymes GPDH-1 and GPDH-2. Taken together, these observations demonstrate that exposure to sorbitol at levels sufficient to induce an adaptive osmotic response extends lifespan in worms and define the osmotic stress response pathway as a longevity pathway conserved between yeast and nematodes.
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Affiliation(s)
| | - Haeri Choi
- Department of Pathology, University of Washington Seattle, WA, USA
| | - Shirley Park
- Department of Pathology, University of Washington Seattle, WA, USA
| | - Billie R Ocampo
- Department of Pathology, University of Washington Seattle, WA, USA
| | - Shiwen Chen
- Department of Pathology, University of Washington Seattle, WA, USA
| | - Anna Le
- Department of Pathology, University of Washington Seattle, WA, USA
| | - George L Sutphin
- Department of Pathology, University of Washington Seattle, WA, USA
| | | | - Erica D Smith
- Department of Cell and Molecular Biology, Northwestern University Chicago, IL, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington Seattle, WA, USA
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19
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Peters MJ, Joehanes R, Pilling LC, Schurmann C, Conneely KN, Powell J, Reinmaa E, Sutphin GL, Zhernakova A, Schramm K, Wilson YA, Kobes S, Tukiainen T, Ramos YF, Göring HHH, Fornage M, Liu Y, Gharib SA, Stranger BE, De Jager PL, Aviv A, Levy D, Murabito JM, Munson PJ, Huan T, Hofman A, Uitterlinden AG, Rivadeneira F, van Rooij J, Stolk L, Broer L, Verbiest MMPJ, Jhamai M, Arp P, Metspalu A, Tserel L, Milani L, Samani NJ, Peterson P, Kasela S, Codd V, Peters A, Ward-Caviness CK, Herder C, Waldenberger M, Roden M, Singmann P, Zeilinger S, Illig T, Homuth G, Grabe HJ, Völzke H, Steil L, Kocher T, Murray A, Melzer D, Yaghootkar H, Bandinelli S, Moses EK, Kent JW, Curran JE, Johnson MP, Williams-Blangero S, Westra HJ, McRae AF, Smith JA, Kardia SLR, Hovatta I, Perola M, Ripatti S, Salomaa V, Henders AK, Martin NG, Smith AK, Mehta D, Binder EB, Nylocks KM, Kennedy EM, Klengel T, Ding J, Suchy-Dicey AM, Enquobahrie DA, Brody J, Rotter JI, Chen YDI, Houwing-Duistermaat J, Kloppenburg M, Slagboom PE, Helmer Q, den Hollander W, Bean S, Raj T, Bakhshi N, Wang QP, Oyston LJ, Psaty BM, Tracy RP, Montgomery GW, Turner ST, Blangero J, Meulenbelt I, Ressler KJ, Yang J, Franke L, Kettunen J, Visscher PM, Neely GG, Korstanje R, Hanson RL, Prokisch H, Ferrucci L, Esko T, Teumer A, van Meurs JBJ, Johnson AD. The transcriptional landscape of age in human peripheral blood. Nat Commun 2015; 6:8570. [PMID: 26490707 PMCID: PMC4639797 DOI: 10.1038/ncomms9570] [Citation(s) in RCA: 407] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 09/07/2015] [Indexed: 02/08/2023] Open
Abstract
Disease incidences increase with age, but the molecular characteristics of ageing that lead to increased disease susceptibility remain inadequately understood. Here we perform a whole-blood gene expression meta-analysis in 14,983 individuals of European ancestry (including replication) and identify 1,497 genes that are differentially expressed with chronological age. The age-associated genes do not harbor more age-associated CpG-methylation sites than other genes, but are instead enriched for the presence of potentially functional CpG-methylation sites in enhancer and insulator regions that associate with both chronological age and gene expression levels. We further used the gene expression profiles to calculate the ‘transcriptomic age' of an individual, and show that differences between transcriptomic age and chronological age are associated with biological features linked to ageing, such as blood pressure, cholesterol levels, fasting glucose, and body mass index. The transcriptomic prediction model adds biological relevance and complements existing epigenetic prediction models, and can be used by others to calculate transcriptomic age in external cohorts. Ageing increases the risk of many diseases. Here the authors compare blood cell transcriptomes of over 14,000 individuals and identify a set of about 1,500 genes that are differently expressed with age, shedding light on transcriptional programs linked to the ageing process and age-associated diseases.
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Affiliation(s)
- Marjolein J Peters
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Roby Joehanes
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Luke C Pilling
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - Claudia Schurmann
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany.,The Charles Bronfman Institute for Personalized Medicine, Genetics of Obesity &Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York 10029, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia 30301, USA
| | - Joseph Powell
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Queensland 4000, Australia.,The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4000, Australia
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - George L Sutphin
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Alexandra Zhernakova
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands
| | - Katharina Schramm
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.,Institute of Human Genetics, Technical University Munich, Munich 85540, Germany
| | - Yana A Wilson
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Sayuko Kobes
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona 85001, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | | | - Yolande F Ramos
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Harald H H Göring
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Myriam Fornage
- Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Sciences, Center at Houston, Texas 77001, USA.,Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, Texas 77001, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, Washington 98101, USA
| | - Barbara E Stranger
- Section of Genetic Medicine, Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois 60290, USA
| | - Philip L De Jager
- Program in Translational NeuroPsychiatric Genomics, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Abraham Aviv
- Center of Human Development and Aging, New Jersey Medical School, Newark 07101, USA
| | - Daniel Levy
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Joanne M Murabito
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,General Internal Medicine Section, Boston University, Boston, Massachusetts 02108, USA
| | - Peter J Munson
- The Mathematical and Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20817, USA
| | - Tianxiao Huan
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000CA, The Netherlands
| | - Jeroen van Rooij
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Lisette Stolk
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Linda Broer
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Michael M P J Verbiest
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Mila Jhamai
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Pascal Arp
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Liina Tserel
- Molecular Pathology, Institute of Biomedicine, University of Tartu, Tartu 0794, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1, UK.,National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE1, UK
| | - Pärt Peterson
- Molecular Pathology, Institute of Biomedicine, University of Tartu, Tartu 0794, Estonia
| | - Silva Kasela
- Institute of Molecular and Cell Biology, Estonian Genome Center, University of Tartu, Tartu 0794, Estonia
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1, UK.,National Institute for Health Research Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE1, UK
| | - Annette Peters
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Cavin K Ward-Caviness
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Christian Herder
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40593, Germany
| | - Melanie Waldenberger
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Michael Roden
- Institute of Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf 40593, Germany.,Division of Endocrinology and Diabetology, University Hospital Düsseldorf, Heinrich Heine University, Düsseldorf 40593, Germany
| | - Paula Singmann
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Sonja Zeilinger
- Institute of Epidemiologie II, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany.,Research Unit of Molecular Epidemiology, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover 30519, Germany
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Hans-Jörgen Grabe
- Department of Psychiatry and Psychotherapy, Helios Hospital Stralsund, University Medicine Greifswald, Greifswald 17489, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Leif Steil
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Thomas Kocher
- Unit of Periodontology, Department of Restorative Dentistry, Periodontology and Endodontology, University Medicine Greifswald, Greifswald 17489, Germany
| | - Anna Murray
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - David Melzer
- Epidemiology and Public Health, University of Exeter Medical School, Exeter EX4 1DB, UK
| | - Hanieh Yaghootkar
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter EX2 5DW, UK
| | | | - Eric K Moses
- Centre for Genetic Origins of Health and Disease, The University of Western Australia, and Faculty of Health Sciences, Curtin University, Perth, Western Australia 9011, Australia
| | - Jack W Kent
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Joanne E Curran
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Matthew P Johnson
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | | | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge 02138, USA.,Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA.,Partners Center for Personalized Genetic Medicine, Boston, Massachusetts 02108, USA
| | - Allan F McRae
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - Jennifer A Smith
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48103, USA
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48103, USA
| | - Iiris Hovatta
- Department of Biosciences, University of Helsinki, Helsinki 00100, Finland.,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki 00100, Finland
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia.,Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB4, UK.,Department of Public Health, Hjelt Institute, University of Helsinki, Helsinki 00100, Finland
| | - Veikko Salomaa
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland
| | - Anjali K Henders
- The Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4000, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4000, Australia
| | - Alicia K Smith
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Divya Mehta
- Max-Planck Institute of Psychiatry, Munich 80331, Germany
| | | | - K Maria Nylocks
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Elizabeth M Kennedy
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia 30301, USA
| | | | - Jingzhong Ding
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina 27101, USA
| | - Astrid M Suchy-Dicey
- Department of Epidemiology, University of Washington, Seattle, Washington 98101, USA
| | - Daniel A Enquobahrie
- Department of Epidemiology, University of Washington, Seattle, Washington 98101, USA
| | - Jennifer Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington 98101, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90501, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California 90501, USA
| | | | - Margreet Kloppenburg
- Department of Rheumatology, Leiden University Medical Center, Leiden 2300RC, The Netherlands.,Department of Clinical Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Quinta Helmer
- Department of Medical Statistics, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Wouter den Hollander
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Shannon Bean
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Towfique Raj
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02138, USA
| | - Noman Bakhshi
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Qiao Ping Wang
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Lisa J Oyston
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, Washington 98195, USA.,Cardiovascular Health Research Unit, Department of Health Services, University of Washington, Seattle, Washington 98195, USA.,Group Health Research Institute, Group Health Cooperative, Seattle, Washington 98195, USA
| | - Russell P Tracy
- Department of Pathology, University of Vermont College of Medicine, Colchester, Vermont 98195, USA
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4000, Australia
| | - Stephen T Turner
- Division of Nephrology and Hypertension, Department of Medicine, Mayo Clinic, Rochester, Minnesota 55901, USA
| | - John Blangero
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas 78201, USA
| | - Ingrid Meulenbelt
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden 2300RC, The Netherlands
| | - Kerry J Ressler
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia 30301, USA
| | - Jian Yang
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700RB, The Netherlands
| | - Johannes Kettunen
- Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki 00131, Finland.,Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00131, Finland.,Computational Medicine, Institute of Health Sciences, Faculty of Medicine, University of Oulu, Oulu 90570, Finland
| | - Peter M Visscher
- The Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4000, Australia.,University of Queensland Diamantina Institute, University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4000, Australia
| | - G Gregory Neely
- Neuroscience Division, Garvan Institute of Medical Research, Australia and Charles Perkins Centre and School of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Ron Korstanje
- Nathan Shock Center of Excellence in the Basic Biology of Aging, The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | - Robert L Hanson
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Phoenix, Arizona 85001, USA
| | - Holger Prokisch
- Institute of Human Genetics, Helmholz Zentrum München - German Research Center for Environmental Health, Neuherberg 85764, Germany.,Institute of Human Genetics, Technical University Munich, Munich 85540, Germany
| | - Luigi Ferrucci
- Clinical Research Branch, National Institute on Aging, Baltimore, Maryland 21218, USA
| | - Tonu Esko
- Estonian Genome Center, University of Tartu, Tartu 0794, Estonia.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge 02138, USA.,Division of Endocrinology, Children's Hospital Boston, Boston, Massachusetts 02108, USA.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Alexander Teumer
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17493, Germany
| | - Joyce B J van Meurs
- Department of Internal Medicine, Erasmus Medical Centre Rotterdam, Rotterdam 3000CA, The Netherlands
| | - Andrew D Johnson
- The National Heart, Lung, and Blood Institute's and Boston University's Framingham Heart Study, Framingham, Massachusetts 01702, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20817, USA
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Vermulst M, Denney AS, Lang MJ, Hung CW, Moore S, Moseley MA, Thompson JW, Madden V, Gauer J, Wolfe KJ, Summers DW, Schleit J, Sutphin GL, Haroon S, Holczbauer A, Caine J, Jorgenson J, Cyr D, Kaeberlein M, Strathern JN, Duncan MC, Erie DA. Corrigendum: Transcription errors induce proteotoxic stress and shorten cellular lifespan. Nat Commun 2015; 6:8738. [PMID: 26465398 DOI: 10.1038/ncomms9738] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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21
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Vermulst M, Denney AS, Lang MJ, Hung CW, Moore S, Moseley MA, Mosely AM, Thompson JW, Thompson WJ, Madden V, Gauer J, Wolfe KJ, Summers DW, Schleit J, Sutphin GL, Haroon S, Holczbauer A, Caine J, Jorgenson J, Cyr D, Kaeberlein M, Strathern JN, Duncan MC, Erie DA. Transcription errors induce proteotoxic stress and shorten cellular lifespan. Nat Commun 2015; 6:8065. [PMID: 26304740 DOI: 10.1038/ncomms9065] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/14/2015] [Indexed: 11/09/2022] Open
Abstract
Transcription errors occur in all living cells; however, it is unknown how these errors affect cellular health. To answer this question, we monitor yeast cells that are genetically engineered to display error-prone transcription. We discover that these cells suffer from a profound loss in proteostasis, which sensitizes them to the expression of genes that are associated with protein-folding diseases in humans; thus, transcription errors represent a new molecular mechanism by which cells can acquire disease phenotypes. We further find that the error rate of transcription increases as cells age, suggesting that transcription errors affect proteostasis particularly in aging cells. Accordingly, transcription errors accelerate the aggregation of a peptide that is implicated in Alzheimer's disease, and shorten the lifespan of cells. These experiments reveal a previously unappreciated role for transcriptional fidelity in cellular health and aging.
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Affiliation(s)
- Marc Vermulst
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Ashley S Denney
- School of Medicine, University of Colorado, Denver, Colorado 80217, USA
| | - Michael J Lang
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Chao-Wei Hung
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Stephanie Moore
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - M Arthur Moseley
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - Arthur M Mosely
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - J Will Thompson
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - William J Thompson
- Proteomics Core Facility, Duke University, Durham, North Carolina 27710, USA
| | - Victoria Madden
- Microscopy Services Laboratory, School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Jacob Gauer
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Katie J Wolfe
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Daniel W Summers
- Department of Developmental Biology, and Hope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | - Jennifer Schleit
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Suraiya Haroon
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Agnes Holczbauer
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Joanne Caine
- CSIRO, Department of Materials Science and Engineering, Parkville 3052, Australia
| | - James Jorgenson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Douglas Cyr
- Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Jeffrey N Strathern
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
| | - Mara C Duncan
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Department of Chemistry, Curriculum in Applied Sciences and Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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22
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Dang W, Sutphin GL, Dorsey JA, Otte GL, Cao K, Perry RM, Wanat JJ, Saviolaki D, Murakami CJ, Tsuchiyama S, Robison B, Gregory BD, Vermeulen M, Shiekhattar R, Johnson FB, Kennedy BK, Kaeberlein M, Berger SL. Inactivation of yeast Isw2 chromatin remodeling enzyme mimics longevity effect of calorie restriction via induction of genotoxic stress response. Cell Metab 2014; 19:952-66. [PMID: 24814484 PMCID: PMC4106248 DOI: 10.1016/j.cmet.2014.04.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 05/30/2013] [Accepted: 03/31/2014] [Indexed: 12/16/2022]
Abstract
ATP-dependent chromatin remodeling is involved in all DNA transactions and is linked to numerous human diseases. We explored functions of chromatin remodelers during cellular aging. Deletion of ISW2, or mutations inactivating the Isw2 enzyme complex, extends yeast replicative lifespan. This extension by ISW2 deletion is epistatic to the longevity effect of calorie restriction (CR), and this mechanism is distinct from suppression of TOR signaling by CR. Transcriptome analysis indicates that isw2Δ partially mimics an upregulated stress response in CR cells. In particular, isw2Δ cells show an increased response to genotoxic stresses, and the DNA repair enzyme Rad51 is important for isw2Δ-mediated longevity. We show that lifespan is also extended in C. elegans by reducing levels of athp-2, a putative ortholog of Itc1/ACF1, a critical subunit of the enzyme complex. Our findings demonstrate that the ISWI class of ATP-dependent chromatin remodeling complexes plays a conserved role during aging and in CR.
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Affiliation(s)
- Weiwei Dang
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - George L Sutphin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jean A Dorsey
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gabriel L Otte
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kajia Cao
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rocco M Perry
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer J Wanat
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | | | | | - Brett Robison
- Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michiel Vermeulen
- Department Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | | | - F Brad Johnson
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Program, University of Pennsylvania, Philadelphia, PA 19104, USA.
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23
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Abstract
Identifying and characterizing the factors that modulate longevity is central to understanding the basic mechanisms of aging. Among model organisms used for research related to aging, the budding yeast has proven to be an important system for defining pathways that influence life span. Replicative life span is defined by the number of daughter cells a mother cell can produce before senescing. Over the past 10 years, we have performed replicative life span analysis on several thousand yeast strains, identifying several hundred genes that influence replicative longevity. In this chapter we describe our method for determining replicative life span. Individual cells are grown on solid media and monitored from their initial undivided state until they undergo senescence. Daughter cells are manually removed using a fiber optic needle and quantified to determine the total number of times each mother cell divides.
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Affiliation(s)
- George L Sutphin
- Department of Pathology, University of Washington, Health Science Building D-514, 357470, Seattle, WA, 98195-7470, USA
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24
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Schleit J, Johnson SC, Bennett CF, Simko M, Trongtham N, Castanza A, Hsieh EJ, Moller RM, Wasko BM, Delaney JR, Sutphin GL, Carr D, Murakami CJ, Tocchi A, Xian B, Chen W, Yu T, Goswami S, Higgins S, Holmberg M, Jeong KS, Kim JR, Klum S, Liao E, Lin MS, Lo W, Miller H, Olsen B, Peng ZJ, Pollard T, Pradeep P, Pruett D, Rai D, Ros V, Singh M, Spector BL, Wende HV, An EH, Fletcher M, Jelic M, Rabinovitch PS, MacCoss MJ, Han JDJ, Kennedy BK, Kaeberlein M. Molecular mechanisms underlying genotype-dependent responses to dietary restriction. Aging Cell 2013; 12:1050-61. [PMID: 23837470 DOI: 10.1111/acel.12130] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2013] [Indexed: 01/11/2023] Open
Abstract
Dietary restriction (DR) increases lifespan and attenuates age-related phenotypes in many organisms; however, the effect of DR on longevity of individuals in genetically heterogeneous populations is not well characterized. Here, we describe a large-scale effort to define molecular mechanisms that underlie genotype-specific responses to DR. The effect of DR on lifespan was determined for 166 single gene deletion strains in Saccharomyces cerevisiae. Resulting changes in mean lifespan ranged from a reduction of 79% to an increase of 103%. Vacuolar pH homeostasis, superoxide dismutase activity, and mitochondrial proteostasis were found to be strong determinants of the response to DR. Proteomic analysis of cells deficient in prohibitins revealed induction of a mitochondrial unfolded protein response (mtUPR), which has not previously been described in yeast. Mitochondrial proteotoxic stress in prohibitin mutants was suppressed by DR via reduced cytoplasmic mRNA translation. A similar relationship between prohibitins, the mtUPR, and longevity was also observed in Caenorhabditis elegans. These observations define conserved molecular processes that underlie genotype-dependent effects of DR that may be important modulators of DR in higher organisms.
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25
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Delaney JR, Chou A, Olsen B, Carr D, Murakami C, Ahmed U, Sim S, An EH, Castanza AS, Fletcher M, Higgins S, Holmberg M, Hui J, Jelic M, Jeong KS, Kim JR, Klum S, Liao E, Lin MS, Lo W, Miller H, Moller R, Peng ZJ, Pollard T, Pradeep P, Pruett D, Rai D, Ros V, Schleit J, Schuster A, Singh M, Spector BL, Sutphin GL, Wang AM, Wasko BM, Vander Wende H, Kennedy BK, Kaeberlein M. End-of-life cell cycle arrest contributes to stochasticity of yeast replicative aging. FEMS Yeast Res 2013; 13:267-76. [PMID: 23336757 DOI: 10.1111/1567-1364.12030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 01/14/2013] [Accepted: 01/14/2013] [Indexed: 11/28/2022] Open
Abstract
There is growing evidence that stochastic events play an important role in determining individual longevity. Studies in model organisms have demonstrated that genetically identical populations maintained under apparently equivalent environmental conditions display individual variation in life span that can be modeled by the Gompertz-Makeham law of mortality. Here, we report that within genetically identical haploid and diploid wild-type populations, shorter-lived cells tend to arrest in a budded state, while cells that arrest in an unbudded state are significantly longer-lived. This relationship is particularly notable in diploid BY4743 cells, where mother cells that arrest in a budded state have a shorter mean life span (25.6 vs. 35.6) and larger coefficient of variance with respect to individual life span (0.42 vs. 0.32) than cells that arrest in an unbudded state. Mutations that cause genomic instability tend to shorten life span and increase the proportion of the population that arrest in a budded state. These observations suggest that randomly occurring damage may contribute to stochasticity during replicative aging by causing a subset of the population to terminally arrest prematurely in the S or G2 phase of the cell cycle.
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Affiliation(s)
- Joe R Delaney
- Department of Pathology, University of Washington, Seattle, WA 98195-7470, USA
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26
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Delaney JR, Ahmed U, Chou A, Sim S, Carr D, Murakami CJ, Schleit J, Sutphin GL, An EH, Castanza A, Fletcher M, Higgins S, Jelic M, Klum S, Muller B, Peng ZJ, Rai D, Ros V, Singh M, Wende HV, Kennedy BK, Kaeberlein M. Stress profiling of longevity mutants identifies Afg3 as a mitochondrial determinant of cytoplasmic mRNA translation and aging. Aging Cell 2013; 12:156-66. [PMID: 23167605 DOI: 10.1111/acel.12032] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2012] [Indexed: 01/05/2023] Open
Abstract
Although environmental stress likely plays a significant role in promoting aging, the relationship remains poorly understood. To characterize this interaction in a more comprehensive manner, we examined the stress response profiles for 46 long-lived yeast mutant strains across four different stress conditions (oxidative, ER, DNA damage, and thermal), grouping genes based on their associated stress response profiles. Unexpectedly, cells lacking the mitochondrial AAA protease gene AFG3 clustered strongly with long-lived strains lacking cytosolic ribosomal proteins of the large subunit. Similar to these ribosomal protein mutants, afg3Δ cells show reduced cytoplasmic mRNA translation, enhanced resistance to tunicamycin that is independent of the ER unfolded protein response, and Sir2-independent but Gcn4-dependent lifespan extension. These data demonstrate an unexpected link between a mitochondrial protease, cytoplasmic mRNA translation, and aging.
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Affiliation(s)
| | - Umema Ahmed
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Annie Chou
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Sylvia Sim
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Daniel Carr
- Department of Pathology; University of Washington; Seattle; WA; USA
| | | | - Jennifer Schleit
- Department of Pathology; University of Washington; Seattle; WA; USA
| | | | - Elroy H. An
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Anthony Castanza
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Marissa Fletcher
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Sean Higgins
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Monika Jelic
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Shannon Klum
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Brian Muller
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Zhao J. Peng
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Dilreet Rai
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Vanessa Ros
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Minnie Singh
- Department of Pathology; University of Washington; Seattle; WA; USA
| | - Helen V. Wende
- Department of Pathology; University of Washington; Seattle; WA; USA
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27
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Delaney JR, Murakami C, Chou A, Carr D, Schleit J, Sutphin GL, An EH, Castanza AS, Fletcher M, Goswami S, Higgins S, Holmberg M, Hui J, Jelic M, Jeong KS, Kim JR, Klum S, Liao E, Lin MS, Lo W, Miller H, Moller R, Peng ZJ, Pollard T, Pradeep P, Pruett D, Rai D, Ros V, Schuster A, Singh M, Spector BL, Wende HV, Wang AM, Wasko BM, Olsen B, Kaeberlein M. Dietary restriction and mitochondrial function link replicative and chronological aging in Saccharomyces cerevisiae. Exp Gerontol 2012; 48:1006-13. [PMID: 23235143 DOI: 10.1016/j.exger.2012.12.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2012] [Revised: 11/27/2012] [Accepted: 12/03/2012] [Indexed: 12/30/2022]
Abstract
Chronological aging of budding yeast cells results in a reduction in subsequent replicative life span through unknown mechanisms. Here we show that dietary restriction during chronological aging delays the reduction in subsequent replicative life span up to at least 23days of chronological age. We further show that among the viable portion of the control population aged 26days, individual cells with the lowest mitochondrial membrane potential have the longest subsequent replicative lifespan. These observations demonstrate that dietary restriction modulates a common molecular mechanism linking chronological and replicative aging in yeast and indicate a critical role for mitochondrial function in this process.
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Affiliation(s)
- Joe R Delaney
- Department of Pathology, University of Washington, Seattle, WA 98195-7470, USA
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28
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Sutphin GL, Bishop E, Yanos ME, Moller RM, Kaeberlein M. Caffeine extends life span, improves healthspan, and delays age-associated pathology in Caenorhabditis elegans. Longev Healthspan 2012; 1:9. [PMID: 24764514 PMCID: PMC3922918 DOI: 10.1186/2046-2395-1-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/12/2012] [Indexed: 12/15/2022]
Abstract
BACKGROUND The longevity of an organism is influenced by both genetic and environmental factors. With respect to genetic factors, a significant effort is being made to identify pharmacological agents that extend life span by targeting pathways with a defined role in the aging process. On the environmental side, the molecular mechanisms responsible for the positive influence of interventions such as dietary restriction are being explored. The environment experienced by humans in modern societies already contains countless compounds that may influence longevity. Understanding the role played by common compounds that substantially affect the aging process will be critical for predicting and interpreting the outcome of introducing new interventions. Caffeine is the most widely used psychoactive drug worldwide. Prior studies in flies, worms, and mice indicate that caffeine may positively impact age-associated neurodegenerative pathology, such as that observed in Alzheimer's disease. RESULTS Here we report that caffeine is capable of extending life span and improving healthspan in Caenorhabditis elegans, a finding that is in agreement with a recently published screen looking for FDA-approved compounds capable of extending worm life span. Life span extension using caffeine displays epistatic interaction with two known longevity interventions: dietary restriction and reduced insulin signaling. Caffeine treatment also delays pathology in a nematode model of polyglutamine disease. CONCLUSIONS The identification of caffeine as a relevant factor in aging and healthspan in worms, combined with prior work in both humans and rodents linking caffeine consumption to reduced risk of age-associated disease, suggests that caffeine may target conserved longevity pathways. Further, it may be important to consider caffeine consumption when developing clinical interventions, particularly those designed to mimic dietary restriction or modulate insulin/IGF-1-like signaling. The positive impact of caffeine on a worm model of polyglutamine disease suggests that chronic caffeine consumption may generally enhance resistance to proteotoxic stress and may be relevant to assessing risk and developing treatments for human diseases like Alzheimer's and Huntington's disease. Future work addressing the relevant targets of caffeine in models of aging and healthspan will help to clarify the underlying mechanisms and potentially identify new molecular targets for disease intervention.
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Affiliation(s)
- George L Sutphin
- Department of Pathology, University of Washington, Box 357470, Seattle, 98195-7470, WA, USA ; Molecular and Cellular Biology Program, University of Washington, Box 357275, Seattle, 98195-7275, WA, USA
| | - Emma Bishop
- Department of Pathology, University of Washington, Box 357470, Seattle, 98195-7470, WA, USA
| | - Melana E Yanos
- Department of Pathology, University of Washington, Box 357470, Seattle, 98195-7470, WA, USA ; Department of Psychology, University of Washington, Box 351525, Seattle, 98195-1525, WA, USA
| | - Richard M Moller
- Department of Pathology, University of Washington, Box 357470, Seattle, 98195-7470, WA, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Box 357470, Seattle, 98195-7470, WA, USA ; Institute of Aging Research, Guangdong Medical College, Dongguan, 523808, China
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29
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Murakami C, Delaney JR, Chou A, Carr D, Schleit J, Sutphin GL, An EH, Castanza AS, Fletcher M, Goswami S, Higgins S, Holmberg M, Hui J, Jelic M, Jeong KS, Kim JR, Klum S, Liao E, Lin MS, Lo W, Miller H, Moller R, Peng ZJ, Pollard T, Pradeep P, Pruett D, Rai D, Ros V, Schuster A, Singh M, Spector BL, Vander Wende H, Wang AM, Wasko BM, Olsen B, Kaeberlein M. pH neutralization protects against reduction in replicative lifespan following chronological aging in yeast. Cell Cycle 2012; 11:3087-96. [PMID: 22871733 DOI: 10.4161/cc.21465] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chronological and replicative aging have been studied in yeast as alternative paradigms for post-mitotic and mitotic aging, respectively. It has been known for more than a decade that cells of the S288C background aged chronologically in rich medium have reduced replicative lifespan relative to chronologically young cells. Here we report replication of this observation in the diploid BY4743 strain background. We further show that the reduction in replicative lifespan from chronological aging is accelerated when cells are chronologically aged under standard conditions in synthetic complete medium rather than rich medium. The loss of replicative potential with chronological age is attenuated by buffering the pH of the chronological aging medium to 6.0, an intervention that we have previously shown can extend chronological lifespan. These data demonstrate that extracellular acidification of the culture medium can cause intracellular damage in the chronologically aging population that is asymmetrically segregated by the mother cell to limit subsequent replicative lifespan.
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30
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Delaney JR, Sutphin GL, Dulken B, Sim S, Kim JR, Robison B, Schleit J, Murakami CJ, Carr D, An EH, Choi E, Chou A, Fletcher M, Jelic M, Liu B, Lockshon D, Moller RM, Pak DN, Peng Q, Peng ZJ, Pham KM, Sage M, Solanky A, Steffen KK, Tsuchiya M, Tsuchiyama S, Johnson S, Raabe C, Suh Y, Zhou Z, Liu X, Kennedy BK, Kaeberlein M. Sir2 deletion prevents lifespan extension in 32 long-lived mutants. Aging Cell 2011; 10:1089-91. [PMID: 21902802 DOI: 10.1111/j.1474-9726.2011.00742.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Activation of Sir2 orthologs is proposed to increase lifespan downstream of dietary restriction. Here, we describe an examination of the effect of 32 different lifespan-extending mutations and four methods of DR on replicative lifespan (RLS) in the short-lived sir2Δ yeast strain. In every case, deletion of SIR2 prevented RLS extension; however, RLS extension was restored when both SIR2 and FOB1 were deleted in several cases, demonstrating that SIR2 is not directly required for RLS extension. These findings indicate that suppression of the sir2Δ lifespan defect is a rare phenotype among longevity interventions and suggest that sir2Δ cells senesce rapidly by a mechanism distinct from that of wild-type cells. They also demonstrate that failure to observe lifespan extension in a short-lived background, such as cells or animals lacking sirtuins, should be interpreted with caution.
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Affiliation(s)
- Joe R Delaney
- Department of Pathology, University of Washington, Seattle, WA, USA
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31
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Abstract
In the past several decades the budding yeast Saccharomyces cerevisiae has emerged as a prominent model for aging research. The creation of a single-gene deletion collection covering the majority of open reading frames in the yeast genome and advances in genomic technologies have opened yeast research to genome-scale screens for a variety of phenotypes. A number of screens have been performed looking for genes that modify secondary age-associated phenotypes such as stress resistance or growth rate. More recently, moderate-throughput methods for measuring replicative life span and high-throughput methods for measuring chronological life span have allowed for the first unbiased screens aimed at directly identifying genes involved in determining yeast longevity. In this chapter we discuss large-scale life span studies performed in yeast and their implications for research related to the basic biology of aging.
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Affiliation(s)
- George L Sutphin
- Department of Pathology and the Molecular and Cellular Biology Program, University of Washington, Seattle, WA, 98195-7470, USA,
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32
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Mehta R, Steinkraus KA, Sutphin GL, Ramos FJ, Shamieh LS, Huh A, Davis C, Chandler-Brown D, Kaeberlein M. Proteasomal regulation of the hypoxic response modulates aging in C. elegans. Science 2009; 324:1196-8. [PMID: 19372390 PMCID: PMC2737476 DOI: 10.1126/science.1173507] [Citation(s) in RCA: 185] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Caenorhabditis elegans von Hippel-Lindau tumor suppressor homolog VHL-1 is a cullin E3 ubiquitin ligase that negatively regulates the hypoxic response by promoting ubiquitination and degradation of the hypoxic response transcription factor HIF-1. Here, we report that loss of VHL-1 significantly increased life span and enhanced resistance to polyglutamine and beta-amyloid toxicity. Deletion of HIF-1 was epistatic to VHL-1, indicating that HIF-1 acts downstream of VHL-1 to modulate aging and proteotoxicity. VHL-1 and HIF-1 control longevity by a mechanism distinct from both dietary restriction and insulin-like signaling. These findings define VHL-1 and the hypoxic response as an alternative longevity and protein homeostasis pathway.
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Affiliation(s)
- Ranjana Mehta
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
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33
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Abstract
Aging is a degenerative process characterized by a progressive deterioration of cellular components and organelles resulting in mortality. The nematode Caenorhabditis elegans has emerged as a principal model used to study the biology of aging. Because virtually every biological subsystem undergoes functional decline with increasing age, life span is the primary endpoint of interest when considering total rate of aging. In nematodes, life span is typically defined as the number of days an animal remains responsive to external stimuli. Nematodes can be propagated either in liquid media or on solid media in plates, and techniques have been developed for measuring life span under both conditions. Here we present a generalized protocol for measuring life span of nematodes maintained on solid nematode growth media and fed a diet of UV-killed bacteria. These procedures can easily be adapted to assay life span under various common conditions, including a diet consisting of live bacteria, dietary restriction, and RNA interference.
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Affiliation(s)
- George L Sutphin
- Department of Pathology, University of Washington, Seattle, WA, USA
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34
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35
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Steinkraus KA, Smith ED, Davis C, Carr D, Pendergrass WR, Sutphin GL, Kennedy BK, Kaeberlein M. Dietary restriction suppresses proteotoxicity and enhances longevity by an hsf-1-dependent mechanism in Caenorhabditis elegans. Aging Cell 2008; 7:394-404. [PMID: 18331616 DOI: 10.1111/j.1474-9726.2008.00385.x] [Citation(s) in RCA: 185] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dietary restriction increases lifespan and slows the onset of age-associated disease in organisms from yeast to mammals. In humans, several age-related diseases are associated with aberrant protein folding or aggregation, including neurodegenerative disorders such as Alzheimer's, Parkinson's, and Huntington's diseases. We report here that dietary restriction dramatically suppresses age-associated paralysis in three nematode models of proteotoxicity. Similar to its longevity-enhancing properties, dietary restriction protects against proteotoxicity by a mechanism distinct from reduced insulin/IGF-1-like signaling. Instead, the heat shock transcription factor, hsf-1, is required for enhanced thermotolerance, suppression of proteotoxicity, and lifespan extension by dietary restriction. These findings demonstrate that dietary restriction confers a general protective effect against proteotoxicity and promotes longevity by a mechanism involving hsf-1.
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36
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Sutphin GL, Kaeberlein M. Dietary restriction by bacterial deprivation increases life span in wild-derived nematodes. Exp Gerontol 2008; 43:130-5. [DOI: 10.1016/j.exger.2007.10.019] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Revised: 10/26/2007] [Accepted: 10/31/2007] [Indexed: 10/22/2022]
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