1
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Sands B, Yun SR, Oshima J, Mendenhall AR. Maternal histone methyltransferases antagonistically regulate monoallelic expression in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576748. [PMID: 38328214 PMCID: PMC10849558 DOI: 10.1101/2024.01.22.576748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Undefined epigenetic programs act to probabilistically silence individual autosomal alleles, generating unique individuals, even from genetic clones. This sort of random monoallelic expression can explain variation in traits and diseases that differences in genes and environments cannot. Here, we developed the nematode Caenorhabditis elegans to study monoallelic expression in whole tissues, and defined a developmental genetic regulation pathway. We found maternal H3K9 histone methyltransferase (HMT) SET-25/SUV39/G9a works with HPL-2/HP1 and LIN-61/L3MBTL2 to randomly silence alleles in the intestinal progenitor E-cell of 8-cell embryos to cause monoallelic expression. SET-25 was antagonized by another maternal H3K9 HMT, MET-2/SETDB1, which works with LIN-65/ATF7ZIP and ARLE-14/ARL14EP to prevent monoallelic expression. The HMT-catalytic SET domains of both MET-2 and SET-25 were required for regulating monoallelic expression. Our data support a model wherein SET-25 and MET-2 regulate histones during development to generate patterns of somatic monoallelic expression that are persistent but not heritable.
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2
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Sands B, Yun S, Mendenhall AR. Introns control stochastic allele expression bias. Nat Commun 2021; 12:6527. [PMID: 34764277 PMCID: PMC8585970 DOI: 10.1038/s41467-021-26798-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Monoallelic expression (MAE) or extreme allele bias can account for incomplete penetrance, missing heritability and non-Mendelian diseases. In cancer, MAE is associated with shorter patient survival times and higher tumor grade. Prior studies showed that stochastic MAE is caused by stochastic epigenetic silencing, in a gene and tissue-specific manner. Here, we used C. elegans to study stochastic MAE in vivo. We found allele bias/MAE to be widespread within C. elegans tissues, presenting as a continuum from fully biallelic to MAE. We discovered that the presence of introns within alleles robustly decreases MAE. We determined that introns control MAE at distinct loci, in distinct cell types, with distinct promoters, and within distinct coding sequences, using a 5'-intron position-dependent mechanism. Bioinformatic analysis showed human intronless genes are significantly enriched for MAE. Our experimental evidence demonstrates a role for introns in regulating MAE, possibly explaining why some mutations within introns result in disease.
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Affiliation(s)
- Bryan Sands
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Soo Yun
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
| | - Alexander R. Mendenhall
- grid.34477.330000000122986657Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA USA
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3
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Shadel GS, Adams PD, Berggren WT, Diedrich JK, Diffenderfer KE, Gage FH, Hah N, Hansen M, Hetzer MW, Molina AJA, Manor U, Marek K, O'Keefe DD, Pinto AFM, Sacco A, Sharpee TO, Shokriev MN, Zambetti S. The San Diego Nathan Shock Center: tackling the heterogeneity of aging. GeroScience 2021; 43:2139-2148. [PMID: 34370163 PMCID: PMC8599742 DOI: 10.1007/s11357-021-00426-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/26/2022] Open
Abstract
Understanding basic mechanisms of aging holds great promise for developing interventions that prevent or delay many age-related declines and diseases simultaneously to increase human healthspan. However, a major confounding factor in aging research is the heterogeneity of the aging process itself. At the organismal level, it is clear that chronological age does not always predict biological age or susceptibility to frailty or pathology. While genetics and environment are major factors driving variable rates of aging, additional complexity arises because different organs, tissues, and cell types are intrinsically heterogeneous and exhibit different aging trajectories normally or in response to the stresses of the aging process (e.g., damage accumulation). Tackling the heterogeneity of aging requires new and specialized tools (e.g., single-cell analyses, mass spectrometry-based approaches, and advanced imaging) to identify novel signatures of aging across scales. Cutting-edge computational approaches are then needed to integrate these disparate datasets and elucidate network interactions between known aging hallmarks. There is also a need for improved, human cell-based models of aging to ensure that basic research findings are relevant to human aging and healthspan interventions. The San Diego Nathan Shock Center (SD-NSC) provides access to cutting-edge scientific resources to facilitate the study of the heterogeneity of aging in general and to promote the use of novel human cell models of aging. The center also has a robust Research Development Core that funds pilot projects on the heterogeneity of aging and organizes innovative training activities, including workshops and a personalized mentoring program, to help investigators new to the aging field succeed. Finally, the SD-NSC participates in outreach activities to educate the general community about the importance of aging research and promote the need for basic biology of aging research in particular.
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Affiliation(s)
- Gerald S Shadel
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - W Travis Berggren
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Jolene K Diedrich
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kenneth E Diffenderfer
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Fred H Gage
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Nasun Hah
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Malene Hansen
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Martin W Hetzer
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Anthony J A Molina
- Divison of Geriatrics, Gerontology and Palliative Care, Department of Medicine, University of California, San Diego, 9500 Gilman Dr, San Diego, CA, 92093, USA
| | - Uri Manor
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Kurt Marek
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - David D O'Keefe
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | | | - Alessandra Sacco
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Tatyana O Sharpee
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Maxim N Shokriev
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Stefania Zambetti
- The Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA, 92037, USA
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4
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Finch CE, Haghani A. Gene-Environment Interactions and Stochastic Variations in the Gero-Exposome. J Gerontol A Biol Sci Med Sci 2021; 76:1740-1747. [PMID: 33580247 PMCID: PMC8436990 DOI: 10.1093/gerona/glab045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Indexed: 12/11/2022] Open
Abstract
The limited heritability of human life spans suggests an important role for gene-environment (G × E) interactions across the life span (T), from gametes to geronts. Multilevel G × E × T interactions of aging phenotypes are conceptualized in the Gero-Exposome as Exogenous and Endogenous domains. Stochastic variations in the Endogenous domain contribute to the diversity of aging phenotypes, shown for the diversity of inbred Caenorhabditis elegans life spans in the same culture environment, and for variegated gene expression of somatic cells in nematodes and mammals. These phenotypic complexities can be analyzed as 3-way interactions of gene, environment, and stochastic variations, the Tripartite Phenotype of Aging. Single-cell analyses provide tools to explore this broadening frontier of biogerontology.
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Affiliation(s)
- Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA
- Dornsife College, University of Southern California, Los Angeles, CA
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
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5
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Zhang J, Burnaevskiy N, Annis J, Han W, Hou D, Ladd P, Lee L, Mendenhall AR, Oshima J, Martin GM. Cell-to-Cell Variation in Gene Expression for Cultured Human Cells Is Controlled in Trans by Diverse Genes: Implications for the Pathobiology of Aging. J Gerontol A Biol Sci Med Sci 2021; 75:2295-2298. [PMID: 31957802 DOI: 10.1093/gerona/glaa027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Indexed: 11/13/2022] Open
Abstract
Cell-to-cell variation in gene expression increases among homologous cells within multiple tissues during aging. We call this phenomenon variegated gene expression (VGE). Long, healthy life requires robust and coordinated gene expression. We posit that nature may have evolved VGE as a bet-hedging mechanism to protect reproductively active populations. The price we may pay is accelerated aging. That hypothesis will require the demonstration that genetic loci are capable of modulating degrees of VGE. While loci controlling VGE in yeast and genes controlling interindividual variation in gene expression in Caenorhabditis elegans have been identified, there has been no compelling evidence for the role of specific genetic loci in modulations of VGE of specific targets in humans. With the assistance of a core facility, we used a customized library of siRNA constructs to screen 1,195 human genes to identify loci contributing to the control of VGE of a gene with relevance to the biology of aging. We identified approximately 50 loci controlling VGE of the prolongevity gene, SIRT1. Because of its partial homology to FOXO3A, a variant of which is enriched in centenarians, our laboratory independently confirmed that the knockdown of FOXF2 greatly diminished VGE of SIRT1 but had little impact upon the VGE of WRN. While the role of these VGE-altering genes on aging in vivo remains to be determined, we hypothesize that some of these genes can be targeted to increase functionality during aging.
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Affiliation(s)
- Jiaming Zhang
- Department of Pathology, University of Washington, Seattle
| | | | - James Annis
- Quellos High-throughput Screening Core, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle
| | - Wenyan Han
- Department of Pathology, University of Washington, Seattle
| | - Deyin Hou
- Department of Pathology, University of Washington, Seattle
| | - Paula Ladd
- Department of Pathology, University of Washington, Seattle
| | - Lin Lee
- Department of Pathology, University of Washington, Seattle
| | | | - Junko Oshima
- Department of Pathology, University of Washington, Seattle
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6
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Mendenhall AR, Lithgow GJ, Kim S, Friedman D, Newell-Stamper BL, Johnson TE. Career Retrospective: Tom Johnson-Genetics, Genomics, Stress, Stochastic Variation, and Aging. J Gerontol A Biol Sci Med Sci 2021; 76:e85-e91. [PMID: 33609361 DOI: 10.1093/gerona/glab050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, Washington, USA.,University of Washington Nathan Shock Center for Excellence in the Basic Biology of Aging, Department of Laboratory Medicine and Pathology, Seattle, Washington, USA
| | | | - Stuart Kim
- Department of Developmental Biology, Stanford University Medical Center, California, USA
| | - David Friedman
- Department of Chemistry, Middle Tennessee State University, Murfreesboro, USA
| | | | - Thomas E Johnson
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA.,University of Colorado, Institute for Behavioral Genetics, Boulder, Colorado, USA
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7
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Kinser HE, Mosley MC, Plutzer IB, Pincus Z. Global, cell non-autonomous gene regulation drives individual lifespan among isogenic C. elegans. eLife 2021; 10:65026. [PMID: 33522488 PMCID: PMC7864635 DOI: 10.7554/elife.65026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/13/2021] [Indexed: 01/04/2023] Open
Abstract
Across species, lifespan is highly variable among individuals within a population. Even genetically identical Caenorhabditis elegans reared in homogeneous environments are as variable in lifespan as outbred human populations. We hypothesized that persistent inter-individual differences in expression of key regulatory genes drives this lifespan variability. As a test, we examined the relationship between future lifespan and the expression of 22 microRNA promoter::GFP constructs. Surprisingly, expression of nearly half of these reporters, well before death, could effectively predict lifespan. This indicates that prospectively long- vs. short-lived individuals have highly divergent patterns of transgene expression and transcriptional regulation. The gene-regulatory processes reported on by two of the most lifespan-predictive transgenes do not require DAF-16, the FOXO transcription factor that is a principal effector of insulin/insulin-like growth factor (IGF-1) signaling. Last, we demonstrate a hierarchy of redundancy in lifespan-predictive ability among three transgenes expressed in distinct tissues, suggesting that they collectively report on an organism-wide, cell non-autonomous process that acts to set each individual’s lifespan.
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Affiliation(s)
- Holly E Kinser
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, United States.,Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Matthew C Mosley
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, United States.,Program in Developmental, Regenerative, and Stem Cell Biology, Washington University in St. Louis, St. Louis, United States
| | - Isaac B Plutzer
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, United States
| | - Zachary Pincus
- Department of Developmental Biology and Department of Genetics, Washington University in St. Louis, St. Louis, United States
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8
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Mendenhall AR, Martin GM, Kaeberlein M, Anderson RM. Cell-to-cell variation in gene expression and the aging process. GeroScience 2021; 43:181-196. [PMID: 33595768 PMCID: PMC8050212 DOI: 10.1007/s11357-021-00339-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/04/2021] [Indexed: 12/11/2022] Open
Abstract
There is tremendous variation in biological traits, and much of it is not accounted for by variation in DNA sequence, including human diseases and lifespan. Emerging evidence points to differences in the execution of the genetic program as a key source of variation, be it stochastic variation or programmed variation. Here we discuss variation in gene expression as an intrinsic property and how it could contribute to variation in traits, including the rate of aging. The review is divided into sections describing the historical context and evidence to date for nongenetic variation, the different approaches that may be used to detect nongenetic variation, and recent findings showing that the amount of variation in gene expression can be both genetically programmed and epigenetically controlled. Finally, we present evidence that changes in cell-to-cell variation in gene expression emerge as part of the aging process and may be linked to disease vulnerability as a function of age. These emerging concepts are likely to be important across the spectrum of biomedical research and may well underpin what we understand as biological aging.
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Affiliation(s)
- Alexander R Mendenhall
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA.
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA.
| | - George M Martin
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Washington, Seattle, WA, USA
- Nathan Shock Center for Excellence in the Basic Biology of Aging, School of Medicine, University of Washington, Seattle, WA, USA
| | - Rozalyn M Anderson
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin and Geriatric Research Education and Clinical Center, William S Middleton Memorial Veterans Hospital, Madison, WI, USA.
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9
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Yee Z, Lim SHY, Ng LF, Gruber J. Inhibition of mTOR decreases insoluble proteins burden by reducing translation in C. elegans. Biogerontology 2020; 22:101-118. [PMID: 33159806 DOI: 10.1007/s10522-020-09906-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/02/2020] [Indexed: 02/07/2023]
Abstract
Aging animals accumulate insoluble proteins as a consequence of a decline of proteostatic maintenance with age. In Caenorhabditis elegans, for instance, levels of detergent-insoluble proteins increase with age. In longer-lived strains of C. elegans, this accumulation occurs more slowly, implying a link to lifespan determination. We further explored this link and found that detergent-insoluble proteins accumulate more rapidly at higher temperatures, a condition where lifespan is short. We employed a C. elegans strain carrying a GFP transcriptional reporter under the control of a heat shock (hsp-16.2) promoter to investigate the dynamics of proteostatic failure in individual nematodes. We found that early, sporadic activation of hsp-16.2 was predictive of shorter remaining lifespan in individual nematodes. Exposure to rapamycin, resulting in reduced mTOR signaling, delayed spurious expression, extended lifespan, and delayed accumulation of insoluble proteins, suggesting that targets downstream of the mTOR pathway regulate the accumulation of insoluble proteins. We specifically explored ribosomal S6 kinase (rsks-1) as one such candidate and found that RNAi against rsks-1 also resulted in less age-dependent accumulation of insoluble proteins and extended lifespan. Our results demonstrate that inhibition of protein translation via reduced mTOR signaling resulted in slower accumulation of insoluble proteins, delayed proteostatic crisis, and extended lifespan in C. elegans.
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Affiliation(s)
- Zhuangli Yee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Shaun Hsien Yang Lim
- Aging Research Laboratory, Science Division, Yale-NUS College, Singapore, Singapore
| | - Li Fang Ng
- Aging Research Laboratory, Science Division, Yale-NUS College, Singapore, Singapore
| | - Jan Gruber
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Aging Research Laboratory, Science Division, Yale-NUS College, Singapore, Singapore.
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10
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Russell JC, Burnaevskiy N, Ma B, Mailig MA, Faust F, Crane M, Kaeberlein M, Mendenhall A. Electrophysiological Measures of Aging Pharynx Function in C. elegans Reveal Enhanced Organ Functionality in Older, Long-lived Mutants. J Gerontol A Biol Sci Med Sci 2020; 74:1173-1179. [PMID: 29165668 DOI: 10.1093/gerona/glx230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 11/16/2017] [Indexed: 02/03/2023] Open
Abstract
The function of the pharynx, an organ in the model system Caenorhabditis elegans, has been correlated with life span and motility (another measure of health) since 1980. In this study, in order to further understand the relationship between organ function and life span, we measured the age-related decline of the pharynx using an electrophysiological approach. We measured and analyzed electropharyngeograms (EPG) of wild type animals, short-lived hsf-1 mutants, and long-lived animals with genetically decreased insulin signaling or increased heat shock pathway signaling; we recorded a total of 2,478 EPGs from 1,374 individuals. As expected, the long-lived daf-2(e1370) and hsf-1OE(uthIs235) animals maintained pharynx function relatively closer to the youthful state during aging, whereas the hsf-1(sy441) and wild type animals' pharynx function deviated significantly further from the youthful state at advanced age. Measures of the amount of variation in organ function can act as biomarkers of youthful physiology as well. Intriguingly, the long-lived animals had greater variation in the duration of pharynx contraction at older ages.
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Affiliation(s)
| | | | - Bridget Ma
- Department of Pathology, University of Washington, Seattle
| | | | - Franklin Faust
- Department of Pathology, University of Washington, Seattle
| | - Matt Crane
- Department of Pathology, University of Washington, Seattle
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11
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Rhoads TW, Clark JP, Gustafson GE, Miller KN, Conklin MW, DeMuth TM, Berres ME, Eliceiri KW, Vaughan LK, Lary CW, Beasley TM, Colman RJ, Anderson RM. Molecular and Functional Networks Linked to Sarcopenia Prevention by Caloric Restriction in Rhesus Monkeys. Cell Syst 2020; 10:156-168.e5. [PMID: 31982367 PMCID: PMC7047532 DOI: 10.1016/j.cels.2019.12.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 08/03/2019] [Accepted: 12/11/2019] [Indexed: 12/13/2022]
Abstract
Caloric restriction (CR) improves survival in nonhuman primates and delays the onset of age-related morbidities including sarcopenia, which is characterized by the age-related loss of muscle mass and function. A shift in metabolism anticipates the onset of muscle-aging phenotypes in nonhuman primates, suggesting a potential role for metabolism in the protective effects of CR. Here, we show that CR induced profound changes in muscle composition and the cellular metabolic environment. Bioinformatic analysis linked these adaptations to proteostasis, RNA processing, and lipid synthetic pathways. At the tissue level, CR maintained contractile content and attenuated age-related metabolic shifts among individual fiber types with higher mitochondrial activity, altered redox metabolism, and smaller lipid droplet size. Biometric and metabolic rate data confirm preserved metabolic efficiency in CR animals that correlated with the attenuation of age-related muscle mass and physical activity. These data suggest that CR-induced reprogramming of metabolism plays a role in delayed aging of skeletal muscle in rhesus monkeys.
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Affiliation(s)
- Timothy W Rhoads
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Josef P Clark
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Grace E Gustafson
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Karl N Miller
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Matthew W Conklin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Tyler M DeMuth
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Mark E Berres
- Biotechnolgoy Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Kevin W Eliceiri
- Laboratory for Optical and Computational Instrumentation, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Laura K Vaughan
- Department of Biostatistics, University of Alabama-Birmingham, Birmingham, AL 35294, USA
| | - Christine W Lary
- Department of Biostatistics, University of Alabama-Birmingham, Birmingham, AL 35294, USA
| | - T Mark Beasley
- Department of Biostatistics, University of Alabama-Birmingham, Birmingham, AL 35294, USA; Geriatric Research Education and Clinical Center, Birmingham/Atlanta Veterans Administration Hospital, Birmingham, AL 35297, USA
| | - Ricki J Colman
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, WI 53715, USA
| | - Rozalyn M Anderson
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA; Geriatric Research Education and Clinical Center, William S. Middleton Memorial Veterans Hospital, Madison, WI 53705, USA.
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12
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Burnaevskiy N, Sands B, Yun S, Tedesco PM, Johnson TE, Kaeberlein M, Brent R, Mendenhall A. Chaperone biomarkers of lifespan and penetrance track the dosages of many other proteins. Nat Commun 2019; 10:5725. [PMID: 31844058 PMCID: PMC6914778 DOI: 10.1038/s41467-019-13664-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 11/11/2019] [Indexed: 12/27/2022] Open
Abstract
Many traits vary among isogenic individuals in homogeneous environments. In microbes, plants and animals, variation in the protein chaperone system affects many such traits. In the animal model C. elegans, the expression level of hsp-16.2 chaperone biomarkers correlates with or predicts the penetrance of mutations and lifespan after heat shock. But the physiological mechanisms causing cells to express different amounts of the biomarker were unknown. Here, we used an in vivo microscopy approach to dissect different contributions to cell-to-cell variation in hsp-16.2 expression in the intestines of young adult animals, which generate the most lifespan predicting signal. While we detected both cell autonomous intrinsic noise and signaling noise, we found both contributions were relatively unimportant. The major contributor to cell-to-cell variation in biomarker expression was general differences in protein dosage. The hsp-16.2 biomarker reveals states of high or low effective dosage for many genes.
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Affiliation(s)
| | - Bryan Sands
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Soo Yun
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Patricia M Tedesco
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Thomas E Johnson
- Department of Integrative Physiology, University of Colorado, Boulder, CO, USA
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
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13
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Crane MM, Sands B, Battaglia C, Johnson B, Yun S, Kaeberlein M, Brent R, Mendenhall A. In vivo measurements reveal a single 5'-intron is sufficient to increase protein expression level in Caenorhabditis elegans. Sci Rep 2019; 9:9192. [PMID: 31235724 PMCID: PMC6591249 DOI: 10.1038/s41598-019-45517-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 06/06/2019] [Indexed: 11/29/2022] Open
Abstract
Introns can increase gene expression levels using a variety of mechanisms collectively referred to as Intron Mediated Enhancement (IME). IME has been measured in cell culture and plant models by quantifying expression of intronless and intron-bearing reporter genes in vitro. We developed hardware and software to implement microfluidic chip-based gene expression quantification in vivo. We altered position, number and sequence of introns in reporter genes controlled by the hsp-90 promoter. Consistent with plant and mammalian studies, we determined a single, natural or synthetic, 5'-intron is sufficient for the full IME effect conferred by three synthetic introns, while a 3'-intron is not. We found coding sequence can affect IME; the same three synthetic introns that increase mcherry protein concentration by approximately 50%, increase mEGFP by 80%. We determined IME effect size is not greatly affected by the stronger vit-2 promoter. Our microfluidic imaging approach should facilitate screens for factors affecting IME and other intron-dependent processes.
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Affiliation(s)
- Matthew M Crane
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Bryan Sands
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Christian Battaglia
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Brock Johnson
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Soo Yun
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Matt Kaeberlein
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Division of Basic Science, Seattle, WA, USA
| | - Alex Mendenhall
- University of Washington, School of Medicine, Department of Pathology, Seattle, WA, USA.
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14
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Stroustrup N. Measuring and modeling interventions in aging. Curr Opin Cell Biol 2018; 55:129-138. [PMID: 30099284 PMCID: PMC6284105 DOI: 10.1016/j.ceb.2018.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/09/2018] [Accepted: 07/13/2018] [Indexed: 02/06/2023]
Abstract
Many dietary, pharmaceutical, and genetic interventions have been found to increase the lifespan of laboratory animals. Several are now being explored for clinical application. To understand the physiologic action and therapeutic potential of interventions in aging, researchers must build quantitative models. Do interventions delay the onset of aging? Slow it down? Merely ameliorate some of its symptoms? If interventions slow some aging mechanisms but accelerate others, can we detect or predict the systemic consequences? Statistical and analytic models provide a crucial framework in which to answer these questions and clarify the systems-level effect of molecular interventions in aging. This review provides a brief survey of approaches to modeling lifespan data and places them in the context of recent experimental work.
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Affiliation(s)
- Nicholas Stroustrup
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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15
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Wentz JM, Mendenhall AR, Bortz DM. Pattern Formation in the Longevity-Related Expression of Heat Shock Protein-16.2 in Caenorhabditis elegans. Bull Math Biol 2018; 80:2669-2697. [PMID: 30097920 DOI: 10.1007/s11538-018-0482-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 07/27/2018] [Indexed: 11/26/2022]
Abstract
Aging in Caenorhabditis elegans is controlled, in part, by the insulin-like signaling and heat shock response pathways. Following thermal stress, expression levels of small heat shock protein-16.2 show a spatial patterning across the 20 intestinal cells that reside along the length of the worm. Here, we present a hypothesized mechanism that could lead to this patterned response and develop a mathematical model of this system to test our hypothesis. We propose that the patterned expression of heat shock protein is caused by a diffusion-driven instability within the pseudocoelom, or fluid-filled cavity, that borders the intestinal cells in C. elegans. This instability is due to the interactions between two classes of insulin-like peptides that serve antagonistic roles. We examine output from the developed model and compare it to experimental data on heat shock protein expression. Given biologically bounded parameters, the model presented is capable of producing patterns similar to what is observed experimentally and provides a first step in mathematically modeling aging-related mechanisms in C. elegans.
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Affiliation(s)
- J M Wentz
- Interdisciplinary Quantitative Biology Graduate Program and Department of Applied Mathematics, University of Colorado, Boulder, CO, 80309-0526, USA
| | - A R Mendenhall
- Department of Pathology, University of Washington, Seattle, WA, 98109-1024, USA
| | - D M Bortz
- Department of Applied Mathematics, University of Colorado, Boulder, CO, 80309-0526, USA.
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16
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Pesce CG, Zdraljevic S, Peria WJ, Bush A, Repetto MV, Rockwell D, Yu RC, Colman-Lerner A, Brent R. Single-cell profiling screen identifies microtubule-dependent reduction of variability in signaling. Mol Syst Biol 2018; 14:e7390. [PMID: 29618636 PMCID: PMC5884679 DOI: 10.15252/msb.20167390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/25/2018] [Accepted: 02/06/2018] [Indexed: 01/01/2023] Open
Abstract
Populations of isogenic cells often respond coherently to signals, despite differences in protein abundance and cell state. Previously, we uncovered processes in the Saccharomyces cerevisiae pheromone response system (PRS) that reduced cell-to-cell variability in signal strength and cellular response. Here, we screened 1,141 non-essential genes to identify 50 "variability genes". Most had distinct, separable effects on strength and variability of the PRS, defining these quantities as genetically distinct "axes" of system behavior. Three genes affected cytoplasmic microtubule function: BIM1, GIM2, and GIM4 We used genetic and chemical perturbations to show that, without microtubules, PRS output is reduced but variability is unaffected, while, when microtubules are present but their function is perturbed, output is sometimes lowered, but its variability is always high. The increased variability caused by microtubule perturbations required the PRS MAP kinase Fus3 and a process at or upstream of Ste5, the membrane-localized scaffold to which Fus3 must bind to be activated. Visualization of Ste5 localization dynamics demonstrated that perturbing microtubules destabilized Ste5 at the membrane signaling site. The fact that such microtubule perturbations cause aberrant fate and polarity decisions in mammals suggests that microtubule-dependent signal stabilization might also operate throughout metazoans.
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Affiliation(s)
| | - Stefan Zdraljevic
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | | | - Alan Bush
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Victoria Repetto
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | | | | | - Alejandro Colman-Lerner
- IFIBYNE-UBA-CONICET and Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Roger Brent
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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17
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Mendenhall A, Crane MM, Tedesco PM, Johnson TE, Brent R. Caenorhabditis elegans Genes Affecting Interindividual Variation in Life-span Biomarker Gene Expression. J Gerontol A Biol Sci Med Sci 2017; 72:1305-1310. [PMID: 28158434 DOI: 10.1093/gerona/glw349] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 12/30/2016] [Indexed: 01/12/2023] Open
Abstract
Genetically identical organisms grown in homogenous environments differ in quantitative phenotypes. Differences in one such trait, expression of a single biomarker gene, can identify isogenic cells or organisms that later manifest different fates. For example, in isogenic populations of young adult Caenorhabditis elegans, differences in Green Fluorescent Protein (GFP) expressed from the hsp-16.2 promoter predict differences in life span. Thus, it is of interest to determine how interindividual differences in biomarker gene expression arise. Prior reports showed that the thermosensory neurons and insulin signaling systems controlled the magnitude of the heat shock response, including absolute expression of hsp-16.2. Here, we tested whether these regulatory signals might also influence variation in hsp-16.2 reporter expression. Genetic experiments showed that the action of AFD thermosensory neurons increases interindividual variation in biomarker expression. Further genetic experimentation showed the insulin signaling system acts to decrease interindividual variation in life-span biomarker expression; in other words, insulin signaling canalizes expression of the hsp-16.2-driven life-span biomarker. Our results show that specific signaling systems regulate not only expression level, but also the amount of interindividual expression variation for a life-span biomarker gene. They raise the possibility that manipulation of these systems might offer means to reduce heterogeneity in the aging process.
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Affiliation(s)
| | | | | | - Thomas E Johnson
- Institute for Behavioral Genetics.,Department of Integrative Physiology.,Biofrontiers Institute, University of Colorado, Boulder
| | - Roger Brent
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
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