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Kron NS, Fieber LA, Baker L, Campbell C, Schmale MC. Host response to Aplysia Abyssovirus 1 in nervous system and gill. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024; 159:105211. [PMID: 38885747 DOI: 10.1016/j.dci.2024.105211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/03/2024] [Accepted: 06/06/2024] [Indexed: 06/20/2024]
Abstract
The California sea hare (Aplysia californica) is a model for age associated cognitive decline. Recent researched identified a novel nidovirus, Aplysia Abyssovirus 1, with broad tropism enriched in the Aplysia nervous system. This virus is ubiquitous in wild and maricultured, young and old animals without obvious pathology. Here we re-evaluated gene expression data from several previous studies to investigate differential expression in the nervous system and gill in response to virus and aging as well as the mutational spectrum observed in the viral sequences obtained from these datasets. Viral load and age were highly correlated, indicating persistent infection. Upregulated genes in response to virus were enriched for immune genes and signatures of ER and proteostatic stress, while downregulated genes were enriched for mitochondrial metabolism. Differential expression with respect to age suggested increased iron accumulation and decreased glycolysis, fatty acid metabolism, and proteasome function. Interaction of gene expression trends associated with viral infection and aging suggest that viral infection likely plays a role in aging in the Aplysia nervous system. Mutation analysis of viral RNA identified signatures suggesting ADAR and AID/APOBEC like deaminase act as part of Aplysia anti-viral defense.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA.
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | - Lydia Baker
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
| | | | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, 4600 Rickenbacker Cswy, Miami, FL, 33149, USA
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2
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Chen YR, Harel I, Singh PP, Ziv I, Moses E, Goshtchevsky U, Machado BE, Brunet A, Jarosz DF. Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate. Dev Cell 2024; 59:1892-1911.e13. [PMID: 38810654 PMCID: PMC11265985 DOI: 10.1016/j.devcel.2024.04.014] [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: 08/30/2023] [Revised: 01/13/2024] [Accepted: 04/15/2024] [Indexed: 05/31/2024]
Abstract
Protein aggregation is a hallmark of age-related neurodegeneration. Yet, aggregation during normal aging and in tissues other than the brain is poorly understood. Here, we leverage the African turquoise killifish to systematically profile protein aggregates in seven tissues of an aging vertebrate. Age-dependent aggregation is strikingly tissue specific and not simply driven by protein expression differences. Experimental interrogation in killifish and yeast, combined with machine learning, indicates that this specificity is linked to protein-autonomous biophysical features and tissue-selective alterations in protein quality control. Co-aggregation of protein quality control machinery during aging may further reduce proteostasis capacity, exacerbating aggregate burden. A segmental progeria model with accelerated aging in specific tissues exhibits selectively increased aggregation in these same tissues. Intriguingly, many age-related protein aggregates arise in wild-type proteins that, when mutated, drive human diseases. Our data chart a comprehensive landscape of protein aggregation during vertebrate aging and identify strong, tissue-specific associations with dysfunction and disease.
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Affiliation(s)
- Yiwen R Chen
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Itamar Harel
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Inbal Ziv
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Eitan Moses
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Uri Goshtchevsky
- The Silberman Institute, the Hebrew University of Jerusalem, Givat Ram, Jerusalem 91904, Israel
| | - Ben E Machado
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Center for the Biology of Aging, Stanford University, Stanford, CA 94305, USA.
| | - Daniel F Jarosz
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
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Liu X, Novak B, Namendorf C, Steigenberger B, Zhang Y, Turck CW. Long-lived proteins and DNA as candidate predictive biomarkers for tissue associated diseases. iScience 2024; 27:109642. [PMID: 38632996 PMCID: PMC11022098 DOI: 10.1016/j.isci.2024.109642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 01/11/2024] [Accepted: 03/26/2024] [Indexed: 04/19/2024] Open
Abstract
Protein turnover is an important mechanism to maintain proteostasis. Long-lived proteins (LLPs) are vulnerable to lose their function due to time-accumulated damages. In this study we employed in vivo stable isotope labeling in mice from birth to postnatal day 89. Quantitative proteomics analysis of ten tissues and plasma identified 2113 LLPs, including widespread and tissue-specific ones. Interestingly, a significant percentage of LLPs was detected in plasma, implying a potential link to age-related cardiovascular diseases. LLPs identified in brains were related to neurodegenerative diseases. In addition, the relative quantification of DNA-derived deoxynucleosides from the same tissues provided information about cellular DNA renewal and showed good correlation with LLPs in the brain. The combined data reveal tissue-specific maps of mouse LLPs that may be involved in pathology due to a low renewal rate and an increased risk of damage. Tissue-derived peripheral LLPs hold promise as biomarkers for aging and age-related diseases.
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Affiliation(s)
- Xiaosong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bozidar Novak
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Kraepelinstr. 2-10, 80804 Munich, Germany
| | - Christian Namendorf
- Max Planck Institute of Psychiatry, Clinical Laboratory, Core Unit Analytics and Mass Spectrometry, Kraepelinstr. 2-10, 80804 Munich, Germany
| | - Barbara Steigenberger
- Mass Spectrometry Core Facility, Max Planck Institute of Biochemistry, D-82152 Martinsried/Munich, Germany
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 100 Haike Road, Shanghai 201210, China
| | - Christoph W. Turck
- Max Planck Institute of Psychiatry, Proteomics and Biomarkers, Kraepelinstr. 2-10, 80804 Munich, Germany
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, and KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-human Primates, and National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650107, China
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D’Angiolini S, Lui M, Mazzon E, Calabrò M. Network Analysis Performed on Transcriptomes of Parkinson's Disease Patients Reveals Dysfunction in Protein Translation. Int J Mol Sci 2024; 25:1299. [PMID: 38279299 PMCID: PMC10816150 DOI: 10.3390/ijms25021299] [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: 12/24/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Parkinson's disease (PD) is a prevalent neurodegenerative disorder characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra region of the brain. The hallmark pathological feature of PD is the accumulation of misfolded proteins, leading to the formation of intracellular aggregates known as Lewy bodies. Recent data evidenced how disruptions in protein synthesis, folding, and degradation are events commonly observed in PD and may provide information on the molecular background behind its etiopathogenesis. In the present study, we used a publicly available transcriptomic microarray dataset of peripheral blood of PD patients and healthy controls (GSE6613) to investigate the potential dysregulation of elements involved in proteostasis-related processes at the transcriptomic level. Our bioinformatics analysis revealed 375 differentially expressed genes (DEGs), of which 281 were down-regulated and 94 were up-regulated. Network analysis performed on the observed DEGs highlighted a cluster of 36 elements mainly involved in the protein synthesis processes. Different enriched ontologies were related to translation initiation and regulation, ribosome structure, and ribosome components nuclear export. Overall, this data consistently points to a generalized impairment of the translational machinery and proteostasis. Dysregulation of these mechanics has been associated with PD pathogenesis. Understanding the precise regulation of such processes may shed light on the molecular mechanisms of PD and provide potential data for early diagnosis.
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Affiliation(s)
| | | | - Emanuela Mazzon
- IRCCS Centro Neurolesi “Bonino-Pulejo”, Via Provinciale Palermo, Contrada Casazza, 98124 Messina, Italy
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Martins AD, Ribeiro JC, Ferreira R, Alves MG, Oliveira PF. Understanding the age-related alterations in the testis-specific proteome. Expert Rev Proteomics 2023; 20:331-343. [PMID: 37878493 DOI: 10.1080/14789450.2023.2274857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
INTRODUCTION Fertility rates in developing countries have declined over the past decades, and the trend of delayed fatherhood is rising as societies develop. The reasons behind the decline in male fertility with advancing age remain mysterious, making it a compelling and crucial area for further research. However, the limited number of studies dedicated to unraveling this enigma poses a challenge. Thus, our objective is to illuminate some of the upregulated and downregulated mechanisms in the male testis during the aging process. AREAS COVERED Herein, we present a critical overview of the studies addressing the alterations of testicular proteome through the aging process, starting from sexually matured young males to end-of-life-expectancy aged males. The comparative studies of the proteomic testicular profile of men with and without spermatogenic impairment are also discussed and key proteins and pathways involved are highlighted. EXPERT OPINION The difficulty of making age-comparative studies, especially of advanced-age study subjects, makes this topic of study quite challenging. Another topic worth mentioning is the heterogeneous nature and vast cellular composition of testicular tissue, which makes proteome data interpretation tricky. The cell type sorting and comorbidities testing in the testicular tissue of the studied subjects would help mitigate these problems.
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Affiliation(s)
- Ana D Martins
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - João C Ribeiro
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Aveiro, Portugal
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
- Laboratory for Integrative and Translational Research in Population Health (ITR), University of Porto, Porto, Portugal
| | - Rita Ferreira
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Marco G Alves
- iBiMED-Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Pedro F Oliveira
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, Aveiro, Portugal
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6
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Wodrich APK, Scott AW, Giniger E. What do we mean by "aging"? Questions and perspectives revealed by studies in Drosophila. Mech Ageing Dev 2023; 213:111839. [PMID: 37354919 PMCID: PMC10330756 DOI: 10.1016/j.mad.2023.111839] [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: 05/01/2023] [Revised: 06/14/2023] [Accepted: 06/21/2023] [Indexed: 06/26/2023]
Abstract
What is the nature of aging, and how best can we study it? Here, using a series of questions that highlight differing perspectives about the nature of aging, we ask how data from Drosophila melanogaster at the organismal, tissue, cellular, and molecular levels shed light on the complex interactions among the phenotypes associated with aging. Should aging be viewed as an individual's increasing probability of mortality over time or as a progression of physiological states? Are all age-correlated changes in physiology detrimental to vigor or are some compensatory changes that maintain vigor? Why do different age-correlated functions seem to change at different rates in a single individual as it ages? Should aging be considered as a single, integrated process across the scales of biological resolution, from organismal to molecular, or must we consider each level of biological scale as a separate, distinct entity? Viewing aging from these differing perspectives yields distinct but complementary interpretations about the properties and mechanisms of aging and may offer a path through the complexities related to understanding the nature of aging.
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Affiliation(s)
- Andrew P K Wodrich
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States; Interdisciplinary Program in Neuroscience, Georgetown University, Washington DC, United States; College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Andrew W Scott
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, National Institutes of Health (NIH), Bethesda, MD, United States.
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Villalobos-Cantor S, Barrett RM, Condon AF, Arreola-Bustos A, Rodriguez KM, Cohen MS, Martin I. Rapid cell type-specific nascent proteome labeling in Drosophila. eLife 2023; 12:83545. [PMID: 37092974 PMCID: PMC10125018 DOI: 10.7554/elife.83545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/09/2023] [Indexed: 04/25/2023] Open
Abstract
Controlled protein synthesis is required to regulate gene expression and is often carried out in a cell type-specific manner. Protein synthesis is commonly measured by labeling the nascent proteome with amino acid analogs or isotope-containing amino acids. These methods have been difficult to implement in vivo as they require lengthy amino acid replacement procedures. O-propargyl-puromycin (OPP) is a puromycin analog that incorporates into nascent polypeptide chains. Through its terminal alkyne, OPP can be conjugated to a fluorophore-azide for directly visualizing nascent protein synthesis, or to a biotin-azide for capture and identification of newly-synthesized proteins. To achieve cell type-specific OPP incorporation, we developed phenylacetyl-OPP (PhAc-OPP), a puromycin analog harboring an enzyme-labile blocking group that can be removed by penicillin G acylase (PGA). Here, we show that cell type-specific PGA expression in Drosophila can be used to achieve OPP labeling of newly-synthesized proteins in targeted cell populations within the brain. Following a brief 2 hr incubation of intact brains with PhAc-OPP, we observe robust imaging and affinity purification of OPP-labeled nascent proteins in PGA-targeted cell populations. We apply this method to show a pronounced age-related decline in neuronal protein synthesis in the fly brain, demonstrating the capability of PhAc-OPP to quantitatively capture in vivo protein synthesis states. This method, which we call POPPi (PGA-dependent OPP incorporation), should be applicable for rapidly visualizing protein synthesis and identifying nascent proteins synthesized under diverse physiological and pathological conditions with cellular specificity in vivo.
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Affiliation(s)
- Stefanny Villalobos-Cantor
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Ruth M Barrett
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alec F Condon
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alicia Arreola-Bustos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Kelsie M Rodriguez
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
- Parkinson Center of Oregon, Oregon Health and Science University, Portland, United States
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8
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Dowling P, Gargan S, Swandulla D, Ohlendieck K. Fiber-Type Shifting in Sarcopenia of Old Age: Proteomic Profiling of the Contractile Apparatus of Skeletal Muscles. Int J Mol Sci 2023; 24:ijms24032415. [PMID: 36768735 PMCID: PMC9916839 DOI: 10.3390/ijms24032415] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/20/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
The progressive loss of skeletal muscle mass and concomitant reduction in contractile strength plays a central role in frailty syndrome. Age-related neuronal impairments are closely associated with sarcopenia in the elderly, which is characterized by severe muscular atrophy that can considerably lessen the overall quality of life at old age. Mass-spectrometry-based proteomic surveys of senescent human skeletal muscles, as well as animal models of sarcopenia, have decisively improved our understanding of the molecular and cellular consequences of muscular atrophy and associated fiber-type shifting during aging. This review outlines the mass spectrometric identification of proteome-wide changes in atrophying skeletal muscles, with a focus on contractile proteins as potential markers of changes in fiber-type distribution patterns. The observed trend of fast-to-slow transitions in individual human skeletal muscles during the aging process is most likely linked to a preferential susceptibility of fast-twitching muscle fibers to muscular atrophy. Studies with senescent animal models, including mostly aged rodent skeletal muscles, have confirmed fiber-type shifting. The proteomic analysis of fast versus slow isoforms of key contractile proteins, such as myosin heavy chains, myosin light chains, actins, troponins and tropomyosins, suggests them as suitable bioanalytical tools of fiber-type transitions during aging.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Stephen Gargan
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Dieter Swandulla
- Institute of Physiology, University of Bonn, D53115 Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
- Correspondence: ; Tel.: +353-1-7083842
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Hwangbo DS, Kwon YJ, Iwanaszko M, Jiang P, Abbasi L, Wright N, Alli S, Hutchison AL, Dinner AR, Braun RI, Allada R. Dietary Restriction Impacts Peripheral Circadian Clock Output Important for Longevity in Drosophila. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.04.522718. [PMID: 36711760 PMCID: PMC9881908 DOI: 10.1101/2023.01.04.522718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Circadian clocks may mediate lifespan extension by caloric or dietary restriction (DR). We find that the core clock transcription factor Clock is crucial for a robust longevity and fecundity response to DR in Drosophila. To identify clock-controlled mediators, we performed RNA-sequencing from abdominal fat bodies across the 24 h day after just 5 days under control or DR diets. In contrast to more chronic DR regimens, we did not detect significant changes in the rhythmic expression of core clock genes. Yet we discovered that DR induced de novo rhythmicity or increased expression of rhythmic clock output genes. Network analysis revealed that DR increased network connectivity in one module comprised of genes encoding proteasome subunits. Adult, fat body specific RNAi knockdown demonstrated that proteasome subunits contribute to DR-mediated lifespan extension. Thus, clock control of output links DR-mediated changes in rhythmic transcription to lifespan extension.
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Affiliation(s)
- Dae-Sung Hwangbo
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- Center for Sleep & Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Yong-Jae Kwon
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Marta Iwanaszko
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Peng Jiang
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- Center for Sleep & Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Ladan Abbasi
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Nicholas Wright
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Sarayu Alli
- Department of Biology, University of Louisville, Louisville, 40292, KY, USA
| | - Alan L. Hutchison
- James Franck Institute, Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Aaron R. Dinner
- James Franck Institute, Department of Chemistry, Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Rosemary I Braun
- Biostatistics Division, Department of Preventive Medicine, Northwestern University, Chicago, IL 60611, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
| | - Ravi Allada
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- Center for Sleep & Circadian Biology, Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL 60208, USA
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Targeting the "hallmarks of aging" to slow aging and treat age-related disease: fact or fiction? Mol Psychiatry 2023; 28:242-255. [PMID: 35840801 PMCID: PMC9812785 DOI: 10.1038/s41380-022-01680-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/09/2023]
Abstract
Aging is a major risk factor for a number of chronic diseases, including neurodegenerative and cerebrovascular disorders. Aging processes have therefore been discussed as potential targets for the development of novel and broadly effective preventatives or therapeutics for age-related diseases, including those affecting the brain. Mechanisms thought to contribute to aging have been summarized under the term the "hallmarks of aging" and include a loss of proteostasis, mitochondrial dysfunction, altered nutrient sensing, telomere attrition, genomic instability, cellular senescence, stem cell exhaustion, epigenetic alterations and altered intercellular communication. We here examine key claims about the "hallmarks of aging". Our analysis reveals important weaknesses that preclude strong and definitive conclusions concerning a possible role of these processes in shaping organismal aging rate. Significant ambiguity arises from the overreliance on lifespan as a proxy marker for aging, the use of models with unclear relevance for organismal aging, and the use of study designs that do not allow to properly estimate intervention effects on aging rate. We also discuss future research directions that should be taken to clarify if and to what extent putative aging regulators do in fact interact with aging. These include multidimensional analytical frameworks as well as designs that facilitate the proper assessment of intervention effects on aging rate.
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11
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Cui M, Cheng C, Zhang L. High-throughput proteomics: a methodological mini-review. J Transl Med 2022; 102:1170-1181. [PMID: 36775443 PMCID: PMC9362039 DOI: 10.1038/s41374-022-00830-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 11/15/2022] Open
Abstract
Proteomics plays a vital role in biomedical research in the post-genomic era. With the technological revolution and emerging computational and statistic models, proteomic methodology has evolved rapidly in the past decade and shed light on solving complicated biomedical problems. Here, we summarize scientific research and clinical practice of existing and emerging high-throughput proteomics approaches, including mass spectrometry, protein pathway array, next-generation tissue microarrays, single-cell proteomics, single-molecule proteomics, Luminex, Simoa and Olink Proteomics. We also discuss important computational methods and statistical algorithms that can maximize the mining of proteomic data with clinical and/or other 'omics data. Various principles and precautions are provided for better utilization of these tools. In summary, the advances in high-throughput proteomics will not only help better understand the molecular mechanisms of pathogenesis, but also to identify the signature signaling networks of specific diseases. Thus, modern proteomics have a range of potential applications in basic research, prognostic oncology, precision medicine, and drug discovery.
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Affiliation(s)
- Miao Cui
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pathology, Mount Sinai West, New York, NY, USA
| | - Chao Cheng
- Department of Medicine, Section of Epidemiology and Population Sciences, Baylor College of Medicine, Houston, TX, USA. .,Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
| | - Lanjing Zhang
- Department of Biological Sciences, Rutgers University, Newark, NJ, USA. .,Department of Pathology, Princeton Medical Center, Plainsboro, NJ, USA. .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA. .,Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ, USA.
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12
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Ge MX, Yu Q, Li GH, Yang LQ, He Y, Li J, Kong QP. Multiple time-series expression trajectories imply dynamic functional changes during cellular senescence. Comput Struct Biotechnol J 2022; 20:4131-4137. [PMID: 36016715 PMCID: PMC9379982 DOI: 10.1016/j.csbj.2022.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/03/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
Cellular senescence is a dynamic process driven by epigenetic and genetic changes. Although some transcriptomic signatures of senescent cells have been discovered, how these senescence-related signals change over time remains largely unclear. Here, we profiled the transcriptome dynamics of human dermal fibroblast (HDF) cells in successive stages of growth from proliferation to senescence. Based on time-series expression profile analysis, we discovered four trajectories (C1, C2, C3, C4) that are dynamically expressed as senescence progresses. While some genes were continuously up-regulated (C4) or down-regulated (C2) with aging, other genes did not change linearly with cell proliferation, but remained stable until entering the senescent state (C1, C3). Further analysis revealed that the four modes were enriched in different biological pathways, including regulation of cellular senescence. These findings provide a new perspective on understanding the dynamic regulatory mechanism of cellular senescence.
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13
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Liu Q, Chang CE, Wooldredge AC, Fong B, Kennedy BK, Zhou C. Tom70-based transcriptional regulation of mitochondrial biogenesis and aging. eLife 2022; 11:e75658. [PMID: 35234609 PMCID: PMC8926401 DOI: 10.7554/elife.75658] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/01/2022] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial biogenesis has two major steps: the transcriptional activation of nuclear genome-encoded mitochondrial proteins and the import of nascent mitochondrial proteins that are synthesized in the cytosol. These nascent mitochondrial proteins are aggregation-prone and can cause cytosolic proteostasis stress. The transcription factor-dependent transcriptional regulations and the TOM-TIM complex-dependent import of nascent mitochondrial proteins have been extensively studied. Yet, little is known regarding how these two steps of mitochondrial biogenesis coordinate with each other to avoid the cytosolic accumulation of these aggregation-prone nascent mitochondrial proteins. Here, we show that in budding yeast, Tom70, a conserved receptor of the TOM complex, moonlights to regulate the transcriptional activity of mitochondrial proteins. Tom70's transcription regulatory role is conserved in Drosophila. The dual roles of Tom70 in both transcription/biogenesis and import of mitochondrial proteins allow the cells to accomplish mitochondrial biogenesis without compromising cytosolic proteostasis. The age-related reduction of Tom70, caused by reduced biogenesis and increased degradation of Tom70, is associated with the loss of mitochondrial membrane potential, mtDNA, and mitochondrial proteins. While loss of Tom70 accelerates aging and age-related mitochondrial defects, overexpressing TOM70 delays these mitochondrial dysfunctions and extends the replicative lifespan. Our results reveal unexpected roles of Tom70 in mitochondrial biogenesis and aging.
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Affiliation(s)
- Qingqing Liu
- Buck Institute for Research on AgingNovatoUnited States
| | | | | | - Benjamin Fong
- Buck Institute for Research on AgingNovatoUnited States
| | - Brian K Kennedy
- Buck Institute for Research on AgingNovatoUnited States
- Healthy Longevity Programme, Yong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
- Centre for Healthy Longevity, National University Health SystemSingaporeSingapore
- Singapore Institute of Clinical Sciences, A(∗)STARSingaporeSingapore
| | - Chuankai Zhou
- Buck Institute for Research on AgingNovatoUnited States
- USC Leonard Davis School of Gerontology, University of Southern CaliforniaLos AngelesUnited States
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14
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Li Y, Bagheri P, Chang P, Zeng A, Hao J, Fung A, Wu JY, Shi L. Direct Imaging of Lipid Metabolic Changes in Drosophila Ovary During Aging Using DO-SRS Microscopy. FRONTIERS IN AGING 2022; 2:819903. [PMID: 35822015 PMCID: PMC9261447 DOI: 10.3389/fragi.2021.819903] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 12/29/2021] [Indexed: 01/09/2023]
Abstract
Emerging studies have shown that lipids and proteins play versatile roles in various aspects of aging. High-resolution in situ optical imaging provides a powerful approach to study the metabolic dynamics of lipids and proteins during aging. Here, we integrated D2O probing and stimulated Raman scattering (DO-SRS) microscopy to directly visualize metabolic changes in aging Drosophila ovary. The subcellular spatial distribution of de novo protein synthesis and lipogenesis in ovary was quantitatively imaged and examined. Our Raman spectra showed that early stages follicles were protein-enriched whereas mature eggs were lipid-enriched. DO-SRS imaging showed a higher protein synthesis in the earlier developing stages and an increased lipid turned over at the late stage. Aged (35 days) flies exhibited a dramatic decrease in metabolic turnover activities of both proteins and lipids, particularly, in the germ stem cell niche of germarium. We found an accumulation of unsaturated lipids in the nurse cells and oocytes in old flies, suggesting that unsaturated lipids may play an important role in the processes of oocyte maturation. We further detected changes in mitochondrial morphology and accumulation of Cytochrome c during aging. To our knowledge, this is the first study that directly visualizes spatiotemporal changes in lipid and protein metabolism in Drosophila ovary during development and aging processes. Our study not only demonstrates the application of a new imaging platform in visualizing metabolic dynamics of lipids and proteins in situ but also unravels how the metabolic activity and lipid distribution change in Drosophila ovary during aging.
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Affiliation(s)
- Yajuan Li
- The Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Pegah Bagheri
- The Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Phyllis Chang
- The Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Audrey Zeng
- The Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Jie Hao
- The Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Anthony Fung
- The Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
| | - Jane Y. Wu
- Department of Neurology, Northwestern University, Chicago, IL, United States
| | - Lingyan Shi
- The Department of Bioengineering, University of California San Diego, La Jolla, CA, United States
- *Correspondence: Lingyan Shi,
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15
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Torrelles JB, Restrepo BI, Bai Y, Ross C, Schlesinger LS, Turner J. The Impact of Aging on the Lung Alveolar Environment, Predetermining Susceptibility to Respiratory Infections. FRONTIERS IN AGING 2022; 3:818700. [PMID: 35821836 PMCID: PMC9261427 DOI: 10.3389/fragi.2022.818700] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/03/2022] [Indexed: 12/15/2022]
Abstract
Respiratory infections are one of the top causes of death in the elderly population, displaying susceptibility factors with increasing age that are potentially amenable to interventions. We posit that with increasing age there are predictable tissue-specific changes that prevent the immune system from working effectively in the lung. This mini-review highlights recent evidence for altered local tissue environment factors as we age focusing on increased tissue oxidative stress with associated immune cell changes, likely driven by the byproducts of age-associated inflammatory disease. Potential intervention points are presented.
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Affiliation(s)
- Jordi B. Torrelles
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Blanca I. Restrepo
- School of Public Health in Brownsville, University of Texas Health Houston, Brownsville, TX, United States
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, TX, United States
| | - Yidong Bai
- Department of Cell Systems and Anatomy, UT-Health San Antonio, San Antonio, TX, United States
| | - Corinna Ross
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
- Soutwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Larry S. Schlesinger
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Joanne Turner
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, TX, United States
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16
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Li L, Conradson DM, Bharat V, Kim MJ, Hsieh CH, Minhas PS, Papakyrikos AM, Durairaj AS, Ludlam A, Andreasson KI, Partridge L, Cianfrocco MA, Wang X. A mitochondrial membrane-bridging machinery mediates signal transduction of intramitochondrial oxidation. Nat Metab 2021; 3:1242-1258. [PMID: 34504353 PMCID: PMC8460615 DOI: 10.1038/s42255-021-00443-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Mitochondria are the main site for generating reactive oxygen species, which are key players in diverse biological processes. However, the molecular pathways of redox signal transduction from the matrix to the cytosol are poorly defined. Here we report an inside-out redox signal of mitochondria. Cysteine oxidation of MIC60, an inner mitochondrial membrane protein, triggers the formation of disulfide bonds and the physical association of MIC60 with Miro, an outer mitochondrial membrane protein. The oxidative structural change of this membrane-crossing complex ultimately elicits cellular responses that delay mitophagy, impair cellular respiration and cause oxidative stress. Blocking the MIC60-Miro interaction or reducing either protein, genetically or pharmacologically, extends lifespan and health-span of healthy fruit flies, and benefits multiple models of Parkinson's disease and Friedreich's ataxia. Our discovery provides a molecular basis for common treatment strategies against oxidative stress.
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Affiliation(s)
- Li Li
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Devon M Conradson
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Vinita Bharat
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Min Joo Kim
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Chung-Han Hsieh
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Paras S Minhas
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Neurosciences Intradepartmental Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Amanda M Papakyrikos
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
- Graduate Program in Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Anthony Ludlam
- Life Sciences Institute & Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Katrin I Andreasson
- Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA
- Program in Immunology, Stanford University, Stanford, CA, USA
| | - Linda Partridge
- Institute of Healthy Ageing, Genetics, Evolution and Environment, University College London, London, UK
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Michael A Cianfrocco
- Life Sciences Institute & Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Xinnan Wang
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Maternal & Child Health Research Institute, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Quantitative Proteomic and Metabolomic Profiling Reveals Altered Mitochondrial Metabolism and Folate Biosynthesis Pathways in the Aging Drosophila Eye. Mol Cell Proteomics 2021; 20:100127. [PMID: 34332122 PMCID: PMC8385154 DOI: 10.1016/j.mcpro.2021.100127] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/09/2021] [Accepted: 07/21/2021] [Indexed: 11/26/2022] Open
Abstract
Aging is associated with increased risk of ocular disease, suggesting that age-associated molecular changes in the eye increase its vulnerability to damage. Although there are common pathways involved in aging at an organismal level, different tissues and cell types exhibit specific changes in gene expression with advanced age. Drosophila melanogaster is an established model system for studying aging and neurodegenerative disease that also provides a valuable model for studying age-associated ocular disease. Flies, like humans, exhibit decreased visual function and increased risk of retinal degeneration with age. Here, we profiled the aging proteome and metabolome of the Drosophila eye and compared these data with age-associated transcriptomic changes from both eyes and photoreceptors to identify alterations in pathways that could lead to age-related phenotypes in the eye. Of note, the proteomic and metabolomic changes observed in the aging eye are distinct from those observed in the head or whole fly, suggesting that tissue-specific changes in protein abundance and metabolism occur in the aging fly. Our integration of the proteomic, metabolomic, and transcriptomic data reveals that changes in metabolism, potentially due to decreases in availability of B vitamins, together with chronic activation of the immune response, may underpin many of the events observed in the aging Drosophila eye. We propose that targeting these pathways in the genetically tractable Drosophila system may help to identify potential neuroprotective approaches for neurodegenerative and age-related ocular diseases. Data are available via ProteomeXchange with identifier PXD027090. Tissue-specific changes in protein abundance occur in the aging Drosophila eye. Increase in mitochondrial metabolism enzyme abundance in the aging eye. Decrease in corneal lens protein abundance and calcium buffering in the aging eye. Dysregulated metabolism impacts vitamin B and methionine metabolism in the aging eye.
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18
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Pras A, Nollen EAA. Regulation of Age-Related Protein Toxicity. Front Cell Dev Biol 2021; 9:637084. [PMID: 33748125 PMCID: PMC7973223 DOI: 10.3389/fcell.2021.637084] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 02/10/2021] [Indexed: 12/23/2022] Open
Abstract
Proteome damage plays a major role in aging and age-related neurodegenerative diseases. Under healthy conditions, molecular quality control mechanisms prevent toxic protein misfolding and aggregation. These mechanisms include molecular chaperones for protein folding, spatial compartmentalization for sequestration, and degradation pathways for the removal of harmful proteins. These mechanisms decline with age, resulting in the accumulation of aggregation-prone proteins that are harmful to cells. In the past decades, a variety of fast- and slow-aging model organisms have been used to investigate the biological mechanisms that accelerate or prevent such protein toxicity. In this review, we describe the most important mechanisms that are required for maintaining a healthy proteome. We describe how these mechanisms decline during aging and lead to toxic protein misassembly, aggregation, and amyloid formation. In addition, we discuss how optimized protein homeostasis mechanisms in long-living animals contribute to prolonging their lifespan. This knowledge might help us to develop interventions in the protein homeostasis network that delay aging and age-related pathologies.
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Affiliation(s)
| | - Ellen A. A. Nollen
- Laboratory of Molecular Neurobiology of Ageing, European Research Institute for the Biology of Ageing, University Medical Centre Groningen, University of Groningen, Groningen, Netherlands
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19
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Vincow ES, Thomas RE, Merrihew GE, MacCoss MJ, Pallanck LJ. Slowed protein turnover in aging Drosophila reflects a shift in cellular priorities. J Gerontol A Biol Sci Med Sci 2021; 76:1734-1739. [PMID: 33453098 DOI: 10.1093/gerona/glab015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
The accumulation of protein aggregates and dysfunctional organelles as organisms age has led to the hypothesis that aging involves general breakdown of protein quality control. We tested this hypothesis using a proteomic and informatic approach in the fruit fly Drosophila melanogaster. Turnover of most proteins was markedly slower in old flies. However, ribosomal and proteasomal proteins maintained high turnover rates, suggesting that the observed slowdowns in protein turnover might not be due to a global failure of quality control. As protein turnover reflects the balance of protein synthesis and degradation, we investigated whether decreases in synthesis or decreases in degradation would best explain the observed slowdowns in protein turnover. We found that while many individual proteins in old flies showed slower turnover due to decreased degradation, an approximately equal number showed slower turnover due to decreased synthesis, and enrichment analyses revealed that translation machinery itself was less abundant. Mitochondrial complex I subunits and glycolytic enzymes were decreased in abundance as well, and proteins involved in glutamine-dependent anaplerosis were increased, suggesting that old flies modify energy production to limit oxidative damage. Together, our findings suggest that age-related proteostasis changes in Drosophila represent a coordinated adaptation rather than a systems collapse.
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Affiliation(s)
- Evelyn S Vincow
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Ruth E Thomas
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Leo J Pallanck
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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20
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Torson AS, Dong YW, Sinclair BJ. Help, there are ‘omics’ in my comparative physiology! J Exp Biol 2020; 223:223/24/jeb191262. [DOI: 10.1242/jeb.191262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
‘Omics’ methods, such as transcriptomics, proteomics, lipidomics or metabolomics, yield simultaneous measurements of many related molecules in a sample. These approaches have opened new opportunities to generate and test hypotheses about the mechanisms underlying biochemical and physiological phenotypes. In this Commentary, we discuss general approaches and considerations for successfully integrating omics into comparative physiology. The choice of omics approach will be guided by the availability of existing resources and the time scale of the process being studied. We discuss the use of whole-organism extracts (common in omics experiments on small invertebrates) because such an approach may mask underlying physiological mechanisms, and we consider the advantages and disadvantages of pooling samples within biological replicates. These methods can bring analytical challenges, so we describe the most easily analyzed omics experimental designs. We address the propensity of omics studies to digress into ‘fishing expeditions’ and show how omics can be used within the hypothetico-deductive framework. With this Commentary, we hope to provide a roadmap that will help newcomers approach omics in comparative physiology while avoiding some of the potential pitfalls, which include ambiguous experiments, long lists of candidate molecules and vague conclusions.
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Affiliation(s)
- Alex S. Torson
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Yun-wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Brent J. Sinclair
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
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21
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Gao Y, Zhu C, Li K, Cheng X, Du Y, Yang D, Fan X, Gaur U, Yang M. Comparative proteomics analysis of dietary restriction in Drosophila. PLoS One 2020; 15:e0240596. [PMID: 33064752 PMCID: PMC7567386 DOI: 10.1371/journal.pone.0240596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/29/2020] [Indexed: 12/19/2022] Open
Abstract
To explore the underlying mechanism of dietary restriction (DR) induced lifespan extension in fruit flies at protein level, we performed proteome sequencing in Drosophila at day 7 (young) and day 42 (old) under DR and ad libitum (AL) conditions. A total of 18629 unique peptides were identified in Uniprot, corresponding to 3,662 proteins. Among them, 383 and 409 differentially expressed proteins (DEPs) were identified from comparison between DR vs AL at day 7 and 42, respectively. Bioinformatics analysis revealed that membrane-related processes, post-transcriptional processes, spliceosome and reproduction related processes, were highlighted significantly. In addition, expression of proteins involved in pathways such as spliceosomes, oxidative phosphorylation, lysosomes, ubiquitination, and riboflavin metabolism was relatively higher during DR. A relatively large number of DEPs were found to participate in longevity and age-related disease pathways. We identified 20 proteins that were consistently regulated during DR and some of which are known to be involved in ageing, such as mTORC1, antioxidant, DNA damage repair and autophagy. In the integration analysis, we found 15 genes that were stably regulated by DR at both transcriptional as well as translational levels. Our results provided a useful dataset for further investigations on the mechanism of DR and aging.
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Affiliation(s)
- Yue Gao
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Chenxing Zhu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Keqin Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Xingyi Cheng
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yanjiao Du
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Deying Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Xiaolan Fan
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
| | - Uma Gaur
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
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22
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Kron NS, Schmale MC, Fieber LA. Changes in Metabolism and Proteostasis Drive Aging Phenotype in Aplysia californica Sensory Neurons. Front Aging Neurosci 2020; 12:573764. [PMID: 33101008 PMCID: PMC7522570 DOI: 10.3389/fnagi.2020.573764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/12/2020] [Indexed: 12/29/2022] Open
Abstract
Aging is associated with cognitive declines that originate in impairments of function in the neurons that make up the nervous system. The marine mollusk Aplysia californica (Aplysia) is a premier model for the nervous system uniquely suited to investigation of neuronal aging due to uniquely identifiable neurons and molecular techniques available in this model. This study describes the molecular processes associated with aging in two populations of sensory neurons in Aplysia by applying RNA sequencing technology across the aging process (age 6-12 months). Differentially expressed genes clustered into four to five coherent expression patterns across the aging time series in the two neuron populations. Enrichment analysis of functional annotations in these neuron clusters revealed decreased expression of pathways involved in energy metabolism and neuronal signaling, suggesting that metabolic and signaling pathways are intertwined. Furthermore, increased expression of pathways involved in protein processing and translation suggests that proteostatic stress also occurs in aging. Temporal overlap of enrichment for energy metabolism, proteostasis, and neuronal function suggests that cognitive impairments observed in advanced age result from the ramifications of broad declines in energy metabolism.
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Affiliation(s)
- Nicholas S Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Michael C Schmale
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Lynne A Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
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23
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Buffenstein R, Lewis KN, Gibney PA, Narayan V, Grimes KM, Smith M, Lin TD, Brown-Borg HM. Probing Pedomorphy and Prolonged Lifespan in Naked Mole-Rats and Dwarf Mice. Physiology (Bethesda) 2020; 35:96-111. [DOI: 10.1152/physiol.00032.2019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Pedomorphy, maintenance of juvenile traits throughout life, is most pronounced in extraordinarily long-lived naked mole-rats. Many of these traits (e.g., slow growth rates, low hormone levels, and delayed sexual maturity) are shared with spontaneously mutated, long-lived dwarf mice. Although some youthful traits likely evolved as adaptations to subterranean habitats (e.g., thermolability), the nature of these intrinsic pedomorphic features may also contribute to their prolonged youthfulness, longevity, and healthspan.
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Affiliation(s)
| | | | - Patrick A. Gibney
- Calico Life Sciences LLC, South San Francisco, California
- Department of Food Science, College of Agriculture and Life Sciences, Stocking Hall, Cornell University, Ithaca, New York
| | - Vikram Narayan
- Calico Life Sciences LLC, South San Francisco, California
| | - Kelly M. Grimes
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Megan Smith
- Calico Life Sciences LLC, South San Francisco, California
| | - Tzuhua D. Lin
- Calico Life Sciences LLC, South San Francisco, California
| | - Holly M. Brown-Borg
- Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, North Dakota
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