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Hafiz Rothi M, Sarkar GC, Haddad JA, Mitchell W, Ying K, Pohl N, Sotomayor-Mena RG, Natale J, Dellacono S, Gladyshev VN, Lieberman Greer E. The 18S rRNA Methyltransferase DIMT-1 Regulates Lifespan in the Germline Later in Life. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.14.594211. [PMID: 38798397 PMCID: PMC11118296 DOI: 10.1101/2024.05.14.594211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Ribosome heterogeneity has emerged as an important regulatory control feature for determining which proteins are synthesized, however, the influence of age on ribosome heterogeneity is not fully understood. Whether mRNA transcripts are selectively translated in young versus old cells and whether dysregulation of this process drives organismal aging is unknown. Here we examined the role of ribosomal RNA (rRNA) methylation in maintaining appropriate translation as organisms age. In a directed RNAi screen, we identified the 18S rRNA N6'-dimethyl adenosine (m6,2A) methyltransferase, dimt-1, as a regulator of C. elegans lifespan and stress resistance. Lifespan extension induced by dimt-1 deficiency required a functional germline and was dependent on the known regulator of protein translation, the Rag GTPase, raga-1, which links amino acid sensing to the mechanistic target of rapamycin complex (mTORC)1. Using an auxin-inducible degron tagged version of dimt-1, we demonstrate that DIMT-1 functions in the germline after mid-life to regulate lifespan. We further found that knock-down of dimt-1 leads to selective translation of transcripts important for stress resistance and lifespan regulation in the C. elegans germline in mid-life including the cytochrome P450 daf-9, which synthesizes a steroid that signals from the germline to the soma to regulate lifespan. We found that dimt-1 induced lifespan extension was dependent on the daf-9 signaling pathway. This finding reveals a new layer of proteome dysfunction, beyond protein synthesis and degradation, as an important regulator of aging. Our findings highlight a new role for ribosome heterogeneity, and specific rRNA modifications, in maintaining appropriate translation later in life to promote healthy aging.
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Affiliation(s)
- M. Hafiz Rothi
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Gautam Chandra Sarkar
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Joseph Al Haddad
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Wayne Mitchell
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Kejun Ying
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Nancy Pohl
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Roberto G. Sotomayor-Mena
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Julia Natale
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Scarlett Dellacono
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women’s Hospital, Harvard Medical School, Boston MA 02115, USA
| | - Eric Lieberman Greer
- Department of Pediatrics, HMS Initiative for RNA Medicine, Harvard Medical School, Boston MA, USA
- Division of Newborn Medicine, Boston Children’s Hospital, Boston MA, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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2
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Li R, Yi Q, Wang J, Miao Y, Chen Q, Xu Y, Tao M. Paeonol promotes longevity and fitness in Caenorhabditis elegans through activating the DAF-16/FOXO and SKN-1/Nrf2 transcription factors. Biomed Pharmacother 2024; 173:116368. [PMID: 38471269 DOI: 10.1016/j.biopha.2024.116368] [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: 11/23/2023] [Revised: 02/17/2024] [Accepted: 02/28/2024] [Indexed: 03/14/2024] Open
Abstract
Paeonol, as one of the most abundant plant-derived polyphenols, has multiple bioactivities including anti-inflammatory, anti-tumor, and anti-cardiovascular diseases. Nevertheless, the anti-aging effects and related mechanisms of paeonol are rarely reported. In this study, we found that paeonol significantly prolonged the mean lifespan of Caenorhabditis elegans (C. elegans) by 28.49% at a dose of 200 μM. Moreover, paeonol promoted the health of C. elegans by increasing the body bending and pharyngeal pumping rates and reducing the lipofuscin accumulation level. Meanwhile, paeonol induced the expression of stress-related genes or proteins by activating the transcription factors DAF-16/FOXO, SKN-1/Nrf2, and HSF-1, which in turn enhanced oxidative and thermal stress tolerance. The mechanism behind the anti-aging effect of paeonol occurred by down-regulating the insulin/IGF-1 signaling (IIS) pathway. Our findings shed new light on the application of paeonol for longevity promotion and human health.
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Affiliation(s)
- Rong Li
- College of Bioengineering/Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, People's Republic of China
| | - Qingping Yi
- College of Bioengineering/Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, People's Republic of China
| | - Jinsong Wang
- College of Bioengineering/Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, People's Republic of China
| | - Yuanxin Miao
- College of Bioengineering/Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, People's Republic of China
| | - Qingchan Chen
- College of Bioengineering/Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, People's Republic of China
| | - Yan Xu
- College of Bioengineering/Hubei Engineering Research Center for Specialty Flowers Biological Breeding, Jingchu University of Technology, Jingmen, People's Republic of China.
| | - Mingfang Tao
- Hubei Key Laboratory of Nutritional Quality and Safety of Agro-products, Institute of Agricultural Quality Standards and Detection Technology, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China.
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3
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Fabrizio P, Alcolei A, Solari F. Considering Caenorhabditis elegans Aging on a Temporal and Tissue Scale: The Case of Insulin/IGF-1 Signaling. Cells 2024; 13:288. [PMID: 38334680 PMCID: PMC10854721 DOI: 10.3390/cells13030288] [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: 12/23/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024] Open
Abstract
The aging process is inherently complex, involving multiple mechanisms that interact at different biological scales. The nematode Caenorhabditis elegans is a simple model organism that has played a pivotal role in aging research following the discovery of mutations extending lifespan. Longevity pathways identified in C. elegans were subsequently found to be conserved and regulate lifespan in multiple species. These pathways intersect with fundamental hallmarks of aging that include nutrient sensing, epigenetic alterations, proteostasis loss, and mitochondrial dysfunction. Here we summarize recent data obtained in C. elegans highlighting the importance of studying aging at both the tissue and temporal scale. We then focus on the neuromuscular system to illustrate the kinetics of changes that take place with age. We describe recently developed tools that enabled the dissection of the contribution of the insulin/IGF-1 receptor ortholog DAF-2 to the regulation of worm mobility in specific tissues and at different ages. We also discuss guidelines and potential pitfalls in the use of these new tools. We further highlight the opportunities that they present, especially when combined with recent transcriptomic data, to address and resolve the inherent complexity of aging. Understanding how different aging processes interact within and between tissues at different life stages could ultimately suggest potential intervention points for age-related diseases.
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Affiliation(s)
- Paola Fabrizio
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS UMR5239, INSERM 1210, University Claude Bernard Lyon 1, 69364 Lyon, France;
| | - Allan Alcolei
- INMG, MeLiS, CNRS UMR 5284, INSERM U1314, University Claude Bernard Lyon 1, 69008 Lyon, France;
| | - Florence Solari
- INMG, MeLiS, CNRS UMR 5284, INSERM U1314, University Claude Bernard Lyon 1, 69008 Lyon, France;
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4
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Bustamante JA, Ceron JS, Gao IT, Ramirez HA, Aviles MV, Bet Adam D, Brice JR, Cuellar RA, Dockery E, Jabagat MK, Karp DG, Lau JKO, Li S, Lopez-Magaña R, Moore RR, Morin BKR, Nzongo J, Rezaeihaghighi Y, Sapienza-Martinez J, Tran TTK, Huang Z, Duthoy AJ, Barnett MJ, Long SR, Chen JC. A protease and a lipoprotein jointly modulate the conserved ExoR-ExoS-ChvI signaling pathway critical in Sinorhizobium meliloti for symbiosis with legume hosts. PLoS Genet 2023; 19:e1010776. [PMID: 37871041 PMCID: PMC10659215 DOI: 10.1371/journal.pgen.1010776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/20/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
Sinorhizobium meliloti is a model alpha-proteobacterium for investigating microbe-host interactions, in particular nitrogen-fixing rhizobium-legume symbioses. Successful infection requires complex coordination between compatible host and endosymbiont, including bacterial production of succinoglycan, also known as exopolysaccharide-I (EPS-I). In S. meliloti EPS-I production is controlled by the conserved ExoS-ChvI two-component system. Periplasmic ExoR associates with the ExoS histidine kinase and negatively regulates ChvI-dependent expression of exo genes, necessary for EPS-I synthesis. We show that two extracytoplasmic proteins, LppA (a lipoprotein) and JspA (a lipoprotein and a metalloprotease), jointly influence EPS-I synthesis by modulating the ExoR-ExoS-ChvI pathway and expression of genes in the ChvI regulon. Deletions of jspA and lppA led to lower EPS-I production and competitive disadvantage during host colonization, for both S. meliloti with Medicago sativa and S. medicae with M. truncatula. Overexpression of jspA reduced steady-state levels of ExoR, suggesting that the JspA protease participates in ExoR degradation. This reduction in ExoR levels is dependent on LppA and can be replicated with ExoR, JspA, and LppA expressed exogenously in Caulobacter crescentus and Escherichia coli. Akin to signaling pathways that sense extracytoplasmic stress in other bacteria, JspA and LppA may monitor periplasmic conditions during interaction with the plant host to adjust accordingly expression of genes that contribute to efficient symbiosis. The molecular mechanisms underlying host colonization in our model system may have parallels in related alpha-proteobacteria.
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Affiliation(s)
- Julian A. Bustamante
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Josue S. Ceron
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Ivan Thomas Gao
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Hector A. Ramirez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Milo V. Aviles
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Demsin Bet Adam
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Jason R. Brice
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rodrigo A. Cuellar
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Eva Dockery
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Miguel Karlo Jabagat
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Donna Grace Karp
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Kin-On Lau
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Suling Li
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Raymondo Lopez-Magaña
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Rebecca R. Moore
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Bethany Kristi R. Morin
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Juliana Nzongo
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Yasha Rezaeihaghighi
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Joseph Sapienza-Martinez
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Tuyet Thi Kim Tran
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Zhenzhong Huang
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
| | - Aaron J. Duthoy
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Melanie J. Barnett
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sharon R. Long
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Joseph C. Chen
- Department of Biology, San Francisco State University, San Francisco, California, United States of America
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5
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Sturm Á, Saskői É, Hotzi B, Tarnóci A, Barna J, Bodnár F, Sharma H, Kovács T, Ari E, Weinhardt N, Kerepesi C, Perczel A, Ivics Z, Vellai T. Downregulation of transposable elements extends lifespan in Caenorhabditis elegans. Nat Commun 2023; 14:5278. [PMID: 37644049 PMCID: PMC10465613 DOI: 10.1038/s41467-023-40957-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Mobility of transposable elements (TEs) frequently leads to insertional mutations in functional DNA regions. In the potentially immortal germline, TEs are effectively suppressed by the Piwi-piRNA pathway. However, in the genomes of ageing somatic cells lacking the effects of the pathway, TEs become increasingly mobile during the adult lifespan, and their activity is associated with genomic instability. Whether the progressively increasing mobilization of TEs is a cause or a consequence of ageing remains a fundamental problem in biology. Here we show that in the nematode Caenorhabditis elegans, the downregulation of active TE families extends lifespan. Ectopic activation of Piwi proteins in the soma also promotes longevity. Furthermore, DNA N6-adenine methylation at TE stretches gradually rises with age, and this epigenetic modification elevates their transcription as the animal ages. These results indicate that TEs represent a novel genetic determinant of ageing, and that N6-adenine methylation plays a pivotal role in ageing control.
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Affiliation(s)
- Ádám Sturm
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - Éva Saskői
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Bernadette Hotzi
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Anna Tarnóci
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - János Barna
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary
| | - Ferenc Bodnár
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Himani Sharma
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Tibor Kovács
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Eszter Ari
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
- HCEMM-BRC Metabolic Systems Biology Research Group, 6726, Szeged, Hungary
- Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network (ELKH), Temesvári krt. 62, 6726, Szeged, Hungary
| | - Nóra Weinhardt
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary
| | - Csaba Kerepesi
- Institute for Computer Science and Control (SZTAKI), 1111, Budapest, Hungary
- Brigham and Women's Hospital & Harvard Medical School, Boston, MA, 02115, USA
| | - András Perczel
- Laboratory of Structural Chemistry and Biology & Hungarian Academy of Sciences (MTA)-ELTE Protein Modelling Research Group, Institute of Chemistry, Eötvös Loránd University, 1117, Budapest, Hungary
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225, Langen, Germany
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University (ELTE), 1117, Budapest, Hungary.
- Eötvös Loránd Research Network (ELKH)-ELTE Genetics Research Group, 1117, Budapest, Hungary.
- Vellab Biotech Ltd., 6722, Szeged, Hungary.
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6
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Roux AE, Yuan H, Podshivalova K, Hendrickson D, Kerr R, Kenyon C, Kelley D. Individual cell types in C. elegans age differently and activate distinct cell-protective responses. Cell Rep 2023; 42:112902. [PMID: 37531250 DOI: 10.1016/j.celrep.2023.112902] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 05/17/2023] [Accepted: 07/14/2023] [Indexed: 08/04/2023] Open
Abstract
Aging is characterized by a global decline in physiological function. However, by constructing a complete single-cell gene expression atlas, we find that Caenorhabditis elegans aging is not random in nature but instead is characterized by coordinated changes in functionally related metabolic, proteostasis, and stress-response genes in a cell-type-specific fashion, with downregulation of energy metabolism being the only nearly universal change. Similarly, the rates at which cells age differ significantly between cell types. In some cell types, aging is characterized by an increase in cell-to-cell variance, whereas in others, variance actually decreases. Remarkably, multiple resilience-enhancing transcription factors known to extend lifespan are activated across many cell types with age; we discovered new longevity candidates, such as GEI-3, among these. Together, our findings suggest that cells do not age passively but instead react strongly, and individualistically, to events that occur during aging. This atlas can be queried through a public interface.
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Affiliation(s)
| | - Han Yuan
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | | | | | - Rex Kerr
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA
| | - Cynthia Kenyon
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
| | - David Kelley
- Calico Life Sciences LLC, South San Francisco, CA 94080, USA.
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7
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Dutta S, Shah RB, Singhal S, Dutta SB, Bansal S, Sinha S, Haque M. Metformin: A Review of Potential Mechanism and Therapeutic Utility Beyond Diabetes. Drug Des Devel Ther 2023; 17:1907-1932. [PMID: 37397787 PMCID: PMC10312383 DOI: 10.2147/dddt.s409373] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 06/10/2023] [Indexed: 07/04/2023] Open
Abstract
Metformin has been designated as one of the most crucial first-line therapeutic agents in the management of type 2 diabetes mellitus. Primarily being an antihyperglycemic agent, metformin also has a plethora of pleiotropic effects on various systems and processes. It acts majorly by activating AMPK (Adenosine Monophosphate-Activated Protein Kinase) in the cells and reducing glucose output from the liver. It also decreases advanced glycation end products and reactive oxygen species production in the endothelium apart from regulating the glucose and lipid metabolism in the cardiomyocytes, hence minimizing the cardiovascular risks. Its anticancer, antiproliferative and apoptosis-inducing effects on malignant cells might prove instrumental in the malignancy of organs like the breast, kidney, brain, ovary, lung, and endometrium. Preclinical studies have also shown some evidence of metformin's neuroprotective role in Parkinson's disease, Alzheimer's disease, multiple sclerosis and Huntington's disease. Metformin exerts its pleiotropic effects through varied pathways of intracellular signalling and exact mechanism in the majority of them remains yet to be clearly defined. This article has extensively reviewed the therapeutic benefits of metformin and the details of its mechanism for a molecule of boon in various conditions like diabetes, prediabetes, obesity, polycystic ovarian disease, metabolic derangement in HIV, various cancers and aging.
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Affiliation(s)
- Siddhartha Dutta
- Department of Pharmacology, All India Institute of Medical Sciences, Rajkot, Gujarat, India
| | - Rima B Shah
- Department of Pharmacology, All India Institute of Medical Sciences, Rajkot, Gujarat, India
| | - Shubha Singhal
- Department of Pharmacology, All India Institute of Medical Sciences, Rajkot, Gujarat, India
| | - Sudeshna Banerjee Dutta
- Department of Medical Surgical Nursing, Shri Anand Institute of Nursing, Rajkot, Gujarat, 360005, India
| | - Sumit Bansal
- Department of Anaesthesiology, All India Institute of Medical Sciences, Rajkot, Gujarat, India
| | - Susmita Sinha
- Department of Physiology, Khulna City Medical College and Hospital, Khulna, Bangladesh
| | - Mainul Haque
- Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur, 57000, Malaysia
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8
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Sanfilippo C, Castrogiovanni P, Vinciguerra M, Imbesi R, Ulivieri M, Fazio F, Cantarella A, Nunnari G, Di Rosa M. Neuro-immune deconvolution analysis of OAS3 as a transcriptomic central node in HIV-associated neurocognitive disorders. J Neurol Sci 2023; 446:120562. [PMID: 36706688 DOI: 10.1016/j.jns.2023.120562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Neurological complications of AIDS (NeuroAIDS) include primary HIV-associated neurocognitive disorder (HAND). OAS3 is an enzyme belonging to the 2', 5' oligoadenylate synthase family induced by type I interferons and involved in the degradation of both viral and endogenous RNA. Here, we used microarray datasets from NCBI of brain samples of non-demented HIV-negative controls (NDC), HIV, deceased patients with HAND and encephalitis (HIVE) (treated and untreated with antiretroviral therapy, ART), and with HAND without HIVE. The HAND/HIVE patients were stratified according to the OAS3 gene expression. The genes positively and negatively correlated to the OAS3 gene expression were used to perform a genomic deconvolution analysis using neuroimmune signatures (NIS) belonging to sixteen signatures. Expression analysis revealed significantly higher OAS3 expression in HAND/HIVE and HAND/HIVE/ART compared with NDC. OAS3 expressed an excellent diagnostic ability to discriminate NDC from HAND/HIVE, HAND from HAND/HIVE, HAND from HAND/HIVE/ART, and HIV from HAND/HIVE. Noteworthy, OAS3 expression levels in the brains of HAND/HIVE patients were positively correlated with viral load in both peripheral blood and cerebrospinal fluid (CSF). Furthermore, deconvolution analysis revealed that the genes positively correlated to OAS3 expression were associated with inflammatory signatures. Neuronal activation profiles were significantly activated by the genes negatively correlated to OAS3 expression levels. Moreover, gene ontology analysis performed on genes characterizing the microglia signature highlighted an immune response as a main biological process. According to our results, genes positively correlated to OAS3 gene expression in the brains of HAND/HIVE patients are associated with inflammatory transcriptomic signatures and likely worse cognitive impairment.
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Affiliation(s)
- Cristina Sanfilippo
- Neurologic Unit, AOU "Policlinico-San Marco", Department of Medical, Surgical Sciences and Advanced Technologies, GF, Ingrassia, University of Catania, Via Santa Sofia n.78, 95100 Catania, Sicily, Italy
| | - Paola Castrogiovanni
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Manlio Vinciguerra
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czech Republic; Department of Translational Stem Cell Biology, Research Institute of the Medical University of Varna, Varna, Bulgaria; Liverpool Center for Cardiovascular Science, Liverpool Johns Moore University & University of Liverpool, Liverpool, UK
| | - Rosa Imbesi
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Martina Ulivieri
- University of California San Diego, Department of Psychiatry, Health Science, San Diego La Jolla, CA, USA
| | - Francesco Fazio
- University of California San Diego, Department of Psychiatry, Health Science, San Diego La Jolla, CA, USA
| | - Antonio Cantarella
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy
| | - Giuseppe Nunnari
- Department of Clinical and Experimental Medicine, Unit of Infectious Diseases, University of Messina, 98124 Messina, Italy
| | - Michelino Di Rosa
- Department of Biomedical and Biotechnological Sciences, Anatomy, Histology and Movement Sciences Section, School of Medicine, University of Catania, 95125 Catania, Italy.
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9
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Shrivastava A, Sandhof CA, Reinle K, Jawed A, Ruger-Herreros C, Schwarz D, Creamer D, Nussbaum-Krammer C, Mogk A, Bukau B. The cytoprotective sequestration activity of small heat shock proteins is evolutionarily conserved. J Cell Biol 2022; 221:213447. [PMID: 36069810 PMCID: PMC9458469 DOI: 10.1083/jcb.202202149] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 11/22/2022] Open
Abstract
The chaperone-mediated sequestration of misfolded proteins into inclusions is a pivotal cellular strategy to maintain proteostasis in Saccharomyces cerevisiae, executed by small heat shock proteins (sHsps) Hsp42 and Btn2. Direct homologs of Hsp42 and Btn2 are absent in other organisms, questioning whether sequestration represents a conserved proteostasis strategy and, if so, which factors are involved. We examined sHsps from Escherchia coli, Caenorhabditis elegans, and humans for their ability to complement the defects of yeast sequestrase mutants. We show that sequestration of misfolded proteins is an original and widespread activity among sHsps executed by specific family members. Sequestrase positive C. elegans' sHsps harbor specific sequence features, including a high content of aromatic and methionine residues in disordered N-terminal extensions. Those sHsps buffer limitations in Hsp70 capacity in C. elegans WT animals and are upregulated in long-lived daf-2 mutants, contributing to lifespan extension. Cellular protection by sequestration of misfolded proteins is, therefore, an evolutionarily conserved activity of the sHsp family.
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Affiliation(s)
- Aseem Shrivastava
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carl Alexander Sandhof
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Kevin Reinle
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Areeb Jawed
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carmen Ruger-Herreros
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominic Schwarz
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Declan Creamer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Carmen Nussbaum-Krammer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Huang M, Hong M, Hou X, Zhu C, Chen D, Chen X, Guang S, Feng X. H3K9me1/2 methylation limits the lifespan of daf-2 mutants in C. elegans. eLife 2022; 11:74812. [PMID: 36125117 PMCID: PMC9514849 DOI: 10.7554/elife.74812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 09/16/2022] [Indexed: 11/29/2022] Open
Abstract
Histone methylation plays crucial roles in the development, gene regulation, and maintenance of stem cell pluripotency in mammals. Recent work shows that histone methylation is associated with aging, yet the underlying mechanism remains unclear. In this work, we identified a class of putative histone 3 lysine 9 mono/dimethyltransferase genes (met-2, set-6, set-19, set-20, set-21, set-32, and set-33), mutations in which induce synergistic lifespan extension in the long-lived DAF-2 (insulin growth factor 1 [IGF-1] receptor) mutant in Caenorhabditis elegans. These putative histone methyltransferase plus daf-2 double mutants not only exhibited an average lifespan nearly three times that of wild-type animals and a maximal lifespan of approximately 100 days, but also significantly increased resistance to oxidative and heat stress. Synergistic lifespan extension depends on the transcription factor DAF-16 (FOXO). mRNA-seq experiments revealed that the mRNA levels of DAF-16 Class I genes, which are activated by DAF-16, were further elevated in the daf-2;set double mutants. Among these genes, tts-1, F35E8.7, ins-35, nhr-62, sod-3, asm-2, and Y39G8B.7 are required for the lifespan extension of the daf-2;set-21 double mutant. In addition, treating daf-2 animals with the H3K9me1/2 methyltransferase G9a inhibitor also extends lifespan and increases stress resistance. Therefore, investigation of DAF-2 and H3K9me1/2 deficiency-mediated synergistic longevity will contribute to a better understanding of the molecular mechanisms of aging and therapeutic applications.
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Affiliation(s)
- Meng Huang
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Minjie Hong
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Xinhao Hou
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Chengming Zhu
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Di Chen
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, China
| | - Xiangyang Chen
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Shouhong Guang
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
| | - Xuezhu Feng
- Department of Obstetrics and Gynecology, University of Science and Technology of China, Hefei, China
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11
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Paiha AP, Laird RA. Pace and shape of senescence in three species of duckweed. Ecol Evol 2022; 12:e9038. [PMID: 35813927 PMCID: PMC9254075 DOI: 10.1002/ece3.9038] [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: 12/17/2021] [Revised: 05/17/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Senescence is progressive bodily deterioration associated with declines in survival and fecundity in older age classes. There is great diversity in patterns of senescence across species, but these patterns can be difficult to compare formally due to variation in the absolute time scales in which species live and die: members of some species live for a matter of days, others for millennia. To address this issue, the “pace‐shape” approach was developed to decouple absolute time from analyses and instead standardize life history traits in terms of average life expectancy, facilitating intra‐ and interspecific comparisons. Here, we use this approach to distinguish the generic form of demographic trajectories (shape) from the time scale on which the trajectories occurred (pace) in three species of tiny, free‐floating aquatic plants known as duckweeds (Lemna gibba L., L. minor L., and L. turionifera Landolt), which have mean lifespans of less than a month under typical lab conditions, and exhibit age‐related declines in survivorship and reproduction. Using a randomized block design in which we tracked a final total of 430 individuals, we report differences in pace and shape among the three species. Specifically, the largest, least‐fecund, and typically longest‐lived species, L. gibba, tended to exhibit more rapid decreases in time‐standardized survivorship and fecundity compared with the other two species. This study emphasizes variation in aging patterns that can be found among plant species, including those in the same genus, and provides further validation for the utility of applying the pace and shape approach in interspecific comparisons.
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Affiliation(s)
- Austin P. Paiha
- Department of Biological Sciences University of Lethbridge Lethbridge Alberta Canada
| | - Robert A. Laird
- Department of Biological Sciences University of Lethbridge Lethbridge Alberta Canada
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12
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The Relaxin-3 Receptor, RXFP3, Is a Modulator of Aging-Related Disease. Int J Mol Sci 2022; 23:ijms23084387. [PMID: 35457203 PMCID: PMC9027355 DOI: 10.3390/ijms23084387] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022] Open
Abstract
During the aging process our body becomes less well equipped to deal with cellular stress, resulting in an increase in unrepaired damage. This causes varying degrees of impaired functionality and an increased risk of mortality. One of the most effective anti-aging strategies involves interventions that combine simultaneous glucometabolic support with augmented DNA damage protection/repair. Thus, it seems prudent to develop therapeutic strategies that target this combinatorial approach. Studies have shown that the ADP-ribosylation factor (ARF) GTPase activating protein GIT2 (GIT2) acts as a keystone protein in the aging process. GIT2 can control both DNA repair and glucose metabolism. Through in vivo co-regulation analyses it was found that GIT2 forms a close coexpression-based relationship with the relaxin-3 receptor (RXFP3). Cellular RXFP3 expression is directly affected by DNA damage and oxidative stress. Overexpression or stimulation of this receptor, by its endogenous ligand relaxin 3 (RLN3), can regulate the DNA damage response and repair processes. Interestingly, RLN3 is an insulin-like peptide and has been shown to control multiple disease processes linked to aging mechanisms, e.g., anxiety, depression, memory dysfunction, appetite, and anti-apoptotic mechanisms. Here we discuss the molecular mechanisms underlying the various roles of RXFP3/RLN3 signaling in aging and age-related disorders.
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13
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McHugh KM, Burke MK. From microbes to mammals: The experimental evolution of aging and longevity across species. Evolution 2022; 76:692-707. [PMID: 35112358 DOI: 10.1111/evo.14442] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/09/2021] [Accepted: 12/01/2021] [Indexed: 01/21/2023]
Abstract
Senescence, the functional deterioration of cells or organisms associated with increased age, is pervasive across the tree of life. Yet our understanding of the genetic and physiological basis underlying age-related declines in health and reproduction remains limited. Experimental evolution allows empirical examination of the question of why aging occurs; imposing selection for age-specific fitness traits shifts patterns of aging in experimental populations, enabling investigations of the variation underlying senescence and the mechanisms governing it. Whole-genome sequencing of experimentally evolved populations may reveal candidate genomic variants underlying particular aging patterns; unfortunately, most study systems suffer from limitations that weaken associations between genotypes and phenotypes. In this review, we provide a survey of experimental evolution studies that have altered population-level patterns of reproductive timing and senescence in a variety of species. We discuss the specific selection conditions that have increased longevity, the phenotypic responses and trade-offs that accompany these increases, and examine genomic data collected from these experiments. Additionally, we consider how selected field studies complement laboratory experiments on life-history evolution. Finally, we address the strengths and weaknesses of existing study systems, and evaluate which model organisms appear most promising for future genomic investigations of the evolutionary biology of aging.
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Affiliation(s)
- Kaitlin M McHugh
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
| | - Molly K Burke
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, 97331
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14
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Wang X, Jiang Q, Song Y, He Z, Zhang H, Song M, Zhang X, Dai Y, Karalay O, Dieterich C, Antebi A, Wu L, Han JJ, Shen Y. Ageing induces tissue‐specific transcriptomic changes in
Caenorhabditis elegans. EMBO J 2022; 41:e109633. [PMID: 35253240 PMCID: PMC9016346 DOI: 10.15252/embj.2021109633] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/09/2022] Open
Abstract
Ageing is a complex process with common and distinct features across tissues. Unveiling the underlying processes driving ageing in individual tissues is indispensable to decipher the mechanisms of organismal longevity. Caenorhabditis elegans is a well‐established model organism that has spearheaded ageing research with the discovery of numerous genetic pathways controlling its lifespan. However, it remains challenging to dissect the ageing of worm tissues due to the limited description of tissue pathology and access to tissue‐specific molecular changes during ageing. In this study, we isolated cells from five major tissues in young and old worms and profiled the age‐induced transcriptomic changes within these tissues. We observed a striking diversity of ageing across tissues and identified different sets of longevity regulators therein. In addition, we found novel tissue‐specific factors, including irx‐1 and myrf‐2, which control the integrity of the intestinal barrier and sarcomere structure during ageing respectively. This study demonstrates the complexity of ageing across worm tissues and highlights the power of tissue‐specific transcriptomic profiling during ageing, which can serve as a resource to the field.
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Affiliation(s)
- Xueqing Wang
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Quanlong Jiang
- CAS Key Laboratory of Computational Biology Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
- Peking‐Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB) Peking University Beijing China
| | - Yuanyuan Song
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Zhidong He
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Hongdao Zhang
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Mengjiao Song
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Xiaona Zhang
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Yumin Dai
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Oezlem Karalay
- Max Planck Institute for Biology of Ageing Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Christoph Dieterich
- Klaus Tschira Institute for Integrative Computational Cardiology and Department of Internal Medicine III University Hospital Heidelberg Heidelberg Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing Cologne Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging‐Associated Diseases (CECAD) University of Cologne Cologne Germany
| | - Ligang Wu
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
| | - Jing‐Dong J Han
- CAS Key Laboratory of Computational Biology Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai China
- Peking‐Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB) Peking University Beijing China
| | - Yidong Shen
- State Key Laboratory of Cell Biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Shanghai China
- University of Chinese Academy of Sciences Beijing China
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15
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Raven N, Klaassen M, Madsen T, Thomas F, Hamede R, Ujvari B. Transmissible cancer influences immune gene expression in an endangered marsupial, the Tasmanian devil (Sarcophilus harrisii). Mol Ecol 2022; 31:2293-2311. [PMID: 35202488 PMCID: PMC9310804 DOI: 10.1111/mec.16408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/14/2022] [Indexed: 11/28/2022]
Abstract
Understanding the effects of wildlife diseases on populations requires insight into local environmental conditions, host defence mechanisms, host life‐history trade‐offs, pathogen population dynamics, and their interactions. The survival of Tasmanian devils (Sarcophilus harrisii) is challenged by a novel, fitness limiting pathogen, Tasmanian devil facial tumour disease (DFTD), a clonally transmissible, contagious cancer. In order to understand the devils’ capacity to respond to DFTD, it is crucial to gain information on factors influencing the devils’ immune system. By using RT‐qPCR, we investigated how DFTD infection in association with intrinsic (sex and age) and environmental (season) factors influences the expression of 10 immune genes in Tasmanian devil blood. Our study showed that the expression of immune genes (both innate and adaptive) differed across seasons, a pattern that was altered when infected with DFTD. The expression of immunogbulins IgE and IgM:IgG showed downregulation in colder months in DFTD infected animals. We also observed strong positive association between the expression of an innate immune gene, CD16, and DFTD infection. Our results demonstrate that sampling across seasons, age groups and environmental conditions are beneficial when deciphering the complex ecoevolutionary interactions of not only conventional host‐parasite systems, but also of host and diseases with high mortality rates, such as transmissible cancers.
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Affiliation(s)
- N Raven
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - M Klaassen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - T Madsen
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
| | - F Thomas
- CREEC/CANECEV (CREES), Montpellier, France.,MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
| | - R Hamede
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia.,School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, Tasmania, 7001, Australia
| | - B Ujvari
- Deakin University, Geelong, School of Life and Environmental Sciences, Centre for Integrative Ecology, Waurn Ponds, Vic, 3216, Australia
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16
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Sun Y, Yu R, Guo HB, Qin H, Dang W. A quantitative yeast aging proteomics analysis reveals novel aging regulators. GeroScience 2021; 43:2573-2593. [PMID: 34241809 DOI: 10.1007/s11357-021-00412-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 06/23/2021] [Indexed: 11/29/2022] Open
Abstract
Calorie restriction (CR) is the most robust longevity intervention, extending lifespan from yeast to mammals. Numerous conserved pathways regulating aging and mediating CR have been identified; however, the overall proteomic changes during these conditions remain largely unexplored. We compared proteomes between young and replicatively aged yeast cells under normal and CR conditions using the Stable-Isotope Labeling by Amino acids in Cell culture (SILAC) quantitative proteomics and discovered distinct signatures in the aging proteome. We found remarkable proteomic similarities between aged and CR cells, including induction of stress response pathways, providing evidence that CR pathways are engaged in aged cells. These observations also uncovered aberrant changes in mitochondria membrane proteins as well as a proteolytic cellular state in old cells. These proteomics analyses help identify potential genes and pathways that have causal effects on longevity.
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Affiliation(s)
- Yu Sun
- Huffington Center On Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ruofan Yu
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hao-Bo Guo
- Department of Computer Science and Engineering, Department of Biology, Geology and Environmental Science, SimCenter, The University of Tennessee At Chattanooga, Chattanooga, TN, 37403, USA
| | - Hong Qin
- Department of Computer Science and Engineering, Department of Biology, Geology and Environmental Science, SimCenter, The University of Tennessee At Chattanooga, Chattanooga, TN, 37403, USA
| | - Weiwei Dang
- Huffington Center On Aging and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
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17
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Network analysis in aged C. elegans reveals candidate regulatory genes of ageing. Biogerontology 2021; 22:345-367. [PMID: 33871732 DOI: 10.1007/s10522-021-09920-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/30/2021] [Indexed: 10/21/2022]
Abstract
Ageing is a biological process guided by genetic and environmental factors that ultimately lead to adverse outcomes for organismal lifespan and healthspan. Determination of molecular pathways that are affected with age and increase disease susceptibility is crucial. The gene expression profile of the ideal ageing model, namely the nematode Caenorhabditis elegans mapped with the microarray technology initially led to the identification of age-dependent gene expression alterations that characterize the nematode's ageing process. The list of differentially expressed genes was then utilized to construct a network of molecular interactions with their first neighbors/interactors using the interactions listed in the WormBase database. The subsequent network analysis resulted in the unbiased selection of 110 candidate genes, among which well-known ageing regulators appeared. More importantly, our approach revealed candidates that have never been linked to ageing before, thus suggesting promising potential targets/ageing regulators.
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18
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Guo S, Yang P, Liang B, Zhou F, Hou L, Kang L, Wang X. Aging features of the migratory locust at physiological and transcriptional levels. BMC Genomics 2021; 22:257. [PMID: 33838645 PMCID: PMC8037904 DOI: 10.1186/s12864-021-07585-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/05/2021] [Indexed: 12/13/2022] Open
Abstract
Background Non-Drosophila insects provide diverse aging types and important complementary systems for studies of aging biology. However, little attention has been paid to the special roles of non-Drosophila insects in aging research. Here, the aging-related features of the migratory locust, Locusta migratoria, were determined at the physiological, cellular, and transcriptional levels. Results In physiological assessments, the flight performance and sperm state of locusts displayed clear aging-related decline in male adults. Transcriptional analyses demonstrated locusts have similar aging-related genes with model species. However, different from those of Drosophila and mammals, the organ-specific aging transcriptional features of locusts were characterized by intensive expression changes in flight muscle and fat body and little transcriptional changes in brain. The predominant transcriptional characteristics of flight muscle and fat body aging were changes in expression of mitochondrion-related genes and detoxification and phagocytosis genes, respectively. Cellular assessments revealed the incidence of mitochondrial abnormalities significantly increased in aged flight muscle, and apoptotic signals and nuclear abnormalities were enhanced in aged fat body but not in brain. In addition, some well-known aging genes and locust aging-related genes (i.e., IAP1, PGRP-SA, and LIPT1), whose roles in aging regulation were rarely reported, were demonstrated to affect lifespan, metabolism, and flight ability of locusts after RNAi. Conclusion This study revealed multi-level aging signatures of locust, thus laying a foundation for further investigation of aging mechanisms in this famous insect in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07585-3.
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Affiliation(s)
- Siyuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bo Liang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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19
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Zulazmi NA, Arulsamy A, Ali I, Zainal Abidin SA, Othman I, Shaikh MF. The utilization of small non-mammals in traumatic brain injury research: A systematic review. CNS Neurosci Ther 2021; 27:381-402. [PMID: 33539662 PMCID: PMC7941175 DOI: 10.1111/cns.13590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/07/2020] [Accepted: 12/14/2020] [Indexed: 12/20/2022] Open
Abstract
Traumatic brain injury (TBI) is the leading cause of death and disability worldwide and has complicated underlying pathophysiology. Numerous TBI animal models have been developed over the past decade to effectively mimic the human TBI pathophysiology. These models are of mostly mammalian origin including rodents and non-human primates. However, the mammalian models demanded higher costs and have lower throughput often limiting the progress in TBI research. Thus, this systematic review aims to discuss the potential benefits of non-mammalian TBI models in terms of their face validity in resembling human TBI. Three databases were searched as follows: PubMed, Scopus, and Embase, for original articles relating to non-mammalian TBI models, published between January 2010 and December 2019. A total of 29 articles were selected based on PRISMA model for critical appraisal. Zebrafish, both larvae and adult, was found to be the most utilized non-mammalian TBI model in the current literature, followed by the fruit fly and roundworm. In conclusion, non-mammalian TBI models have advantages over mammalian models especially for rapid, cost-effective, and reproducible screening of effective treatment strategies and provide an opportunity to expedite the advancement of TBI research.
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Affiliation(s)
- Nurul Atiqah Zulazmi
- Neuropharmacology Research LaboratoryJeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangor Darul EhsanMalaysia
| | - Alina Arulsamy
- Neuropharmacology Research LaboratoryJeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangor Darul EhsanMalaysia
| | - Idrish Ali
- Department of NeuroscienceCentral Clinical SchoolThe Alfred HospitalMonash UniversityMelbourneVic.Australia
| | - Syafiq Asnawi Zainal Abidin
- Neuropharmacology Research LaboratoryJeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangor Darul EhsanMalaysia
- Liquid Chromatography Mass Spectrometry (LCMS) PlatformJeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangor Darul EhsanMalaysia
| | - Iekhsan Othman
- Neuropharmacology Research LaboratoryJeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangor Darul EhsanMalaysia
- Liquid Chromatography Mass Spectrometry (LCMS) PlatformJeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangor Darul EhsanMalaysia
| | - Mohd. Farooq Shaikh
- Neuropharmacology Research LaboratoryJeffrey Cheah School of Medicine and Health SciencesMonash University MalaysiaSelangor Darul EhsanMalaysia
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20
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Sex-specific responses to cold in a very cold-tolerant, northern Drosophila species. Heredity (Edinb) 2021; 126:695-705. [PMID: 33510465 PMCID: PMC8182794 DOI: 10.1038/s41437-020-00398-2] [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: 07/28/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 01/30/2023] Open
Abstract
Organisms can plastically alter resource allocation in response to changing environmental factors. For example, in harsh conditions, organisms are expected to shift investment from reproduction toward survival; however, the factors and mechanisms that govern the magnitude of such shifts are relatively poorly studied. Here we compared the impact of cold on males and females of the highly cold-tolerant species Drosophila montana at the phenotypic and transcriptomic levels. Although both sexes showed similar changes in cold tolerance and gene expression in response to cold treatment, indicating that the majority of changes are concordant between the sexes, we identified a clear reduction in sexually dimorphic gene expression, suggesting that preparing for the colder season involves reducing investment in sex-specific traits. This reduction was larger in males than females, as expected if male sexual traits are more condition-dependent than female traits, as predicted by theory. Gene expression changes were primarily associated with shifts in metabolic profile, which likely play a role in increasing cold tolerance. Finally, we found that the expression of immune genes was reduced following cold treatment, suggesting that reduced investment in costly immune function may be important in helping flies survive colder periods.
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21
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Molecular Basis of Neuronal Autophagy in Ageing: Insights from Caenorhabditis elegans. Cells 2021; 10:cells10030694. [PMID: 33800981 PMCID: PMC8004021 DOI: 10.3390/cells10030694] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/17/2021] [Accepted: 03/18/2021] [Indexed: 01/19/2023] Open
Abstract
Autophagy is an evolutionarily conserved degradation process maintaining cell homeostasis. Induction of autophagy is triggered as a response to a broad range of cellular stress conditions, such as nutrient deprivation, protein aggregation, organelle damage and pathogen invasion. Macroautophagy involves the sequestration of cytoplasmic contents in a double-membrane organelle referred to as the autophagosome with subsequent degradation of its contents upon delivery to lysosomes. Autophagy plays critical roles in development, maintenance and survival of distinct cell populations including neurons. Consequently, age-dependent decline in autophagy predisposes animals for age-related diseases including neurodegeneration and compromises healthspan and longevity. In this review, we summarize recent advances in our understanding of the role of neuronal autophagy in ageing, focusing on studies in the nematode Caenorhabditis elegans.
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22
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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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Zia A, Farkhondeh T, Pourbagher-Shahri AM, Samarghandian S. The Roles of mitochondrial dysfunction and Reactive Oxygen Species in Aging and Senescence. Curr Mol Med 2021; 22:37-49. [PMID: 33602082 DOI: 10.2174/1566524021666210218112616] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/16/2020] [Accepted: 12/23/2020] [Indexed: 11/22/2022]
Abstract
The aging process deteriorates organs' function at different levels, causing its progressive decline to resist stress, damage, and disease. In addition to alterations in metabolic control and gene expression, the rate of aging has been connected with the generation of high amounts of Reactive Oxygen Species (ROS). The essential perspective in free radical biology is that reactive oxygen species (ROS) and free radicals are toxic, mostly cause direct biological damage to targets, and are thus a major cause of oxidative stress. Different enzymatic and non-enzymatic compounds in the cells have roles in neutralizing this toxicity. Oxidative damage in aging is mostly high in particular molecular targets, such as mitochondrial DNA and aconitase, and oxidative stress in mitochondria can cause tissue aging across intrinsic apoptosis. Mitochondria's function and morphology are impaired through aging, following a decrease in the membrane potential by an increase in peroxide generation and size of the organelles. Telomeres may be the significant trigger of replicative senescence. Oxidative stress accelerates telomere loss, whereas antioxidants slow it down. Oxidative stress is a crucial modulator of telomere shortening, and that telomere-driven replicative senescence is mainly a stress response. The age-linked mitochondrial DNA mutation and protein dysfunction aggregate in some organs like the brain and skeletal muscle, thus contributing considerably to these post-mitotic tissues' aging. The aging process is mostly due to accumulated damage done by harmful species in some macromolecules such proteins, DNA, and lipids. The degradation of non-functional, oxidized proteins is a crucial part of the antioxidant defenses of cells, in which the clearance of these proteins occurs through autophagy in the cells, which is known as mitophagy for mitochondria.
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Affiliation(s)
- Aliabbas Zia
- Department of Biochemistry, Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran. Iran
| | - Tahereh Farkhondeh
- Medical Toxicology and Drug Abuse Research Center (MTDRC), Birjand University of Medical Sciences, Birjand. Iran
| | | | - Saeed Samarghandian
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur. Iran
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The aging proteostasis decline: From nematode to human. Exp Cell Res 2021; 399:112474. [PMID: 33434530 PMCID: PMC7868887 DOI: 10.1016/j.yexcr.2021.112474] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/21/2020] [Accepted: 01/02/2021] [Indexed: 02/08/2023]
Abstract
The aging proteostasis decline manifests in a failure of aging cells and organisms to properly respond to proteotoxic challenges. This proteostasis collapse has long been considered a hallmark of aging in nematodes, and has recently been shown to occur also in human cells upon entry to senescence, opening the way to exploring the phenomenon in the broader context of human aging. Cellular senescence is part of the normal human physiology of aging, with senescent cell accumulation as a prominent feature of aged tissues. Being highly resistant to cell death, senescent cells, as they accumulate, become pro-inflammatory and promote disease. Here we discuss the causes of human senescence proteostasis decline, in view of the current literature on nematodes, on the one hand, and senescence, on the other hand. We review two major aspects of the phenomenon: (1) the decline in transcriptional activation of stress-response pathways, and (2) impairments in proteasome function. We further outline potential underlying mechanisms of transcriptional proteostasis decline, focusing on reduced chromatin dynamics and compromised nuclear integrity. Finally, we discuss potential strategies for reinforcing proteostasis as a means to improve organismal health and address the relationship to senolytics.
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Razgonova MP, Zakharenko AM, Golokhvast KS, Thanasoula M, Sarandi E, Nikolouzakis K, Fragkiadaki P, Tsoukalas D, Spandidos DA, Tsatsakis A. Telomerase and telomeres in aging theory and chronographic aging theory (Review). Mol Med Rep 2020; 22:1679-1694. [PMID: 32705188 PMCID: PMC7411297 DOI: 10.3892/mmr.2020.11274] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 06/24/2020] [Indexed: 01/03/2023] Open
Abstract
The current review focuses on the connection of telomerase and telomeres with aging. In this review, we describe the changes in telomerase and telomere length (TEL) during development, their role in carcinogenesis processes, and the consequences of reduced telomerase activity. More specifically, the connection of TEL in peripheral blood cells with the development of aging‑associated diseases is discussed. The review provides systematic data on the role of telomerase in mitochondria, the biology of telomeres in stem cells, as well as the consequences of the forced expression of telomerase (telomerization) in human cells. Additionally, it presents the effects of chronic stress exposure on telomerase activity, the effect of TEL on fertility, and the effect of nutraceutical supplements on TEL. Finally, a comparative review of the chronographic theory of aging, presented by Olovnikov is provided based on currently available scientific research on telomere, telomerase activity, and the nature of aging by multicellular organisms.
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Affiliation(s)
- Mayya P. Razgonova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Alexander M. Zakharenko
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
| | - Kirill S. Golokhvast
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190000 Saint-Petersburg, Russia
- Far Eastern Federal University, 690950 Vladivostok, Russia
- Pacific Geographical Institute, Far Eastern Branch of The Russian Academy of Sciences, 690041 Vladivostok, Russia
| | - Maria Thanasoula
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | - Evangelia Sarandi
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | | | - Persefoni Fragkiadaki
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
- Spin-Off Toxplus S.A., 71601 Heraklion, Greece
| | - Dimitris Tsoukalas
- Metabolomic Μedicine, Health Clinics for Autoimmune and Chronic Diseases, 10674 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, Heraklion 71003, Greece
| | - Aristidis Tsatsakis
- Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece
- Spin-Off Toxplus S.A., 71601 Heraklion, Greece
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Dahiya R, Mohammad T, Alajmi MF, Rehman MT, Hasan GM, Hussain A, Hassan MI. Insights into the Conserved Regulatory Mechanisms of Human and Yeast Aging. Biomolecules 2020; 10:E882. [PMID: 32526825 PMCID: PMC7355435 DOI: 10.3390/biom10060882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 05/22/2020] [Accepted: 05/27/2020] [Indexed: 12/12/2022] Open
Abstract
Aging represents a significant biological process having strong associations with cancer, diabetes, and neurodegenerative and cardiovascular disorders, which leads to progressive loss of cellular functions and viability. Astonishingly, age-related disorders share several genetic and molecular mechanisms with the normal aging process. Over the last three decades, budding yeast Saccharomyces cerevisiae has emerged as a powerful yet simple model organism for aging research. Genetic approaches using yeast RLS have led to the identification of hundreds of genes impacting lifespan in higher eukaryotes. Numerous interventions to extend yeast lifespan showed an analogous outcome in multi-cellular eukaryotes like fruit flies, nematodes, rodents, and humans. We collected and analyzed a multitude of observations from published literature and provide the contribution of yeast in the understanding of aging hallmarks most applicable to humans. Here, we discuss key pathways and molecular mechanisms that underpin the evolutionarily conserved aging process and summarize the current understanding and clinical applicability of its trajectories. Gathering critical information on aging biology would pave the way for future investigation targeted at the discovery of aging interventions.
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Affiliation(s)
- Rashmi Dahiya
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
| | - Mohamed F. Alajmi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (M.T.R.); (A.H.)
| | - Md. Tabish Rehman
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (M.T.R.); (A.H.)
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj 11942, Saudi Arabia;
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (M.F.A.); (M.T.R.); (A.H.)
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India;
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Wan J, Sun G, Dicent J, Patel DS, Lu H. smFISH in chips: a microfluidic-based pipeline to quantify in situ gene expression in whole organisms. LAB ON A CHIP 2020; 20:266-273. [PMID: 31788681 PMCID: PMC8146400 DOI: 10.1039/c9lc00896a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Gene expression and genetic regulatory networks in multi-cellular organisms control complex physiological processes ranging from cellular differentiation to development to aging. Traditional methods to investigate gene expression relationships rely on using bulk, pooled-population assays (e.g. RNA-sequencing and RT-PCR) to compare gene expression levels in hypo- or hyper-morphic mutant animals (e.g. gain-of-function or knockout). This approach is limited, especially in complex gene networks, as these genetic mutations may affect the expressions of related genes in unforseen ways. In contrast, we developed a microfluidic-based pipeline to discover gene relationships in a single genetic background. The microfluidic device provides efficient reagent exchange and the ability to track individual animals. By automating a robust microfluidic reagent exchange strategy, we adapted and validated single molecule fluorescent in situ hybridization (smFISH) on-chip and combined this technology with live-imaging of fluorescent transcriptional reporters. Together, this multi-level information enabled us to quantify a gene expression relationship with single-animal resolution. While this microfluidic-based pipeline is optimized for live-imaging and smFISH C. elegans studies, the strategy is highly-adaptable to other biological models as well as combining other live and end-point biological assays, such as behavior-based toxicology screening and immunohistochemistry.
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Affiliation(s)
- Jason Wan
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Gongchen Sun
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Jocelyn Dicent
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Hang Lu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA. and School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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Exploring Target Genes Involved in the Effect of Quercetin on the Response to Oxidative Stress in Caenorhabditis elegans. Antioxidants (Basel) 2019; 8:antiox8120585. [PMID: 31775265 PMCID: PMC6943653 DOI: 10.3390/antiox8120585] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 01/09/2023] Open
Abstract
Quercetin is one the most abundant flavonoids in the human diet. Although it is well known that quercetin exhibits a range of biological activities, the mechanisms behind these activities remain unresolved. The aim of this work is to progress in the knowledge of the molecular mechanisms involved in the biological effects of quercetin using Caenorhabditis elegans as a model organism. With this aim, the nematode has been used to explore the ability of this flavonoid to modulate the insulin/insulin-like growth factor 1(IGF-1) signaling pathway (IIS) and the expression of some genes related to stress response. Different methodological approaches have been used, i.e., assays in knockout mutant worms, gene expression assessment by RT-qPCR, and C. elegans transgenic strains expressing green fluorescent protein (GFP) reporters. The results showed that the improvement of the oxidative stress resistance of C. elegans induced by quercetin could be explained, at least in part, by the modulation of the insulin signaling pathway, involving genes age-1, akt-1, akt-2, daf-18, sgk-1, daf-2, and skn-1. However, this effect could be independent of the transcription factors DAF-16 and HSF-1 that regulate this pathway. Moreover, quercetin was also able to increase expression of hsp-16.2 in aged worms. This observation could be of particular interest to explain the effects of enhanced lifespan and greater resistance to stress induced by quercetin in C. elegans, since the expression of many heat shock proteins diminishes in aging worms.
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29
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Sun G, Wan J, Lu H. Rapid and multi-cycle smFISH enabled by microfluidic ion concentration polarization for in-situ profiling of tissue-specific gene expression in whole C. elegans. BIOMICROFLUIDICS 2019; 13:064101. [PMID: 31700560 PMCID: PMC6824911 DOI: 10.1063/1.5124827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
Understanding gene regulation networks in multicellular organisms is crucial to decipher many complex physiological processes ranging from development to aging. One technique to characterize gene expression with tissue-specificity in whole organisms is single-molecule fluorescence in situ hybridization (smFISH). However, this protocol requires lengthy incubation times, and it is challenging to achieve multiplexed smFISH in a whole organism. Multiplexing techniques can yield transcriptome-level information, but they require sequential probing of different genes. The inefficient macromolecule exchange through diffusion-dominant transport across dense tissues is the major bottleneck. In this work, we address this challenge by developing a microfluidic/electrokinetic hybrid platform to enable multicycle smFISH in an intact model organism, Caenorhabditis elegans. We integrate an ion concentration polarization based ion pump with a microfluidic array to rapidly deliver and remove gene-specific probes and stripping reagents on demand in individual animals. Using our platform, we can achieve rapid smFISH, an order of magnitude faster than traditional smFISH protocols. We also demonstrate the capability to perform multicycle smFISH on the same individual samples, which is impossible to do off-chip. Our method hence provides a powerful tool to study individual-specific, spatially resolvable, and large-scale gene expression in whole organisms.
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Affiliation(s)
- Gongchen Sun
- School of Chemical & Biomolecular Engineering,
Georgia Institute of Technology, Atlanta, Georgia
30332, USA
| | - Jason Wan
- Wallace H. Coulter Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University,
Atlanta, Georgia 30332, USA
| | - Hang Lu
- School of Chemical & Biomolecular Engineering,
Georgia Institute of Technology, Atlanta, Georgia
30332, USA
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30
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Chaudhuri P, Imam HT, Essig Y, Krasauskas J, Webb SM, Blindauer CA, Stürzenbaum SR. Molecular genetic and biochemical characterization of a putative family of zinc metalloproteins in Caenorhabditis elegans. Metallomics 2019; 10:1814-1823. [PMID: 30444224 PMCID: PMC6336089 DOI: 10.1039/c8mt00169c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The first characterization of W08E12.2, W08E12.3, W08E12.4 and W08E12.5, four putative metalloproteins in C. elegans. (A) phase contrast microscopy, (B) fluorescence microscopy of PW08E12.3;W08E12.4::GFP.
Four highly similar genes (W08E12.2, W08E12.3, W08E12.4 and W08E12.5) which are consecutively aligned on chromosome IV of the C. elegans genome are predicted to code for small (120–141aa) yet cysteine rich (18–19 cysteines) proteins. Cloning and sequencing of the genomic regions of the isoforms confirmed the presence and order of all genes. The generation of transgenic worms strains with an integrated single copy or extrachromosomal multi-copy PW08E12.3;W08E12.4::GFP uncovered that W08E12.3 and W08E12.4 are constitutively expressed in the pharynx and significantly induced in worms exposed to 100 μM Zn. Knockdown by RNAi did not have a marked consequence on reproductive performance nor was a Zn-dependent effect on nematode growth observed. However, RNAi of these genes led to an accumulation of Zn in the intestinal cells. W08E12.3 was recombinantly expressed in E. coli and the purified protein was shown to be able to bind up to 6.5 Zn molecules at neutral pH. Zn-binding was acid-labile and the apo protein was observed at pH < 4.3. This characterization suggests W08E12.2, W08E12.3, W08E12.4 and W08E12.5 belong to a family of putative Metalloproteins which, akin to metallothioneins, may play an important role in Zn-sensing, homeostasis and/or detoxification.
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Affiliation(s)
- Poulami Chaudhuri
- King's College London, School of Population Health & Environmental Sciences, Faculty of Life Sciences & Medicine, 150 Stamford Street, London, SE1 9NH, UK.
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Miansari M, Mehta MD, Schilling JM, Kurashina Y, Patel HH, Friend J. Inducing Mild Traumatic Brain Injury in C. elegans via Cavitation-Free Surface Acoustic Wave-Driven Ultrasonic Irradiation. Sci Rep 2019; 9:12775. [PMID: 31485018 PMCID: PMC6726767 DOI: 10.1038/s41598-019-47295-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/15/2019] [Indexed: 12/13/2022] Open
Abstract
Mild traumatic brain injury is an all-too-common outcome from modern warfare and sport, and lacks a reproducible model for assessment of potential treatments and protection against it. Here we consider the use of surface acoustic wave (SAW) irradiation of C. elegans worms—without cavitation—as a potential, ethically reasonable animal-on-a-chip model for inducing traumatic brain injury in an animal, producing significant effects on memory and learning that could prove useful in a model that progress from youth to old age in but a few weeks. We show a significant effect by SAW on the ability of worms to learn post-exposure through associative learning chemotaxis. At higher SAW intensity, we find immediate, thorough, but temporary paralysis of the worms. We further explore the importance of homogeneous exposure of the worms to the SAW-driven ultrasound, an aspect poorly controlled in past efforts, if at all, and demonstrate the absence of cavitation through a change in fluids from a standard media for the worms to the exceedingly viscous polyvinyl alcohol. Likewise, we demonstrate that acoustic streaming, when present, is not directly responsible for paralysis nor learning disabilities induced in the worm, but is beneficial at low amplitudes to ensuring homogeneous ultrasound exposure.
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Affiliation(s)
- Morteza Miansari
- Medically Advanced Devices Laboratory, Center for Medical Devices, Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, 92093, CA, United States of America.,Department of Mechanical Engineering, Babol Noshirvani University of Technology, P.O. Box 484, Babol, Iran.,Department of Cancer Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Babol, Iran
| | - Meghna D Mehta
- Department of Anesthesiology, University of California San Diego, 9500 Gilman Dr MC0801, La Jolla, 92093, California, USA
| | - Jan M Schilling
- Department of Anesthesiology, University of California San Diego, 9500 Gilman Dr MC0801, La Jolla, 92093, California, USA
| | - Yuta Kurashina
- Medically Advanced Devices Laboratory, Center for Medical Devices, Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, 92093, CA, United States of America.,School of Materials and Chemical Technology, Tokyo Institute of Technology, Nagatsuta, Yokohama, 4259, Japan
| | - Hemal H Patel
- Department of Anesthesiology, University of California San Diego, 9500 Gilman Dr MC0801, La Jolla, 92093, California, USA
| | - James Friend
- Medically Advanced Devices Laboratory, Center for Medical Devices, Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive MC0411, La Jolla, 92093, CA, United States of America.
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Finch CE, Kulminski AM. The Alzheimer's Disease Exposome. Alzheimers Dement 2019; 15:1123-1132. [PMID: 31519494 PMCID: PMC6788638 DOI: 10.1016/j.jalz.2019.06.3914] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/06/2019] [Accepted: 06/12/2019] [Indexed: 12/29/2022]
Abstract
INTRODUCTION Environmental factors are poorly understood in the etiology of Alzheimer's disease (AD) and related dementias. The importance of environmental factors in gene environment interactions (GxE) is suggested by wide individual differences in cognitive loss, even for carriers of AD-risk genetic variants. RESULTS AND DISCUSSION We propose the "AD exposome" to comprehensively assess the modifiable environmental factors relevant to genetic underpinnings of cognitive aging and AD. Analysis of endogenous and exogenous environmental factors requires multi-generational consideration of these interactions over age and time (GxExT). New computational approaches to the multi-level complexities may identify accessible interventions for individual brain aging. International collaborations on diverse populations are needed to identify the most relevant exposures over the life course for GxE interactions.
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Affiliation(s)
- Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
| | - Alexander M Kulminski
- Biodemography of Aging Research Unit, Social Science Research Institute, Duke University, Durham, NC, USA.
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Li S, Zhao H, Zhang P, Liang C, Zhang Y, Hsu A, Dong M. DAF-16 stabilizes the aging transcriptome and is activated in mid-aged Caenorhabditis elegans to cope with internal stress. Aging Cell 2019; 18:e12896. [PMID: 30773782 PMCID: PMC6516157 DOI: 10.1111/acel.12896] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 11/03/2018] [Indexed: 12/31/2022] Open
Abstract
The roles and regulatory mechanisms of transcriptome changes during aging are unclear. It has been proposed that the transcriptome suffers decay during aging owing to age‐associated down‐regulation of transcription factors. In this study, we characterized the role of a transcription factor DAF‐16, which is a highly conserved lifespan regulator, in the normal aging process of Caenorhabditis elegans. We found that DAF‐16 translocates into the nucleus in aged wild‐type worms and activates the expression of hundreds of genes in response to age‐associated cellular stress. Most of the age‐dependent DAF‐16 targets are different from the canonical DAF‐16 targets downstream of insulin signaling. This and other evidence suggest that activation of DAF‐16 during aging is distinct from activation of DAF‐16 due to reduced signaling from DAF‐2. Further analysis showed that it is due in part to a loss of proteostasis during aging. We also found that without daf‐16, dramatic gene expression changes occur as early as on adult day 2, indicating that DAF‐16 acts to stabilize the transcriptome during normal aging. Our results thus reveal that normal aging is not simply a process in which the gene expression program descends into chaos due to loss of regulatory activities; rather, there is active transcriptional regulation during aging.
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Affiliation(s)
- Shang‐Tong Li
- School of Life Sciences Tsinghua University Beijing China
- Peking University‐Tsinghua University‐National Institute of Biological Sciences (PTN) Joint Graduate Program Beijing China
- National Institute of Biological Sciences Beijing China
| | - Han‐Qing Zhao
- National Institute of Biological Sciences Beijing China
| | - Pan Zhang
- National Institute of Biological Sciences Beijing China
| | - Chung‐Yi Liang
- Research Center for Healthy Aging China Medical University Taichung Taiwan
| | | | - Ao‐Lin Hsu
- Research Center for Healthy Aging China Medical University Taichung Taiwan
- Institute of Biochemistry and Molecular Biology National Yang‐Ming University Taipei Taiwan
- Department of Internal Medicine, Division of Geriatric and Palliative Medicine University of Michigan Ann Arbor Michigan
| | - Meng‐Qiu Dong
- National Institute of Biological Sciences Beijing China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University Beijing China
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Son HG, Altintas O, Kim EJE, Kwon S, Lee SV. Age-dependent changes and biomarkers of aging in Caenorhabditis elegans. Aging Cell 2019; 18:e12853. [PMID: 30734981 PMCID: PMC6413654 DOI: 10.1111/acel.12853] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 08/28/2018] [Accepted: 09/11/2018] [Indexed: 12/13/2022] Open
Abstract
Caenorhabditis elegans is an exceptionally valuable model for aging research because of many advantages, including its genetic tractability, short lifespan, and clear age‐dependent physiological changes. Aged C. elegans display a decline in their anatomical and functional features, including tissue integrity, motility, learning and memory, and immunity. Caenorhabditis elegans also exhibit many age‐associated changes in the expression of microRNAs and stress‐responsive genes and in RNA and protein quality control systems. Many of these age‐associated changes provide information on the health of the animals and serve as valuable biomarkers for aging research. Here, we review the age‐dependent changes in C. elegans and their utility as aging biomarkers indicative of the physiological status of aging.
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Affiliation(s)
- Heehwa G. Son
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
| | - Ozlem Altintas
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang South Korea
| | - Eun Ji E. Kim
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
| | - Sujeong Kwon
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
| | - Seung‐Jae V. Lee
- Department of Life Sciences Pohang University of Science and Technology Pohang South Korea
- School of Interdisciplinary Bioscience and Bioengineering Pohang University of Science and Technology Pohang South Korea
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Dzakah EE, Waqas A, Wei S, Yu B, Wang X, Fu T, Liu L, Shan G. Loss of miR-83 extends lifespan and affects target gene expression in an age-dependent manner in Caenorhabditis elegans. J Genet Genomics 2018; 45:651-662. [PMID: 30595472 DOI: 10.1016/j.jgg.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 10/11/2018] [Accepted: 11/06/2018] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are short non-coding RNAs that are involved in the post-transcriptional regulation of protein-coding genes. miRNAs modulate lifespan and the aging process in a variety of organisms. In this study, we identified a role of miR-83 in regulating lifespan of Caenorhabditis elegans. mir-83 mutants exhibited extended lifespan, and the overexpression of miR-83 was sufficient to decrease the prolonged lifespan of the mutants. We observed upregulation of the expression levels of a set of miR-83 target genes in young mir-83 mutant adults; while different sets of genes were upregulated in older mir-83 mutant adults. In vivo assays showed that miR-83 regulated expression of target genes including din-1, spp-9 and col-178, and we demonstrated that daf-16 and din-1 were required for the extension of lifespan in the mir-83 mutants. The regulation of din-1 by miR-83 during aging resulted in the differential expression of din-1 targets such as gst-4 and gst-10. In daf-2 mutants, the expression level of miR-83 was significantly reduced compared to wild-type animals. We identified a role for miR-83 in modulating lifespan in C. elegans and provided molecular insights into its functional mechanism.
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Affiliation(s)
- Emmanuel Enoch Dzakah
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; Department of Molecular Biology and Biotechnology, School of Biological Sciences, College of Agriculture and Natural Sciences, University of Cape Coast, Cape Coast 03321, Ghana
| | - Ahmed Waqas
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Shuai Wei
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Bin Yu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Xiaolin Wang
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Tao Fu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Lei Liu
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Ge Shan
- Division of Molecular Medicine, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China; CAS Centre for Excellence in Molecular Cell Science, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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36
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Song R, Sarnoski EA, Acar M. The Systems Biology of Single-Cell Aging. iScience 2018; 7:154-169. [PMID: 30267677 PMCID: PMC6153419 DOI: 10.1016/j.isci.2018.08.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/30/2018] [Accepted: 08/29/2018] [Indexed: 12/12/2022] Open
Abstract
Aging is a leading cause of human morbidity and mortality, but efforts to slow or reverse its effects are hampered by an incomplete understanding of its multi-faceted origins. Systems biology, the use of quantitative and computational methods to understand complex biological systems, offers a toolkit well suited to elucidating the root cause of aging. We describe the known components of the aging network and outline innovative techniques that open new avenues of investigation to the aging research community. We propose integration of the systems biology and aging fields, identifying areas of complementarity based on existing and impending technological capabilities.
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Affiliation(s)
- Ruijie Song
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA
| | - Ethan A Sarnoski
- Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA
| | - Murat Acar
- Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, 300 George Street, Suite 501, New Haven, CT 06511, USA; Systems Biology Institute, Yale University, 850 West Campus Drive, West Haven, CT 06516, USA; Department of Molecular Cellular and Developmental Biology, Yale University, 219 Prospect Street, New Haven, CT 06511, USA; Department of Physics, Yale University, 217 Prospect Street, New Haven, CT 06511, USA.
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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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Park MR, Ryu S, Maburutse BE, Oh NS, Kim SH, Oh S, Jeong SY, Jeong DY, Oh S, Kim Y. Probiotic Lactobacillus fermentum strain JDFM216 stimulates the longevity and immune response of Caenorhabditis elegans through a nuclear hormone receptor. Sci Rep 2018; 8:7441. [PMID: 29748542 PMCID: PMC5945636 DOI: 10.1038/s41598-018-25333-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 03/23/2018] [Indexed: 01/14/2023] Open
Abstract
Here, we examined the functionality of Lactobacillus fermentum strain JDFM216, a newly isolated probiotic bacterium, using a Caenorhabditis elegans model. We determined bacterial colonization in the intestinal tract of C. elegans by plate counting and transmission electron microscopy and examined the survival of C. elegans using a solid killing assay. In addition, we employed DNA microarray analysis, quantitative real time-polymerase chain reaction, and immunoblotting assays to explore health-promoting pathways induced by probiotic bacteria in C. elegans. Initially, we found that the probiotic bacterium L. fermentum strain JDFM216 was not harmful to the C. elegans host. Conditioning with JDFM216 led to its colonization in the nematode intestine and enhanced resistance in nematodes exposed to food-borne pathogens, including Staphylococcus aureus and Escherichia coli O157:H7. Interestingly, this probiotic strain significantly prolonged the life span of C. elegans. Whole-transcriptome analysis and transgenic worm assays revealed that the health-promoting effects of JDFM216 were mediated by a nuclear hormone receptor (NHR) family and PMK-1 signaling. Taken together, we described a new C. elegans-based system to screen novel probiotic activity and demonstrated that preconditioning with the probiotic L. fermentum strain JDFM216 may positively stimulate the longevity of the C. elegans host via specific pathway.
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Affiliation(s)
- Mi Ri Park
- Department of Animal Science and Institute of Milk Genomics, Chonbuk National University, Jeonju, 54896, Korea
| | - Sangdon Ryu
- Department of Animal Science and Institute of Milk Genomics, Chonbuk National University, Jeonju, 54896, Korea
| | - Brighton E Maburutse
- Department of Animal Science and Institute of Milk Genomics, Chonbuk National University, Jeonju, 54896, Korea
| | - Nam Su Oh
- R&D Center, Seoul Dairy Cooperative, Ansan, Gyeonggi, 15407, South Korea
| | - Sae Hun Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Sejong Oh
- Department of Animal Science, Chonnam National University, Gwangju, 61186, Korea
| | - Seong-Yeop Jeong
- Microbial Institute for Fermentation Industry, Sunchang, Jeonbuk, 56048, Republic of Korea
| | - Do-Youn Jeong
- Microbial Institute for Fermentation Industry, Sunchang, Jeonbuk, 56048, Republic of Korea
| | - Sangnam Oh
- Department of Functional Food and Biotechnology, Jeonju University, Jeonju, 55069, Republic of Korea.
| | - Younghoon Kim
- Department of Animal Science and Institute of Milk Genomics, Chonbuk National University, Jeonju, 54896, Korea.
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39
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Xu J, Guo Y, Sui T, Wang Q, Zhang Y, Zhang R, Wang M, Guan S, Wang L. Molecular mechanisms of anti-oxidant and anti-aging effects induced by convallatoxin in Caenorhabditis elegans. Free Radic Res 2018; 51:529-544. [PMID: 28503972 DOI: 10.1080/10715762.2017.1331037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Convallatoxin is widely used as a cardiac glycoside in acute and chronic congestive heart-failure and paroxysmal tachycardia, with many effects and underlying protective mechanisms on inflammation and cellular proliferation. However, convallatoxin has not been investigated in its antioxidant effects and lifespan extension in Caenorhabditis elegans. In this study, we found that convallatoxin (20 μM) could significantly prolong the lifespan of wild-type C. elegans up to 16.3% through daf-16, but not sir-2.1 signalling and increased thermotolerance and resistance to paraquat-induced oxidative stress. Convallatoxin also improved pharyngeal pumping, locomotion, reduced lipofuscin accumulation and reactive oxygen species levels in C. elegans, which were attributed to hormesis, free radical-scavenging effects in vivo, and up-regulation of stress resistance-related proteins, such as SOD-3 and HSP-16.1. Furthermore, aging-associated genes daf-16, sod-3, and ctl-2 also appeared to contribute to the stress-resistance effect of convallatoxin. In summary, this study demonstrates that convallatoxin can protect against heat and oxidative stress and extend the lifespan of C. elegans, pointing it as a potential novel drug for retarding the aging process in humans.
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Affiliation(s)
- Jia Xu
- a School of Life Science , Jilin University , Changchun , PR China
| | - Youming Guo
- a School of Life Science , Jilin University , Changchun , PR China
| | - Tianzhuo Sui
- a School of Life Science , Jilin University , Changchun , PR China
| | - Qifei Wang
- b College of Chemistry , Jilin University , Changchun , PR China
| | - Yue Zhang
- a School of Life Science , Jilin University , Changchun , PR China
| | - Ruining Zhang
- a School of Life Science , Jilin University , Changchun , PR China
| | - Mingyang Wang
- a School of Life Science , Jilin University , Changchun , PR China
| | - Shuwen Guan
- a School of Life Science , Jilin University , Changchun , PR China
| | - Liping Wang
- a School of Life Science , Jilin University , Changchun , PR China
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40
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Abstract
Ageing leads to dramatic changes in the physiology of many different tissues resulting in a spectrum of pathology. Nonetheless, many lines of evidence suggest that ageing is driven by highly conserved cell intrinsic processes, and a set of unifying hallmarks of ageing has been defined. Here, we survey reports of age-linked changes in basal gene expression across eukaryotes from yeast to human and identify six gene expression hallmarks of cellular ageing: downregulation of genes encoding mitochondrial proteins; downregulation of the protein synthesis machinery; dysregulation of immune system genes; reduced growth factor signalling; constitutive responses to stress and DNA damage; dysregulation of gene expression and mRNA processing. These encompass widely reported features of ageing such as increased senescence and inflammation, reduced electron transport chain activity and reduced ribosome synthesis, but also reveal a surprising lack of gene expression responses to known age-linked cellular stresses. We discuss how the existence of conserved transcriptomic hallmarks relates to genome-wide epigenetic differences underlying ageing clocks, and how the changing transcriptome results in proteomic alterations where data is available and to variations in cell physiology characteristic of ageing. Identification of gene expression events that occur during ageing across distant organisms should be informative as to conserved underlying mechanisms of ageing, and provide additional biomarkers to assess the effects of diet and other environmental factors on the rate of ageing.
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Affiliation(s)
- Stephen Frenk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599-3280, USA
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41
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Brehme M, Voisine C. Model systems of protein-misfolding diseases reveal chaperone modifiers of proteotoxicity. Dis Model Mech 2017; 9:823-38. [PMID: 27491084 PMCID: PMC5007983 DOI: 10.1242/dmm.024703] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chaperones and co-chaperones enable protein folding and degradation, safeguarding the proteome against proteotoxic stress. Chaperones display dynamic responses to exogenous and endogenous stressors and thus constitute a key component of the proteostasis network (PN), an intricately regulated network of quality control and repair pathways that cooperate to maintain cellular proteostasis. It has been hypothesized that aging leads to chronic stress on the proteome and that this could underlie many age-associated diseases such as neurodegeneration. Understanding the dynamics of chaperone function during aging and disease-related proteotoxic stress could reveal specific chaperone systems that fail to respond to protein misfolding. Through the use of suppressor and enhancer screens, key chaperones crucial for proteostasis maintenance have been identified in model organisms that express misfolded disease-related proteins. This review provides a literature-based analysis of these genetic studies and highlights prominent chaperone modifiers of proteotoxicity, which include the HSP70-HSP40 machine and small HSPs. Taken together, these studies in model systems can inform strategies for therapeutic regulation of chaperone functionality, to manage aging-related proteotoxic stress and to delay the onset of neurodegenerative diseases.
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Affiliation(s)
- Marc Brehme
- Joint Research Center for Computational Biomedicine (JRC-COMBINE), RWTH Aachen University, 52062 Aachen, Germany
| | - Cindy Voisine
- Department of Biology, Northeastern Illinois University, Chicago, IL 60625, USA
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42
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Angeles-Albores D, Leighton DHW, Tsou T, Khaw TH, Antoshechkin I, Sternberg PW. The Caenorhabditis elegans Female-Like State: Decoupling the Transcriptomic Effects of Aging and Sperm Status. G3 (BETHESDA, MD.) 2017; 7:2969-2977. [PMID: 28751504 PMCID: PMC5592924 DOI: 10.1534/g3.117.300080] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 07/04/2017] [Indexed: 12/22/2022]
Abstract
Understanding genome and gene function in a whole organism requires us to fully comprehend the life cycle and the physiology of the organism in question. Caenorhabditis elegans XX animals are hermaphrodites that exhaust their sperm after 3 d of egg-laying. Even though C. elegans can live for many days after cessation of egg-laying, the molecular physiology of this state has not been as intensely studied as other parts of the life cycle, despite documented changes in behavior and metabolism. To study the effects of sperm depletion and aging of C. elegans during the first 6 d of adulthood, we measured the transcriptomes of first-day adult hermaphrodites and sixth-day sperm-depleted adults, and, at the same time points, mutant fog-2(lf) worms that have a feminized germline phenotype. We found that we could separate the effects of biological aging from sperm depletion. For a large subset of genes, young adult fog-2(lf) animals had the same gene expression changes as sperm-depleted sixth-day wild-type hermaphrodites, and these genes did not change expression when fog-2(lf) females reached the sixth day of adulthood. Taken together, this indicates that changing sperm status causes a change in the internal state of the worm, which we call the female-like state. Our data provide a high-quality picture of the changes that happen in global gene expression throughout the period of early aging in the worm.
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Affiliation(s)
- David Angeles-Albores
- Department of Biology and Biological Engineering, and Howard Hughes Medical Institute, Caltech, Pasadena, California 91125
| | - Daniel H W Leighton
- Department of Biology and Biological Engineering, and Howard Hughes Medical Institute, Caltech, Pasadena, California 91125
- Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Institute, University of California, Los Angeles, California 90095
| | - Tiffany Tsou
- Department of Biology and Biological Engineering, and Howard Hughes Medical Institute, Caltech, Pasadena, California 91125
| | - Tiffany H Khaw
- Department of Biology and Biological Engineering, and Howard Hughes Medical Institute, Caltech, Pasadena, California 91125
| | - Igor Antoshechkin
- Department of Biology and Biological Engineering, Caltech, Pasadena, California 91125
| | - Paul W Sternberg
- Department of Biology and Biological Engineering, and Howard Hughes Medical Institute, Caltech, Pasadena, California 91125
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Baxi K, Ghavidel A, Waddell B, Harkness TA, de Carvalho CE. Regulation of Lysosomal Function by the DAF-16 Forkhead Transcription Factor Couples Reproduction to Aging in Caenorhabditis elegans. Genetics 2017; 207:83-101. [PMID: 28696216 PMCID: PMC5586388 DOI: 10.1534/genetics.117.204222] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Aging in eukaryotes is accompanied by widespread deterioration of the somatic tissue. Yet, abolishing germ cells delays the age-dependent somatic decline in Caenorhabditis elegans In adult worms lacking germ cells, the activation of the DAF-9/DAF-12 steroid signaling pathway in the gonad recruits DAF-16 activity in the intestine to promote longevity-associated phenotypes. However, the impact of this pathway on the fitness of normally reproducing animals is less clear. Here, we explore the link between progeny production and somatic aging and identify the loss of lysosomal acidity-a critical regulator of the proteolytic output of these organelles-as a novel biomarker of aging in C. elegans The increase in lysosomal pH in older worms is not a passive consequence of aging, but instead is timed with the cessation of reproduction, and correlates with the reduction in proteostasis in early adult life. Our results further implicate the steroid signaling pathway and DAF-16 in dynamically regulating lysosomal pH in the intestine of wild-type worms in response to the reproductive cycle. In the intestine of reproducing worms, DAF-16 promotes acidic lysosomes by upregulating the expression of v-ATPase genes. These findings support a model in which protein clearance in the soma is linked to reproduction in the gonad via the active regulation of lysosomal acidification.
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Affiliation(s)
- Kunal Baxi
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Ata Ghavidel
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Brandon Waddell
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Troy A Harkness
- Department of Anatomy and Cell Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
| | - Carlos E de Carvalho
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan S7N5E2, Canada
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44
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Identification of a T cell gene expression clock obtained by exploiting a MZ twin design. Sci Rep 2017; 7:6005. [PMID: 28729616 PMCID: PMC5519672 DOI: 10.1038/s41598-017-05694-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 06/01/2017] [Indexed: 02/02/2023] Open
Abstract
Many studies investigated age-related changes in gene expression of different tissues, with scarce agreement due to the high number of affecting factors. Similarly, no consensus has been reached on which genes change expression as a function of age and not because of environment. In this study we analysed gene expression of T lymphocytes from 27 healthy monozygotic twin couples, with ages ranging over whole adult lifespan (22 to 98 years). This unique experimental design allowed us to identify genes involved in normative aging, which expression changes independently from environmental factors. We obtained a transcriptomic signature with 125 genes, from which chronological age can be estimated. This signature has been tested in two datasets of same cell type hybridized over two different platforms, showing a significantly better performance compared to random signatures. Moreover, the same signature was applied on a dataset from a different cell type (human muscle). A lower performance was obtained, indicating the possibility that the signature is T cell-specific. As a whole our results suggest that this approach can be useful to identify age-modulated genes.
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45
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Dhondt I, Petyuk VA, Bauer S, Brewer HM, Smith RD, Depuydt G, Braeckman BP. Changes of Protein Turnover in Aging Caenorhabditis elegans. Mol Cell Proteomics 2017; 16:1621-1633. [PMID: 28679685 DOI: 10.1074/mcp.ra117.000049] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Indexed: 11/06/2022] Open
Abstract
Protein turnover rates severely decline in aging organisms, including C. elegans However, limited information is available on turnover dynamics at the individual protein level during aging. We followed changes in protein turnover at one-day resolution using a multiple-pulse 15N-labeling and accurate mass spectrometry approach. Forty percent of the proteome shows gradual slowdown in turnover with age, whereas only few proteins show increased turnover. Decrease in protein turnover was consistent for only a minority of functionally related protein subsets, including tubulins and vitellogenins, whereas randomly diverging turnover patterns with age were the norm. Our data suggests increased heterogeneity of protein turnover of the translation machinery, whereas protein turnover of ubiquitin-proteasome and antioxidant systems are well-preserved over time. Hence, we presume that maintenance of quality control mechanisms is a protective strategy in aging worms, although the ultimate proteome collapse is inescapable.
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Affiliation(s)
- Ineke Dhondt
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium
| | - Vladislav A Petyuk
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Sophie Bauer
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium
| | - Heather M Brewer
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D Smith
- §Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Geert Depuydt
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium.,¶Laboratory for Functional Genomics and Proteomics, Department of Biology, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Bart P Braeckman
- From the ‡Laboratory for Aging Physiology and Molecular Evolution, Biology Department, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent Belgium;
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46
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Stegeman R, Weake VM. Transcriptional Signatures of Aging. J Mol Biol 2017; 429:2427-2437. [PMID: 28684248 DOI: 10.1016/j.jmb.2017.06.019] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 06/02/2017] [Accepted: 06/28/2017] [Indexed: 12/31/2022]
Abstract
Genome-wide studies of aging have identified subsets of genes that show age-related changes in expression. Although the types of genes that are age regulated vary among different tissues and organisms, some patterns emerge from these large data sets. First, aging is associated with a broad induction of stress response pathways, although the specific genes and pathways involved differ depending on cell type and species. In contrast, a wide variety of functional classes of genes are downregulated with age, often including tissue-specific genes. Although the upregulation of age-regulated genes is likely to be governed by stress-responsive transcription factors, questions remain as to why particular genes are susceptible to age-related transcriptional decline. Here, we discuss recent findings showing that splicing is misregulated with age. While defects in splicing could lead to changes in protein isoform levels, they could also impact gene expression through nonsense-mediated decay of intron-retained transcripts. The discovery that splicing is misregulated with age suggests that other aspects of gene expression, such as transcription elongation, termination, and polyadenylation, must also be considered as potential mechanisms for age-related changes in transcript levels. Moreover, the considerable variation between genome-wide aging expression studies indicates that there is a critical need to analyze the transcriptional signatures of aging in single-cell types rather than whole tissues. Since age-associated decreases in gene expression could contribute to a progressive decline in cellular function, understanding the mechanisms that determine the aging transcriptome provides a potential target to extend healthy cellular lifespan.
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Affiliation(s)
- R Stegeman
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - V M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, West Lafayette, IN 47907, USA.
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Churgin MA, Jung SK, Yu CC, Chen X, Raizen DM, Fang-Yen C. Longitudinal imaging of Caenorhabditis elegans in a microfabricated device reveals variation in behavioral decline during aging. eLife 2017; 6. [PMID: 28537553 PMCID: PMC5484621 DOI: 10.7554/elife.26652] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/22/2017] [Indexed: 12/28/2022] Open
Abstract
The roundworm C. elegans is a mainstay of aging research due to its short lifespan and easily manipulable genetics. Current, widely used methods for long-term measurement of C. elegans are limited by low throughput and the difficulty of performing longitudinal monitoring of aging phenotypes. Here we describe the WorMotel, a microfabricated device for long-term cultivation and automated longitudinal imaging of large numbers of C. elegans confined to individual wells. Using the WorMotel, we find that short-lived and long-lived strains exhibit patterns of behavioral decline that do not temporally scale between individuals or populations, but rather resemble the shortest and longest lived individuals in a wild type population. We also find that behavioral trajectories of worms subject to oxidative stress resemble trajectories observed during aging. Our method is a powerful and scalable tool for analysis of C. elegans behavior and aging. DOI:http://dx.doi.org/10.7554/eLife.26652.001 Aging affects almost all living things, yet little is known about the biological changes that occur as we get older. Scientists often study aging in the microscopic roundworm Caenorhabditis elegans because it reproduces quickly and its lifespan is short (about 2–3 weeks on average). To date, investigations have helped to reveal genes that affect overall lifespan. However, it is not known how much these genes also affect the animal’s healthy lifespan or “healthspan”, that is to say, the length of time before advancing age begins to negatively affect health. Until now, studies with worms have often been limited because measuring health and aging required time-consuming and difficult manual experiments. This also meant that worms were studied together as groups, rather than as individuals, providing a simplified picture of what was going on. An automated system in which many single worms can be analyzed and assessed would provide a much more detailed view of the effects of aging on health. Churgin et al. have now developed a device called the WorMotel to allow simultaneous automated examination of 240 worms throughout their entire adult lifespan. The WorMotel is a rectangular slab of clear silicone rubber with small wells in it. A single worm is confined in each well with a source of bacteria for food, and a camera is used to track and monitor each worm’s behavior over time. This device confirmed that worms move more slowly as they get older, which was taken to be a measurement of the worms’ declining health. Worms that lived the longest declined over the first few days and then had a long plateau of very low activity before eventually dying. Short-lived worms became slower and died fairly promptly. Churgin et al. also showed that the worms with mutations that increase lifespan declined in a similar way to the longest-lived normal worms, and that mutants with shorter lifespans declined like the shortest-lived normal worms. Also, normal worms that had been exposed to a chemical called paraquat – which stresses the worm's cells and shortens the worm’s lifespans to a few days – slowed down in a similar manner as aging worms, suggesting that the stress is similar to the aging process. Tools like the WorMotel can improve our understanding of the links between lifespan and healthspan. The tool is designed to be versatile and can be used with standard imaging systems and automated tools, meaning it can be scaled up to deal with tens of thousands of worms at once. Churgin et al. are now using the WorMotel to find other genes that influence healthspan and understand how they contribute to deteriorating health as animals age. Aging affects us all and learning more about healthspan could lead to drugs or interventions to help more people to live healthily for longer. DOI:http://dx.doi.org/10.7554/eLife.26652.002
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Affiliation(s)
- Matthew A Churgin
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, United States
| | - Sang-Kyu Jung
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, United States
| | - Chih-Chieh Yu
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, United States
| | - Xiangmei Chen
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, United States
| | - David M Raizen
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Christopher Fang-Yen
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, United States.,Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
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Investigating the specific core genetic-and-epigenetic networks of cellular mechanisms involved in human aging in peripheral blood mononuclear cells. Oncotarget 2017; 7:8556-79. [PMID: 26895224 PMCID: PMC4890987 DOI: 10.18632/oncotarget.7388] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 02/03/2016] [Indexed: 12/26/2022] Open
Abstract
Aging is an inevitable part of life for humans, and slowing down the aging process has become a main focus of human endeavor. Here, we applied a systems biology approach to construct protein-protein interaction networks, gene regulatory networks, and epigenetic networks, i.e. genetic and epigenetic networks (GENs), of elderly individuals and young controls. We then compared these GENs to extract aging mechanisms using microarray data in peripheral blood mononuclear cells, microRNA (miRNA) data, and database mining. The core GENs of elderly individuals and young controls were obtained by applying principal network projection to GENs based on Principal Component Analysis. By comparing the core networks, we identified that to overcome the accumulated mutation of genes in the aging process the transcription factor JUN can be activated by stress signals, including the MAPK signaling, T-cell receptor signaling, and neurotrophin signaling pathways through DNA methylation of BTG3, G0S2, and AP2B1 and the regulations of mir-223 let-7d, and mir-130a. We also address the aging mechanisms in old men and women. Furthermore, we proposed that drugs designed to target these DNA methylated genes or miRNAs may delay aging. A multiple drug combination comprising phenylalanine, cholesterol, and palbociclib was finally designed for delaying the aging process.
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Ma X, Zhan G, Sleumer MC, Chen S, Liu W, Zhang MQ, Liu X. Analysis of C. elegans muscle transcriptome using trans-splicing-based RNA tagging (SRT). Nucleic Acids Res 2016; 44:e156. [PMID: 27557708 PMCID: PMC5137427 DOI: 10.1093/nar/gkw734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/03/2016] [Accepted: 08/11/2016] [Indexed: 01/02/2023] Open
Abstract
Current approaches to profiling tissue-specific gene expression in C. elegans require delicate manipulation and are difficult under certain conditions, e.g. from dauer or aging worms. We have developed an easy and robust method for tissue-specific RNA-seq by taking advantage of the endogenous trans-splicing process. In this method, transgenic worms are generated in which a spliced leader (SL) RNA gene is fused with a sequence tag and driven by a tissue-specific promoter. Only in the tissue of interest, the tagged SL RNA gene is transcribed and then trans-spliced onto mRNAs. The tag allows enrichment and sequencing of mRNAs from that tissue only. As a proof of principle, we profiled the muscle transcriptome, which showed high coverage and efficient enrichment of muscle specific genes, with low background noise. To demonstrate the robustness of our method, we profiled muscle gene expression in dauer larvae and aging worms, revealing gene expression changes consistent with the physiology of these stages. The resulting muscle transcriptome also revealed 461 novel RNA transcripts, likely muscle-expressed long non-coding RNAs. In summary, the splicing-based RNA tagging (SRT) method provides a convenient and robust tool to profile trans-spliced genes and identify novel transcripts in a tissue-specific manner, with a low false positive rate.
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Affiliation(s)
- Xiaopeng Ma
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,PTN (Peking University-Tsinghua University-National Institute of Biological Sciences) Joint Graduate Program, Beijing 100084, China
| | - Ge Zhan
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Monica C Sleumer
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Siyu Chen
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Weihong Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Michael Q Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Departmental of Biological Sciences, Center for Systems Biology, The University of Texas at Dallas, TX 75080, USA.,Division of Bioinformatics, TNLIST, School of Information Sciences, Tsinghua University, Beijing 100084, China
| | - Xiao Liu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Yashin AI, Arbeev KG, Wu D, Arbeeva L, Kulminski A, Kulminskaya I, Akushevich I, Ukraintseva SV. How Genes Modulate Patterns of Aging-Related Changes on the Way to 100: Biodemographic Models and Methods in Genetic Analyses of Longitudinal Data. NORTH AMERICAN ACTUARIAL JOURNAL : NAAJ 2016; 20:201-232. [PMID: 27773987 PMCID: PMC5070546 DOI: 10.1080/10920277.2016.1178588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
BACKGROUND AND OBJECTIVE To clarify mechanisms of genetic regulation of human aging and longevity traits, a number of genome-wide association studies (GWAS) of these traits have been performed. However, the results of these analyses did not meet expectations of the researchers. Most detected genetic associations have not reached a genome-wide level of statistical significance, and suffered from the lack of replication in the studies of independent populations. The reasons for slow progress in this research area include low efficiency of statistical methods used in data analyses, genetic heterogeneity of aging and longevity related traits, possibility of pleiotropic (e.g., age dependent) effects of genetic variants on such traits, underestimation of the effects of (i) mortality selection in genetically heterogeneous cohorts, (ii) external factors and differences in genetic backgrounds of individuals in the populations under study, the weakness of conceptual biological framework that does not fully account for above mentioned factors. One more limitation of conducted studies is that they did not fully realize the potential of longitudinal data that allow for evaluating how genetic influences on life span are mediated by physiological variables and other biomarkers during the life course. The objective of this paper is to address these issues. DATA AND METHODS We performed GWAS of human life span using different subsets of data from the original Framingham Heart Study cohort corresponding to different quality control (QC) procedures and used one subset of selected genetic variants for further analyses. We used simulation study to show that approach to combining data improves the quality of GWAS. We used FHS longitudinal data to compare average age trajectories of physiological variables in carriers and non-carriers of selected genetic variants. We used stochastic process model of human mortality and aging to investigate genetic influence on hidden biomarkers of aging and on dynamic interaction between aging and longevity. We investigated properties of genes related to selected variants and their roles in signaling and metabolic pathways. RESULTS We showed that the use of different QC procedures results in different sets of genetic variants associated with life span. We selected 24 genetic variants negatively associated with life span. We showed that the joint analyses of genetic data at the time of bio-specimen collection and follow up data substantially improved significance of associations of selected 24 SNPs with life span. We also showed that aging related changes in physiological variables and in hidden biomarkers of aging differ for the groups of carriers and non-carriers of selected variants. CONCLUSIONS . The results of these analyses demonstrated benefits of using biodemographic models and methods in genetic association studies of these traits. Our findings showed that the absence of a large number of genetic variants with deleterious effects may make substantial contribution to exceptional longevity. These effects are dynamically mediated by a number of physiological variables and hidden biomarkers of aging. The results of these research demonstrated benefits of using integrative statistical models of mortality risks in genetic studies of human aging and longevity.
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Affiliation(s)
- Anatoliy I. Yashin
- Professor, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102E, Durham, NC 27705, USA. Tel.: (+1) 919-668-2713; Fax: (+1) 919-684-3861
| | - Konstantin G. Arbeev
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102F, Durham, NC 27705, USA. Tel.: (+1) 919-668-2707; Fax: (+1) 919-684-3861
| | - Deqing Wu
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A104, Durham, NC 27705, USA. Tel.: (+1) 919-684-6126; Fax: (+1) 919-684-3861
| | - Liubov Arbeeva
- Statistician, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102G, Durham, NC 27705, USA. Tel.: (+1) 919-613-0715; Fax: (+1) 919-684-3861
| | - Alexander Kulminski
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A106, Durham, NC 27705, USA. Tel.: (+1) 919-684-4962; Fax: (+1) 919-684-3861
| | - Irina Kulminskaya
- Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A102D, Durham, NC 27705, USA. Tel.: (+1) 919-681-8232; Fax: (+1) 919-684-3861
| | - Igor Akushevich
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A107, Durham, NC 27705, USA. Tel.: (+1) 919-668-2715; Fax: (+1) 919-684-3861
| | - Svetlana V. Ukraintseva
- Sr. Research Scientist, Center for Population Health and Aging, Duke University, 2024 W. Main Street, Room A105, Durham, NC 27705, USA. Tel.: (+1) 919-668-2712; Fax: (+1) 919-684-3861
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