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Munkhzul C, Yi SS, Kim J, Lee S, Kim H, Moon JS, Lee M. The microRNA-mediated gene regulatory network in the hippocampus and hypothalamus of the aging mouse. PLoS One 2023; 18:e0291943. [PMID: 37943864 PMCID: PMC10635555 DOI: 10.1371/journal.pone.0291943] [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: 05/15/2023] [Accepted: 09/09/2023] [Indexed: 11/12/2023] Open
Abstract
Aging leads to time-dependent functional decline of all major organs. In particular, the aging brain is prone to cognitive decline and several neurodegenerative diseases. Various studies have attempted to understand the aging process and underlying molecular mechanisms by monitoring changes in gene expression in the aging mouse brain using high-throughput sequencing techniques. However, the effect of microRNA (miRNA) on the post-transcriptional regulation of gene expression has not yet been comprehensively investigated. In this study, we performed global analysis of mRNA and miRNA expression simultaneously in the hypothalamus and hippocampus of young and aged mice. We identified aging-dependent differentially expressed genes, most of which were specific either to the hypothalamus or hippocampus. However, genes related to immune response-related pathways were enriched in upregulated differentially expressed genes, whereas genes related to metabolism-related pathways were enriched in downregulated differentially expressed genes in both regions of the aging brain. Furthermore, we identified many differentially expressed miRNAs, including three that were upregulated and three that were downregulated in both the hypothalamus and hippocampus. The two downregulated miRNAs, miR-322-3p, miR-542-3p, and the upregulated protein-encoding coding gene C4b form a regulatory network involved in complement and coagulation cascade pathways in the hypothalamus and hippocampus of the aging brain. These results advance our understanding of the miRNA-mediated gene regulatory network and its influence on signaling pathways in the hypothalamus and hippocampus of the aging mouse brain.
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Affiliation(s)
- Choijamts Munkhzul
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, Korea
| | - Sun Shin Yi
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Korea
| | - Junhyung Kim
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, Korea
| | - Seongsoo Lee
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju, Korea
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Korea
| | - Hyuntae Kim
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju, Korea
| | - Jong-Seok Moon
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, Korea
| | - Mihye Lee
- Soonchunhyang Institute of Medi-Bio Science, Soonchunhyang University, Cheonan, Korea
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, Korea
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2
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Madelaire CB, Klink AC, Israelsen WJ, Hindle AG. Fibroblasts as an experimental model system for the study of comparative physiology. Comp Biochem Physiol B Biochem Mol Biol 2022; 260:110735. [PMID: 35321853 DOI: 10.1016/j.cbpb.2022.110735] [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: 12/30/2021] [Revised: 03/15/2022] [Accepted: 03/17/2022] [Indexed: 10/18/2022]
Abstract
Mechanistic evaluations of processes that underlie organism-level physiology often require reductionist approaches. Dermal fibroblasts offer one such approach. These cells are easily obtained from minimally invasive skin biopsy, making them appropriate for the study of protected and/or logistically challenging species. Cell culture approaches permit extensive and fine-scale sampling regimes as well as gene manipulation techniques that are not feasible in vivo. Fibroblast isolation and culture protocols are outlined here for primary cells, and the benefits and drawbacks of immortalization are discussed. We show examples of physiological metrics that can be used to characterize primary cells (oxygen consumption, translation, proliferation) and readouts that can be informative in understanding cell-level responses to environmental stress (lactate production, heat shock protein induction). Importantly, fibroblasts may display fidelity to whole animal physiological phenotypes, facilitating their study. Fibroblasts from Antarctic Weddell seals show greater resilience to low temperatures and hypoxia exposure than fibroblasts from humans or rats. Fibroblast oxygen consumption rates are not affected by temperature stress in the heat-tolerant camel, whereas similar temperature exposures depress mitochondrial metabolism in fibroblasts from rhinoceros. Finally, dermal fibroblasts from a hibernator, the meadow jumping mouse, better resist experimental cooling than a fibroblast line from the laboratory mouse, with the hibernator demonstrating a greater maintenance of homeostatic processes such as protein translation. These results exemplify the parallels that can be drawn between fibroblast physiology and expectations in vivo, and provide evidence for the power of fibroblasts as a model system to understand comparative physiology and biomedicine.
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Affiliation(s)
- Carla B Madelaire
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - Amy C Klink
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA
| | - William J Israelsen
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA; Skroot Laboratory, Inc., Ames, IA, USA
| | - Allyson G Hindle
- School of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV, USA.
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3
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Otero-Albiol D, Carnero A. Cellular senescence or stemness: hypoxia flips the coin. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:243. [PMID: 34325734 PMCID: PMC8323321 DOI: 10.1186/s13046-021-02035-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/05/2021] [Indexed: 01/10/2023]
Abstract
Cellular senescence is a complex physiological state whose main feature is proliferative arrest. Cellular senescence can be considered the reverse of cell immortalization and continuous tumor growth. However, cellular senescence has many physiological functions beyond being a putative tumor suppressive trait. It remains unknown whether low levels of oxygen or hypoxia, which is a feature of every tissue in the organism, modulate cellular senescence, altering its capacity to suppress the limitation of proliferation. It has been observed that the lifespan of mammalian primary cells is increased under low oxygen conditions. Additionally, hypoxia promotes self-renewal and pluripotency maintenance in adult and embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and cancer stem cells (CSCs). In this study, we discuss the role of hypoxia facilitating senescence bypass during malignant transformation and acquisition of stemness properties, which all contribute to tumor development and cancer disease aggressiveness.
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Affiliation(s)
- Daniel Otero-Albiol
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Avda. Manuel Siurot s/n, 41013, Seville, Spain.,CIBER de CANCER, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla, IBIS, Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Avda. Manuel Siurot s/n, 41013, Seville, Spain. .,CIBER de CANCER, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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4
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Penninckx S, Pariset E, Acuna AU, Lucas S, Costes SV. Considering Cell Proliferation to Optimize Detection of Radiation-Induced 53BP1 Positive Foci in 15 Mouse Strains Ex Vivo. Radiat Res 2021; 195:47-59. [PMID: 33181852 DOI: 10.1667/rade-20-00165.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/05/2020] [Indexed: 11/03/2022]
Abstract
Due to high metabolic activity, proliferating cells continuously generate free radicals, which induce DNA double-strand breaks (DSB). Fluorescently tagged nuclear foci of DNA repair protein 53 binding protein-1 (53BP1) are used as a standard metric for measuring DSB formation at baseline and in response to environmental insults such as radiation. Here we demonstrate that the background level of spontaneous 53BP1+ foci formation can be modeled mathematically as a function of cell confluence, which is a metric of their proliferation rate. This model was validated using spontaneous 53BP1+ foci data from 72 cultures of primary skin fibroblasts derived from 15 different strains of mice, showing a ∼10-fold decrease from low to full confluence that is independent of mouse strain. On the other hand, the baseline level of spontaneous 53BP1+ foci in a fully confluent cell population was strain-dependent, suggesting genomic associations, and correlated with radiation sensitivity based on previous measurements in the same cell lines. Finally, we have developed an online open-access tool to correct for the effect of cell confluence on 53BP1+ foci-based quantification of DSB. This tool provides guidelines for the number of cells required to reach statistical significance for the detection of DSB induced by low doses of ionizing radiation as a function of confluence and time postirradiation.
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Affiliation(s)
- Sébastien Penninckx
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720.,Namur Research Institute for Life Science (NARILIS - LARN), University of Namur, 5000 Namur, Belgium
| | - Eloise Pariset
- Universities Space Research Association (USRA), Mountain View, California 94043.,Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035
| | - Ana Uriarte Acuna
- Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035.,Wyle Laboratories, KBR, Inc., Houston, Texas 77002
| | - Stephane Lucas
- Namur Research Institute for Life Science (NARILIS - LARN), University of Namur, 5000 Namur, Belgium
| | - Sylvain V Costes
- Space Biosciences Division, NASA Ames Research Center, Mountain View, California 94035
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5
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Connective tissue fibroblasts from highly regenerative mammals are refractory to ROS-induced cellular senescence. Nat Commun 2019; 10:4400. [PMID: 31562333 PMCID: PMC6764955 DOI: 10.1038/s41467-019-12398-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
A surveillance system in mammals constantly monitors cell activity to protect against aberrant proliferation in response to damage, injury and oncogenic stress. Here we isolate and culture connective tissue fibroblasts from highly regenerative mammals (Acomys and Oryctolagus) to determine how these cells interpret signals that normally induce cellular senescence in non-regenerating mammals (Mus and Rattus). While H2O2 exposure substantially decreases cell proliferation and increases p53, p21, p16, and p19 in cells from mice and rats, cells from spiny mice and rabbits are highly resistant to H2O2. Quantifying oxygen consumption and mitochondrial stability, we demonstrate that increased intracellular H2O2 is rapidly detoxified in regenerating species, but overwhelms antioxidant scavenging in cells from non-regenerative mammals. However, pretreatment with N-acetylcysteine (NAC) protects mouse and rat cells from ROS-induced cellular senescence. Collectively, our results show that intrinsic cellular differences in stress-sensing mechanisms partially explain interspecific variation in regenerative ability. In regenerative animals, how cells respond to injury signals inducing senescence is unclear. Here, the authors show that cells from highly regenerative mammals are resistant to ROS-induced cellular senescence, but non-regenerating species exhibit mitochondrial dysfunction/senescence in response to hydrogen peroxide exposure.
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You K, Parikh P, Khandalavala K, Wicher SA, Manlove L, Yang B, Roesler A, Roos BB, Teske JJ, Britt RD, Pabelick CM, Prakash YS. Moderate hyperoxia induces senescence in developing human lung fibroblasts. Am J Physiol Lung Cell Mol Physiol 2019; 317:L525-L536. [PMID: 31411059 DOI: 10.1152/ajplung.00067.2019] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hyperoxia exposure in premature infants increases the risk of subsequent lung diseases, such as asthma and bronchopulmonary dysplasia. Fibroblasts help maintain bronchial and alveolar integrity. Thus, understanding mechanisms by which hyperoxia influences fibroblasts is critical. Cellular senescence is increasingly recognized as important to the pathophysiology of multiple diseases. We hypothesized that clinically relevant moderate hyperoxia (<50% O2) induces senescence in developing fibroblasts. Using primary human fetal lung fibroblasts, we investigated effects of 40% O2 on senescence, endoplasmic reticulum (ER) stress, and autophagy pathways. Fibroblasts were exposed to 21% or 40% O2 for 7 days with etoposide as a positive control to induce senescence, evaluated by morphological changes, β-galactosidase activity, and DNA damage markers. Senescence-associated secretory phenotype (SASP) profile of inflammatory and profibrotic markers was further assessed. Hyperoxia decreased proliferation but increased cell size. SA-β-gal activity and DNA damage response, cell cycle arrest in G2/M phase, and marked upregulation of phosphorylated p53 and p21 were noted. Reduced autophagy was noted with hyperoxia. mRNA expression of proinflammatory and profibrotic factors (TNF-α, IL-1, IL-8, MMP3) was elevated by hyperoxia or etoposide. Hyperoxia increased several SASP factors (PAI-1, IL1-α, IL1-β, IL-6, LAP, TNF-α). The secretome of senescent fibroblasts promoted extracellular matrix formation by naïve fibroblasts. Overall, we demonstrate that moderate hyperoxia enhances senescence in primary human fetal lung fibroblasts with reduced autophagy but not enhanced ER stress. The resulting SASP is profibrotic and may contribute to abnormal repair in the lung following hyperoxia.
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Affiliation(s)
- Kai You
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China.,Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
| | - Pavan Parikh
- Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, Minnesota
| | - Karl Khandalavala
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China
| | - Sarah A Wicher
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China
| | - Logan Manlove
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China
| | - Binxia Yang
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China
| | - Annie Roesler
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China
| | - Ben B Roos
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China
| | - Jacob J Teske
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China
| | - Rodney D Britt
- Center for Perinatal Research, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Department of Pediatrics, The Ohio State University, Columbus, Ohio
| | - Christina M Pabelick
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China.,Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
| | - Y S Prakash
- Department of Neonatology, Shengjing Hospital of China Medical University, Shenyang City, China.,Department of Anesthesiology and Perioperative Medicine, Mayo Clinic, Rochester, Minnesota
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Taormina G, Ferrante F, Vieni S, Grassi N, Russo A, Mirisola MG. Longevity: Lesson from Model Organisms. Genes (Basel) 2019; 10:genes10070518. [PMID: 31324014 PMCID: PMC6678192 DOI: 10.3390/genes10070518] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/31/2022] Open
Abstract
Research on longevity and healthy aging promises to increase our lifespan and decrease the burden of degenerative diseases with important social and economic effects. Many aging theories have been proposed, and important aging pathways have been discovered. Model organisms have had a crucial role in this process because of their short lifespan, cheap maintenance, and manipulation possibilities. Yeasts, worms, fruit flies, or mammalian models such as mice, monkeys, and recently, dogs, have helped shed light on aging processes. Genes and molecular mechanisms that were found to be critical in simple eukaryotic cells and species have been confirmed in humans mainly by the functional analysis of mammalian orthologues. Here, we review conserved aging mechanisms discovered in different model systems that are implicated in human longevity as well and that could be the target of anti-aging interventions in human.
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Affiliation(s)
- Giusi Taormina
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Federica Ferrante
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Salvatore Vieni
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Nello Grassi
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Antonio Russo
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy
| | - Mario G Mirisola
- Dipartimento di Discipline Chirurgiche, Oncologiche e Stomatologiche, Università di Palermo, Via del Vespro 129, 90100 Palermo, Italy.
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Keeley TP, Mann GE. Defining Physiological Normoxia for Improved Translation of Cell Physiology to Animal Models and Humans. Physiol Rev 2019; 99:161-234. [PMID: 30354965 DOI: 10.1152/physrev.00041.2017] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The extensive oxygen gradient between the air we breathe (Po2 ~21 kPa) and its ultimate distribution within mitochondria (as low as ~0.5-1 kPa) is testament to the efforts expended in limiting its inherent toxicity. It has long been recognized that cell culture undertaken under room air conditions falls short of replicating this protection in vitro. Despite this, difficulty in accurately determining the appropriate O2 levels in which to culture cells, coupled with a lack of the technology to replicate and maintain a physiological O2 environment in vitro, has hindered addressing this issue thus far. In this review, we aim to address the current understanding of tissue Po2 distribution in vivo and summarize the attempts made to replicate these conditions in vitro. The state-of-the-art techniques employed to accurately determine O2 levels, as well as the issues associated with reproducing physiological O2 levels in vitro, are also critically reviewed. We aim to provide the framework for researchers to undertake cell culture under O2 levels relevant to specific tissues and organs. We envisage that this review will facilitate a paradigm shift, enabling translation of findings under physiological conditions in vitro to disease pathology and the design of novel therapeutics.
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Affiliation(s)
- Thomas P Keeley
- King's British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, Faculty of Life Sciences and Medicine, King's College London , London , United Kingdom
| | - Giovanni E Mann
- King's British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, Faculty of Life Sciences and Medicine, King's College London , London , United Kingdom
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Ke Z, Mallik P, Johnson AB, Luna F, Nevo E, Zhang ZD, Gladyshev VN, Seluanov A, Gorbunova V. Translation fidelity coevolves with longevity. Aging Cell 2017; 16:988-993. [PMID: 28707419 PMCID: PMC5595694 DOI: 10.1111/acel.12628] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 12/26/2022] Open
Abstract
Whether errors in protein synthesis play a role in aging has been a subject of intense debate. It has been suggested that rare mistakes in protein synthesis in young organisms may result in errors in the protein synthesis machinery, eventually leading to an increasing cascade of errors as organisms age. Studies that followed generally failed to identify a dramatic increase in translation errors with aging. However, whether translation fidelity plays a role in aging remained an open question. To address this issue, we examined the relationship between translation fidelity and maximum lifespan across 17 rodent species with diverse lifespans. To measure translation fidelity, we utilized sensitive luciferase‐based reporter constructs with mutations in an amino acid residue critical to luciferase activity, wherein misincorporation of amino acids at this mutated codon re‐activated the luciferase. The frequency of amino acid misincorporation at the first and second codon positions showed strong negative correlation with maximum lifespan. This correlation remained significant after phylogenetic correction, indicating that translation fidelity coevolves with longevity. These results give new life to the role of protein synthesis errors in aging: Although the error rate may not significantly change with age, the basal rate of translation errors is important in defining lifespan across mammals.
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Affiliation(s)
- Zhonghe Ke
- Department of Biology; University of Rochester; Rochester NY USA
| | - Pramit Mallik
- Department of Biology; University of Rochester; Rochester NY USA
| | - Adam B. Johnson
- Department of Biology; University of Rochester; Rochester NY USA
| | - Facundo Luna
- Instituto de Investigaciones Marinas y Costeras; CONICET-UNMdP; Mar del Plata Argentina
| | - Eviatar Nevo
- Institute of Evolution; University of Haifa; Haifa 3498838 Israel
| | - Zhengdong D. Zhang
- Department of Genetics; Albert Einstein College of Medicine; Bronx NY USA
| | - Vadim N. Gladyshev
- Division of Genetics; Department of Medicine, Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Andrei Seluanov
- Department of Biology; University of Rochester; Rochester NY USA
| | - Vera Gorbunova
- Department of Biology; University of Rochester; Rochester NY USA
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