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Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, Salfati EL, Blanchette M, Munding EM, Bhakta M, Chew YC, Guo W, Yang X, Maybury-Lewis S, Tian X, Ross JM, Coppotelli G, Meer MV, Rogers-Hammond R, Vera DL, Lu YR, Pippin JW, Creswell ML, Dou Z, Xu C, Mitchell SJ, Das A, O'Connell BL, Thakur S, Kane AE, Su Q, Mohri Y, Nishimura EK, Schaevitz L, Garg N, Balta AM, Rego MA, Gregory-Ksander M, Jakobs TC, Zhong L, Wakimoto H, El Andari J, Grimm D, Mostoslavsky R, Wagers AJ, Tsubota K, Bonasera SJ, Palmeira CM, Seidman JG, Seidman CE, Wolf NS, Kreiling JA, Sedivy JM, Murphy GF, Green RE, Garcia BA, Berger SL, Oberdoerffer P, Shankland SJ, Gladyshev VN, Ksander BR, Pfenning AR, Rajman LA, Sinclair DA. Loss of epigenetic information as a cause of mammalian aging. Cell 2024; 187:1312-1313. [PMID: 38428398 DOI: 10.1016/j.cell.2024.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
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2
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Petrashen AP, Verdesca AD, Kreiling JA, Sedivy JM. Regulation of the somatotropic axis by MYC-mediated miRNA repression. Front Cell Dev Biol 2023; 11:1269860. [PMID: 37908640 PMCID: PMC10615138 DOI: 10.3389/fcell.2023.1269860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
The transcription factor MYC is overexpressed in many human cancers and has a significant causal role in tumor incidence and progression. In contrast, Myc +/- heterozygous mice, which have decreased MYC expression, exhibit a 10-20% increase in lifespan and a decreased incidence or progression of several age-related diseases. Myc heterozygous mice were also reported to have decreased mTOR and IGF1 signaling, two pathways whose reduced activity is associated with longevity in diverse species. Given MYC's downstream role in these pathways, the downregulation of mTOR and IGF1 signaling in Myc heterozygotes suggests the presence of feedback loops within this regulatory network. In this communication we provide further evidence that the reduction of Myc expression in Myc +/- heterozygous mice provokes a female-specific decrease in circulating IGF1 as well as a reduction of IGF1 protein in the liver. In particular, reduced Myc expression led to upregulation of miRNAs that target the Igf1 transcript, thereby inhibiting its translation and leading to decreased IGF1 protein levels. Using Argonaute (AGO)-CLIP-sequencing we found enrichment of AGO binding in the Igf1 transcript at the target sites of let-7, miR-122, and miR-29 in female, but not male Myc heterozygotes. Upregulation of the liver-specific miR-122 in primary hepatocytes in culture and in vivo in mice resulted in significant downregulation of IGF1 protein, but not mRNA. Reduced levels of IGF1 increased GH production in the pituitary through a well-documented negative-feedback relationship. In line with this, we found that IGF1 levels in bone (where miR-122 is not expressed) were unchanged, consistent with the decreased incidence of osteoporosis in female Myc heterozygotes, despite decreased circulating IGF1.
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Affiliation(s)
| | | | | | - John M. Sedivy
- Center on the Biology of Aging, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, United States
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3
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McKerrow W, Kagermazova L, Doudican N, Frazzette N, Kaparos E, Evans SA, Rocha A, Sedivy JM, Neretti N, Carucci J, Boeke J, Fenyö D. LINE-1 retrotransposon expression in cancerous, epithelial and neuronal cells revealed by 5' single-cell RNA-Seq. Nucleic Acids Res 2023; 51:2033-2045. [PMID: 36744437 PMCID: PMC10018344 DOI: 10.1093/nar/gkad049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 02/07/2023] Open
Abstract
LINE-1 retrotransposons are sequences capable of copying themselves to new genomic loci via an RNA intermediate. New studies implicate LINE-1 in a range of diseases, especially in the context of aging, but without an accurate understanding of where and when LINE-1 is expressed, a full accounting of its role in health and disease is not possible. We therefore developed a method-5' scL1seq-that makes use of a widely available library preparation method (10x Genomics 5' single cell RNA-seq) to measure LINE-1 expression in tens of thousands of single cells. We recapitulated the known pattern of LINE-1 expression in tumors-present in cancer cells, absent from immune cells-and identified hitherto undescribed LINE-1 expression in human epithelial cells and mouse hippocampal neurons. In both cases, we saw a modest increase with age, supporting recent research connecting LINE-1 to age related diseases.
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Affiliation(s)
- Wilson McKerrow
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Larisa Kagermazova
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Nicole Doudican
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, NY, USA
| | - Nicholas Frazzette
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, NY, USA
| | - Efiyenia Ismini Kaparos
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Shane A Evans
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - Azucena Rocha
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
- Center on the Biology of Aging, Brown University, Providence, RI, USA
| | - Nicola Neretti
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, USA
| | - John Carucci
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn,NY11201, USA
| | - David Fenyö
- Institute for Systems Genetics, NYU Langone Health, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
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4
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Yang JH, Hayano M, Griffin PT, Amorim JA, Bonkowski MS, Apostolides JK, Salfati EL, Blanchette M, Munding EM, Bhakta M, Chew YC, Guo W, Yang X, Maybury-Lewis S, Tian X, Ross JM, Coppotelli G, Meer MV, Rogers-Hammond R, Vera DL, Lu YR, Pippin JW, Creswell ML, Dou Z, Xu C, Mitchell SJ, Das A, O'Connell BL, Thakur S, Kane AE, Su Q, Mohri Y, Nishimura EK, Schaevitz L, Garg N, Balta AM, Rego MA, Gregory-Ksander M, Jakobs TC, Zhong L, Wakimoto H, El Andari J, Grimm D, Mostoslavsky R, Wagers AJ, Tsubota K, Bonasera SJ, Palmeira CM, Seidman JG, Seidman CE, Wolf NS, Kreiling JA, Sedivy JM, Murphy GF, Green RE, Garcia BA, Berger SL, Oberdoerffer P, Shankland SJ, Gladyshev VN, Ksander BR, Pfenning AR, Rajman LA, Sinclair DA. Loss of epigenetic information as a cause of mammalian aging. Cell 2023; 186:305-326.e27. [PMID: 36638792 PMCID: PMC10166133 DOI: 10.1016/j.cell.2022.12.027] [Citation(s) in RCA: 156] [Impact Index Per Article: 156.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 08/09/2022] [Accepted: 12/15/2022] [Indexed: 01/13/2023]
Abstract
All living things experience an increase in entropy, manifested as a loss of genetic and epigenetic information. In yeast, epigenetic information is lost over time due to the relocalization of chromatin-modifying proteins to DNA breaks, causing cells to lose their identity, a hallmark of yeast aging. Using a system called "ICE" (inducible changes to the epigenome), we find that the act of faithful DNA repair advances aging at physiological, cognitive, and molecular levels, including erosion of the epigenetic landscape, cellular exdifferentiation, senescence, and advancement of the DNA methylation clock, which can be reversed by OSK-mediated rejuvenation. These data are consistent with the information theory of aging, which states that a loss of epigenetic information is a reversible cause of aging.
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Affiliation(s)
- Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA.
| | - Motoshi Hayano
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Ophthalmology, Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Patrick T Griffin
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - João A Amorim
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; IIIUC-Institute of Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
| | - Michael S Bonkowski
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - John K Apostolides
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Elias L Salfati
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | | | | | - Mital Bhakta
- Cantata/Dovetail Genomics, Scotts Valley, CA, USA
| | | | - Wei Guo
- Zymo Research Corporation, Irvine, CA, USA
| | | | - Sun Maybury-Lewis
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Xiao Tian
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Jaime M Ross
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Giuseppe Coppotelli
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Margarita V Meer
- Department of Medicine, Brigham and Women's Hospital, HMS, Boston, MA, USA
| | - Ryan Rogers-Hammond
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Daniel L Vera
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Yuancheng Ryan Lu
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Jeffrey W Pippin
- Division of Nephrology, University of Washington, Seattle, WA, USA
| | - Michael L Creswell
- Division of Nephrology, University of Washington, Seattle, WA, USA; Georgetown University School of Medicine, Washington, DC, USA
| | - Zhixun Dou
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Caiyue Xu
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Abhirup Das
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Pharmacology, UNSW, Sydney, NSW, Australia
| | | | - Sachin Thakur
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Alice E Kane
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Qiao Su
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Yasuaki Mohri
- Department of Stem Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Emi K Nishimura
- Department of Stem Cell Biology, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Neha Garg
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Ana-Maria Balta
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - Meghan A Rego
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | | | - Tatjana C Jakobs
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, HMS, Boston, MA, USA
| | - Lei Zhong
- The Massachusetts General Hospital Cancer Center, HMS, Boston, MA, USA
| | | | - Jihad El Andari
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, BioQuant, Heidelberg, Germany
| | - Dirk Grimm
- Department of Infectious Diseases/Virology, Section Viral Vector Technologies, Medical Faculty, University of Heidelberg, BioQuant, Heidelberg, Germany
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, HMS, Boston, MA, USA
| | - Amy J Wagers
- Paul F. Glenn Center for Biology of Aging Research, Harvard Stem Cell Institute, Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Joslin Diabetes Center, Boston, MA, USA
| | - Kazuo Tsubota
- Department of Ophthalmology, Department of Neuropsychiatry, Keio University School of Medicine, Tokyo, Japan
| | - Stephen J Bonasera
- Division of Geriatrics, University of Nebraska Medical Center, Durham Research Center II, Omaha, NE, USA
| | - Carlos M Palmeira
- Department of Life Sciences, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | | | | | - Norman S Wolf
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Jill A Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - George F Murphy
- Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Richard E Green
- Department of Biomolecular Engineering, UCSC, Santa Cruz, CA, USA
| | - Benjamin A Garcia
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shelley L Berger
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital, HMS, Boston, MA, USA
| | - Bruce R Ksander
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, HMS, Boston, MA, USA
| | - Andreas R Pfenning
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Luis A Rajman
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA
| | - David A Sinclair
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA.
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5
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Romero MA, Mumford PW, Roberson PA, Osburn SC, Young KC, Sedivy JM, Roberts MD. Translational Significance of the LINE-1 Jumping Gene in Skeletal Muscle. Exerc Sport Sci Rev 2022; 50:185-193. [PMID: 35749745 PMCID: PMC9651911 DOI: 10.1249/jes.0000000000000301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Retrotransposons are gene segments that proliferate in the genome, and the Long INterspersed Element 1 (LINE-1 or L1) retrotransposon is active in humans. Although older mammals show enhanced skeletal muscle L1 expression, exercise generally reverses this trend. We hypothesize skeletal muscle L1 expression influences muscle physiology, and additional innovative investigations are needed to confirm this hypothesis.
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Affiliation(s)
- Matthew A. Romero
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California USA
| | - Petey W. Mumford
- Department of Exercise Science, Lindenwood University, St. Charles, Missouri USA
| | - Paul A. Roberson
- Department of Cellular and Molecular Physiology, College of Medicine, The Pennsylvania State University, Hershey, Pennsylvania USA
| | | | - Kaelin C. Young
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center on the Biology of Aging, Brown University, Providence, Rhode Island, USA
| | - Michael D. Roberts
- School of Kinesiology, Auburn University, Auburn, Alabama USA
- Department of Cell Biology and Physiology, Edward Via College of Osteopathic Medicine-Auburn, Auburn, Alabama, USA
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6
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Zhang S, Huntington KE, Kun B, Zhou L, Kreiling J, Sedivy JM, El-Deiry WS. Abstract 5297: ONC201 suppresses cancer cell growth in a reconstructed tumor microenvironment that includes chemotherapy-induced senescent fibroblasts. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-5297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cellular senescence and its associated secretory phenotype (SASP) can promote cancer progression in the tumor microenvironment (TME). The TME includes tumor cells, stromal cells, immune cells, endothelial cells, and extracellular matrix. Senescent cancer-associated fibroblasts (CAF) may contribute to tumor growth and therapy resistance. Targeting senescent CAF by means of removal, modulation of the SASP, or through cellular reprogramming might provide therapeutic avenues for treating cancer. We investigated the impact of chemotherapy-induced fibroblast senescence in the TME on tumor growth and response to cancer therapy. Expression of cytokines in chemo-induced senescent fibroblasts and cancer cells was assessed by bulk and single cell cytokine profiling. As expected, there were alterations in SASP factors with increased pro-tumorigenic immune factors and decreased anti-tumor cytokines during IMR90 etoposide-induced fibroblast senescence. We co-cultured luciferase-labeled HT29 cancer cells with senescent IMR90 and found that the senescent fibroblasts promoted HT29 cell growth in culture and accelerated xenograft tumor formation in mice. We next inhibited cellular senescence and its SASP with the senolytic drug ABT263 or the senostatic/senomorphic drug lamivudine (3TC). Both ABT263 and 3TC significantly reduced bioluminescence of HT29-Luc cells co-cultured with senescent IMR90 compared to non-treated IMR90 cells. Therapy-induced senescence confers 5-Fluorouracil (5-FU) resistance in colorectal cancer. We found that 5-FU treatment significantly reduced colony formation of HT29 cells in the presence of proliferating or senescent IMR90 cells, with a lesser reduction in the presence of the senescent IMR90 cells. This suggests that a microenvironment that includes senescent cells promotes tumor cell resistance to 5-FU. We hypothesize that SASP factors might confer cancer cell resistance to 5-FU treatment. Cytokine profiling showed that TRAIL expression is reduced in senescent cells. Treatment with the TRAIL-inducer ONC201 reduced colony formation and cell viability of HT29 cells co-cultured with senescent IMR90 fibroblasts. Single-cell cytokine profiling showed subpopulations of cancer cells with increased polyfunctionality strength index (PSI, secretion of more than 2 dominant types of cytokines per cell in a population). Combined treatment with ABT263 and ONC201 synergically reduced viability HT29 cells co-cultured with senescent IMR90, and this correlated with reduced PSI. Our results indicate that TME targeting by increasing antitumor cytokines in conjunction with senolytic therapies can inhibit tumor growth. We are continuing to unravel the cytokine landscape of chemotherapy-induced cell senescence to gain insights into therapeutic strategies targeting chemotherapy-induced TME-senescence and drug resistance.
Citation Format: Shengliang Zhang, Kelsey E. Huntington, Bianca Kun, Lanlan Zhou, Jill Kreiling, John M. Sedivy, Wafik S. El-Deiry. ONC201 suppresses cancer cell growth in a reconstructed tumor microenvironment that includes chemotherapy-induced senescent fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5297.
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7
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Taylor JR, Wood JG, Mizerak E, Hinthorn S, Liu J, Finn M, Gordon S, Zingas L, Chang C, Klein MA, Denu JM, Gorbunova V, Seluanov A, Boeke JD, Sedivy JM, Helfand SL. Sirt6 regulates lifespan in Drosophila melanogaster. Proc Natl Acad Sci U S A 2022; 119:e2111176119. [PMID: 35091469 PMCID: PMC8812521 DOI: 10.1073/pnas.2111176119] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/01/2021] [Indexed: 01/13/2023] Open
Abstract
Sirt6 is a multifunctional enzyme that regulates diverse cellular processes such as metabolism, DNA repair, and aging. Overexpressing Sirt6 extends lifespan in mice, but the underlying cellular mechanisms are unclear. Drosophila melanogaster are an excellent model to study genetic regulation of lifespan; however, despite extensive study in mammals, very little is known about Sirt6 function in flies. Here, we characterized the Drosophila ortholog of Sirt6, dSirt6, and examined its role in regulating longevity; dSirt6 is a nuclear and chromatin-associated protein with NAD+-dependent histone deacetylase activity. dSirt6 overexpression (OE) in flies produces robust lifespan extension in both sexes, while reducing dSirt6 levels shortens lifespan. dSirt6 OE flies have normal food consumption and fertility but increased resistance to oxidative stress and reduced protein synthesis rates. Transcriptomic analyses reveal that dSirt6 OE reduces expression of genes involved in ribosome biogenesis, including many dMyc target genes. dSirt6 OE partially rescues many effects of dMyc OE, including increased nuclear size, up-regulation of ribosome biogenesis genes, and lifespan shortening. Last, dMyc haploinsufficiency does not convey additional lifespan extension to dSirt6 OE flies, suggesting dSirt6 OE is upstream of dMyc in regulating lifespan. Our results provide insight into the mechanisms by which Sirt6 OE leads to longer lifespan.
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Affiliation(s)
- Jackson R Taylor
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Jason G Wood
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Evan Mizerak
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Samuel Hinthorn
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Julianna Liu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Matthew Finn
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Sarah Gordon
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Louis Zingas
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Chengyi Chang
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Mark A Klein
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726
| | - John M Denu
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53726
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627
- Department of Medicine, University of Rochester, Rochester, NY 14627
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627
- Department of Medicine, University of Rochester, Rochester, NY 14627
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016
- Department of Biomedical Engineering, Tandon School of Engineering, Brooklyn, NY 11201
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912
| | - Stephen L Helfand
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912;
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8
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Gorbunova V, Seluanov A, Mita P, McKerrow W, Fenyö D, Boeke JD, Linker SB, Gage FH, Kreiling JA, Petrashen AP, Woodham TA, Taylor JR, Helfand SL, Sedivy JM. The role of retrotransposable elements in ageing and age-associated diseases. Nature 2021; 596:43-53. [PMID: 34349292 PMCID: PMC8600649 DOI: 10.1038/s41586-021-03542-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023]
Abstract
The genomes of virtually all organisms contain repetitive sequences that are generated by the activity of transposable elements (transposons). Transposons are mobile genetic elements that can move from one genomic location to another; in this process, they amplify and increase their presence in genomes, sometimes to very high copy numbers. In this Review we discuss new evidence and ideas that the activity of retrotransposons, a major subgroup of transposons overall, influences and even promotes the process of ageing and age-related diseases in complex metazoan organisms, including humans. Retrotransposons have been coevolving with their host genomes since the dawn of life. This relationship has been largely competitive, and transposons have earned epithets such as 'junk DNA' and 'molecular parasites'. Much of our knowledge of the evolution of retrotransposons reflects their activity in the germline and is evident from genome sequence data. Recent research has provided a wealth of information on the activity of retrotransposons in somatic tissues during an individual lifespan, the molecular mechanisms that underlie this activity, and the manner in which these processes intersect with our own physiology, health and well-being.
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Affiliation(s)
- Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, New York 14627, USA
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, New York 14627, USA
| | - Paolo Mita
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA
| | - David Fenyö
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA.,Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn 11201, NY, USA
| | - Sara B. Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jill A. Kreiling
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Anna P. Petrashen
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Trenton A. Woodham
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Jackson R. Taylor
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Stephen L. Helfand
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - John M. Sedivy
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.,Corresponding author
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9
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Newton JC, Naik MT, Li GY, Murphy EL, Fawzi NL, Sedivy JM, Jogl G. Phase separation of the LINE-1 ORF1 protein is mediated by the N-terminus and coiled-coil domain. Biophys J 2021; 120:2181-2191. [PMID: 33798566 DOI: 10.1016/j.bpj.2021.03.028] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 02/24/2021] [Accepted: 03/23/2021] [Indexed: 10/21/2022] Open
Abstract
Long interspersed nuclear element-1 (L1) is a retrotransposable element that autonomously replicates in the human genome, resulting in DNA damage and genomic instability. Activation of L1 in senescent cells triggers a type I interferon response and age-associated inflammation. Two open reading frames encode an ORF1 protein functioning as messenger RNA chaperone and an ORF2 protein providing catalytic activities necessary for retrotransposition. No function has been identified for the conserved, disordered N-terminal region of ORF1. Using microscopy and NMR spectroscopy, we demonstrate that ORF1 forms liquid droplets in vitro in a salt-dependent manner and that interactions between its N-terminal region and coiled-coil domain are necessary for phase separation. Mutations disrupting blocks of charged residues within the N-terminus impair phase separation, whereas some mutations within the coiled-coil domain enhance phase separation. Demixing of the L1 particle from the cytosol may provide a mechanism to protect the L1 transcript from degradation.
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Affiliation(s)
- Jocelyn C Newton
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Mandar T Naik
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island
| | - Grace Y Li
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Eileen L Murphy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Nicolas L Fawzi
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
| | - Gerwald Jogl
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.
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10
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Chini CCS, Peclat TR, Warner GM, Kashyap S, Espindola-Netto JM, de Oliveira GC, Gomez LS, Hogan KA, Tarragó MG, Puranik AS, Agorrody G, Thompson KL, Dang K, Clarke S, Childs BG, Kanamori KS, Witte MA, Vidal P, Kirkland AL, De Cecco M, Chellappa K, McReynolds MR, Jankowski C, Tchkonia T, Kirkland JL, Sedivy JM, van Deursen JM, Baker DJ, van Schooten W, Rabinowitz JD, Baur JA, Chini EN. CD38 ecto-enzyme in immune cells is induced during aging and regulates NAD + and NMN levels. Nat Metab 2020; 2:1284-1304. [PMID: 33199925 PMCID: PMC8752031 DOI: 10.1038/s42255-020-00298-z] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/10/2020] [Indexed: 11/14/2022]
Abstract
Decreased NAD+ levels have been shown to contribute to metabolic dysfunction during aging. NAD+ decline can be partially prevented by knockout of the enzyme CD38. However, it is not known how CD38 is regulated during aging, and how its ecto-enzymatic activity impacts NAD+ homeostasis. Here we show that an increase in CD38 in white adipose tissue (WAT) and the liver during aging is mediated by accumulation of CD38+ immune cells. Inflammation increases CD38 and decreases NAD+. In addition, senescent cells and their secreted signals promote accumulation of CD38+ cells in WAT, and ablation of senescent cells or their secretory phenotype decreases CD38, partially reversing NAD+ decline. Finally, blocking the ecto-enzymatic activity of CD38 can increase NAD+ through a nicotinamide mononucleotide (NMN)-dependent process. Our findings demonstrate that senescence-induced inflammation promotes accumulation of CD38 in immune cells that, through its ecto-enzymatic activity, decreases levels of NMN and NAD+.
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Affiliation(s)
- Claudia C S Chini
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Thais R Peclat
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Gina M Warner
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Sonu Kashyap
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Jair Machado Espindola-Netto
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Guilherme C de Oliveira
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Lilian S Gomez
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Kelly A Hogan
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Mariana G Tarragó
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Amrutesh S Puranik
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
- Division of Rheumatology, Department of Medicine, NYU Langone Health, New York, NY, USA
| | - Guillermo Agorrody
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Katie L Thompson
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | | | | | - Bennett G Childs
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Karina S Kanamori
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Micaela A Witte
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Paola Vidal
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Anna L Kirkland
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Marco De Cecco
- Center on the Biology of Aging and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
- Astellas Institute for Regenerative Medicine, Marlborough, MA, USA
| | - Karthikeyani Chellappa
- Department of Physiology and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Melanie R McReynolds
- Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Connor Jankowski
- Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Tamara Tchkonia
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - James L Kirkland
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - John M Sedivy
- Center on the Biology of Aging and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Jan M van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Darren J Baker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Joseph A Baur
- Department of Physiology and Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Eduardo N Chini
- Signal Transduction and Molecular Nutrition Laboratory, Kogod Aging Center, Department of Anesthesiology and Perioperative Medicine, Mayo Clinic College of Medicine, Rochester, MN, USA.
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11
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Sedivy JM. Glutamine Transporter as a Target of mTOR Signaling Modulating Longevity. FASEB J 2020. [DOI: 10.1096/fasebj.2020.34.s1.00209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Ito T, Teo YV, Evans SA, Neretti N, Sedivy JM. Regulation of Cellular Senescence by Polycomb Chromatin Modifiers through Distinct DNA Damage- and Histone Methylation-Dependent Pathways. Cell Rep 2019; 22:3480-3492. [PMID: 29590617 PMCID: PMC5915310 DOI: 10.1016/j.celrep.2018.03.002] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 01/09/2018] [Accepted: 02/28/2018] [Indexed: 01/07/2023] Open
Abstract
Polycomb group (PcG) factors maintain facultative heterochromatin and mediate many important developmental and differentiation processes. EZH2, a PcG histone H3 lysine-27 methyltransferase, is repressed in senescent cells. We show here that downregulation of EZH2 promotes senescence through two distinct mechanisms. First, depletion of EZH2 in proliferating cells rapidly initiates a DNA damage response prior to a reduction in the levels of H3K27me3 marks. Second, the eventual loss of H3K27me3 induces p16 (CDKN2A) gene expression independent of DNA damage and potently activates genes of the senescence-associated secretory phenotype (SASP). The progressive depletion of H3K27me3 marks can be viewed as a molecular "timer" to provide a window during which cells can repair DNA damage. EZH2 is regulated transcriptionally by WNT and MYC signaling and posttranslationally by DNA damage-triggered protein turnover. These mechanisms provide insights into the processes that generate senescent cells during aging.
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Affiliation(s)
- Takahiro Ito
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Yee Voan Teo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Shane A Evans
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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13
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Murphy KR, Baggett B, Cooper LL, Lu Y, O-Uchi J, Sedivy JM, Terentyev D, Koren G. Enhancing Autophagy Diminishes Aberrant Ca 2+ Homeostasis and Arrhythmogenesis in Aging Rabbit Hearts. Front Physiol 2019; 10:1277. [PMID: 31636573 PMCID: PMC6787934 DOI: 10.3389/fphys.2019.01277] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
Aim Aging in humans is associated with a 10–40-fold greater incidence of sudden cardiac death from malignant tachyarrhythmia. We have reported that thiol oxidation of ryanodine receptors (RyR2s) by mitochondria-derived reactive oxygen species (mito-ROS) contributes to defective Ca2+ homeostasis in cardiomyocytes (CMs) from aging rabbit hearts. However, mechanisms responsible for the increase in mito-ROS in the aging heart remain poorly understood. Here we test the hypothesis that age-associated decrease in autophagy is a major contributor to enhanced mito-ROS production and thereby pro-arrhythmic disturbances in Ca2+ homeostasis. Methods and Results Ventricular tissues from aged rabbits displayed significant downregulation of proteins involved in mitochondrial autophagy compared with tissues from young controls. Blocking autophagy with chloroquine increased total ROS production in primary rabbit CMs and mito-ROS production in HL-1 CMs. Furthermore, chloroquine treatment of HL-1 cells depolarized mitochondrial membrane potential (Δψm) to 50% that of controls. Blocking autophagy significantly increased oxidation of RyR2, resulting in enhanced propensity to pro-arrhythmic spontaneous Ca2+ release under β-adrenergic stimulation. Aberrant Ca2+ release was abolished by treatment with the mito-ROS scavenger mito-TEMPO. Importantly, the autophagy enhancer Torin1 and ATG7 overexpression reduced the rate of mito-ROS production and restored both Δψm and defective Ca2+ handling in CMs derived from aged rabbit hearts. Conclusion Decreased autophagy is a major cause of increased mito-ROS production in the aging heart. Our data suggest that promoting autophagy may reduce pathologic mito-ROS during normal aging and reduce pro-arrhythmic spontaneous Ca2+ release via oxidized RyR2s.
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Affiliation(s)
- Kevin R Murphy
- Cardiovascular Research Center at the Cardiovascular Institute, Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, RI, United States.,Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Brett Baggett
- Cardiovascular Research Center at the Cardiovascular Institute, Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, RI, United States.,Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Leroy L Cooper
- Cardiovascular Research Center at the Cardiovascular Institute, Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, RI, United States.,Department of Biology, Vassar College, Poughkeepsie, NY, United States
| | - Yichun Lu
- Cardiovascular Research Center at the Cardiovascular Institute, Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Jin O-Uchi
- Cardiovascular Research Center at the Cardiovascular Institute, Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - John M Sedivy
- Department of Molecular Biology, Cellular Biology and Biochemistry, Brown University, Providence, RI, United States
| | - Dmitry Terentyev
- Cardiovascular Research Center at the Cardiovascular Institute, Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, RI, United States
| | - Gideon Koren
- Cardiovascular Research Center at the Cardiovascular Institute, Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, RI, United States
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14
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De Cecco M, Ito T, Petrashen AP, Elias AE, Skvir NJ, Criscione SW, Caligiana A, Brocculi G, Adney EM, Boeke JD, Le O, Beauséjour C, Ambati J, Ambati K, Simon M, Seluanov A, Gorbunova V, Slagboom PE, Helfand SL, Neretti N, Sedivy JM. Author Correction: L1 drives IFN in senescent cells and promotes age-associated inflammation. Nature 2019; 572:E5. [PMID: 31296937 DOI: 10.1038/s41586-019-1350-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An Amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Takahiro Ito
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Anna P Petrashen
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Amy E Elias
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Nicholas J Skvir
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Steven W Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Alberto Caligiana
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Greta Brocculi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Emily M Adney
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Oanh Le
- Centre de Recherche CHU Ste-Justine, and Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada
| | - Christian Beauséjour
- Centre de Recherche CHU Ste-Justine, and Department of Pharmacology and Physiology, Université de Montréal, Montréal, Québec, Canada
| | - Jayakrishna Ambati
- Center for Advanced Vision Science and Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kameshwari Ambati
- Center for Advanced Vision Science and Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Stephen L Helfand
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA.
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15
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Zhao X, Petrashen AP, Sanders JA, Peterson AL, Sedivy JM. SLC1A5 glutamine transporter is a target of MYC and mediates reduced mTORC1 signaling and increased fatty acid oxidation in long-lived Myc hypomorphic mice. Aging Cell 2019; 18:e12947. [PMID: 30909319 PMCID: PMC6516164 DOI: 10.1111/acel.12947] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/11/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
Mice that express reduced levels of the c‐Myc gene (Myc+/− heterozygotes) are long‐lived. Myc hypomorphic mice display reduced rates of protein translation and decreased activity of the mammalian target of rapamycin (mTOR) complex 1 (mTORC1). Given the prominent effect of mTOR on aging, lower mTORC1 activity could contribute to the exceptional longevity and enhanced healthspan of Myc+/− animals. However, given the downstream position of MYC in these signaling cascades, the mechanism through which mTORC1 activity is downregulated in Myc+/− mice is not understood. We report that the high‐affinity glutamine transporter SLC1A5, which is critical for activation of mTORC1 activity by amino acids, is a transcriptional target of MYC. Myc+/− cells display decreased Slc1a5 gene expression that leads to lower glutamine uptake and consequently reduced mTORC1 activity. Decreased mTORC1 activity in turn mediates an elevation of fatty acid oxidation (FAO) by indirectly upregulating the expression of carnitine palmitoyltransferase 1a (Cpt1a) that mediates the rate‐limiting step of β‐oxidation. Increased FAO has been noted in a number of long‐lived mouse models. Taken together, our results show that transcriptional feedback loops regulated by MYC modulate upstream signaling pathways such as mTOR and impact FAO on an organismal level.
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Affiliation(s)
- Xiaoai Zhao
- Department of Molecular Biology, Cell Biology and Biochemistry, and Center on the Biology of Aging Brown University Providence Rhode Island
| | - Anna P. Petrashen
- Department of Molecular Biology, Cell Biology and Biochemistry, and Center on the Biology of Aging Brown University Providence Rhode Island
| | - Jennifer A. Sanders
- Department of Pediatrics Rhode Island Hospital and Brown University Providence Rhode Island
| | - Abigail L. Peterson
- Department of Molecular Biology, Cell Biology and Biochemistry, and Center on the Biology of Aging Brown University Providence Rhode Island
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, and Center on the Biology of Aging Brown University Providence Rhode Island
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16
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Simon M, Van Meter M, Ablaeva J, Ke Z, Gonzalez RS, Taguchi T, De Cecco M, Leonova KI, Kogan V, Helfand SL, Neretti N, Roichman A, Cohen HY, Meer MV, Gladyshev VN, Antoch MP, Gudkov AV, Sedivy JM, Seluanov A, Gorbunova V. LINE1 Derepression in Aged Wild-Type and SIRT6-Deficient Mice Drives Inflammation. Cell Metab 2019; 29:871-885.e5. [PMID: 30853213 PMCID: PMC6449196 DOI: 10.1016/j.cmet.2019.02.014] [Citation(s) in RCA: 247] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 11/02/2018] [Accepted: 02/22/2019] [Indexed: 01/07/2023]
Abstract
Mice deficient for SIRT6 exhibit a severely shortened lifespan, growth retardation, and highly elevated LINE1 (L1) activity. Here we report that SIRT6-deficient cells and tissues accumulate abundant cytoplasmic L1 cDNA, which triggers strong type I interferon response via activation of cGAS. Remarkably, nucleoside reverse-transcriptase inhibitors (NRTIs), which inhibit L1 retrotransposition, significantly improved health and lifespan of SIRT6 knockout mice and completely rescued type I interferon response. In tissue culture, inhibition of L1 with siRNA or NRTIs abrogated type I interferon response, in addition to a significant reduction of DNA damage markers. These results indicate that L1 activation contributes to the pathologies of SIRT6 knockout mice. Similarly, L1 transcription, cytoplasmic cDNA copy number, and type I interferons were elevated in the wild-type aged mice. As sterile inflammation is a hallmark of aging, we propose that modulating L1 activity may be an important strategy for attenuating age-related pathologies.
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Affiliation(s)
- Matthew Simon
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Michael Van Meter
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Julia Ablaeva
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Zhonghe Ke
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Raul S Gonzalez
- Department of Pathology, University of Rochester Medical Center, Rochester, NY 14627, USA
| | - Taketo Taguchi
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Marco De Cecco
- Institute for Translational Research, Ariel University, Ariel, Israel
| | - Katerina I Leonova
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Valeria Kogan
- Institute for Translational Research, Ariel University, Ariel, Israel
| | - Stephen L Helfand
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Asael Roichman
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Haim Y Cohen
- Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Margarita V Meer
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Marina P Antoch
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Andrei V Gudkov
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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17
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Newton JC, Jogl G, Sedivy JM. Determining the mechanism of LINE-1 ribonucleoprotein particle assembly and inhibition by nucleoside reverse transcriptase inhibitors. Acta Crystallogr A Found Adv 2018. [DOI: 10.1107/s0108767318097799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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18
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Bacalini MG, Deelen J, Pirazzini C, De Cecco M, Giuliani C, Lanzarini C, Ravaioli F, Marasco E, van Heemst D, Suchiman HED, Slieker R, Giampieri E, Recchioni R, Marcheselli F, Salvioli S, Vitale G, Olivieri F, Spijkerman AMW, Dollé MET, Sedivy JM, Castellani G, Franceschi C, Slagboom PE, Garagnani P. Systemic Age-Associated DNA Hypermethylation of ELOVL2 Gene: In Vivo and In Vitro Evidences of a Cell Replication Process. J Gerontol A Biol Sci Med Sci 2017; 72:1015-1023. [PMID: 27672102 DOI: 10.1093/gerona/glw185] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 08/26/2016] [Indexed: 12/17/2022] Open
Abstract
Epigenetic remodeling is one of the major features of the aging process. We recently demonstrated that DNA methylation of ELOVL2 and FHL2 CpG islands is highly correlated with age in whole blood. Here we investigated several aspects of age-associated hypermethylation of ELOVL2 and FHL2. We showed that ELOVL2 methylation is significantly different in primary dermal fibroblast cultures from donors of different ages. Using epigenomic data from public resources, we demonstrated that most of the tissues show ELOVL2 and FHL2 hypermethylation with age. Interestingly, ELOVL2 hypermethylation was not found in tissues with very low replication rate. We demonstrated that ELOVL2 hypermethylation is associated with in vitro cell replication rather than with senescence. We confirmed intra-individual hypermethylation of ELOVL2 and FHL2 in longitudinally assessed participants from the Doetinchem Cohort Study. Finally we showed that, although the methylation of the two loci is not associated with longevity/mortality in the Leiden Longevity Study, ELOVL2 methylation is associated with cytomegalovirus status in nonagenarians, which could be informative of a higher number of replication events in a fraction of whole-blood cells. Collectively, these results indicate that ELOVL2 methylation is a marker of cell divisions occurring during human aging.
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Affiliation(s)
- Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy.,Personal Genomics S.r.l., Verona, Italy
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands.,Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Catia Lanzarini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | | | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine
| | - Diana van Heemst
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - H Eka D Suchiman
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Roderick Slieker
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Enrico Giampieri
- Department of Physics and Astronomy, University of Bologna, Italy
| | - Rina Recchioni
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Fiorella Marcheselli
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Giovanni Vitale
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Italy
| | - Fabiola Olivieri
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy.,IRCCS Institute of Neurological Sciences, Bologna, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
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19
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Waaijer MEC, Croco E, Westendorp RGJ, Slagboom PE, Sedivy JM, Lorenzini A, Maier AB. DNA damage markers in dermal fibroblasts in vitro reflect chronological donor age. Aging (Albany NY) 2016; 8:147-57. [PMID: 26830451 PMCID: PMC4761719 DOI: 10.18632/aging.100890] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The aging process is accompanied by an accumulation of cellular damage, which compromises the viability and function of cells and tissues. We aim to further explore the association between in vitro DNA damage markers and the chronological age of the donor, as well as long-lived family membership and presence of cardiovascular diseases. Therefore, numbers of 53BP1 foci, telomere-associated foci (TAF) and micronuclei were measured in cultured dermal fibroblasts obtained from three age groups of donors (mean age 22, 63 and 90 years). Fibroblasts were cultured without a stressor and with 0.6 μM rotenone for 3 days. We found that 53BP1 foci and TAF were more frequently present in fibroblasts of old donors compared to middle-aged and young donors. No association between micronuclei and donor age was found. Within the fibroblasts of the middle-aged donors we did not find associations between DNA damage markers and long-lived family membership or cardiovascular disease. Results were comparable when fibroblasts were stressed in vitro with rotenone. In conclusion, we found that DNA damage foci of cultured fibroblasts are significantly associated with the chronological age, but not biological age, of the donor.
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Affiliation(s)
- Mariëtte E C Waaijer
- Department of Gerontology and Geriatrics, Leiden University Medical Center, 2300 RC Leiden, the Netherlands
| | - Eleonora Croco
- Department for Life Quality Studies, University of Bologna, 40126 Bologna, Italy
| | - Rudi G J Westendorp
- Department of Public Health and Center for Healthy Aging, Faculty of Health and Medical Sciences, University of Copenhagen, 1123 Copenhagen, Denmark
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.,Netherlands Consortium for Healthy Aging, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
| | - Antonello Lorenzini
- Department of Biomedical and Neuromotor Sciences, University of Bologna, 40126 Bologna, Italy
| | - Andrea B Maier
- Department of Internal Medicine, Section of Gerontology and Geriatrics, VU University Medical Center, 1007 MB Amsterdam, The Netherlands.,Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Parkville VIC 3050, Australia
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20
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Kumari A, Iwasaki T, Folk WP, Abdulovic-Cui AL, Pyndiah S, Prendergast GC, Sedivy JM, Sakamuro D. Abstract PR09: c-MYC preserves genomic integrity during DNA replication: a paradigm shift of c-MYC. Mol Cancer Res 2016. [DOI: 10.1158/1557-3125.cellcycle16-pr09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
During DNA synthesis, single-stranded DNA breaks (SSBs) are easily produced by mitogenic and oxidative stresses. Although SSBs are naturally converted to double-stranded DNA breaks (DSBs) at the collapse of replication forks, the integrity of chromosomal DNA is regularly maintained during DNA synthesis. Because DNA replication is a fundamental biological process involved in homeostasis, we hypothesized that an S-phase-associated guardian of the genome constantly stimulates cellular DSB repair machinery during DNA replication. The p53 tumor suppressor is known to act as the guardian of the genome. However, in response to DSBs, p53 not only activates G1 arrest, but also represses RAD51, a key component of homologous recombination (HR), an error-free DSB repair mechanism. Moreover, p53 is regularly dormant in actively growing cells. Thus, p53 cannot be the S-phase-associated DNA-repair enhancer.
In this study, we show that the c-MYC transcription factor, which promotes DNA replication, concomitantly stimulates ataxia telangiectasia mutated kinase (ATM), γH2AX formation, and DSB repair by repressing BIN1. As an E2F1 corepressor, BIN1 suppressed the human ATM promoter, whereas via protein-protein interaction, BIN1 negatively regulated ATM auto-phosphorylation at serine 1981, a critical step for ATM activation. Accordingly, even before DSBs were formed, impaired BIN1 was sufficient to enhance ATM-dependent phosphorylation of histone H2AX at serine 139 (forming γH2AX), which has been widely used as a biomarker of DSBs. Reduced BIN1-dependent γH2AX foci formation was accompanied by the phosphorylation of MDC1 (mediator of DNA damage checkpoint protein 1) and 53BP1 foci. Furthermore, loss of BIN1 substantially accelerated cellular DSB-repair activity, which was reversed by the depletion of BRCA2, a critical player of HR. Intriguingly, activated c-MYC recruited the chromatin-remodeling factor BRG1 to and transcriptionally repressed the BIN1 promoter, thus indirectly liberating ATM expression. Because c-MYC robustly increases γH2AX foci, the oncoprotein has been thought to induce real DSBs. However, c-MYC silencing did not diminish γH2AX foci in the absence of BIN1, suggesting that c-MYC-induced γH2AX foci formation is chiefly attributable to c-MYC-induced decrease in BIN1 and following ATM reactivation in a manner independent of DSBs. Our study identifies c-MYC-associated γH2AX as a novel warning beacon of imminent DSBs and establishes a new paradigm for c-MYC in facilitating DSB-repair signaling during DNA replication.
This abstract is also being presented as Poster B20.
Citation Format: Alpana Kumari, Tetsushi Iwasaki, Walson P. Folk, Amy L. Abdulovic-Cui, Slovénie Pyndiah, George C. Prendergast, John M. Sedivy, Daitoku Sakamuro. c-MYC preserves genomic integrity during DNA replication: a paradigm shift of c-MYC. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Cancer Cell Cycle - Tumor Progression and Therapeutic Response; Feb 28-Mar 2, 2016; Orlando, FL. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(11_Suppl):Abstract nr PR09.
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Abstract
Free circulating or cell‐free DNA (cfDNA), possibly from dying cells that release their contents into the blood as they break down, have become of major interest as a source for noninvasive diagnostics. Recent work demonstrated the uptake of human cfDNA in mouse cells in vitro and in vivo, accompanied by the activation of a cellular DNA damage response (DDR) and the appearance of apoptotic proteins in the host cells. By acting as a source of mobile genetic elements, cfDNA could be a continuous source of DNA mutagenesis of healthy cells in the body throughout life, promoting progressive cellular aging in vivo. As such, cfDNA may causally contribute to multiple aging‐related diseases, such as cancer, diabetes, and Alzheimer's disease.
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Affiliation(s)
- Silvia Gravina
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461 USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry Brown University Providence RI 02912 USA
| | - Jan Vijg
- Department of Genetics Albert Einstein College of Medicine Bronx NY 10461 USA
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22
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Criscione SW, De Cecco M, Siranosian B, Zhang Y, Kreiling JA, Sedivy JM, Neretti N. Reorganization of chromosome architecture in replicative cellular senescence. Sci Adv 2016; 2:e1500882. [PMID: 26989773 PMCID: PMC4788486 DOI: 10.1126/sciadv.1500882] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 12/02/2015] [Indexed: 05/02/2023]
Abstract
Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells.
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Affiliation(s)
- Steven W. Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Benjamin Siranosian
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Yue Zhang
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Jill A. Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
- Corresponding author. E-mail:
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23
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Borghesan M, Fusilli C, Rappa F, Panebianco C, Rizzo G, Oben JA, Mazzoccoli G, Faulkes C, Pata I, Agodi A, Rezaee F, Minogue S, Warren A, Peterson A, Sedivy JM, Douet J, Buschbeck M, Cappello F, Mazza T, Pazienza V, Vinciguerra M. DNA Hypomethylation and Histone Variant macroH2A1 Synergistically Attenuate Chemotherapy-Induced Senescence to Promote Hepatocellular Carcinoma Progression. Cancer Res 2016; 76:594-606. [PMID: 26772755 DOI: 10.1158/0008-5472.can-15-1336] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 11/02/2015] [Indexed: 12/11/2022]
Abstract
Aging is a major risk factor for progression of liver diseases to hepatocellular carcinoma (HCC). Cellular senescence contributes to age-related tissue dysfunction, but the epigenetic basis underlying drug-induced senescence remains unclear. macroH2A1, a variant of histone H2A, is a marker of senescence-associated heterochromatic foci that synergizes with DNA methylation to silence tumor-suppressor genes in human fibroblasts. In this study, we investigated the relationship between macroH2A1 splice variants, macroH2A1.1 and macroH2A1.2, and liver carcinogenesis. We found that protein levels of both macroH2A1 isoforms were increased in the livers of very elderly rodents and humans, and were robust immunohistochemical markers of human cirrhosis and HCC. In response to the chemotherapeutic and DNA-demethylating agent 5-aza-deoxycytidine (5-aza-dC), transgenic expression of macroH2A1 isoforms in HCC cell lines prevented the emergence of a senescent-like phenotype and induced synergistic global DNA hypomethylation. Conversely, macroH2A1 depletion amplified the antiproliferative effects of 5-aza-dC in HCC cells, but failed to enhance senescence. Senescence-associated secretory phenotype and whole-transcriptome analyses implicated the p38 MAPK/IL8 pathway in mediating macroH2A1-dependent escape of HCC cells from chemotherapy-induced senescence. Furthermore, chromatin immunoprecipitation sequencing revealed that this hepatic antisenescence state also required active transcription that could not be attributed to genomic occupancy of these histones. Collectively, our findings reveal a new mechanism by which drug-induced senescence is epigenetically regulated by macroH2A1 and DNA methylation and suggest macroH2A1 as a novel biomarker of hepatic senescence that could potentially predict prognosis and disease progression.
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Affiliation(s)
- Michela Borghesan
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom. Division of Internal Medicine, Department of Medical Sciences, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Caterina Fusilli
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza"-Mendel Laboratory, Rome, Italy
| | - Francesca Rappa
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, Palermo, Italy
| | - Concetta Panebianco
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Giovanni Rizzo
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom
| | - Jude A Oben
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom
| | - Gianluigi Mazzoccoli
- Division of Internal Medicine, Department of Medical Sciences, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Chris Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Illar Pata
- Department of Gene Technology, Tallinn University of Technology (TTU), IVEX Lab, Tallinn, Estonia
| | - Antonella Agodi
- Department GF Ingrassia, University of Catania, Catania, Italy
| | - Farhad Rezaee
- Department of Cell Biology, University Medical Center Groningen, Groningen, the Netherlands
| | - Shane Minogue
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom
| | - Alessandra Warren
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom. Centre for Education and Research on Aging (CERA) and the ANZAC Research Institute, Concord RG Hospital, University of Sydney, Sydney, Australia
| | - Abigail Peterson
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Julien Douet
- Institute for Predictive and Personalized Medicine of Cancer, Campus Can Ruti, Badalona, Spain. Josep Carreras Institute for Leukaemia Research, Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain
| | - Marcus Buschbeck
- Institute for Predictive and Personalized Medicine of Cancer, Campus Can Ruti, Badalona, Spain. Josep Carreras Institute for Leukaemia Research, Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain
| | - Francesco Cappello
- Department of Experimental Biomedicine and Clinical Neurosciences, Section of Human Anatomy, University of Palermo, Palermo, Italy. Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy
| | - Tommaso Mazza
- Bioinformatics Unit, IRCCS "Casa Sollievo della Sofferenza"-Mendel Laboratory, Rome, Italy
| | - Valerio Pazienza
- Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy
| | - Manlio Vinciguerra
- Institute for Liver and Digestive Health, Royal Free Hospital, University College London, London, United Kingdom. Gastroenterology Unit, IRCCS "Casa Sollievo della Sofferenza" Hospital, San Giovanni Rotondo, Italy. Euro-Mediterranean Institute of Science and Technology (IEMEST), Palermo, Italy. School of Science and Technology, Nottingham Trent University, Nottingham, United Kingdom.
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24
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Abstract
Abstract
MYC is a highly pleiotropic transcription factor whose deregulation promotes cancer. We find that Myc haploinsufficient (Myc+/–) mice exhibit increased lifespan. They show resistance to several age-associated pathologies, including osteoporosis, cardiac fibrosis and immunosenescence. They also appear to be more active, with a higher metabolic rate and healthier lipid metabolism. Transcriptomic analysis reveals a gene expression signature enriched for metabolic and immune processes. The ancestral role of MYC as a regulator of ribosome biogenesis is reflected in reduced protein translation, which is inversely correlated with longevity. We also observe changes in nutrient and energy sensing pathways, including reduced serum IGF-1, increased AMPK activity, and decreased AKT, TOR and S6K activities. In contrast to observations in other longevity models, Myc+/– mice do not show improvements in stress management pathways. Our findings indicate that MYC activity has a significant impact on longevity and multiple aspects of mammalian healthspan.
Citation Format: John M. Sedivy. Reduced expression of MYC increases longevity and enhances healthspan. [abstract]. In: Proceedings of the AACR Special Conference on Myc: From Biology to Therapy; Jan 7-10, 2015; La Jolla, CA. Philadelphia (PA): AACR; Mol Cancer Res 2015;13(10 Suppl):Abstract nr IA20.
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25
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Longo VD, Antebi A, Bartke A, Barzilai N, Brown‐Borg HM, Caruso C, Curiel TJ, Cabo R, Franceschi C, Gems D, Ingram DK, Johnson TE, Kennedy BK, Kenyon C, Klein S, Kopchick JJ, Lepperdinger G, Madeo F, Mirisola MG, Mitchell JR, Passarino G, Rudolph KL, Sedivy JM, Shadel GS, Sinclair DA, Spindler SR, Suh Y, Vijg J, Vinciguerra M, Fontana L. Interventions to Slow Aging in Humans: Are We Ready? Aging Cell 2015; 14:497-510. [PMID: 25902704 PMCID: PMC4531065 DOI: 10.1111/acel.12338] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2015] [Indexed: 12/17/2022] Open
Abstract
The workshop entitled ‘Interventions to Slow Aging in Humans: Are We Ready?’ was held in Erice, Italy, on October 8–13, 2013, to bring together leading experts in the biology and genetics of aging and obtain a consensus related to the discovery and development of safe interventions to slow aging and increase healthy lifespan in humans. There was consensus that there is sufficient evidence that aging interventions will delay and prevent disease onset for many chronic conditions of adult and old age. Essential pathways have been identified, and behavioral, dietary, and pharmacologic approaches have emerged. Although many gene targets and drugs were discussed and there was not complete consensus about all interventions, the participants selected a subset of the most promising strategies that could be tested in humans for their effects on healthspan. These were: (i) dietary interventions mimicking chronic dietary restriction (periodic fasting mimicking diets, protein restriction, etc.); (ii) drugs that inhibit the growth hormone/IGF-I axis; (iii) drugs that inhibit the mTOR–S6K pathway; or (iv) drugs that activate AMPK or specific sirtuins. These choices were based in part on consistent evidence for the pro-longevity effects and ability of these interventions to prevent or delay multiple age-related diseases and improve healthspan in simple model organisms and rodents and their potential to be safe and effective in extending human healthspan. The authors of this manuscript were speakers and discussants invited to the workshop. The following summary highlights the major points addressed and the conclusions of the meeting.
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26
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Hofmann JW, Zhao X, De Cecco M, Peterson AL, Pagliaroli L, Manivannan J, Hubbard GB, Ikeno Y, Zhang Y, Feng B, Li X, Serre T, Qi W, Van Remmen H, Miller RA, Bath KG, de Cabo R, Xu H, Neretti N, Sedivy JM. Reduced expression of MYC increases longevity and enhances healthspan. Cell 2015; 160:477-88. [PMID: 25619689 DOI: 10.1016/j.cell.2014.12.016] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 10/21/2014] [Accepted: 12/03/2014] [Indexed: 01/18/2023]
Abstract
MYC is a highly pleiotropic transcription factor whose deregulation promotes cancer. In contrast, we find that Myc haploinsufficient (Myc(+/-)) mice exhibit increased lifespan. They show resistance to several age-associated pathologies, including osteoporosis, cardiac fibrosis, and immunosenescence. They also appear to be more active, with a higher metabolic rate and healthier lipid metabolism. Transcriptomic analysis reveals a gene expression signature enriched for metabolic and immune processes. The ancestral role of MYC as a regulator of ribosome biogenesis is reflected in reduced protein translation, which is inversely correlated with longevity. We also observe changes in nutrient and energy sensing pathways, including reduced serum IGF-1, increased AMPK activity, and decreased AKT, TOR, and S6K activities. In contrast to observations in other longevity models, Myc(+/-) mice do not show improvements in stress management pathways. Our findings indicate that MYC activity has a significant impact on longevity and multiple aspects of mammalian healthspan.
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Affiliation(s)
- Jeffrey W Hofmann
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Xiaoai Zhao
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Abigail L Peterson
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Luca Pagliaroli
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Jayameenakshi Manivannan
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Gene B Hubbard
- Department of Cellular and Structural Biology, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yuji Ikeno
- Department of Cellular and Structural Biology, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Yongqing Zhang
- Translational Gerontology Branch, National Institute on Aging, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - Bin Feng
- Hallett Center for Diabetes and Endocrinology, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Xiaxi Li
- Department of Cognitive, Linguistic, and Psychological Sciences, Brown University, Providence, RI 02912, USA
| | - Thomas Serre
- Department of Cognitive, Linguistic, and Psychological Sciences, Brown University, Providence, RI 02912, USA
| | - Wenbo Qi
- Department of Cellular and Structural Biology, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Holly Van Remmen
- Department of Cellular and Structural Biology, Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kevin G Bath
- Department of Cognitive, Linguistic, and Psychological Sciences, Brown University, Providence, RI 02912, USA
| | - Rafael de Cabo
- Translational Gerontology Branch, National Institute on Aging, 251 Bayview Boulevard, Suite 100, Baltimore, MD 21224, USA
| | - Haiyan Xu
- Hallett Center for Diabetes and Endocrinology, Rhode Island Hospital, Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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27
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Affiliation(s)
- Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Jef D Boeke
- Institute for Systems Genetics, New York University Langone Medical Center, New York, NY 10016, USA
| | - Stephen L Helfand
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.
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Criscione SW, Zhang Y, Thompson W, Sedivy JM, Neretti N. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics 2014; 15:583. [PMID: 25012247 PMCID: PMC4122776 DOI: 10.1186/1471-2164-15-583] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 07/03/2014] [Indexed: 12/11/2022] Open
Abstract
Background Repetitive elements comprise at least 55% of the human genome with more recent estimates as high as two-thirds. Most of these elements are retrotransposons, DNA sequences that can insert copies of themselves into new genomic locations by a “copy and paste” mechanism. These mobile genetic elements play important roles in shaping genomes during evolution, and have been implicated in the etiology of many human diseases. Despite their abundance and diversity, few studies investigated the regulation of endogenous retrotransposons at the genome-wide scale, primarily because of the technical difficulties of uniquely mapping high-throughput sequencing reads to repetitive DNA. Results Here we develop a new computational method called RepEnrich to study genome-wide transcriptional regulation of repetitive elements. We show that many of the Long Terminal Repeat retrotransposons in humans are transcriptionally active in a cell line-specific manner. Cancer cell lines display increased RNA Polymerase II binding to retrotransposons than cell lines derived from normal tissue. Consistent with increased transcriptional activity of retrotransposons in cancer cells we found significantly higher levels of L1 retrotransposon RNA expression in prostate tumors compared to normal-matched controls. Conclusions Our results support increased transcription of retrotransposons in transformed cells, which may explain the somatic retrotransposition events recently reported in several types of cancers. Electronic Supplementary Material Supplementary material is available for this article at 10.1186/1471-2164-15-583 and is accessible for authorized users.
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Affiliation(s)
| | | | | | | | - Nicola Neretti
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA.
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Nelson DM, McBryan T, Jeyapalan JC, Sedivy JM, Adams PD. A comparison of oncogene-induced senescence and replicative senescence: implications for tumor suppression and aging. Age (Dordr) 2014; 36:9637. [PMID: 24647599 PMCID: PMC4082585 DOI: 10.1007/s11357-014-9637-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 02/24/2014] [Indexed: 04/16/2023]
Abstract
Cellular senescence is a stable proliferation arrest associated with an altered secretory pathway, the senescence-associated secretory phenotype. However, cellular senescence is initiated by diverse molecular triggers, such as activated oncogenes and shortened telomeres, and is associated with varied and complex physiological endpoints, such as tumor suppression and tissue aging. The extent to which distinct triggers activate divergent modes of senescence that might be associated with different physiological endpoints is largely unknown. To begin to address this, we performed gene expression profiling to compare the senescence programs associated with two different modes of senescence, oncogene-induced senescence (OIS) and replicative senescence (RS [in part caused by shortened telomeres]). While both OIS and RS are associated with many common changes in gene expression compared to control proliferating cells, they also exhibit substantial differences. These results are discussed in light of potential physiological consequences, tumor suppression and aging.
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Affiliation(s)
- David M. Nelson
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- />Beatson Institute for Cancer Research, Glasgow, UK
| | - Tony McBryan
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- />Beatson Institute for Cancer Research, Glasgow, UK
| | - Jessie C. Jeyapalan
- />Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912 USA
| | - John M. Sedivy
- />Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912 USA
| | - Peter D. Adams
- />Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- />Beatson Institute for Cancer Research, Glasgow, UK
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Hofmann JW, McBryan T, Adams PD, Sedivy JM. The effects of aging on the expression of Wnt pathway genes in mouse tissues. Age (Dordr) 2014; 36:9618. [PMID: 24488586 PMCID: PMC4082588 DOI: 10.1007/s11357-014-9618-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 01/12/2014] [Indexed: 05/19/2023]
Abstract
The Wnt signaling pathway is involved in the regulation of tissue patterning and organ development during embryogenesis and continues to contribute to the maintenance of tissue homeostasis in adulthood. Recently, Wnt signaling has also been implicated in the establishment and progression of replicative cellular senescence. Given the known roles of tissue homeostasis and cellular senescence in aging, we sought to determine whether Wnt signaling changes with age. We examined the expression of 84 Wnt pathway-related genes in the liver, lung, skeletal muscle, and brain tissue from young and old mice. Expression changes were compared with those seen in cellular senescence, and transcription factors that might mediate these changes were predicted bioinformatically. In aggregate, our data are indicative of a general decrease in Wnt signaling with age, especially in the lung and brain. Furthermore, the set of genes that are differentially expressed with age is distinct from the genes differentially expressed in cellular senescence. The transcription factors predicted to regulate these changes, Nf-κB, Myb, Nkx2-1, Nr5a2, and Ep300, are known to regulate inflammation, differentiation, lipid metabolism, and chromatin remodeling, all of which have previously been implicated in aging. Although our study does not address whether altered Wnt signaling is a cause or an effect of aging, the presence of a relationship between the two provides a starting point for further investigation.
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Affiliation(s)
- Jeffrey W. Hofmann
- />Department of Molecular Biology, Cell Biology and Biochemistry, Laboratories for Molecular Medicine, Brown University, Providence, RI 02903 USA
| | - Tony McBryan
- />Beatson Institute for Cancer Research and Institute for Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Peter D. Adams
- />Beatson Institute for Cancer Research and Institute for Cancer Sciences, University of Glasgow, Glasgow, UK
| | - John M. Sedivy
- />Department of Molecular Biology, Cell Biology and Biochemistry, Laboratories for Molecular Medicine, Brown University, Providence, RI 02903 USA
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De Cecco M, Criscione SW, Peterson AL, Neretti N, Sedivy JM, Kreiling JA. Transposable elements become active and mobile in the genomes of aging mammalian somatic tissues. Aging (Albany NY) 2013; 5:867-83. [PMID: 24323947 PMCID: PMC3883704 DOI: 10.18632/aging.100621] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 12/06/2013] [Indexed: 12/15/2022]
Abstract
Transposable elements (TEs) were discovered by Barbara McClintock in maize and have since been found to be ubiquitous in all living organisms. Transposition is mutagenic and organisms have evolved mechanisms to repress the activity of their endogenous TEs. Transposition in somatic cells is very low, but recent evidence suggests that it may be derepressed in some cases, such as cancer development. We have found that during normal aging several families of retrotransposable elements (RTEs) start being transcribed in mouse tissues. In advanced age the expression culminates in active transposition. These processes are counteracted by calorie restriction (CR), an intervention that slows down aging. Retrotransposition is also activated in age-associated, naturally occurring cancers in the mouse. We suggest that somatic retrotransposition is a hitherto unappreciated aging process. Mobilization of RTEs is likely to be an important contributor to the progressive dysfunction of aging cells.
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Affiliation(s)
- Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, RI 02903, USA
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Abstract
Here we present and develop the hypothesis that the derepression of endogenous retrotransposable elements (RTEs) – genomic parasites – is an important and hitherto under-unexplored molecular aging process that can potentially occur in most tissues. We further envision that the activation and continued presence of retrotransposition contribute to age-associated tissue degeneration and pathology. Chromatin is a complex and dynamic structure that needs to be maintained in a functional state throughout our lifetime. Studies of diverse species have revealed that chromatin undergoes extensive rearrangements during aging. Cellular senescence, an important component of mammalian aging, has recently been associated with decreased heterochromatinization of normally silenced regions of the genome. These changes lead to the expression of RTEs, culminating in their transposition. RTEs are common in all kingdoms of life, and comprise close to 50% of mammalian genomes. They are tightly controlled, as their activity is highly destabilizing and mutagenic to their resident genomes.
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Affiliation(s)
- John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, USA
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Abstract
Cellular senescence is a state of irreversible cell cycle arrest that has been documented to both suppress cancer and promote aging. Although not well understood, extensive nuclear changes, including the remodeling of chromatin, take place as cells become senescent. In this issue, Ivanov et al. (2013. J. Cell Biol.http://dx.doi.org/jcb.201212110) report that chromatin fragments are released from the nuclei of senescent cells and are subsequently targeted for processing through the autophagy/lysosomal pathway.
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Affiliation(s)
- Darren J Baker
- Department of Pediatrics and Adolescent Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
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Sedivy JM, van Deursen JM. Why do we grow old: is it because our cells just wear out, we run out of cells (or both), and what can we do about it? Longev Healthspan 2013; 2:7. [PMID: 24472649 PMCID: PMC3922936 DOI: 10.1186/2046-2395-2-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 03/21/2013] [Indexed: 11/27/2022]
Abstract
Longevity & Healthspan, a new BioMed Central journal, has launched a thematic series on cellular senescence and aging, a quickly evolving field critical to our understanding of the biology of aging.
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Affiliation(s)
- John M Sedivy
- Department of Molecular Biology Cell Biology and Biochemistry, Laboratories for Molecular Medicine, Brown University, 70 Ship Street, Providence, RI 02903, USA.
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35
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De Cecco M, Criscione SW, Peckham EJ, Hillenmeyer S, Hamm EA, Manivannan J, Peterson AL, Kreiling JA, Neretti N, Sedivy JM. Genomes of replicatively senescent cells undergo global epigenetic changes leading to gene silencing and activation of transposable elements. Aging Cell 2013; 12:247-56. [PMID: 23360310 DOI: 10.1111/acel.12047] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2013] [Indexed: 11/28/2022] Open
Abstract
Replicative cellular senescence is an important tumor suppression mechanism and also contributes to aging. Progression of both cancer and aging include significant epigenetic components, but the chromatin changes that take place during cellular senescence are not known. We used formaldehyde assisted isolation of regulatory elements (FAIRE) to map genome-wide chromatin conformations. In contrast to growing cells, whose genomes are rich with features of both open and closed chromatin, FAIRE profiles of senescent cells are significantly smoothened. This is due to FAIRE signal loss in promoters and enhancers of active genes, and FAIRE signal gain in heterochromatic gene-poor regions. Chromatin of major retrotransposon classes, Alu, SVA and L1, becomes relatively more open in senescent cells, affecting most strongly the evolutionarily recent elements, and leads to an increase in their transcription and ultimately transposition. Constitutive heterochromatin in centromeric and peri-centromeric regions also becomes relatively more open, and the transcription of satellite sequences increases. The peripheral heterochromatic compartment (PHC) becomes less prominent, and centromere structure becomes notably enlarged. These epigenetic changes progress slowly after the onset of senescence, with some, such as mobilization of retrotransposable elements becoming prominent only at late times. Many of these changes have also been noted in cancer cells.
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Affiliation(s)
- Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Steven W. Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Edward J. Peckham
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Sara Hillenmeyer
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Eliza A. Hamm
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Jayameenakshi Manivannan
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Abigail L. Peterson
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Jill A. Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics; Brown University; Providence; 02912; RI; USA
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Waaijer MEC, Parish WE, Strongitharm BH, van Heemst D, Slagboom PE, de Craen AJM, Sedivy JM, Westendorp RGJ, Gunn DA, Maier AB. The number of p16INK4a positive cells in human skin reflects biological age. Aging Cell 2012; 11:722-5. [PMID: 22612594 DOI: 10.1111/j.1474-9726.2012.00837.x] [Citation(s) in RCA: 178] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Cellular senescence is a defense mechanism in response to molecular damage which accumulates with aging. Correspondingly, the number of senescent cells has been reported to be greater in older than in younger subjects and furthermore associates with age-related pathologies. Inter-individual differences exist in the rate at which a person ages (biological age). Here, we studied whether younger biological age is related to fewer senescent cells in middle-aged individuals with the propensity for longevity, using p16INK4a as a marker for cellular senescence. We observed that a younger biological age associates with lower levels of p16INK4a positive cells in human skin.
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Affiliation(s)
- Mariëtte E C Waaijer
- Department of Gerontology and Geriatrics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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Moen EL, Wen S, Anwar T, Cross-Knorr S, Brilliant K, Birnbaum F, Rahaman S, Sedivy JM, Moss SF, Chatterjee D. Regulation of RKIP function by Helicobacter pylori in gastric cancer. PLoS One 2012; 7:e37819. [PMID: 22662230 PMCID: PMC3360604 DOI: 10.1371/journal.pone.0037819] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Accepted: 04/24/2012] [Indexed: 01/01/2023] Open
Abstract
Helicobacter pylori (H. pylori) is a gram-negative, spiral-shaped bacterium that infects more than half of the world's population and is a major cause of gastric adenocarcinoma. The mechanisms that link H. pylori infection to gastric carcinogenesis are not well understood. In the present study, we report that the Raf-kinase inhibitor protein (RKIP) has a role in the induction of apoptosis by H. pylori in gastric epithelial cells. Western blot and luciferase transcription reporter assays demonstrate that the pathogenicity island of H. pylori rapidly phosphorylates RKIP, which then localizes to the nucleus where it activates its own transcription and induces apoptosis. Forced overexpression of RKIP enhances apoptosis in H. pylori-infected cells, whereas RKIP RNA inhibition suppresses the induction of apoptosis by H. pylori infection. While inducing the phosphorylation of RKIP, H. pylori simultaneously targets non-phosphorylated RKIP for proteasome-mediated degradation. The increase in RKIP transcription and phosphorylation is abrogated by mutating RKIP serine 153 to valine, demonstrating that regulation of RKIP activity by H. pylori is dependent upon RKIP's S153 residue. In addition, H. pylori infection increases the expression of Snail, a transcriptional repressor of RKIP. Our results suggest that H. pylori utilizes a tumor suppressor protein, RKIP, to promote apoptosis in gastric cancer cells.
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Affiliation(s)
- Erika L. Moen
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
- Centers of Biomedical Research Excellence (COBRE), Rhode Island Hospital, Providence, Rhode Island, United States of America
| | - Sicheng Wen
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
| | - Talha Anwar
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
| | - Sam Cross-Knorr
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
- Centers of Biomedical Research Excellence (COBRE), Rhode Island Hospital, Providence, Rhode Island, United States of America
| | - Kate Brilliant
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
- Centers of Biomedical Research Excellence (COBRE), Rhode Island Hospital, Providence, Rhode Island, United States of America
| | - Faith Birnbaum
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
| | - Sherida Rahaman
- Department of Pathobiology Graduate Program, Brown Univesity, Providence, Rhode Island, United States of America
| | - John M. Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Steven F. Moss
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
| | - Devasis Chatterjee
- Department of Medicine, Rhode Island Hospital, Providence, Rhode Island, United States of America
- Centers of Biomedical Research Excellence (COBRE), Rhode Island Hospital, Providence, Rhode Island, United States of America
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Sanders JA, Schorl C, Patel A, Sedivy JM, Gruppuso PA. Postnatal liver growth and regeneration are independent of c-myc in a mouse model of conditional hepatic c-myc deletion. BMC Physiol 2012; 12:1. [PMID: 22397685 PMCID: PMC3353165 DOI: 10.1186/1472-6793-12-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 03/07/2012] [Indexed: 12/27/2022]
Abstract
BACKGROUND The transcription factor c-myc regulates genes involved in hepatocyte growth, proliferation, metabolism, and differentiation. It has also been assigned roles in liver development and regeneration. In previous studies, we made the unexpected observation that c-Myc protein levels were similar in proliferating fetal liver and quiescent adult liver with c-Myc displaying nucleolar localization in the latter. In order to investigate the functional role of c-Myc in adult liver, we have developed a hepatocyte-specific c-myc knockout mouse, c-mycfl/fl;Alb-Cre. RESULTS Liver weight to body weight ratios were similar in control and c-myc deficient mice. Liver architecture was unaffected. Conditional c-myc deletion did not result in compensatory induction of other myc family members or in c-Myc's binding partner Max. Floxed c-myc did have a negative effect on Alb-Cre expression at 4 weeks of age. To explore this relationship further, we used the Rosa26 reporter line to assay Cre activity in the c-myc floxed mice. No significant difference in Alb-Cre activity was found between control and c-mycfl/fl mice. c-myc deficient mice were studied in a nonproliferative model of liver growth, fasting for 48 hr followed by a 24 hr refeeding period. Fasting resulted in a decrease in liver mass and liver protein, both of which recovered upon 24 h of refeeding in the c-mycfl/fl;Alb-Cre animals. There was also no effect of reducing c-myc on recovery of liver mass following 2/3 partial hepatectomy. CONCLUSIONS c-Myc appears to be dispensable for normal liver growth during the postnatal period, restoration of liver mass following partial hepatectomy and recovery from fasting.
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Affiliation(s)
- Jennifer A Sanders
- Department of Pediatrics, Rhode Island Hospital and Brown University, Providence, RI 02903, USA.
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De Cecco M, Jeyapalan J, Zhao X, Tamamori-Adachi M, Sedivy JM. Nuclear protein accumulation in cellular senescence and organismal aging revealed with a novel single-cell resolution fluorescence microscopy assay. Aging (Albany NY) 2012; 3:955-67. [PMID: 22006542 PMCID: PMC3229972 DOI: 10.18632/aging.100372] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Replicative cellular senescence was discovered some 50 years ago. The phenotypes of senescent cells have been investigated extensively in cell culture, and found to affect essentially all aspects of cellular physiology. The relevance of cellular senescence in the context of age-associated pathologies as well as normal aging is a topic of active and ongoing interest. Considerable effort has been devoted to biomarker discovery to enable the microscopic detection of single senescent cells in tissues. One characteristic of senescent cells documented very early in cell culture studies was an increase in cell size and total protein content, but whether this occurs in vivo is not known. A limiting factor for studies of protein content and localization has been the lack of suitable fluorescence microscopy tools. We have developed an easy and flexible method, based on the merocyanine dye known as NanoOrange, to visualize and quantitatively measure total protein levels by high resolution fluorescence microscopy. NanoOrange staining can be combined with antibody-based immunofluorescence, thus providing both specific target and total protein information in the same specimen. These methods are optimally combined with automated image analysis platforms for high throughput analysis. We document here increasing protein content and density in nuclei of senescent human and mouse fibroblasts in vitro, and in liver nuclei of aged mice in vivo. Additionally, in aged liver nuclei NanoOrange revealed protein-dense foci that colocalize with centromeric heterochromatin.
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Affiliation(s)
- Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA
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Zwolinska AK, Heagle Whiting A, Beekman C, Sedivy JM, Marine JC. Suppression of Myc oncogenic activity by nucleostemin haploinsufficiency. Oncogene 2011; 31:3311-21. [PMID: 22081066 DOI: 10.1038/onc.2011.507] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleostemin (NS), a nucleolar GTPase, is highly expressed in stem/progenitor cells and in most cancer cells. However, little is known about the regulation of its expression. Here, we identify the NS gene as a novel direct transcriptional target of the c-Myc oncoprotein. We show that Myc overexpression enhances NS transcription in cultured cells and in pre-neoplastic B cells from Eμ-myc transgenic mice. Consistent with NS being downstream of Myc, NS expression parallels that of Myc in a large panel of human cancer cell lines. Using chromatin immunoprecipitation we show that c-Myc binds to a well-conserved E-box in the NS promoter. Critically, we show NS haploinsufficiency profoundly delays Myc-induced cancer formation in vivo. NS+/-Eμ-myc transgenic mice have much slower rates of B-cell lymphoma development, with life spans twice that of their wild-type littermates. Moreover, we demonstrate that NS is essential for the proliferation of Myc-overexpressing cells in cultured cells and in vivo: impaired lymphoma development was associated with a drastic decrease of c-Myc-induced proliferation of pre-tumoural B cells. Finally, we provide evidence that in cell culture NS controls cell proliferation independently of p53 and that NS haploinsufficiency significantly delays lymphomagenesis in p53-deficient mice. Together these data indicate that NS functions downstream of Myc as a rate-limiting regulator of cell proliferation and transformation, independently from its putative role within the p53 pathway. Targeting NS is therefore expected to compromise early tumour development irrespectively of the p53 status.
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Affiliation(s)
- A K Zwolinska
- Laboratory for Molecular Cancer Biology, Department of Biomedical Molecular Biology, VIB-UGent, Technologiepark, Ghent, Belgium
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41
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Yap CS, Peterson AL, Castellani G, Sedivy JM, Neretti N. Kinetic profiling of the c-Myc transcriptome and bioinformatic analysis of repressed gene promoters. Cell Cycle 2011; 10:2184-96. [PMID: 21623162 DOI: 10.4161/cc.10.13.16249] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Mammalian c-Myc is a member of a small family of three related proto-oncogenic transcription factors. c-Myc has an unusually broad array of regulatory functions, which include roles in cell cycle and apoptosis, a variety of metabolic functions, cell differentiation, senescence, and stem cell maintenance. c-Myc modulates the expression of a very large number of genes, but the magnitude of the majority of the regulatory effects is only 2-fold or less. c-Myc can both activate and repress the promoters of its target genes. Identification of genes directly regulated by c-Myc has been an enduring question in the field. We report here microarray expression profiling of a high resolution time course of c-Myc induction, using fibroblast cells in which c-Myc activity can be modulated from null to physiological. The c-Myc transcriptome dataset presented is the largest reported to date with 4,186 differentially regulated genes (1,826 upregulated, 2,360 downregulated, 1% FDR). The gene expression patterns fit well with the known biological functions of c-Myc. We describe several novel findings and present tools for further data mining. Although the mechanisms of transcriptional activation by c-Myc are well understood, how c-Myc represses an even greater number of genes remains incompletely described. One mechanism involves the binding of c-Myc to other, positively acting transcription factors, and interfering with their activities. We identified rapid-response genes likely to be direct c-Myc targets, and analyzed the promoters of the repressed genes to identify transcription factors that could be targets of c-Myc repression.
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Affiliation(s)
- Chui-Sun Yap
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
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42
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Kreiling JA, Tamamori-Adachi M, Sexton AN, Jeyapalan JC, Munoz-Najar U, Peterson AL, Manivannan J, Rogers ES, Pchelintsev NA, Adams PD, Sedivy JM. Age-associated increase in heterochromatic marks in murine and primate tissues. Aging Cell 2011; 10:292-304. [PMID: 21176091 DOI: 10.1111/j.1474-9726.2010.00666.x] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Chromatin is highly dynamic and subject to extensive remodeling under many physiologic conditions. Changes in chromatin that occur during the aging process are poorly documented and understood in higher organisms, such as mammals. We developed an immunofluorescence assay to quantitatively detect, at the single cell level, changes in the nuclear content of chromatin-associated proteins. We found increased levels of the heterochromatin-associated proteins histone macro H2A (mH2A) and heterochromatin protein 1 beta (HP1β) in human fibroblasts during replicative senescence in culture, and for the first time, an age-associated increase in these heterochromatin marks in several tissues of mice and primates. Mouse lung was characterized by monophasic mH2A expression histograms at both ages, and an increase in mean staining intensity at old age. In the mouse liver, we observed increased age-associated localization of mH2A to regions of pericentromeric heterochromatin. In the skeletal muscle, we found two populations of cells with either low or high mH2A levels. This pattern of expression was similar in mouse and baboon, and showed a clear increase in the proportion of nuclei with high mH2A levels in older animals. The frequencies of cells displaying evidence of increased heterochromatinization are too high to be readily accounted for by replicative or oncogene-induced cellular senescence, and are prominently found in terminally differentiated, postmitotic tissues that are not conventionally thought to be susceptible to senescence. Our findings distinguish specific chromatin states in individual cells of mammalian tissues, and provide a foundation to investigate further the progressive epigenetic changes that occur during aging.
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Kreiling JA, Tamamori-Adachi M, Sexton AN, Jeyapalan JC, Munoz-Najar U, Peterson AL, Manivannan J, Rogers ES, Pchelintsev NA, Adams PD, Sedivy JM. Age-associated increase in heterochromatic marks in murine and primate tissues. Aging Cell 2011. [PMID: 21176091 DOI: 10.1111/j.1474-9726.2010.00666.x.age-associated] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Chromatin is highly dynamic and subject to extensive remodeling under many physiologic conditions. Changes in chromatin that occur during the aging process are poorly documented and understood in higher organisms, such as mammals. We developed an immunofluorescence assay to quantitatively detect, at the single cell level, changes in the nuclear content of chromatin-associated proteins. We found increased levels of the heterochromatin-associated proteins histone macro H2A (mH2A) and heterochromatin protein 1 beta (HP1β) in human fibroblasts during replicative senescence in culture, and for the first time, an age-associated increase in these heterochromatin marks in several tissues of mice and primates. Mouse lung was characterized by monophasic mH2A expression histograms at both ages, and an increase in mean staining intensity at old age. In the mouse liver, we observed increased age-associated localization of mH2A to regions of pericentromeric heterochromatin. In the skeletal muscle, we found two populations of cells with either low or high mH2A levels. This pattern of expression was similar in mouse and baboon, and showed a clear increase in the proportion of nuclei with high mH2A levels in older animals. The frequencies of cells displaying evidence of increased heterochromatinization are too high to be readily accounted for by replicative or oncogene-induced cellular senescence, and are prominently found in terminally differentiated, postmitotic tissues that are not conventionally thought to be susceptible to senescence. Our findings distinguish specific chromatin states in individual cells of mammalian tissues, and provide a foundation to investigate further the progressive epigenetic changes that occur during aging.
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Affiliation(s)
- Jill A Kreiling
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
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Alves H, Munoz-Najar U, De Wit J, Renard AJS, Hoeijmakers JHJ, Sedivy JM, Van Blitterswijk C, De Boer J. A link between the accumulation of DNA damage and loss of multi-potency of human mesenchymal stromal cells. J Cell Mol Med 2011; 14:2729-38. [PMID: 19818093 PMCID: PMC3539748 DOI: 10.1111/j.1582-4934.2009.00931.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Human mesenchymal stromal cells (hMSCs) represent an attractive cell source for clinic applications. Besides being multi-potent, recent clinical trials suggest that they secrete both trophic and immunomodulatory factors, allowing allogenic MSCs to be used in a wider variety of clinical situations. The yield of prospective isolation is however very low, making expansion a required step toward clinical applications. Unfortunately, this leads to a significant decrease in their stemness. To identify the mechanism behind loss of multi-potency, hMSCs were expanded until replicative senescence and the concomitant molecular changes were characterized at regular intervals. We observed that, with time of culture, loss of multi-potency was associated with both the accumulation of DNA damage and the respective activation of the DNA damage response pathway, suggesting a correlation between both phenomena. Indeed, exposing hMSCs to DNA damage agents led to a significant decrease in the differentiation potential. We also showed that hMSCs are susceptible to accumulate DNA damage upon in vitro expansion, and that although hMSCs maintained an effective nucleotide excision repair activity, there was a progressive accumulation of DNA damage. We propose a model in which DNA damage accumulation contributes to the loss of differentiation potential of hMSCs, which might not only compromise their potential for clinical applications but also contribute to the characteristics of tissue ageing.
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Affiliation(s)
- Hugo Alves
- Department of Tissue Regeneration, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands.
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Abstract
Organismal aging and longevity are influenced by many complex interacting factors. Epigenetics has recently emerged as another possible determinant of aging. Here, we review some of the epigenetic pathways that contribute to cellular senescence and age-associated phenotypes. Strategies aimed to reverse age-linked epigenetic alterations may lead to the development of new therapeutic interventions to delay or alleviate some of the most debilitating age-associated diseases.
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Affiliation(s)
- Ursula Muñoz-Najar
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02903, USA.
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Antebi A, Cuervo AM, Sedivy JM, Martin GM. Announcement. Aging Cell 2011. [DOI: 10.1111/j.1474-9726.2010.00664.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Sedivy JM. Phosphatidylenthanolamine Binding Protein aka Raf Kinase Inhibitor Protein: A Brief History of Its Discovery and the Remarkable Diversity of Biological Functions. ACTA ACUST UNITED AC 2011; 2:1-12. [PMID: 23227430 DOI: 10.1615/forumimmundisther.v2.i1.20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Phosphatidylethanolamine-binding protein (PEBP) was identified almost three decades ago as an abundant protein in bovine brain. PEBP is the prototype of a highly conserved family of proteins represented in all three major phylogenetic divisions, eukaryota, bacteria, and archaea, with no significant sequence homology to other proteins. PEBP proteins have been studied in many species. The most thoroughly explored biological role of PEBP is that of a modulator of intracellular signaling pathways, which is mediated by its ability to bind and inhibit a number of protein kinases. The first such interaction that came to light was with the Raf1 kinase, and PEBP is thus widely referred to in the literature under its alternate name RKIP (Raf kinase inhibitory protein). The activity of RKIP itself is subject to regulation by phosphorylation. Intriguingly, PEBP has also been reported to possess additional, and diverse, biological functions unrelated to protein kinase networks that remain to be investigated in detail. Recent findings that RKIP may function as a suppressor of cancer metastasis are of great interest and importance. Prognostic and therapeutic applications of RKIP in human cancer were the subject of the first international workshop on RKIP that was held at the University of California, Los Angeles, in March 2010. This paper was presented at the workshop as a summary of the history of this still small but rapidly evolving field.
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Affiliation(s)
- John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Laboratories for Molecular Medicine, Brown University, 70 Ship Street, Providence, RI 02903; Tel.: 401-863-7631;
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Abstract
Mammalian c-Myc is a member of a small family of three closely related transcription factors. The Myc family of proto-oncogenes are among the most potent activators of tumorigenesis, and are frequently overexpressed in diverse cancers. c-Myc has an unusually broad array of regulatory functions, which include, in addition to roles in the cell cycle and apoptosis, effects on a variety of metabolic functions, cell differentiation, senescence, and stem cell maintenance. A significant number of c-Myc interacting proteins have already been defined, but it is widely believed that the c-Myc interactome is vastly larger than currently documented. In addition to interactions with components of the transcription machinery, transcription independent nuclear interactions with the DNA replication and RNA processing pathways have been reported. Cytoplasmic roles of c-Myc have also been recently substantiated. Recent advances in proteomics have opened new possibilities for the isolation of protein complexes under native conditions and confidently identifying the components using ultrasensitive, high mass accuracy and high resolution mass spectrometry techniques. In this communication we report a new tandem affinity purification (TAP) c-Myc interaction screen that employed new cell lines with near-physiological levels of c-Myc expression with multi-dimensional protein identification techniques (MudPIT) for the detection and quantification of proteins. Both label-free and the recently developed stable isotope labeling with amino acids in cell culture (SILAC) methodologies were used. Combined data from multiple biological replicates provided a dataset of 418 non-redundant proteins, 389 of which are putative novel interactors. This new information should significantly advance our understanding of this interesting and important master regulator.
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Affiliation(s)
- Pooja Agrawal
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
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Paul E, Cronan R, Weston PJ, Boekelheide K, Sedivy JM, Lee SY, Wiest DL, Resnick MB, Klysik JE. Disruption of Supv3L1 damages the skin and causes sarcopenia, loss of fat, and death. Mamm Genome 2009; 20:92-108. [PMID: 19145458 DOI: 10.1007/s00335-008-9168-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 12/03/2008] [Indexed: 01/26/2023]
Abstract
Supv3L1 is a conserved and ubiquitously expressed helicase found in numerous tissues and cell types of many species. In human cells, SUPV3L1 was shown to suppress apoptotic death and sister chromatid exchange, and impair mitochondrial RNA metabolism and protein synthesis. In vitro experiments revealed binding of SUPV3L1 to BLM and WRN proteins, suggesting a role in genome maintenance processes. Disruption of the Supv3L1 gene in the mouse has been reported to be embryonic lethal at early developmental stages. We generated a conditional mouse in which the phenotypes associated with the removal of exon 14 can be tested in a variety of tissues. Disruption mediated by a Mx1 promoter-driven Cre displayed a postnatal growth delay, reduced lifespan, loss of adipose tissue and muscle mass, and severe skin abnormalities manifesting as ichthyosis, thickening of the epidermis, and atrophy of the dermis and subcutaneous tissue. Using a tamoxifen-activatable Esr1/Cre driver, Supv3L1 disruption resulted in growth retardation and aging phenotypes, including loss of adipose tissue and muscle mass, kyphosis, cachexia, and premature death. Many of the abnormalities seen in the Mx1-Cre mice, such as hyperkeratosis characterized by profound scaling of feet and tail, could also be detected in tamoxifen-inducible Cre mice. Conditional ablation of Supv3L1 in keratinocytes confirmed atrophic changes in the skin and ichthyosis-like changes. Together, these data indicate that Supv3L1 is important for the maintenance of the skin barrier. In addition, loss of Supv3L1 function leads to accelerated aging-like phenotypes.
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Affiliation(s)
- Erin Paul
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship St., Providence, RI 02903, USA
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Abstract
Cellular senescence, first observed and defined using in vitro cell culture studies, is an irreversible cell cycle arrest which can be triggered by a variety of factors. Emerging evidence suggests that cellular senescence acts as an in vivo tumor suppression mechanism by limiting aberrant proliferation. It has also been postulated that cellular senescence can occur independently of cancer and contribute to the physiological processes of normal organismal aging. Recent data have demonstrated the in vivo accumulation of senescent cells with advancing age. Some characteristics of senescent cells, such as the ability to modify their extracellular environment, could play a role in aging and age-related pathology. In this review, we examine current evidence that links cellular senescence and organismal aging.
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Affiliation(s)
- Jessie C Jeyapalan
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
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